Science.gov

Sample records for aligned base pairs

  1. Galaxy pairs align with Galactic filaments

    NASA Astrophysics Data System (ADS)

    Tempel, E.; Tamm, A.

    2015-04-01

    Context. Gravitational collapse theory and numerical simulations suggest that the velocity field within large-scale galaxy filaments is dominated by motions along the filaments. Aims: Our aim is to check whether observational data reveal any preferred orientation of galaxy pairs with respect to the underlying filaments as a result of the expectedly anisotropic velocity field. Methods: We use galaxy pairs and galaxy filaments identified from Sloan Digital Sky Survey data. For filament extraction, we use the Bisous model that is based on the marked point process technique. During the filament detection, we use the centre point of each pair instead of the positions of galaxies to avoid a built-in influence of pair orientation on the filament construction. For pairs lying within filaments (3012 cases), we calculate the angle between the line connecting the galaxies of each pair and their host filaments. To avoid redshift-space distortions, the angle is measured in the plane of the sky. Results: The alignment analysis shows that the orientation of galaxy pairs correlates strongly with their host filaments. The alignment signal is stronger for loose pairs, with at least 25% excess of aligned pairs compared to a random distribution. The alignment of galaxy pairs and filaments measured from the observational data is in good agreement with the alignment in the Millennium simulation and thus provides support to the ΛCDM formalism.

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

    PubMed

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

    2011-10-24

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

  3. Projection-Based Volume Alignment

    PubMed Central

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

    2013-01-01

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

  4. Base pairing and base mis-pairing in nucleic acids

    NASA Technical Reports Server (NTRS)

    Wang, A. H. J.; Rich, A.

    1986-01-01

    In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

  5. Combining Multiple Pairwise Structure-based Alignments

    SciTech Connect

    2014-11-12

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  8. Pair-eigenstates and mutual alignment of coupled molecular rotors in a magnetic field.

    PubMed

    Sharma, Ketan; Friedrich, Bretislav

    2016-05-11

    We examine the rotational states of a pair of polar (2)Σ molecules subject to a uniform magnetic field. The electric dipole-dipole interaction between the molecules creates entangled pair-eigenstates of two types. In one type, the Zeeman interaction between the inherently paramagnetic molecules and the magnetic field destroys the entanglement of the pair-eigenstates, whereas in the other type it does not. The pair-eigenstates exhibit numerous intersections, which become avoided for pair-eigenstates comprised of individual states that meet the selection rules ΔJi = 0, ± 1, ΔNi = 2n (n = 0, ±1, ±2,…), and ΔMi = 0, ± 1 imposed by the electric dipole-dipole operator. Here Ji, Ni and Mi are the total, rotational and projection angular momentum quantum numbers of molecules i = 1, 2 in the absence of the electric dipole-dipole interaction. We evaluate the mutual alignment of the pair-eigenstates and find it to be independent of the magnetic field, except for states that undergo avoided crossings, in which case the alignment of the interacting states is interchanged at the magnetic field corresponding to the crossing point. We present an analytic model which provides ready estimates of the pairwise alignment cosine that characterises the mutual alignment of the pair of coupled rotors. PMID:27126576

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

    PubMed

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

    2012-11-01

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

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

    DOEpatents

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

    2013-06-18

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

  11. Alignment and Integration Techniques for Mirror Segment Pairs on the Constellation X Telescope

    NASA Technical Reports Server (NTRS)

    Hadjimichael, Theo; Lehan, John; Olsen, Larry; Owens, Scott; Saha, Timo; Wallace, Tom; Zhang, Will

    2007-01-01

    We present the concepts behind current alignment and integration techniques for testing a Constellation-X primary-secondary mirror segment pair in an x-ray beam line test. We examine the effects of a passive mount on thin glass x-ray mirror segments, and the issues of mount shape and environment on alignment. We also investigate how bonding and transfer to a permanent housing affects the quality of the final image, comparing predicted results to a full x-ray test on a primary secondary pair.

  12. Combining Multiple Pairwise Structure-based Alignments

    2014-11-12

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

  13. Alignment of paired molecules of C60 within a hexagonal platform networked through hydrogen-bonds.

    PubMed

    Hisaki, Ichiro; Nakagawa, Shoichi; Sato, Hiroyasu; Tohnai, Norimitsu

    2016-07-28

    We demonstrate, for the first time, that a hydrogen-bonded low-density organic framework can be applied as a platform to achieve periodic alignment of paired molecules of C60, which is the smallest example of a finite-numbered cluster of C60. The framework is a layered assembly of a hydrogen-bonded 2D hexagonal network (LA-H-HexNet) composed of dodecadehydrotribenzo[18]annulene derivatives. PMID:27417325

  14. Report on Pairing-based Cryptography

    PubMed Central

    Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

    2015-01-01

    This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST’s position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed. PMID:26958435

  15. Report on Pairing-based Cryptography.

    PubMed

    Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

    2015-01-01

    This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed. PMID:26958435

  16. Methodological Alignment in Design-Based Research

    ERIC Educational Resources Information Center

    Hoadley, Christopher M.

    2004-01-01

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

  17. Graph-based molecular alignment (GMA).

    PubMed

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

    2007-01-01

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

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

    SciTech Connect

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

    2015-11-01

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

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

    SciTech Connect

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

    2006-03-15

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

  20. Multiple Sequence Alignment Based on Chaotic PSO

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  4. QUADRUPOLE BEAM-BASED ALIGNMENT AT RHIC.

    SciTech Connect

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

    2005-05-16

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

  5. Automated DNA Base Pair Calling Algorithm

    1999-07-07

    The procedure solves the problem of calling the DNA base pair sequence from two channel electropherogram separations in an automated fashion. The core of the program involves a peak picking algorithm based upon first, second, and third derivative spectra for each electropherogram channel, signal levels as a function of time, peak spacing, base pair signal to noise sequence patterns, frequency vs ratio of the two channel histograms, and confidence levels generated during the run. Themore » ratios of the two channels at peak centers can be used to accurately and reproducibly determine the base pair sequence. A further enhancement is a novel Gaussian deconvolution used to determine the peak heights used in generating the ratio.« less

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

    PubMed

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

    2012-01-01

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

  7. Radical-pair based avian magnetoreception

    NASA Astrophysics Data System (ADS)

    Procopio, Maria; Ritz, Thorsten

    2014-03-01

    Behavioural experiments suggest that migratory birds possess a magnetic compass sensor able to detect the direction of the geomagnetic. One hypothesis for the basis of this remarkable sensory ability is that the coherent quantum spin dynamics of photoinduced radical pair reactions transduces directional magnetic information from the geomagnetic field into changes of reaction yields, possibly involving the photoreceptor cryptochrome in the birds retina. The suggested radical-pair based avian magnetoreception has attracted attention in the field of quantum biology as an example of a biological sensor which might exploit quantum coherences for its biological function. Investigations on such a spin-based sensor have focussed on uncovering the design features for the design of a biomimetic magnetic field sensor. We study the effects of slow fluctuations in the nuclear spin environment on the directional signal. We quantitatively evaluate the robustness of signals under fluctuations on a timescale longer than the lifetime of a radical pair, utilizing two models of radical pairs. Our results suggest design principles for building a radical-pair based compass sensor that is both robust and highly directional sensitive.

  8. MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs.

    PubMed

    Cheng, Hua; Kim, Bong-Hyun; Grishin, Nick V

    2008-03-01

    We describe MALIDUP (manual alignments of duplicated domains), a database of 241 pairwise structure alignments for homologous domains originated by internal duplication within the same polypeptide chain. Since duplicated domains within a protein frequently diverge in function and thus in sequence, this would be the first database of structurally similar homologs that is not strongly biased by sequence or functional similarity. Our manual alignments in most cases agree with the automatic structural alignments generated by several commonly used programs. This carefully constructed database could be used in studies on protein evolution and as a reference for testing structure alignment programs. The database is available at http://prodata.swmed.edu/malidup. PMID:17932926

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  10. Effective Electrocardiogram Steganography Based on Coefficient Alignment.

    PubMed

    Yang, Ching-Yu; Wang, Wen-Fong

    2016-03-01

    This study presents two types of data hiding methods based on coefficient alignment for electrocardiogram (ECG) signals, namely, lossy and reversible ECG steganographys. The lossy method is divided into high-quality and high-capacity ECG steganography, both of which are capable of hiding confidential patient data in ECG signals. The reversible data hiding method can not only hide secret messages but also completely restore the original ECG signal after bit extraction. Simulations confirmed that the perceived quality generated by the lossy ECG steganography methods was good, while hiding capacity was acceptable. In addition, these methods have a certain degree of robustness, which is rare in conventional ECG stegangraphy schemes. Moreover, the proposed reversible ECG steganography method can not only successfully extract hidden messages but also completely recover the original ECG data. PMID:26711443

  11. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

    PubMed

    Moriya, Yuki; Yamada, Takuji; Okuda, Shujiro; Nakagawa, Zenichi; Kotera, Masaaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2016-03-28

    Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes. PMID:26822930

  12. Cell pairing using microwell array electrodes based on dielectrophoresis.

    PubMed

    Yoshimura, Yuki; Tomita, Masahiro; Mizutani, Fumio; Yasukawa, Tomoyuki

    2014-07-15

    We report a simple device with an array of 10,000 (100 × 100) microwells for producing vertical pairs of cells in individual microwells with a rapid manipulation based on positive dielectrophoresis (p-DEP). The areas encircled with micropoles which fabricated from an electrical insulating photosensitive polymer were used as microwells. The width (14 μm) and depth (25 μm) of the individual microwells restricted the size to two vertically aligned cells. The DEP device for the manipulation of cells consisted of a microfluidic channel with an upper indium tin oxide (ITO) electrode and a lower microwell array electrode fabricated on an ITO substrate. Mouse myeloma cells stained in green were trapped within 1 s in the microwells by p-DEP by applying an alternating current voltage between the upper ITO and the lower microwell array electrode. The cells were retained inside the wells even after switching off the voltage and washing with a fluidic flow. Other myeloma cells stained in blue were then trapped in the microwells occupied by the cells stained in green to form the vertical cell pairing in the microwells. Cells stained in different colors were paired within only 1 min and a pairing efficiency of over 50% was achieved. PMID:24947270

  13. Graphene/Lead (Pb)-based Cooper -pair splitter

    NASA Astrophysics Data System (ADS)

    Borzenets, Ivan; Shimazaki, Yuya; Jones, Gareth; Russo, Saverio; Yamamoto, Michihisa; Tarucha, Seigo

    2015-03-01

    We have fabricated a Cooper-pair splitter device based on a superconductor- two normal leads, ``Y'' shaped junction with graphene as the base material. (Compared to nanowire-based devices, the two dimensional nature of graphene allows for the normal leads to be placed arbitrarily close together and in a non-parallel arrangement.) The superconducting lead is created by contacting graphene with lead (Pb), thus inducing a supercurrent via the proximity effect. The normal metal leads are patterned into quantum dots by etching nano-constrictions with self-aligned side gates. Quantum dots strongly suppress two electron processes, allowing only one electron to pass at a time. Thus, the Cooper-pair splitting efficiency is enhanced as the split electrons must necessarily tunnel through different quantum dots. Using a DC measurement we have demonstrated enhanced currents though both normal leads when both quantum dots are in resonance and the input lead is in the superconducting regime: demonstrating Cooper-pair splitting. (This is contrary to the classical regime of currents though a three resistor junction.) Shot noise measurements would demonstrate that the split electrons tunnel at the same time. Demonstrating that the split electrons have opposite spin would show that such a device could be used as a source of quantum entangled electrons.

  14. Method for sequencing DNA base pairs

    DOEpatents

    Sessler, Andrew M.; Dawson, John

    1993-01-01

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source.

  15. Signature scheme based on bilinear pairs

    NASA Astrophysics Data System (ADS)

    Tong, Rui Y.; Geng, Yong J.

    2013-03-01

    An identity-based signature scheme is proposed by using bilinear pairs technology. The scheme uses user's identity information as public key such as email address, IP address, telephone number so that it erases the cost of forming and managing public key infrastructure and avoids the problem of user private generating center generating forgery signature by using CL-PKC framework to generate user's private key.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  17. Method for sequencing DNA base pairs

    DOEpatents

    Sessler, A.M.; Dawson, J.

    1993-12-14

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 6 figures.

  18. Base pair analogs in the gas phase.

    PubMed

    Roscioli, Joseph R; Pratt, David W

    2003-11-25

    A rotationally resolved electronic spectrum of the gas-phase dimer 2-aminopyridine.2-pyridone, an analog of the adenine.thymine base pair, has been observed and assigned, leading to precise measurements of its moments of inertia and preliminary determinations of its structure. A Watson-Crick configuration results, with N...H-N and N-H...O hydrogen bond lengths of 2.898 and 2.810 A, respectively. The two bases are found not to be coplanar; a dihedral angle of 6.1 degrees between the base planes is also estimated from the measured moments of inertia. Possible chemical and biological implications of these results are discussed. PMID:14612563

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

    SciTech Connect

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

    1995-12-01

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

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

    ERIC Educational Resources Information Center

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

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

  1. Chunk Alignment for Corpus-Based Machine Translation

    ERIC Educational Resources Information Center

    Kim, Jae Dong

    2011-01-01

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

  2. Local alignment of two-base encoded DNA sequence

    PubMed Central

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

    2009-01-01

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

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

    PubMed Central

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

    2008-01-01

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

  4. NMR analysis of base-pair opening kinetics in DNA

    PubMed Central

    Szulik, Marta W.; Voehler, Markus; Stone, Michael P.

    2014-01-01

    Base pairing in nucleic acids plays a crucial role in their structure and function. Differences in the base pair opening and closing kinetics of individual double stranded DNA sequences or between chemically modified base pairs provide insight into the recognition of these base pairs by DNA processing enzymes. This unit describes how to quantify the kinetics for localized base pairs by observing changes in the imino proton signals by nuclear magnetic resonance spectroscopy. The determination of all relevant parameters using state of the art techniques and NMR instrumentation, including cryoprobes, is discussed. PMID:25501592

  5. Nucleic acid duplexes incorporating a dissociable covalent base pair

    NASA Technical Reports Server (NTRS)

    Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1999-01-01

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

  6. Nucleic acid duplexes incorporating a dissociable covalent base pair.

    PubMed

    Gao, K; Orgel, L E

    1999-12-21

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure. PMID:10611299

  7. An Accurate Scalable Template-based Alignment Algorithm.

    PubMed

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

    2012-12-31

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

  8. Natural versus artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies.

    PubMed

    Hirao, Ichiro; Kimoto, Michiko; Yamashige, Rie

    2012-12-18

    Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously. Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids. As researchers developing unnatural base pairs, they use repeated "proof of concept" experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the

  9. Efficient PCR amplification by an unnatural base pair system.

    PubMed

    Kimoto, Michiko; Kawai, Rie; Mitsui, Tsuneo; Yokoyama, Shigeyuki; Hirao, Ichiro

    2008-01-01

    Expansion of the genetic alphabet by an unnatural base pair system enables the site-specific incorporation of extra functional components into nucleic acids and proteins. In this system, PCR amplification of DNA templates containing unnatural base pairs is essential for modern biotechnology. We present a new unnatural base pair system, in which DNA duplexes containing the unnatural base pairs can be efficiently amplified by PCR. The system also provides a method for the site-specific incorporation of functional components into amplified DNA fragments by PCR, using unnatural base substrates linked with functional groups of interest. PMID:18776457

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

    PubMed Central

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-01-01

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

  11. Evidence for a spin-aligned neutron-proton paired phase from the level structure of (92)Pd.

    PubMed

    Cederwall, B; Moradi, F Ghazi; Bäck, T; Johnson, A; Blomqvist, J; Clément, E; de France, G; Wadsworth, R; Andgren, K; Lagergren, K; Dijon, A; Jaworski, G; Liotta, R; Qi, C; Nyakó, B M; Nyberg, J; Palacz, M; Al-Azri, H; Algora, A; de Angelis, G; Ataç, A; Bhattacharyya, S; Brock, T; Brown, J R; Davies, P; Di Nitto, A; Dombrádi, Zs; Gadea, A; Gál, J; Hadinia, B; Johnston-Theasby, F; Joshi, P; Juhász, K; Julin, R; Jungclaus, A; Kalinka, G; Kara, S O; Khaplanov, A; Kownacki, J; La Rana, G; Lenzi, S M; Molnár, J; Moro, R; Napoli, D R; Singh, B S Nara; Persson, A; Recchia, F; Sandzelius, M; Scheurer, J-N; Sletten, G; Sohler, D; Söderström, P-A; Taylor, M J; Timár, J; Valiente-Dobón, J J; Vardaci, E; Williams, S

    2011-01-01

    Shell structure and magic numbers in atomic nuclei were generally explained by pioneering work that introduced a strong spin-orbit interaction to the nuclear shell model potential. However, knowledge of nuclear forces and the mechanisms governing the structure of nuclei, in particular far from stability, is still incomplete. In nuclei with equal neutron and proton numbers (N = Z), enhanced correlations arise between neutrons and protons (two distinct types of fermions) that occupy orbitals with the same quantum numbers. Such correlations have been predicted to favour an unusual type of nuclear superfluidity, termed isoscalar neutron-proton pairing, in addition to normal isovector pairing. Despite many experimental efforts, these predictions have not been confirmed. Here we report the experimental observation of excited states in the N = Z = 46 nucleus (92)Pd. Gamma rays emitted following the (58)Ni((36)Ar,2n)(92)Pd fusion-evaporation reaction were identified using a combination of state-of-the-art high-resolution γ-ray, charged-particle and neutron detector systems. Our results reveal evidence for a spin-aligned, isoscalar neutron-proton coupling scheme, different from the previous prediction. We suggest that this coupling scheme replaces normal superfluidity (characterized by seniority coupling) in the ground and low-lying excited states of the heaviest N = Z nuclei. Such strong, isoscalar neutron-proton correlations would have a considerable impact on the nuclear level structure and possibly influence the dynamics of rapid proton capture in stellar nucleosynthesis. PMID:21179086

  12. Theory of nodal s ± -wave pairing symmetry in the Pu-based 115 superconductor family.

    PubMed

    Das, Tanmoy; Zhu, Jian-Xin; Graf, Matthias J

    2015-01-01

    The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-Tc superconductors and predict the presence of a nodal s(±) wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface "hot-spots" in the inter-band scattering channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s(±) wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry. PMID:25721375

  13. Alignment fixture

    DOEpatents

    Bell, Grover C.; Gibson, O. Theodore

    1980-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Wheeler, Ward C.

    2003-01-01

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

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

    PubMed

    Wheeler, Ward C

    2003-06-01

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

  16. An ensemble of SVM classifiers based on gene pairs.

    PubMed

    Tong, Muchenxuan; Liu, Kun-Hong; Xu, Chungui; Ju, Wenbin

    2013-07-01

    In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of base classifiers. The effectiveness of the GA-ESP classifier is evaluated on both binary-class and multi-class datasets. PMID:23668348

  17. On the internal d-wave structure of s+/- pairs in Iron-based Superconductors

    NASA Astrophysics Data System (ADS)

    Ong, Tze Tzen; Coleman, Piers

    2014-03-01

    A key issue in understanding the high temperature iron-based superconductors concerns the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. Whereas electronically paired superconductors generally avoid the Coulomb interaction through the formation of higher angular momentum pairs, iron based superconductors involve s-wave (s+/-) pairs with zero angular momentum. By taking account of the orbital degrees of freedom of the iron atoms, here we show that the s+/- pairs in these materials possess hidden d-wave symmetry, forming orbital triplets in which the the d-wave angular momentum of the pairs is compensated by the internal angular momentum of the orbitals. The recent observation of a gap with octahedral structure in KFe2As2 materials can be understood as a transition to a ``high spin'' configuration of the d-wave orbital triplets, through the alignment of the two angular momentum components of the pair. We acknowledge funding from DOE grant DE-FG02-99ER45790.

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

    PubMed

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

    2015-08-01

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

  19. Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms.

    PubMed

    Bartenhagen, Christoph; Dugas, Martin

    2016-01-01

    Structural variation (SV) plays an important role in genetic diversity among the population in general and specifically in diseases such as cancer. Modern next-generation sequencing (NGS) technologies provide paired-end sequencing data at high depth with increasing read lengths. This development enabled the analysis of split-reads to detect SV breakpoints with single-nucleotide resolution. But ambiguous mappings and breakpoint sequences with further co-occurring mutations hamper split-read alignments against a reference sequence. The trade-off between high sensitivity and low false-positive rate is problematic and often requires a lot of fine-tuning of the analysis method based on knowledge about its algorithm and the characteristics of the data set. We present SoftSV, a method for exact breakpoint detection for small and large deletions, inversions, tandem duplications and inter-chromosomal translocations, which relies solely on the mutual alignment of soft-clipped reads within the neighborhood of discordantly mapped paired-end reads. Unlike other SV detection algorithms, our approach does not require thresholds regarding sequencing coverage or mapping quality. We evaluate SoftSV together with eight approaches (Breakdancer, Clever, CREST, Delly, GASVPro, Pindel, Socrates and SoftSearch) on simulated and real data sets. Our results show that sensitive and reliable SV detection is subject to many different factors like read length, sequence coverage and SV type. While most programs have their individual drawbacks, our greedy approach turns out to be the most robust and sensitive on many experimental setups. Sensitivities above 85% and positive predictive values between 80 and 100% could be achieved consistently for all SV types on simulated data sets starting at relatively short 75 bp reads and low 10-15× sequence coverage. PMID:25998133

  20. Image-based temporal alignment of echocardiographic sequences

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  1. LSST Telescope Alignment Plan Based on Nodal Aberration Theory

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  2. Base-pairing promotes leader selection to prime in vitro influenza genome transcription.

    PubMed

    Geerts-Dimitriadou, Christina; Zwart, Mark P; Goldbach, Rob; Kormelink, Richard

    2011-01-01

    The requirements for alignment of capped leader sequences along the viral genome during influenza transcription initiation (cap-snatching) have long been an enigma. In this study, competition experiments using an in vitro transcription assay revealed that influenza virus transcriptase prefers leader sequences with base complementarity to the 3'-ultimate residues of the viral template, 10 or 11 nt from the 5' cap. Internal priming at the 3'-penultimate residue, as well as prime-and-realign was observed. The nucleotide identity immediately 5' of the base-pairing residues also affected cap donor usage. Application to the in vitro system of RNA molecules with increased base complementarity to the viral RNA template showed stronger reduction of globin RNA leader initiated influenza transcription compared to those with a single base-pairing possibility. Altogether the results indicated an optimal cap donor consensus sequence of (7m)G-(N)(7-8)-(A/U/G)-(A/U)-AGC-3'. PMID:21051068

  3. Fast statistical alignment.

    PubMed

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

    2009-05-01

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

  4. Structure of 2,4-Diaminopyrimidine - Theobromine Alternate Base Pairs

    NASA Technical Reports Server (NTRS)

    Gengeliczki, Zsolt; Callahan, Michael P.; Kabelac, Martin; Rijs, Anouk M.; deVries, Mattanjah S.

    2011-01-01

    We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine. We have found the four lowest energy structures, which include the Watson-Crick base pairing motif. This Watson-Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.

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

    NASA Astrophysics Data System (ADS)

    Münch, Jürgen; Heidrich, Jens; Mandić, Vladimir

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

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

    SciTech Connect

    T. Satogata, J. Ziegler

    2011-03-01

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

  7. Dual AFM probes alignment based on vision guidance

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

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

    SciTech Connect

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

    2011-03-04

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

  9. Beam-based alignment measurements of the LANSCE linac

    SciTech Connect

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

    2004-01-01

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

  10. A point matching algorithm based on reference point pair

    NASA Astrophysics Data System (ADS)

    Zou, Huanxin; Zhu, Youqing; Zhou, Shilin; Lei, Lin

    2016-03-01

    Outliers and occlusions are important degradation in the real application of point matching. In this paper, a novel point matching algorithm based on the reference point pairs is proposed. In each iteration, it firstly eliminates the dubious matches to obtain the relatively accurate matching points (reference point pairs), and then calculates the shape contexts of the removed points with reference to them. After re-matching the removed points, the reference point pairs are combined to achieve better correspondences. Experiments on synthetic data validate the advantages of our method in comparison with some classical methods.

  11. Calix[4]pyrrole-based ion pair receptors.

    PubMed

    Kim, Sung Kuk; Sessler, Jonathan L

    2014-08-19

    Ion pair receptors, which are able to bind concurrently both a cation and an anion, often display higher selectivity and affinity for specific ion pairs than simple ion receptors capable of recognizing primarily either a cation or an anion. This enhancement in recognition function is attributable to direct or indirect cooperative interactions between cobound ions via electrostatic attractions between oppositely charged ions, as well as to positive allosteric effects. In addition, by virtue of binding the counterions of the targeted ion, ion pair receptors can minimize the solvation of the counterions, which can otherwise have a negative effect on the interactions between the receptors and the targeted ions. As a result of their more favorable interactions, ion pair receptors are attractive for use in applications, such as extraction and sensing, where control of the binding interactions is advantageous. In this Account, we illustrate this potential in the context of ion pair receptors based on the calix[4]pyrrole scaffold. Both simple ditopic ion pair receptors, containing sites for the recognition of a single anion and single cation, and so-called multitopic ion pair receptors will be discussed. The latter systems differ from conventional, so-called ditopic ion pair receptors in that they contain more than one binding site for a given targeted ion (e.g., a cation). This permits a level of selectivity and control over binding function not normally seen for simple ion or ion pair receptors containing one or two binding sites, respectively. Calix[4]pyrroles are macrocyclic compounds consisting of four pyrrole units linked via fully substituted sp(3) hybridized meso carbon atoms. They are effective receptors for Lewis basic anions (e.g., halides) in typical organic media and under certain conditions will recognize ion pairs containing charge diffuse cations, such as a small alkylammonium, imidazolium, or cesium cations. The calix[4]pyrrole framework is further

  12. The 6-thioguanine/5-methyl-2-pyrimidinone base pair.

    PubMed Central

    Rappaport, H P

    1988-01-01

    As part of a program to determine the physical possibility of expanding the number of types of base pairs in DNA, the pairing stabilities of the analog bases 6-thioguanine (GS) and 5-methyl-2-pyrimidinone (TH) in oligodeoxynucleotides were measured. Procedures were developed to synthesize oligodeoxynucleotides with the analog bases. The sequences of the synthesized oligomers were T-C-G-A-C-G-G-X-Y-C-C-G. An enzymatic procedure was developed to measure relative association constants of oligomer pairs with the self complementary reference oligomer, X = A and Y = T, K(T/A) = K. The results were K(C/G) = (5 +/- .5)K, K(TH/GS) = K/(1 +/- .5), K(T/G) = K/(9 +/- 3), K(TH/G) = K/(25 +/- 5), K(C/GS) less than K/30, K(TH/A) less than K/40, K(T/GS) less than K/40, K(C/A) less than K/40. The results with the standard bases are consistent with other methods of measurement. The stability of the base pair GS/TH is approximately the same as the standard base pair A/T. PMID:3412886

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

    SciTech Connect

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

    2010-07-21

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

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

    SciTech Connect

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

    2010-12-20

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

  15. Femtosecond molecular dynamics of tautomerization in model base pairs

    NASA Astrophysics Data System (ADS)

    Douhal, A.; Kim, S. K.; Zewail, A. H.

    1995-11-01

    HYDROGEN bonds commonly lend robustness and directionality to molecular recognition processes and supramolecular structures1,2. In particular, the two or three hydrogen bonds in Watson-Crick base pairs bind the double-stranded DNA helix and determine the complementarity of the pairing. Watson and Crick pointed out3, however, that the possible tautomers of base pairs, in which hydrogen atoms become attached to the donor atom of the hydrogen bond, might disturb the genetic code, as the tautomer is capable of pairing with different partners. But the dynamics of hydrogen bonds in general, and of this tautomerization process in particular, are not well understood. Here we report observations of the femtosecond dynamics of tautomerization in model base pairs (7-azaindole dimers) containing two hydrogen bonds. Because of the femtosecond resolution of proton motions, we are able to examine the cooperativity of formation of the tautomer (in which the protons on each base are shifted sequentially to the other base), and to determine the characteristic timescales of the motions in a solvent-free environment. We find that the first step occurs on a timescale of a few hundred femtoseconds, whereas the second step, to form the full tautomer, is much slower, taking place within several picoseconds; the timescales are changed significantly by replacing hydrogen with deuterium. These results establish the molecular basis of the dynamics and the role of quantum tunnelling.

  16. Image alignment

    DOEpatents

    Dowell, Larry Jonathan

    2014-04-22

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

  17. Understanding the kinetic mechanism of RNA single base pair formation

    PubMed Central

    Xu, Xiaojun; Yu, Tao; Chen, Shi-Jie

    2016-01-01

    RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. PMID:26699466

  18. Geometric nomenclature and classification of RNA base pairs.

    PubMed Central

    Leontis, N B; Westhof, E

    2001-01-01

    Non-Watson-Crick base pairs mediate specific interactions responsible for RNA-RNA self-assembly and RNA-protein recognition. An unambiguous and descriptive nomenclature with well-defined and nonoverlapping parameters is needed to communicate concisely structural information about RNA base pairs. The definitions should reflect underlying molecular structures and interactions and, thus, facilitate automated annotation, classification, and comparison of new RNA structures. We propose a classification based on the observation that the planar edge-to-edge, hydrogen-bonding interactions between RNA bases involve one of three distinct edges: the Watson-Crick edge, the Hoogsteen edge, and the Sugar edge (which includes the 2'-OH and which has also been referred to as the Shallow-groove edge). Bases can interact in either of two orientations with respect to the glycosidic bonds, cis or trans relative to the hydrogen bonds. This gives rise to 12 basic geometric types with at least two H bonds connecting the bases. For each geometric type, the relative orientations of the strands can be easily deduced. High-resolution examples of 11 of the 12 geometries are presently available. Bifurcated pairs, in which a single exocyclic carbonyl or amino group of one base directly contacts the edge of a second base, and water-inserted pairs, in which single functional groups on each base interact directly, are intermediate between two of the standard geometries. The nomenclature facilitates the recognition of isosteric relationships among base pairs within each geometry, and thus facilitates the recognition of recurrent three-dimensional motifs from comparison of homologous sequences. Graphical conventions are proposed for displaying non-Watson-Crick interactions on a secondary structure diagram. The utility of the classification in homology modeling of RNA tertiary motifs is illustrated. PMID:11345429

  19. How do base-pairing small RNAs evolve?

    PubMed Central

    Updegrove, Taylor B.; Shabalina, Svetlana A.; Storz, Gisela

    2015-01-01

    The increasing numbers of characterized base-pairing small RNAs (sRNAs) and the identification of these regulators in a broad range of bacteria are allowing comparisons between species and explorations of sRNA evolution. In this review, we describe some examples of trans-encoded base-pairing sRNAs that are species-specific and others that are more broadly distributed. We also describe examples of sRNA orthologs where different features are conserved. These examples provide the background for a discussion of mechanisms of sRNA evolution and selective pressures on the sRNAs and their mRNA target(s). PMID:25934120

  20. The thermodynamics and kinetics of a nucleotide base pair.

    PubMed

    Wang, Yujie; Gong, Sha; Wang, Zhen; Zhang, Wenbing

    2016-03-21

    The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian. PMID:27004898

  1. The thermodynamics and kinetics of a nucleotide base pair

    NASA Astrophysics Data System (ADS)

    Wang, Yujie; Gong, Sha; Wang, Zhen; Zhang, Wenbing

    2016-03-01

    The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.

  2. biobambam: tools for read pair collation based algorithms on BAM files

    PubMed Central

    2014-01-01

    Background Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. Results In this paper we introduce biobambam, a set of tools based on the efficient collation of alignments in BAM files by read name. The employed collation algorithm avoids time and space consuming sorting of alignments by read name where this is possible without using more than a specified amount of main memory. Using this algorithm tasks like duplicate marking in BAM files and conversion of BAM files to the FastQ format can be performed very efficiently with limited resources. We also make the collation algorithm available in the form of an API for other projects. This API is part of the libmaus package. Conclusions In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities our approach can often perform an equivalent task more efficiently in terms of the required main memory and run-time. Our BAM to FastQ conversion is faster than all widely known alternatives including Picard and bamUtil. Our duplicate marking is about as fast as the closest competitor bamUtil for small data sets and faster than all known alternatives on large and complex data sets.

  3. Ultrafast dynamics in DNA base pairs following ultraviolet excitation.

    NASA Astrophysics Data System (ADS)

    Orr-Ewing, Andrew

    2015-03-01

    Photo-protective mechanisms in DNA are essential to maintain the integrity of the genetic code by preventing damage from absorption of solar ultraviolet (UV) radiation. We have used time-resolved infra-red (TRIR) spectroscopy to observe the dynamics of Watson-Crick nucleobase pairs following absorption of femtosecond UV laser pulses. The base pairs are prepared as nucleosides in solution, and photo-induced dynamics are probed in the carbonyl and N-H bond stretching regions using broadband IR pulses with picosecond time resolution. Results will be presented for the guanine-cytosine (G-C) base pair, contrasting the rapid recovery of ground-state products (the photo-protection pathway) with formation of other photoproducts which might represent photo-damage mechanisms. This work is a collaboration with the group of Prof F. Temps (Christian-Albrechts-Universitat zu Kiel). This research is supported by ERC Advanced Grant 290966 CAPRI.

  4. Systematic Detection of Epistatic Interactions Based on Allele Pair Frequencies

    PubMed Central

    Ackermann, Marit; Beyer, Andreas

    2012-01-01

    Epistatic genetic interactions are key for understanding the genetic contribution to complex traits. Epistasis is always defined with respect to some trait such as growth rate or fitness. Whereas most existing epistasis screens explicitly test for a trait, it is also possible to implicitly test for fitness traits by searching for the over- or under-representation of allele pairs in a given population. Such analysis of imbalanced allele pair frequencies of distant loci has not been exploited yet on a genome-wide scale, mostly due to statistical difficulties such as the multiple testing problem. We propose a new approach called Imbalanced Allele Pair frequencies (ImAP) for inferring epistatic interactions that is exclusively based on DNA sequence information. Our approach is based on genome-wide SNP data sampled from a population with known family structure. We make use of genotype information of parent-child trios and inspect 3×3 contingency tables for detecting pairs of alleles from different genomic positions that are over- or under-represented in the population. We also developed a simulation setup which mimics the pedigree structure by simultaneously assuming independence of the markers. When applied to mouse SNP data, our method detected 168 imbalanced allele pairs, which is substantially more than in simulations assuming no interactions. We could validate a significant number of the interactions with external data, and we found that interacting loci are enriched for genes involved in developmental processes. PMID:22346757

  5. Experimental demonstration of wavelength domain rogue-free ONU based on wavelength-pairing for TDM/WDM optical access networks.

    PubMed

    Lee, Jie Hyun; Park, Heuk; Kang, Sae-Kyoung; Lee, Joon Ki; Chung, Hwan Seok

    2015-11-30

    In this study, we propose and experimentally demonstrate a wavelength domain rogue-free ONU based on wavelength-pairing of downstream and upstream signals for time/wavelength division-multiplexed optical access networks. The wavelength-pairing tunable filter is aligned to the upstream wavelength channel by aligning it to one of the downstream wavelength channels. Wavelength-pairing is implemented with a compact and cyclic Si-AWG integrated with a Ge-PD. The pairing filter covered four 100 GHz-spaced wavelength channels. The feasibility of the wavelength domain rogue-free operation is investigated by emulating malfunction of the misaligned laser. The wavelength-pairing tunable filter based on the Si-AWG blocks the upstream signal in the non-assigned wavelength channel before data collision with other ONUs. PMID:26698745

  6. Social Networks-Based Adaptive Pairing Strategy for Cooperative Learning

    ERIC Educational Resources Information Center

    Chuang, Po-Jen; Chiang, Ming-Chao; Yang, Chu-Sing; Tsai, Chun-Wei

    2012-01-01

    In this paper, we propose a grouping strategy to enhance the learning and testing results of students, called Pairing Strategy (PS). The proposed method stems from the need of interactivity and the desire of cooperation in cooperative learning. Based on the social networks of students, PS provides members of the groups to learn from or mimic…

  7. Nanogenerators based on vertically aligned InN nanowires.

    PubMed

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

    2016-01-28

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

  8. Beam based alignment of C-shaped quadrupole magnets

    SciTech Connect

    Portmann, G.; Robin, D.

    1998-06-01

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

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

    SciTech Connect

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

    2014-03-01

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

  10. Deformability-based microfluidic cell pairing and fusion.

    PubMed

    Dura, Burak; Liu, Yaoping; Voldman, Joel

    2014-08-01

    We present a microfluidic cell pairing device capable of sequential trapping and pairing of hundreds of cells using passive hydrodynamics and flow-induced deformation. We describe the design and operation principles of our device and show its applicability for cell fusion. Using our device, we achieved both homotypic and heterotypic cell pairing, demonstrating efficiencies up to 80%. The platform is compatible with fusion protocols based on biological, chemical and physical stimuli with fusion yields up to 95%. Our device further permits its disconnection from the fluidic hardware enabling its transportation for imaging and culture while maintaining cell registration on chip. Our design principles and cell trapping technique can readily be applied for different cell types and can be extended to trap and fuse multiple (>2) cell partners as demonstrated by our preliminary experiments. PMID:24898933

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  12. Configurations of base-pair complexes in solutions. [nucleotide chemistry

    NASA Technical Reports Server (NTRS)

    Egan, J. T.; Nir, S.; Rein, R.; Macelroy, R.

    1978-01-01

    A theoretical search for the most stable conformations (i.e., stacked or hydrogen bonded) of the base pairs A-U and G-C in water, CCl4, and CHCl3 solutions is presented. The calculations of free energies indicate a significant role of the solvent in determining the conformations of the base-pair complexes. The application of the continuum method yields preferred conformations in good agreement with experiment. Results of the calculations with this method emphasize the importance of both the electrostatic interactions between the two bases in a complex, and the dipolar interaction of the complex with the entire medium. In calculations with the solvation shell method, the last term, i.e., dipolar interaction of the complex with the entire medium, was added. With this modification the prediction of the solvation shell model agrees both with the continuum model and with experiment, i.e., in water the stacked conformation of the bases is preferred.

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

    SciTech Connect

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

    2011-03-23

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  16. Theory of nodal s±-wave pairing symmetry in the Pu-based 115 superconductor family

    SciTech Connect

    Das, Tanmoy; Zhu, Jian -Xin; Graf, Matthias J.

    2015-02-27

    The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-Tc superconductors and predict the presence of a nodal s⁺⁻ wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scattering channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s⁺⁻ wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry.

  17. Theory of nodal s±-wave pairing symmetry in the Pu-based 115 superconductor family

    DOE PAGESBeta

    Das, Tanmoy; Zhu, Jian -Xin; Graf, Matthias J.

    2015-02-27

    The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-Tc superconductors and predict the presence of a nodal s⁺⁻ wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scattering channel,more » which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s⁺⁻ wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry.« less

  18. Theory of nodal s±-wave pairing symmetry in the Pu-based 115 superconductor family

    PubMed Central

    Das, Tanmoy; Zhu, Jian-Xin; Graf, Matthias J.

    2015-01-01

    The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-Tc superconductors and predict the presence of a nodal s+− wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface “hot-spots” in the inter-band scattering channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s+− wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry. PMID:25721375

  19. Semiautomated improvement of RNA alignments

    PubMed Central

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

    2007-01-01

    We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture of the SARSE editor makes it a flexible tool to improve all RNA alignments with relatively little human intervention. Online documentation and software are available at http://sarse.ku.dk. PMID:17804647

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

    PubMed Central

    2014-01-01

    Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD). The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing -mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown) organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows. PMID:25133391

  1. Synthesis, base pairing and structure studies of geranylated RNA.

    PubMed

    Wang, Rui; Vangaveti, Sweta; Ranganathan, Srivathsan V; Basanta-Sanchez, Maria; Haruehanroengra, Phensinee; Chen, Alan; Sheng, Jia

    2016-07-27

    Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella Typhimurium The geranylated residues are located in the first anticodon position of tRNAs specific for lysine, glutamine and glutamic acid. This big hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. We aimed to systematically study the structure, function and biosynthesis mechanism of this geranylation pathway, as well as answer the question of why nature uses such a hydrophobic modification in hydrophilic RNA systems. Recently, we have synthesized the deoxy-analog of S-geranyluridine and showed the geranylated T-G pair is much stronger than the geranylated T-A pair and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation that the geranylated tRNA(Glu) UUC recognizes GAG more efficiently than GAA. In this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA oligos. We also report extensive molecular simulation studies to explore the structural features of the geranyl group in the context of A-form RNA and its effect on codon-anticodon interaction during ribosome binding. PMID:27307604

  2. Microwave and THz sensing using slab-pair-based metamaterials

    SciTech Connect

    Kenanakis, G.; Shen, Nianhai; Mavidis, Ch.; Katsarakis, N.; Kafesaki, M.; Soukoulis, Costas M.; Economou, E.N.

    2012-10-15

    In this work the sensing capability of an artificial magnetic metamaterial based on pairs of metal slabs is demonstrated, both theoretically and experimentally, in the microwave regime. The demonstration is based on transmission measurements and simulations monitoring the shift of the magnetic resonance frequency as one changes a thin dielectric layer placed between the slabs of the pairs. Strong dependence of the magnetic resonance frequency on both the permittivity and the thickness of the dielectric layer under detection was observed. The sensitivity to the dielectrics′ permittivity (ε) is larger for dielectrics of low ε values, which makes the approach suitable for sensing organic materials also in the THz regime. The capability of our approach for THz sensing is also demonstrated through simulations.

  3. Charge Transport in DNA with Five Base Pairs

    NASA Astrophysics Data System (ADS)

    Lee, Sunhee; Hedin, Eric; Joe, Yong

    2008-10-01

    Recently, much interest has arisen in the process of charge transport through DNA due to its fundamental roles in biological processes and in possible novel molecular electronics. We investigate quantum mechanical electron transmission along the long axis of the DNA molecule using a one-dimensional tight-binding model. In this system, we consider a single central conduction channel in which individual sites represent a base-pair formed by either AT (TA) or GC (CG) pairs coupled via hydrogen bonds. The sites are linked by a hopping amplitude, or quantum overlap integral. The sugar-phosphate backbone and the hopping amplitude between each site of the base and the backbone are incorporated into an energy-dependent on-site potential in the main DNA site. For the sake of simplicity, a simple DNA molecule segment with five base pairs is studied, and the transmission for different values of on-site energy is calculated to determine the influence of mismatch (impurity) effects in the DNA sequence. Finally, we present results for the temperature dependence of the transmission, and the current-voltage characteristics in order to examine the extent and efficiency of charge migration. *One of the authors (E.R.H) is partially supported by a grant from the Center for Energy Research, Education, and Service (CERES) at Ball State University.

  4. Hydrophobic, Non-Hydrogen-Bonding Bases and Base Pairs in DNA

    PubMed Central

    Schweitzer, Barbara A.; Kool, Eric T.

    2009-01-01

    We report the properties of hydrophobic isosteres of pyrimidines and purines in synthetic DNA duplexes. Phenyl nucleosides 1 and 2 are nonpolar isosteres of the natural thymidine nucleoside, and indole nucleoside 3 is an analog of the complementary purine 2-aminodeoxyadenosine. The nucleosides were incorporated into synthetic oligodeoxynucleotides and were paired against each other and against the natural bases. Thermal denaturation experiments were used to measure the stabilities of the duplexes at neutral pH. It is found that the hydrophobic base analogs are nonselective in pairing with the four natural bases but selective for pairing with each other rather than with the natural bases. For example, compound 2 selectively pairs with itself rather than with A, T, G, or C; the magnitude of this selectivity is found to be 6.5–9.3 °C in Tm or 1.5–1.8 kcal/mol in free energy (25 °C). All possible hydrophobic pairing combinations of 1, 2, and 3 were examined. Results show that the pairing affinity depends on the nature of the pairs and on position in the duplex. The highest affinity pairs are found to be the 1–1 and 2–2 self-pairs and the 1–2 heteropair. The best stabilization occurs when the pairs are placed at the ends of duplexes rather than internally; the internal pairs may be destabilized by imperfect steric mimicry which leads to non-ideal duplex structure. In some cases the hydrophobic pairs are significantly stabilizing to the DNA duplex; for example, when situated at the end of a duplex, the 1–1 pair is more stabilizing than a T–A pair. When situated internally, the affinity of the 1–1 pair is the same as, or slightly better than, the analogous T–T mismatch pair, which is known to have two hydrogen bonds. The studies raise the possibility that hydrogen bonds may not always be required for the formation of stable duplex DNA-like structure. In addition, the results point out the importance of solvation and desolvation in natural base pairing

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

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

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

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

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-11-16

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

  7. Coherent Pair Production in Deformed Crystals with a Complex Base

    NASA Astrophysics Data System (ADS)

    Mkrtchyan, A. R.; Saharian, A. A.; Parazian, V. V.

    We investigate the coherent electron-positron pair creation by high-energy photons in a periodically deformed single crystal with a complex base. The formula for the corresponding differential cross-section is derived for an arbitrary deformation field. The conditions are specified under which the influence of the deformation is considerable. The case is considered in detail when the photon enters into the crystal at small angles with respect to a crystallographic axis. The results of the numerical calculations are presented for SiO2 single crystal and Moliere parametrization of the screened atomic potentials in the case of the deformation field generated by the acoustic wave of S type. In dependence of the parameters, the presence of deformation can either enhance or reduce the pair creation cross-section. This can be used to control the parameters of the positron sources for storage rings and colliders.

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

    PubMed

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

    2012-09-01

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

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

    SciTech Connect

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

    2003-01-29

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

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

    PubMed Central

    Razmara, Jafar; Deris, Safaai; Parvizpour, Sepideh

    2011-01-01

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

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

    SciTech Connect

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

    2015-09-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    SciTech Connect

    Ziegler, J.; Satogata, T.

    2011-03-28

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

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

    PubMed

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

    2015-09-01

    Initially in the Indus-2 storage ring, the closed orbit distortion (COD) could be best corrected to 1.3 mm rms in the horizontal and 0.43 mm rms in the vertical plane. The strength of the corrector magnets required high values for COD correction. This revealed that offsets in COD readout by the beam position monitors (BPMs) played a role in not achieving a rms COD lower than the above value. Thus, the offset between the electrical center of BPMs and the magnetic center of the nearest quadrupole magnet could be estimated using the beam based alignment (BBA) method. It prefers that the quadrupole magnet is able to be controlled individually and active shunt power supply (ASPS) system was designed for this purpose that works efficiently. This paper describes the methodology of BBA, topology of ASPS and its performance, and COD minimization using the measured BPM offsets. After BBA, the COD could be reduced to 0.45 mm rms and 0.2 mm rms in horizontal and vertical planes, respectively. PMID:26429436

  15. Physics of base-pairing dynamics in DNA

    NASA Astrophysics Data System (ADS)

    Manghi, Manoel; Destainville, Nicolas

    2016-05-01

    As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque-driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain orientational degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain orientational degrees of freedom can be integrated out, and the quasi-static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.

  16. Base pairing properties of O/sup 6/-methylguanine

    SciTech Connect

    Williams, L.D.; Shaw, B.R.

    1986-05-01

    Alkyl adducts at the O/sup 6/ position of guanine are understood to be particularly important in the process of mutagenesis. The hydrogen bonding interactions of O/sup 6/-methylguanine (O/sup 6/MeG) with potential base complements in chloroform-d have been investigated by /sup 1/H NMR. For these studies, the authors have employed nucleosides with ribose hydroxyls blocked by triisopropylsilyl groups. The authors have seen that O/sup 6/MeG forms a mispair with thymine (T). However, only under certain circumstances does O/sup 6/MeG interact with cytosine (C). Although no observable interaction occurs between unprotonated C and O/sup 6/MeG, protonated C does base pair with O/sup 6/MeG. Assuming that RNA and DNA polymerases incorporate the physiologically predominant (unionized) form of each base, which may then be protonated, the data accounts both for the coding preference of O/sup 6/MeG for T and for the relatively high stability of the O/sup 6/MeG:C base pair in oligonucleotides.

  17. Constructing optimal backbone segments for joining fixed DNA base pairs.

    PubMed Central

    Mazur, J; Jernigan, R L; Sarai, A

    1996-01-01

    A method is presented to link a sequence of space-fixed base pairs by the sugar-phosphate segments of single nucleotides and to evaluate the effects in the backbone caused by this positioning of the bases. The entire computational unit comprises several nucleotides that are energy-minimized, subject to constraints imposed by the sugar-phosphate backbone segments being anchored to space-fixed base pairs. The minimization schemes are based on two stages, a conjugate gradient method followed by a Newton-Raphson algorithm. Because our purpose is to examine the response, or relaxation, of an artificially stressed backbone, it is essential to be able to obtain, as closely as possible, a lowest minimum energy conformation of the backbone segment in conformational space. For this purpose, an algorithm is developed that leads to the generation of an assembly of many local energy minima. From these sets of local minima, one conformation corresponding to the one with the lowest minimum is then selected and designated to represent the backbone segment at its minimum. The effective electrostatic potential of mean force is expressed in terms of adjustable parameters that incorporate solvent screening action in the Coulombic interactions between charged backbone atoms; these parameters are adjusted to obtain the best fit of the nearest-neighbor phosphorous atoms in an x-ray structure. PMID:8874023

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

    PubMed

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

    2014-03-01

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

  19. Detection of base-pair mismatches in DNA using graphene-based nanopore device

    NASA Astrophysics Data System (ADS)

    Kundu, Sourav; Karmakar, S. N.

    2016-04-01

    We present a unique way to detect base-pair mismatches in DNA, leading to a different epigenetic disorder by the method of nanopore sequencing. Based on a tight-binding formulation of a graphene-based nanopore device, using the Green’s function approach we study the changes in the electronic transport properties of the device as we translocate a double-stranded DNA through the nanopore embedded in a zigzag graphene nanoribbon. In the present work we are not only successful in detecting the usual AT and GC pairs but also a set of possible mismatches in the complementary base pairing.

  20. Comparison of Kilovoltage Cone-Beam Computed Tomography With Megavoltage Projection Pairs for Paraspinal Radiosurgery Patient Alignment and Position Verification

    SciTech Connect

    Kriminski, Sergey A. Lovelock, D. Michael; Seshan, Venkatraman E.; Ali, Imad; Munro, Peter; Amols, Howard I.; Fuks, Zvi; Bilsky, Mark; Yamada, Yoshiya

    2008-08-01

    Purpose: Implanted gold markers and megavoltage (MV) portal imaging are commonly used for setup verification of paraspinal tumors treated with high-dose, single-fraction radiotherapy. We investigated whether the use of kilovoltage cone-beam computed tomography (CBCT) imaging eliminates the need for marker implantation. Methods and Materials: Patients with paraspinal disease who were eligible for single-fraction stereotactic body radiotherapy were accrued to an institutional review board-approved protocol. Each of 16 patients underwent implantation of fiducial markers near the target. The markers were visible on the MV images. Three MV image pairs were acquired for each patient (initial, verification, and final) and were registered to the reference images. Every MV pair was complemented by a CBCT scan. CBCT image registration was performed automatically by maximizing the mutual information using a region of interest that excluded the markers. The corrections, as determined from the MV images, were compared with these from CBCT and were used for actual patient setup. Results: The mean and standard deviation of the absolute values of the differences between the CBCT and MV corrections were 1.0 {+-} 0.7, 1.0 {+-} 0.6, and 1.0 {+-} 0.8 mm for the left-right, anteroposterior, and superoinferior directions, respectively. The absolute differences between the corresponding pre- and post-treatment kilovoltage CBCT image registration were 0.6 {+-} 0.5, 0.6 {+-} 0.5, and 1.0 {+-} 0.8 mm. Conclusion: The setup corrections found using CBCT without the use of implanted markers were consistent with the marker registration on MV projections. CBCT has additional advantages, including better positioning precision and robust automatic three-dimensional registration, as well as eliminating the need for invasive marker implantation. We have adopted CBCT for the setup of all single-fraction paraspinal patients. Our data have also demonstrated that target displacements during treatment

  1. Using Pair Programming to Teach CAD Based Engineering Graphics

    ERIC Educational Resources Information Center

    Leland, Robert P.

    2010-01-01

    Pair programming was introduced into a course in engineering graphics that emphasizes solid modeling using SolidWorks. In pair programming, two students work at a single computer, and periodically trade off roles as driver (hands on the keyboard and mouse) and navigator (discuss strategy and design issues). Pair programming was used in a design…

  2. Nonclassically paired photons from sources based on cold atoms

    NASA Astrophysics Data System (ADS)

    Głódź, Małgorzata; Janowicz, Maciej; Kowalski, Krzysztof; Szonert, Jerzy

    2015-01-01

    In this short review some essentials concerning creation and testing of nonclassically correlated photons (biphotons) are given. In the introduction we remind the role which the experimentally produced entangled states have been playing for the foundations of the quantum physics, by witnessing against the model of local hidden variables. The well established sources of biphotons are based on spontaneous parametric down conversion in nonlinear crystals. A popular source with two BBO crystals is described, which generates pairs of photons nearly maximally entangled in polarization. Crystalbased sources rely on intrinsically broadband transitions, therefore thus produced biphotons are also broadband. Additional efforts (like applying optical cavities) are needed to reach narrowband biphotons which would comply with the requirements of some implementations in the quantum communication science. The topical issue of our article is a review of another, more recent approaches based on narrowband transitions between levels in cold atoms. Such method provides naturally narrowband biphotons. First, the principles are given of an atomic source of nonclassically paired photons, which is operated in a pulsed write-read mode. Such source is based on two separated in time Raman transitions triggered successively in two Λ-schemes. Next, cw-mode sources based (mainly) on spontaneous four wave mixing process (SFWM) are presented in a generic four-level scheme. Some underlying physics is sketched and profiles of biphoton correlation functions in the time domain are explained. Among other presented SFWM sources, one proves in testing high degree entanglement of generated biphotons, both in time-frequency and polarization (hyperentanglement).

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

    PubMed

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

    2014-01-01

    The initial alignment of the Inertial Measurement Unit (IMU) is an important process of INS to determine the coordinate transformation matrix which is used in the integration of Global Positioning Systems (GPS) with Inertial Navigation Systems (INS). In this paper a novel alignment method for a disturbed base, such as a vehicle disturbed by wind outdoors, implemented with the aid of a Vondrak low pass filter, is proposed. The basic principle of initial alignment including coarse alignment and fine alignment is introduced first. The spectral analysis is processed to compare the differences between the characteristic error of INS force observation on a stationary base and on disturbed bases. In order to reduce the high frequency noise in the force observation more accurately and more easily, a Vondrak low pass filter is constructed based on the spectral analysis result. The genetic algorithms method is introduced to choose the smoothing factor in the Vondrak filter and the corresponding objective condition is built. The architecture of the proposed alignment method with the Vondrak low pass filter is shown. Furthermore, simulated experiments and actual experiments were performed to validate the new algorithm. The results indicate that, compared with the conventional alignment method, the Vondrak filter could eliminate the high frequency noise in the force observation and the proposed alignment method could improve the attitude accuracy. At the same time, only one parameter needs to be set, which makes the proposed method easier to implement than other low-pass filter methods. PMID:25513826

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

    PubMed Central

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

    2014-01-01

    The initial alignment of the Inertial Measurement Unit (IMU) is an important process of INS to determine the coordinate transformation matrix which is used in the integration of Global Positioning Systems (GPS) with Inertial Navigation Systems (INS). In this paper a novel alignment method for a disturbed base, such as a vehicle disturbed by wind outdoors, implemented with the aid of a Vondrak low pass filter, is proposed. The basic principle of initial alignment including coarse alignment and fine alignment is introduced first. The spectral analysis is processed to compare the differences between the characteristic error of INS force observation on a stationary base and on disturbed bases. In order to reduce the high frequency noise in the force observation more accurately and more easily, a Vondrak low pass filter is constructed based on the spectral analysis result. The genetic algorithms method is introduced to choose the smoothing factor in the Vondrak filter and the corresponding objective condition is built. The architecture of the proposed alignment method with the Vondrak low pass filter is shown. Furthermore, simulated experiments and actual experiments were performed to validate the new algorithm. The results indicate that, compared with the conventional alignment method, the Vondrak filter could eliminate the high frequency noise in the force observation and the proposed alignment method could improve the attitude accuracy. At the same time, only one parameter needs to be set, which makes the proposed method easier to implement than other low-pass filter methods. PMID:25513826

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

    ERIC Educational Resources Information Center

    Morton, Christopher

    2013-01-01

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

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

    SciTech Connect

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

    2008-04-02

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

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

    SciTech Connect

    Emma, P.

    1992-03-01

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

  8. Prokaryotic Phylogeny Based on Complete Genomes Without Sequence Alignment

    NASA Astrophysics Data System (ADS)

    Hao, Bailin; Qi, Ji; Wang, Bin

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

  9. CATO: The Clone Alignment Tool.

    PubMed

    Henstock, Peter V; LaPan, Peter

    2016-01-01

    High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1) a top-level summary of the top candidate sequences aligned to each reference sequence, 2) a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3) a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow. PMID:27459605

  10. CATO: The Clone Alignment Tool

    PubMed Central

    Henstock, Peter V.; LaPan, Peter

    2016-01-01

    High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1) a top-level summary of the top candidate sequences aligned to each reference sequence, 2) a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3) a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow. PMID:27459605

  11. Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies.

    PubMed

    Roy, Ashim; Panigrahi, Swati; Bhattacharyya, Malyasri; Bhattacharyya, Dhananjay

    2008-03-27

    The importance of non-Watson-Crick base pairs in the three-dimensional structure of RNA is now well established. The structure and stability of these noncanonical base pairs are, however, poorly understood. We have attempted to understand structural features of 33 frequently occurring base pairs using density functional theory. These are of three types, namely (i) those stabilized by two or more polar hydrogen bonds between the bases, (ii) those having one polar and another C-H...O/N type interactions, and (iii) those having one H-bond between the bases and another involving one of the sugars linked to the bases. We found that the base pairs having two polar H-bonds are very stable as compared to those having one C-H...O/N interaction. Our quantitatively analysis of structures of these optimized base pairs indicates that they possess a different amount of nonplanarity with large propeller or buckle values as also observed in the crystal structures. We further found that geometry optimization does not modify the hydrogen-bonding pattern, as values of shear and open angle of the base pairs remain conserved. The structures of initial crystal geometry and final optimized geometry of some base pairs having only one polar H-bond and a C-H...O/N interaction, however, are significantly different, indicating the weak nature of the nonpolar interaction. The base pair flexibility, as measured from normal-mode analysis, in terms of the intrinsic standard deviations of the base pair structural parameters are in conformity with those calculated from RNA crystal structures. We also noticed that deformation of a base pair along the stretch direction is impossible for all of the base pairs, and movements of the base pairs along shear and open are also quite restricted. The base pair opening mode through alteration of propeller or buckle is considerably less restricted for most of the base pairs. PMID:18318519

  12. Prokaryotic Phylogeny Based on Complete Genomes Without Sequence Alignment

    NASA Astrophysics Data System (ADS)

    Hao, Bailin; Qi, Ji; Wang, Bin

    2003-04-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  15. hst2galign: an Automated Galaxy-based Alignment Routine

    NASA Astrophysics Data System (ADS)

    Anderson, Jay; Ogaz, Sara

    2014-10-01

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

  16. Observation of a vh{sub 11/2} pair alignment in neutron-rich {sup 118}Pd

    SciTech Connect

    Zhang, X. Q.; Hamilton, J. H.; Ramayya, A. V.; Zhu, S. J.; Hwang, J. K.; Beyer, C. J.; Kormicki, J.; Jones, E. F.; Gore, P. M.; Babu, B. R. S.

    2001-02-01

    The yrast band was significantly extended to 14{sup +} and the {gamma} band to 5{sup +} in neutron-rich {sup 118}Pd by measuring the {gamma}-{gamma}-{gamma} coincidences emitted from the spontaneous fission of {sup 252}Cf with Gammasphere. The first band crossing was observed in the yrast band in {sup 118}Pd at a frequency of {Dirac_h}{omega}{approx}0.36 MeV at the starting point of the backbending, which is similar to that found in {sup 112-116}Pd. The first bandbending in the yrast cascade in {sup 118}Pd is interpreted to be built on a two h{sub 11/2} neutron configuration based on its similarity to the yrast bands in even-even {sup 112-116}Pd. Our result indicates {sup 118}Pd still maintains a prolate shape. The quasineutron Routhian calculations indicate a lower crossing frequency for the h{sub 11/2} level.

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

    NASA Astrophysics Data System (ADS)

    Shen, Li; Makedon, Fillia; Saykin, Andrew

    2004-05-01

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

  18. Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.

    PubMed

    Sponer, Judit E; Spacková, Nad'a; Kulhanek, Petr; Leszczynski, Jerzy; Sponer, Jirí

    2005-03-17

    Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions. PMID:16838999

  19. Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA.

    PubMed

    Vengut-Climent, Empar; Gómez-Pinto, Irene; Lucas, Ricardo; Peñalver, Pablo; Aviñó, Anna; Fonseca Guerra, Célia; Bickelhaupt, F Matthias; Eritja, Ramón; González, Carlos; Morales, Juan C

    2016-07-18

    Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside-RNA recognition, glucose-nucleobase pairs have been examined. Deoxyoligonucleotides with a 6-deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6-Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6-deoxyglucose-guanine pair closely resembles a purine-pyrimidine geometry. Quantum chemical calculations indicate that glucose-purine pairs are as stable as a natural T-A pair. PMID:27328804

  20. Evaluation of the Quantitative Accuracy of 3D Reconstruction of Edentulous Jaw Models with Jaw Relation Based on Reference Point System Alignment

    PubMed Central

    Li, Weiwei; Yuan, Fusong; Lv, Peijun; Wang, Yong; Sun, Yuchun

    2015-01-01

    Objectives To apply contact measurement and reference point system (RPS) alignment techniques to establish a method for 3D reconstruction of the edentulous jaw models with centric relation and to quantitatively evaluate its accuracy. Methods Upper and lower edentulous jaw models were clinically prepared, 10 pairs of resin cylinders with same size were adhered to axial surfaces of upper and lower models. The occlusal bases and the upper and lower jaw models were installed in the centric relation position. Faro Edge 1.8m was used to directly obtain center points of the base surface of the cylinders (contact method). Activity 880 dental scanner was used to obtain 3D data of the cylinders and the center points were fitted (fitting method). 3 pairs of center points were used to align the virtual model to centric relation. An observation coordinate system was interactively established. The straight-line distances in the X (horizontal left/right), Y (horizontal anterior/posterior), and Z (vertical) between the remaining 7 pairs of center points derived from contact method and fitting method were measured respectively and analyzed using a paired t-test. Results The differences of the straight-line distances of the remaining 7 pairs of center points between the two methods were X: 0.074 ± 0.107 mm, Y: 0.168 ± 0.176 mm, and Z: −0.003± 0.155 mm. The results of paired t-test were X and Z: p >0.05, Y: p <0.05. Conclusion By using contact measurement and the reference point system alignment technique, highly accurate reconstruction of the vertical distance and centric relation of a digital edentulous jaw model can be achieved, which meets the design and manufacturing requirements of the complete dentures. The error of horizontal anterior/posterior jaw relation was relatively large. PMID:25659133

  1. Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism

    PubMed Central

    Yusupov, Marat; Yusupova, Gulnara

    2014-01-01

    The natural bases of nucleic acids have a strong preference for one tautomer form, guaranteeing fidelity in their hydrogen bonding potential. However, base pairs observed in recent crystal structures of polymerases and ribosomes are best explained by an alternative base tautomer, leading to the formation of base pairs with Watson-Crick-like geometries. These observations set limits to geometric selection in molecular recognition of complementary Watson-Crick pairs for fidelity in replication and translation processes. PMID:24765524

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

    SciTech Connect

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

    2005-05-16

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

  3. Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs

    SciTech Connect

    Wu, Yuan-Yan; Bao, Lei; Zhang, Xi; Tan, Zhi-Jie

    2015-03-28

    Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5–50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ∼6 bps at each helix end. Correspondingly, the apparent persistence length l{sub p} of short DNAs increases gradually from ∼29 nm to ∼45 nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ∼6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with l{sub p} ∼ 50 nm.

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

    PubMed Central

    Yang, Zhengfan; Penczek, Pawel A.

    2008-01-01

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

  5. Raising the barrier for photoinduced DNA charge injection with a cyclohexyl artificial base pair.

    PubMed

    Singh, Arunoday P N; Harris, Michelle A; Young, Ryan M; Miller, Stephen A; Wasielewski, Michael R; Lewis, Frederick D

    2015-01-01

    The effects of an artificial cyclohexyl base pair on the quantum yields of fluorescence and dynamics of charge separation and charge recombination have been investigated for several synthetic DNA hairpins. The hairpins possess stilbenedicarboxamide, perylenediimide, or naphthalenediimide linkers and base-paired stems. In the absence of the artificial base pair hole injection into both adenine and guanine purine bases is exergonic and irreversible, except in the case of stilbene with adenine for which it is slightly endergonic and reversible. Insertion of the artificial base pair renders hole injection endergonic or isoergonic except in the case of the powerful naphthalene acceptor for which it remains exergonic. Both hole injection and charge recombination are slower for the naphthalene acceptor in the presence of the artificial base pair than in its absence. The effect of an artificial base pair on charge separation and charge recombination in hairpins possessing stilbene and naphthalene acceptor linkers and a stilbenediether donor capping group has also been investigated. In the case of the stilbene acceptor-stilbene donor capped hairpins photoinduced charge separation across six base pairs is efficient in the absence of the artificial base pair but does not occur in its presence. In the case of the naphthalene acceptor-stilbene donor capped hairpins the artificial base pair slows but does not stop charge separation and charge recombination, leading to the formation of long-lived charge separated states. PMID:26442603

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

    NASA Astrophysics Data System (ADS)

    Brandt, Rasmus; Mochaourab, Rami; Bengtsson, Mats

    2016-04-01

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

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

    PubMed

    Gladish, James C; Duncan, Donald D

    2014-06-20

    It is well known that in liquid crystal (LC)-based active polarimetry, alignment and temperature effects impact polarimeter performance. Practically speaking, when constructing a polarimetric measurement system from LC variable retarders (LCVRs), unavoidable alignment and temperature uncertainties will occur, leading to systematic error that propagates to the Mueller matrix. Typical calibration methods use only a single metric to assess polarimeter performance (the condition number) and often ignore the relationship between systematic error and specific Mueller matrix elements. Here we explore alignment and temperature effects in a Stokes generator and polarimeter, each consisting of two LCVRs, through a series of simulations to calibrate the polarimeter and measure the Mueller matrix of air. We achieve this by modifying an existing LCVR model to incorporate alignment and temperature effects. This new approach offers insight into employing LCVRs individually and associating particular Mueller matrix element error with specific LCVR effects. PMID:24979431

  8. Terahertz detectors arrays based on orderly aligned InN nanowires

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Gao, Yang; Luo, Liaofu

    2012-01-15

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

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

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  11. A comprehensive classification of nucleic acid structural families based on strand direction and base pairing.

    PubMed Central

    Lavery, R; Zakrzewska, K; Sun, J S; Harvey, S C

    1992-01-01

    We propose a classification of DNA structures formed from 1 to 4 strands, based only on relative strand directions, base to strand orientation and base pairing geometries. This classification and its associated notation enable all nucleic acids to be grouped into structural families and bring to light possible structures which have not yet been observed experimentally. It also helps in understanding transitions between families and can assist in the design of multistrand structures. PMID:1383936

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

    PubMed

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

    2014-04-01

    The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This 'sequence-like' representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/ . PMID:23659291

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

    PubMed

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

    2015-11-01

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

  14. Database of non-canonical base pairs found in known RNA structures

    NASA Technical Reports Server (NTRS)

    Nagaswamy, U.; Voss, N.; Zhang, Z.; Fox, G. E.

    2000-01-01

    Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

  15. Alternative radical pairs for cryptochrome-based magnetoreception.

    PubMed

    Lee, Alpha A; Lau, Jason C S; Hogben, Hannah J; Biskup, Till; Kattnig, Daniel R; Hore, P J

    2014-06-01

    There is growing evidence that the remarkable ability of animals, in particular birds, to sense the direction of the Earth's magnetic field relies on magnetically sensitive photochemical reactions of the protein cryptochrome. It is generally assumed that the magnetic field acts on the radical pair [FAD•- TrpH•+] formed by the transfer of an electron from a group of three tryptophan residues to the photo-excited flavin adenine dinucleotide cofactor within the protein. Here, we examine the suitability of an [FAD•- Z•] radical pair as a compass magnetoreceptor, where Z• is a radical in which the electron spin has no hyperfine interactions with magnetic nuclei, such as hydrogen and nitrogen. Quantum spin dynamics simulations of the reactivity of [FAD•- Z•] show that it is two orders of magnitude more sensitive to the direction of the geomagnetic field than is [FAD•- TrpH•+] under the same conditions (50 µT magnetic field, 1 µs radical lifetime). The favourable magnetic properties of [FAD•- Z•] arise from the asymmetric distribution of hyperfine interactions among the two radicals and the near-optimal magnetic properties of the flavin radical. We close by discussing the identity of Z• and possible routes for its formation as part of a spin-correlated radical pair with an FAD radical in cryptochrome. PMID:24671932

  16. Reversed-phase ion-pair liquid chromatography method for purification of duplex DNA with single base pair resolution

    PubMed Central

    Wysoczynski, Christina L.; Roemer, Sarah C.; Dostal, Vishantie; Barkley, Robert M.; Churchill, Mair E. A.; Malarkey, Christopher S.

    2013-01-01

    Obtaining quantities of highly pure duplex DNA is a bottleneck in the biophysical analysis of protein–DNA complexes. In traditional DNA purification methods, the individual cognate DNA strands are purified separately before annealing to form DNA duplexes. This approach works well for palindromic sequences, in which top and bottom strands are identical and duplex formation is typically complete. However, in cases where the DNA is non-palindromic, excess of single-stranded DNA must be removed through additional purification steps to prevent it from interfering in further experiments. Here we describe and apply a novel reversed-phase ion-pair liquid chromatography purification method for double-stranded DNA ranging in lengths from 17 to 51 bp. Both palindromic and non-palindromic DNA can be readily purified. This method has the unique ability to separate blunt double-stranded DNA from pre-attenuated (n-1, n-2, etc) synthesis products, and from DNA duplexes with single base pair overhangs. Additionally, palindromic DNA sequences with only minor differences in the central spacer sequence of the DNA can be separated, and the purified DNA is suitable for co-crystallization of protein–DNA complexes. Thus, double-stranded ion-pair liquid chromatography is a useful approach for duplex DNA purification for many applications. PMID:24013567

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

    NASA Technical Reports Server (NTRS)

    Rakoczy, John; Steincamp, James; Taylor, Jaime

    2003-01-01

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

  18. Choline Ions Stabilize A-T Base Pairs by Fitting into Minor Groove

    NASA Astrophysics Data System (ADS)

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Sugimoto, Naoki

    In a Watson-Crick base paired DNA duplex, G-C base pairs are more stable than A-T base pairs. However, in solvent containing choline ions, the stabilities of these base pairs are reversed. To elucidate the mechanism through which choline ions exert this effect from a microscopic viewpoint, we performed molecular dynamics simulations. We found that choline ions interact with a DNA duplex through multiple hydrogen bonds. The affinity of choline ion for the minor groove of A-T base pairs was higher than that for the major groove. The binding of choline ions to the minor groove of A-T base pairs supports groove formation without disturbing the formation of hydrogen bonds between the base pairs. In contrast, choline ions inhibit the formation of hydrogen bonds between G-C base pairs by binding to atoms of these bases that are involved in Watson-Crick hydrogen bonding. These findings will help us understand the stabilities of canonical DNA structures under the crowded conditions inside cells.

  19. Development of artificial nucleic acid that recognizes a CG base pair in triplex DNA formation.

    PubMed

    Hari, Yoshiyuki

    2013-01-01

    An oligonucleotide that can form a triplex with double-stranded DNA is called a triplex-forming oligonucleotide (TFO). TFOs have gained considerable attention because of their potential as gene targeting tools. However, triplex DNA formation involves inherent problems for practical use. The most important problem is that natural nucleotides in TFO do not have sufficient affinity and base pair-selectivity to pyrimidine-purine base pair, like a CG or TA base pair, within dsDNA. This suggests that dsDNA region including a CG or TA base pair cannot be targeted. Therefore, artificial nucleotides, especially with non-natural nucleobases, capable of direct recognition of a CG or TA base pair via hydrogen bond formation have been developed; however, nucleotides with better selectivity and stronger affinity are necessary for implementing this dsDNA-targeting technology using TFOs. Under such a background, we considered that facile and efficient synthesis of various nucleobase derivatives in TFOs would be useful for finding an ideal nucleobase for recognition of a CG or TA base pair because detailed and rational exploration of nucleobase structures is facilitated. Recently, to develop a nucleobase recognizing a CG base pair, we have used post-elongation modification, i.e., modification after oligonucleotide synthesis, for the facile synthesis of nucleobase derivatives. This review mainly summarizes our recent findings on the development of artificial nucleobases and nucleotides for recognition of a CG base pair in triplexes formed between dsDNA and TFOs. PMID:24189561

  20. Conducting Task-Based Interviews with Pairs of Children: Consensus, Conflict, Knowledge Construction and Turn Taking

    ERIC Educational Resources Information Center

    Houssart, Jenny; Evens, Hilary

    2011-01-01

    This article explores theoretical and methodological issues associated with task-based interviews conducted with pairs of children. We explore different approaches to interviews from sociological, psychological and subject-based perspectives. Our interviews, concerning mathematical questions and carried out with pairs of 10 and 11-year-olds, are…

  1. The Impact of a Peer-Learning Agent Based on Pair Programming in a Programming Course

    ERIC Educational Resources Information Center

    Han, Keun-Woo; Lee, EunKyoung; Lee, YoungJun

    2010-01-01

    This paper analyzes the educational effects of a peer-learning agent based on pair programming in programming courses. A peer-learning agent system was developed to facilitate the learning of a programming language through the use of pair programming strategies. This system is based on the role of a peer-learning agent from pedagogical and…

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

    PubMed

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

    2015-09-15

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

  3. Curriculum Alignment Research Suggests that Alignment Can Improve Student Achievement

    ERIC Educational Resources Information Center

    Squires, David

    2012-01-01

    Curriculum alignment research has developed showing the relationship among three alignment categories: the taught curriculum, the tested curriculum and the written curriculum. Each pair (for example, the taught and the written curriculum) shows a positive impact for aligning those results. Following this, alignment results from the Third…

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

    PubMed

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

    2016-08-11

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2016-07-01

    It is well documented that electrospun tissue engineering scaffolds can be fabricated with variable degrees of fiber alignment to produce scaffolds with anisotropic mechanical properties. Several attempts have been made to quantify the degree of fiber alignment within an electrospun scaffold using image-based methods. However, these methods are limited by the inability to produce a quantitative measure of alignment that can be used to make comparisons across publications. Therefore, we have developed a new approach to quantifying the alignment present within a scaffold from scanning electron microscopic (SEM) images. The alignment is determined by using the Sobel approximation of the image gradient to determine the distribution of gradient angles with an image. This data was fit to a Von Mises distribution to find the dispersion parameter κ, which was used as a quantitative measure of fiber alignment. We fabricated four groups of electrospun polycaprolactone (PCL) + Gelatin scaffolds with alignments ranging from κ = 1.9 (aligned) to κ = 0.25 (random) and tested our alignment quantification method on these scaffolds. It was found that our alignment quantification method could distinguish between scaffolds of different alignments more accurately than two other published methods. Additionally, the alignment parameter κ was found to be a good predictor the mechanical anisotropy of our electrospun scaffolds. The ability to quantify fiber alignment within and make direct comparisons of scaffold fiber alignment across publications can reduce ambiguity between published results where cells are cultured on "highly aligned" fibrous scaffolds. This could have important implications for characterizing mechanics and cellular behavior on aligned tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1680-1686, 2016. PMID:26939754

  7. Lewis pair polymerization by classical and frustrated Lewis pairs: acid, base and monomer scope and polymerization mechanism.

    PubMed

    Zhang, Yuetao; Miyake, Garret M; John, Mallory G; Falivene, Laura; Caporaso, Lucia; Cavallo, Luigi; Chen, Eugene Y-X

    2012-08-14

    Classical and frustrated Lewis pairs (LPs) of the strong Lewis acid (LA) Al(C(6)F(5))(3) with several Lewis base (LB) classes have been found to exhibit exceptional activity in the Lewis pair polymerization (LPP) of conjugated polar alkenes such as methyl methacrylate (MMA) as well as renewable α-methylene-γ-butyrolactone (MBL) and γ-methyl-α-methylene-γ-butyrolactone (γ-MMBL), leading to high molecular weight polymers, often with narrow molecular weight distributions. This study has investigated a large number of LPs, consisting of 11 LAs as well as 10 achiral and 4 chiral LBs, for LPP of 12 monomers of several different types. Although some more common LAs can also be utilized for LPP, Al(C(6)F(5))(3)-based LPs are far more active and effective than other LA-based LPs. On the other hand, several classes of LBs, when paired with Al(C(6)F(5))(3), can render highly active and effective LPP of MMA and γ-MMBL; such LBs include phosphines (e.g., P(t)Bu(3)), chiral chelating diphosphines, N-heterocyclic carbenes (NHCs), and phosphazene superbases (e.g., P(4)-(t)Bu). The P(4)-(t)Bu/Al(C(6)F(5))(3) pair exhibits the highest activity of the LP series, with a remarkably high turn-over frequency of 9.6 × 10(4) h(-1) (0.125 mol% catalyst, 100% MMA conversion in 30 s, M(n) = 2.12 × 10(5) g mol(-1), PDI = 1.34). The polymers produced by LPs at RT are typically atactic (P(γ)MMBL with ∼47% mr) or syndio-rich (PMMA with ∼70-75% rr), but highly syndiotactic PMMA with rr ∼91% can be produced by chiral or achiral LPs at -78 °C. Mechanistic studies have identified and structurally characterized zwitterionic phosphonium and imidazolium enolaluminates as the active species of the current LPP system, which are formed by the reaction of the monomer·Al(C(6)F(5))(3) adduct with P(t)Bu(3) and NHC bases, respectively. Kinetic studies have revealed that the MMA polymerization by the (t)Bu(3)P/Al(C(6)F(5))(3) pair is zero-order in monomer concentration after an initial

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    PubMed

    Witman, S; Gefen, A; Barnea, O

    2007-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Hu, Ya-bin; Wang, Miao

    2015-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    Serin, Gökhan

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  15. Pairing state with a time-reversal symmetry breaking in FeAs-based superconductors

    SciTech Connect

    Lee, Wei-Sheng

    2010-05-26

    We investigate the competition between the extended s{+-} wave and dx2-y2 -wave pairing order parameters in the iron-based superconductors. Because of the frustrating pairing interactions among the electron and the hole fermi pockets, a time-reversal symmetry breaking s + id pairing state could be favored. We analyze this pairing state within the Ginzburg-Landau theory, and explore the experimental consequences. In such a state, spatial inhomogeneity induces supercurrent near a non-magnetic impurity and the corners of a square sample. The resonance mode between the s{+-} and dx2?y2 -wave order parameters can be detected through the B1g-Raman spectroscopy.

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

    PubMed

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

    2015-12-01

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

  17. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues

    SciTech Connect

    Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri; Sumpter, Bobby G; Fuentes-Cabrera, Miguel A; Vazquez-Mayagoitia, Alvaro

    2010-01-01

    Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.

  18. Thermodynamics of the formation of Ag(I)-mediated azole base pairs in DNA duplexes.

    PubMed

    Schweizer, Kristina; Léon, J Christian; Ravoo, Bart Jan; Müller, Jens

    2016-07-01

    Isothermal titration calorimetry was applied to determine the thermodynamic parameters for the specific binding of Ag(I) ions to a series of DNA duplexes comprising Im:Im or Tr:Tr mispairs to form metal-mediated Im-Ag(I)-Im or Tr-Ag(I)-Tr base pairs (Im=imidazole nucleoside; Tr=1.2,4-triazole nucleoside). A total of seven different duplexes are discussed, incorporating one to three artificial base pairs in neighboring or non-neighboring positions. The association constant related to the formation of Tr-Ag(I)-Tr base pairs is estimated to be <10(3)M(-1). In contrast, Im-Ag(I)-Im base pairs are much more stable. The intrinsic association constant for their formation is in the order of 10(6)M(-1) and is therefore larger than that for the formation of T-Hg(II)-T and C-Ag(I)-C base pairs consisting of natural nucleobases. Two neighboring Im-Ag(I)-Im base pairs form cooperatively, whereas two remotely located Im-Ag(I)-Im base pairs form non-cooperatively. In general, the specific binding of Ag(I) to Im:Im-containing duplexes is enthalpically driven, with a significant additional entropic contribution in most cases. PMID:27032292

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

    PubMed Central

    Katoh, Kazutaka; Standley, Daron M.

    2016-01-01

    Motivation: We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction. Results: The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, the effect of the proposed method is slightly negative in real protein-based benchmarks, and mostly neutral in simulation-based benchmarks. This approach is based on natural biological reasoning and should be compatible with many methods based on dynamic programming for multiple sequence alignment. Availability and implementation: The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/ Contact: katoh@ifrec.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153688

  20. An essential non-Watson-Crick base pair motif in 3'UTR to mediate selenoprotein translation.

    PubMed Central

    Walczak, R; Carbon, P; Krol, A

    1998-01-01

    The SECIS element is an RNA hairpin in the 3'UTR of selenoprotein mRNAs required for decoding UGA selenocysteine codons. Our experimentally derived 2D structure model for the SECIS RNA revealed the conservation of four consecutive non-Watson-Crick base pairs, with a central G.A/A.G tandem. The present study was dedicated to gaining insight into the role of this quartet of base pairs. The effects of mutations introduced into the SECIS quartet of the glutathione peroxidase (GPx) cDNA, an enzyme with selenocysteine in its active center, were reported in vivo by the GPx activity. The detrimental consequence of an all-Watson-Crick mutant quartet disclosed the paramount importance of the non-Watson-Crick base pairs for GPx activity. Next, structure probing established that base pair changes in the central G.A/A.G tandem, predicted by the model to be structurally unfavorable, effectively led to local opening of the helix at the quartet. A concomitant abolition of GPx activity was observed, arising from translational impairment of full-length GPx. In contrast, an isosteric base pair replacement in the tandem did not affect base pairing in the quartet, leading to an almost wt GPx activity. Collectively, the data provided conclusive evidence for the functional relevance of these non-Watson-Crick base pairs in vivo, thus identifying a noncanonical RNA motif crucial to SECIS function in mediating selenoprotein translation. Within the quartet, the prominent requirement for the central G.A/A.G tandem is highlighted, our previous structural model and the mutagenesis data presented here strongly arguing in favor of a sheared arrangement for the G.A base pairs. The SECIS RNA is therefore another member to be added to the growing list of RNAs containing building blocks of non-Watson-Crick base pairs, required for structure and/or function. PMID:9436910

  1. Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins

    PubMed Central

    Renaud, Nicolas; Berlin, Yuri A.; Ratner, Mark A.

    2013-01-01

    Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine base pair shifts from the beginning to the end of the sequence. Although these results are in agreement with recent experimental findings, the mechanism governing the charge migration along these sequences is revisited here. Instead of the phenomenological two-step hopping mechanism via the guanine base, the charge propagation occurs through a delocalization of the hole density along the base pair stack. Furthermore, the variations of the charge transfer with the position of the guanine base are explained by the impact of the base pair substitutions on the delocalized conduction channels. PMID:23980166

  2. Alignments of RNA structures.

    PubMed

    Blin, Guillaume; Denise, Alain; Dulucq, Serge; Herrbach, Claire; Touzet, Hélène

    2010-01-01

    We describe a theoretical unifying framework to express the comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences and encompasses the main existing models for RNA structure comparison based on trees and arc-annotated sequences with a variety of edit operations. It also gives rise to edit models that have not been studied yet. We provide a thorough analysis of the alignment hierarchy, including a new polynomial-time algorithm and an NP-completeness proof. The polynomial-time algorithm involves biologically relevant edit operations such as pairing or unpairing nucleotides. It has been implemented in a software, called gardenia, which is available at the Web server http://bioinfo.lifl.fr/RNA/gardenia. PMID:20431150

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

    PubMed Central

    Hatje, Klas; Kollmar, Martin

    2012-01-01

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

  4. A cohesin-based structural platform supporting homologous chromosome pairing in meiosis.

    PubMed

    Ding, Da-Qiao; Haraguchi, Tokuko; Hiraoka, Yasushi

    2016-08-01

    The pairing and recombination of homologous chromosomes during the meiotic prophase is necessary for the accurate segregation of chromosomes in meiosis. However, the mechanism by which homologous chromosomes achieve this pairing has remained an open question. Meiotic cohesins have been shown to affect chromatin compaction; however, the impact of meiotic cohesins on homologous pairing and the fine structures of cohesion-based chromatin remain to be determined. A recent report using live-cell imaging and super-resolution microscopy demonstrated that the lack of meiotic cohesins alters the chromosome axis structures and impairs the pairing of homologous chromosomes. These results suggest that meiotic cohesin-based chromosome axis structures are crucial for the pairing of homologous chromosomes. PMID:26856595

  5. Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson–Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine

    PubMed Central

    2016-01-01

    5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5′-CG-3′ sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5′-T8X9G10-3′ sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A5:T8, whereas 5caC did not. At the oxidized base pair G4:X9, 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C3:G10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G4:X9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes. PMID:25632825

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

    PubMed Central

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

    2015-01-01

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

  7. SURVEY AND SUMMARY: The non-Watson–Crick base pairs and their associated isostericity matrices

    PubMed Central

    Leontis, Neocles B.; Stombaugh, Jesse; Westhof, Eric

    2002-01-01

    RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson–Crick base pairing, forming motifs that mediate long-range RNA–RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases contain the annotation of such base pairs. An unambiguous and descriptive nomenclature was proposed recently in which RNA base pairs were classified by the base edges participating in the interaction (Watson–Crick, Hoogsteen/CH or sugar edge) and the orientation of the glycosidic bonds relative to the hydrogen bonds (cis or trans). Twelve basic geometric families were identified and all 12 have been observed in crystal structures. For each base pairing family, we present here the 4 × 4 ‘isostericity matrices’ summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U. Whenever available, a representative example of each observed base pair from X-ray crystal structures (3.0 Å resolution or better) is provided or, otherwise, theoretically plausible models. This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs. PMID:12177293

  8. Isomers of the DNA bases and their possible role in base pair mismatch

    NASA Astrophysics Data System (ADS)

    Michaelian, Karo; Romero, Aldo

    2004-03-01

    We have found stable isomers of the two DNA purines, adenine and guanine, in global searches using a force field potential and ab initio local relaxations. The stability characteristics were investigated by searching for the lowest energy connecting saddles, and by using Car-Parrinello molecular dynamics. Expected equilibrium concentrations and possible non-equilibrium production mechanisms are discussed. It is suggested that these isomers may play a role in base-pair miss-match leading to point mutation of the gnome, and in a number of other important biological processes based on the purine structures.

  9. Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs

    PubMed Central

    Wright, A.; Krousel-Wood, M.; Thomas, E. J.; McCoy, J. A.; Sittig, D. F.

    2015-01-01

    Summary Background Clinical knowledge bases of problem-medication pairs are necessary for many informatics solutions that improve patient safety, such as clinical summarization. However, developing these knowledge bases can be challenging. Objective We sought to validate a previously developed crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large, non-university health care system with a widely used, commercially available electronic health record. Methods We first retrieved medications and problems entered in the electronic health record by clinicians during routine care during a six month study period. Following the previously published approach, we calculated the link frequency and link ratio for each pair then identified a threshold cutoff for estimated problem-medication pair appropriateness through clinician review; problem-medication pairs meeting the threshold were included in the resulting knowledge base. We selected 50 medications and their gold standard indications to compare the resulting knowledge base to the pilot knowledge base developed previously and determine its recall and precision. Results The resulting knowledge base contained 26,912 pairs, had a recall of 62.3% and a precision of 87.5%, and outperformed the pilot knowledge base containing 11,167 pairs from the previous study, which had a recall of 46.9% and a precision of 83.3%. Conclusions We validated the crowdsourcing approach for generating a knowledge base of problem-medication pairs in a large non-university health care system with a widely used, commercially available electronic health record, indicating that the approach may be generalizable across healthcare settings and clinical systems. Further research is necessary to better evaluate the knowledge, to compare crowdsourcing with other approaches, and to evaluate if incorporating the knowledge into electronic health records improves patient outcomes. PMID:26171079

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  11. An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules

    PubMed Central

    Kimoto, Michiko; Kawai, Rie; Mitsui, Tsuneo; Yokoyama, Shigeyuki; Hirao, Ichiro

    2009-01-01

    Toward the expansion of the genetic alphabet, we present an unnatural base pair system for efficient PCR amplification, enabling the site-specific incorporation of extra functional components into DNA. This system can be applied to conventional PCR protocols employing DNA templates containing unnatural bases, natural and unnatural base triphosphates, and a 3′→5′ exonuclease-proficient DNA polymerase. For highly faithful and efficient PCR amplification involving the unnatural base pairing, we identified the natural-base sequences surrounding the unnatural bases in DNA templates by an in vitro selection technique, using a DNA library containing the unnatural base. The system facilitates the site-specific incorporation of a variety of modified unnatural bases, linked with functional groups of interest, into amplified DNA. DNA fragments (0.15 amol) containing the unnatural base pair can be amplified 107-fold by 30 cycles of PCR, with <1% total mutation rate of the unnatural base pair site. Using the system, we demonstrated efficient PCR amplification and functionalization of DNA fragments for the extremely sensitive detection of zeptomol-scale target DNA molecules from mixtures with excess amounts (pmol scale) of foreign DNA species. This unnatural base pair system will be applicable to a wide range of DNA/RNA-based technologies. PMID:19073696

  12. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.

    PubMed

    Chawla, Mohit; Oliva, Romina; Bujnicki, Janusz M; Cavallo, Luigi

    2015-08-18

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. 'modified base pairs'. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson-Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in. PMID:26117545

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

    PubMed

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

    2015-11-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2006-10-01

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

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Castellano, Richard; Akin, Cevat; Shan, Jerry

    2014-11-01

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

  18. Structural Implications of Homopyrimidine Base Pairs in the Parallel-Stranded d(YGA) Motif.

    PubMed

    Tripathi, Shailesh; Paukstelis, Paul J

    2016-06-16

    DNA can adopt many other structures beyond the canonical B-form double helix. These alternative DNA structures have become increasingly significant as new biological roles are found for them. Additionally, there has been a growing interest in using non-canonical base pairs to provide structural diversity for designing DNA architectures for nanotechnology applications. We recently described the crystal structure of d(ACTCGGATGAT), which forms a tetraplex through parallel-stranded homo-base pairs and nucleobase intercalation. The homoduplex region contains a d(YGA⋅YGA) motif observed in crystal and solution structures. Here, we examine the structural implications of the homopyrimidine base pair within this motif. We determined crystal structures of two variants that differ from the original structure in the homopyrimidine base pairs and number of d(YGA) motifs. Our results show that the intercalation-locked tetraplex motif is predictable in these different sequence contexts and that substituting C⋅C base pairs for T⋅T base pairs introduces asymmetry to the homoduplex. These results have important implications for utilizing d(YGA) motifs in DNA crystal design and could provide a basis for understanding how local structures could be associated with repeat expansions. PMID:26629965

  19. Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion

    PubMed Central

    Wenke, Belinda B.; Huiting, Leah N.; Frankel, Elisa B.; Lane, Benjamin F.; Núñez, Megan E.

    2014-01-01

    The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair Kop. In the normal duplex Kop decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a Kop of 8×10−7. In contrast, base pair opening at the 5’T of the thymine dimer is facile. The 5’T of the dimer has the largest equilibrium constant (Kop =3×10−4) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3’T of the dimer is much more stable than by the 5’T, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5’ side more than on the 3’ side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions. PMID:24328089

  20. Fluorescent Protein Based FRET Pairs with Improved Dynamic Range for Fluorescence Lifetime Measurements.

    PubMed

    George Abraham, Bobin; Sarkisyan, Karen S; Mishin, Alexander S; Santala, Ville; Tkachenko, Nikolai V; Karp, Matti

    2015-01-01

    Fluorescence Resonance Energy Transfer (FRET) using fluorescent protein variants is widely used to study biochemical processes in living cells. FRET detection by fluorescence lifetime measurements is the most direct and robust method to measure FRET. The traditional cyan-yellow fluorescent protein based FRET pairs are getting replaced by green-red fluorescent protein variants. The green-red pair enables excitation at a longer wavelength which reduces cellular autofluorescence and phototoxicity while monitoring FRET. Despite the advances in FRET based sensors, the low FRET efficiency and dynamic range still complicates their use in cell biology and high throughput screening. In this paper, we utilized the higher lifetime of NowGFP and screened red fluorescent protein variants to develop FRET pairs with high dynamic range and FRET efficiency. The FRET variations were analyzed by proteolytic activity and detected by steady-state and time-resolved measurements. Based on the results, NowGFP-tdTomato and NowGFP-mRuby2 have shown high potentials as FRET pairs with large fluorescence lifetime dynamic range. The in vitro measurements revealed that the NowGFP-tdTomato has the highest Förster radius for any fluorescent protein based FRET pairs yet used in biological studies. The developed FRET pairs will be useful for designing FRET based sensors and studies employing Fluorescence Lifetime Imaging Microscopy (FLIM). PMID:26237400

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

    PubMed

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

    2014-01-01

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

  2. Tunnel conductance of Watson-Crick nucleoside-base pairs from telegraph noise.

    PubMed

    Chang, Shuai; He, Jin; Lin, Lisha; Zhang, Peiming; Liang, Feng; Young, Michael; Huang, Shuo; Lindsay, Stuart

    2009-05-01

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor of two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break. PMID:19420603

  3. Tunnel Conductance of Watson-Crick Nucleoside-Base Pairs from Telegraph Noise

    PubMed Central

    Chang, Shuai; He, Jin; Lin, Lisha; Zhang, Peiming; Liang, Feng; Young, Michael; Huang, Shuo; Lindsay, Stuart

    2009-01-01

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base-pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break. PMID:19420603

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

    PubMed Central

    Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  5. Addendum to "Quantum wireless multihop communication based on arbitrary Bell pairs and teleportation"

    NASA Astrophysics Data System (ADS)

    Wang, Kan; Gong, Yan-Xiao; Yu, Xu-Tao; Lu, Sheng-Li

    2014-10-01

    In our previous work [Phys. Rev. A 89, 022329 (2014), 10.1103/PhysRevA.89.022329], we proposed a teleportation-based quantum communication scheme in a quantum wireless multihop network with arbitrary types of Bell pairs shared between adjacent nodes. Here we revised the scheme by introducing a result-mapping method for halving the classical communication cost, with which the source and intermediate nodes map the measurement outcomes to those corresponding to the target Bell pair type assigned by the destination node. A routing protocol is utilized to piggyback the target Bell pair type notification information which introduces no extra communication cost.

  6. Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing.

    PubMed

    Tatsumi, Kaori; Nishimura, Osamu; Itomi, Kazu; Tanegashima, Chiharu; Kuraku, Shigehiro

    2015-05-01

    In de novo genome sequencing, mate-pair reads are crucial for scaffolding assembled contigs. However, preparation of mate-pair libraries is not a trivial task, even when using one of the latest approaches, the Nextera Mate Pair Sample Prep Kit from Illumina. To reduce cost and enhance library yield and fidelity when using this kit, we have modified the manufacturer's protocol based on (i) variable tagmentation conditions, (ii) intensive DNA shearing to decrease library insert length, and (iii) sequencing on an Illumina HiSeq with >150 cycles. Finally, we provide additional suggestions for further improvement in the application of this kit. PMID:25967904

  7. Multi-hop teleportation based on W state and EPR pairs

    NASA Astrophysics Data System (ADS)

    Hai-Tao, Zhan; Xu-Tao, Yu; Pei-Ying, Xiong; Zai-Chen, Zhang

    2016-05-01

    Multi-hop teleportation has significant value due to long-distance delivery of quantum information. Many studies about multi-hop teleportation are based on Bell pairs, partially entangled pairs or W state. The possibility of multi-hop teleportation constituted by partially entangled pairs relates to the number of nodes. The possibility of multi-hop teleportation constituted by double W states is after n-hop teleportation. In this paper, a multi-hop teleportation scheme based on W state and EPR pairs is presented and proved. The successful possibility of quantum information transmitted hop by hop through intermediate nodes is deduced. The possibility of successful transmission is after n-hop teleportation. Project supported by the National Natural Science Foundation of China (Grant No. 61571105), the Prospective Future Network Project of Jiangsu Province, China (Grant No. BY2013095-1-18), and the Independent Project of State Key Laboratory of Millimeter Waves, China (Grant No. Z201504).

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  9. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

    PubMed Central

    Chawla, Mohit; Oliva, Romina; Bujnicki, Janusz M.; Cavallo, Luigi

    2015-01-01

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in. PMID:26117545

  10. Isoalloxazine derivatives promote photocleavage of natural RNAs at G.U base pairs embedded within helices.

    PubMed Central

    Burgstaller, P; Hermann, T; Huber, C; Westhof, E; Famulok, M

    1997-01-01

    We have recently shown that isoalloxazine derivatives are able to photocleave RNA specifically at G.U base pairs embedded within a helical stack. The reaction involves the selective molecular recognition of G.U base pairs by the isoalloxazine ring and the removal of one nucleoside downstream of the uracil residue. Divalent metal ions are absolutely required for cleavage. Here we extend our studies to complex natural RNA molecules with known secondary and tertiary structures, such as tRNAs and a group I intron (td). G.U pairs were cleaved in accordance with the phylogenetically and experimentally derived secondary and tertiary structures. Tandem G.U pairs or certain G.U pairs located at a helix extremity were not affected. These new cleavage data, together with the RNA crystal structure, allowed us to perform molecular dynamics simulations to provide a structural basis for the observed specificity. We present a stable structural model for the ternary complex of the G. U-containing helical stack, the isoalloxazine molecule and a metal ion. This model provides significant new insight into several aspects of the cleavage phenomenon, mechanism and specificity for G. U pairs. Our study shows that in large natural RNAs a secondary structure motif made of an unusual base pair can be recognized and cleaved with high specificity by a low molecular weight molecule. This photocleavage reaction thus opens up the possibility of probing the accessibility of G.U base pairs, which are endowed with specific structural and functional roles in numerous structured and catalytic RNAs and interactions of RNA with proteins, in folded RNAs. PMID:9321652

  11. New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.

    PubMed

    Zhou, Huiqing; Hintze, Bradley J; Kimsey, Isaac J; Sathyamoorthy, Bharathwaj; Yang, Shan; Richardson, Jane S; Al-Hashimi, Hashim M

    2015-04-20

    Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C1' distance across the bp) to search for HG bps in X-ray structures of DNA duplexes in the Protein Data Bank. The survey identifies 106 A•T and 34 G•C HG bps in DNA duplexes, many of which are undocumented in the literature. It also uncovers HG-like bps with syn purines lacking HG hydrogen bonds or constricted C1'-C1' distances that are analogous to conformations that have been proposed to populate the WC-to-HG transition pathway. The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5'-purine. HG bps induce small local perturbations in neighboring bps and, surprisingly, a small but significant degree of DNA bending (∼14°) directed toward the major groove. The survey provides insights into the preferences and structural consequences of HG bps in duplex DNA. PMID:25813047

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

    PubMed

    Sun, Hu; Yuao, Tao

    2012-06-01

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

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

    PubMed

    Fendrick, A Mark; Zank, Daniel C

    2013-11-01

    When consumers are required to pay the same out-of-pocket amount for pulmonary services for which clinical benefits depend on patient characteristics, clinical indication, and provider choice, there is an enormous potential for both underutilization and overutilization. Unlike most current one-size-fits-all health plan designs, value-based insurance design (V-BID) explicitly acknowledges clinical heterogeneity across the continuum of care. By adding clinical nuance to benefit design, V-BID seeks to align consumer and provider incentives with value, encouraging the use of high-value services and discouraging the use of low-value interventions. This article describes the concept of V-BID; creates a framework for its development in pulmonary medicine; and outlines how this concept aligns with research, care delivery, and payment reform initiatives. PMID:23929504

  14. Superconductivity, magnetism, and pairing symmetry in Fe-based superconductors

    NASA Astrophysics Data System (ADS)

    Eremin, Ilya

    2009-03-01

    We analyze antiferromagnetism and superconductivity within the renormalization group(RG) technique in novel Fe-based superconductors using the itinerant model of small electron and hole pockets near (0; 0) and (π,π), respectively, originating from the two strongly hybridized orbitals. We find that, for this model, the bare interactions in the Cooper channel are repulsive, and superconductivity does not occur at the mean-field level. However, under RG the effective interaction in the superconducting channel changes sign and becomes attractive. Furthermore, the effective interactions in antiferromagnetic and superconducting channels logarithmically flow towards the same absolute values at low energies, i.e., both must be treated on equal footings. The magnetic instability comes first for equal sizes of the two pockets, but looses to superconductivity upon doping. The superconducting gap has no nodes, but changes sign between the two Fermi surfaces (extended s-wave symmetry). We argue that the T dependencies of the spin susceptibility and NMR relaxation rate for such state are exponential only at very low T, and can be well fitted by power-laws over a wide T range below Tc. We further show that below Tc excitonic resonance appears in the spin excitations spectrum. [4pt] [1] M. Korshunov, and I. Eremin, Phys. Rev. B 78, 140509(R) (2008) [0pt] [2] A.V. Chubukov, D. Efremov, I. Eremin, Phys. Rev. B 78, 134512 (2008). [0pt] [3] M.M. Korshunov and I. Eremin, Europhys. Lett. 83, 67003 (2008).

  15. Charge transport in DNA oligonucleotides with various base-pairing patterns.

    PubMed

    Kratochvílová, Irena; Todorciuc, Tatiana; Král, Karel; Nemec, Hynek; Buncek, Martin; Sebera, Jakub; Zális, Stanislav; Vokácová, Zuzana; Sychrovský, Vladimír; Bednárová, Lucie; Mojzes, Peter; Schneider, Bohdan

    2010-04-22

    We combined various experimental (scanning tunneling microscopy and Raman spectroscopy) and theoretical (density functional theory and molecular dynamics) approaches to study the relationships between the base-pairing patterns and the charge transfer properties in DNA 32-mer duplexes that may be relevant for identification and repair of defects in base pairing of the genetic DNA and for DNA use in nanotechnologies. Studied were two fully Watson-Crick (W-C)-paired duplexes, one mismatched (containing three non-W-C pairs), and three with base pairs chemically removed. The results show that the charge transport varies strongly between these duplexes. The conductivity of the mismatched duplex is considerably lower than that of the W-C-paired one despite the fact that their structural integrities and thermal stabilities are comparable. Structurally and thermally much less stable abasic duplexes have still lower conductivity but not markedly different from the mismatched duplex. All duplexes are likely to conduct by the hole mechanism, and water orbitals increase the charge transport probability. PMID:20353252

  16. Biochemical evidence for the requirement of Hoogsteen base pairing for replication by human DNA polymerase iota.

    PubMed

    Johnson, Robert E; Prakash, Louise; Prakash, Satya

    2005-07-26

    Because of the near geometric identity of Watson-Crick (W-C) GxC and AxT base pairs, a given DNA polymerase forms the four possible correct base pairs with nearly identical catalytic efficiencies. However, human DNA polymerase iota (Pol iota), a member of the Y family of DNA polymerases, exhibits a marked template specificity, being more efficient at incorporating the correct nucleotide opposite template purines than opposite pyrimidines. By using 7-deazaadenine and 7-deazaguanine as the templating residues, which disrupt Hoogsteen base pair formation, we show that, unlike the other DNA polymerases belonging to the A, B, or Y family, DNA synthesis by Pol iota is severely inhibited by these N7-modified bases. These observations provide biochemical evidence that, during normal DNA synthesis, template purines adopt a syn conformation in the Pol iota active site, enabling the formation of a Hoogsteen base pair with the incoming pyrimidine nucleotide. Additionally, mutational studies with Leu-62, which lies in close proximity to the templating residue in the Pol iota ternary complex, have indicated that both factors, steric constraints within the active site and the stability provided by the hydrogen bonds in the Hoogsteen base pair, contribute to the efficiency of correct nucleotide incorporation opposite template purines by Pol iota. PMID:16014707

  17. Generation of arbitrary vector fields based on a pair of orthogonal elliptically polarized base vectors.

    PubMed

    Xu, Danfeng; Gu, Bing; Rui, Guanghao; Zhan, Qiwen; Cui, Yiping

    2016-02-22

    We present an arbitrary vector field with hybrid polarization based on the combination of a pair of orthogonal elliptically polarized base vectors on the Poincaré sphere. It is shown that the created vector field is only dependent on the latitude angle 2χ but is independent on the longitude angle 2ψ on the Poincaré sphere. By adjusting the latitude angle 2χ, which is related to two identical waveplates in a common path interferometric arrangement, one could obtain arbitrary type of vector fields. Experimentally, we demonstrate the generation of such kind of vector fields and confirm the distribution of state of polarization by the measurement of Stokes parameters. Besides, we investigate the tight focusing properties of these vector fields. It is found that the additional degree of freedom 2χ provided by arbitrary vector field with hybrid polarization allows one to control the spatial structure of polarization and to engineer the focusing field. PMID:26907066

  18. Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

    PubMed Central

    Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

    2014-01-01

    The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson–Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo. PMID:24399194

  19. Molecular mechanism of base pairing infidelity during DNA duplication upon one-electron oxidation

    PubMed Central

    Reynisson, Jóhannes

    2010-01-01

    The guanine radical cation (G•+) is formed by one-electron oxidation from its parent guanine (G). G•+ is rapidly deprotonated in the aqueous phase resulting in the formation of the neutral guanine radical [G(-H)•]. The loss of proton occurs at the N1 nitrogen, which is involved in the classical Watson-Crick base pairing with cytosine (C). Employing the density functional theory (DFT), it has been observed that a new shifted base pairing configuration is formed between G(-H)• and C constituting only two hydrogen bonds after deprotonation occurs. Using the DFT method, G(-H)• was paired with thymine (T), adenine (A) and G revealing substantial binding energies comparable to those of classical G-C and A-T base pairs. Hence, G(-H)• does not display any particular specificity for C compared to the other bases. Taking into account the long lifetime of the G(-H)• radical in the DNA helix (5 s) and the rapid duplication rate of DNA during mitosis/meiosis (5-500 bases per s), G(-H)• can pair promiscuously leading to errors in the duplication process. This scenario constitutes a new mechanism which explains how one-electron oxidation of the DNA double helix can lead to mutations. PMID:21603305

  20. Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate.

    PubMed

    Tateishi-Karimata, Hisae; Nakano, Miki; Sugimoto, Naoki

    2014-01-01

    The instability of Hoogsteen base pairs relative to Watson-Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson-Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson-Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo. PMID:24399194

  1. On the conditions for enhanced transport through molecular junctions based on metal centres ligated by pairs of pyridazino-derived ligands

    SciTech Connect

    Ding, Bei; Washington, Victoria; Dunietz, Barry D

    2010-10-10

    Transport properties of a Ni bis-η{sup 2} complex ligated by a pair of bi-pyridazino derivative are considered. This complex provides the opportunity to avoid perpendicular alignment of the ligand π planes. We study the effects of π-bonding and of intramolecular hydrogen bonding between the ligands as mediated by the metal centre on electron transport. The complicated effect of the electronic structure equilibration with the electrodes on the transport is discussed. The analysis at the electronic structure level provides guidelines to design a molecular bridge that is based on metal complexation with effective electronic transport.

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

    NASA Astrophysics Data System (ADS)

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

    1996-03-01

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

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

    PubMed

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

    2014-06-01

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

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

    PubMed

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

    2007-02-19

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

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

    SciTech Connect

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

    2009-01-29

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

  6. PAIRS, The GIS-Based Incident Response System for Pennsylvania, and NASA

    NASA Technical Reports Server (NTRS)

    Conrad, Eric; Arbegast, Daniel; Maynard, Nancy; Vicente, Gilberto

    2003-01-01

    Over the past several years the Pennsylvania Departments of Environmental Protection (DEP), Health (DOH), and Agriculture (PDA) built the GIs-based Pennsylvania West Nile Surveillance System. That system has become a model for collecting data that has a field component, laboratory component, reporting and mapping component, and a public information component. Given the success of the West Nile Virus System and the events of September 11, 2001, DEP then embarked on the development of the Pennsylvania Incident Response System, or PAIRS. PAIRS is an effective GIs-based approach to providing a system for response to incidents of any kind, including terrorism because it is building upon the existing experience, infrastructure and databases that were successfully developed to respond to the West Nile Virus by DEP, DOH, and PDA. The proposed system can be described as one that supports data acquisition, laboratory forensics, decision making/response, and communications. Decision makers will have tools to view and analyze data from various sources and, at the same time, to communicate with the large numbers of people responding to the same incident. Recent collaborations with NASA partners are creating mechanisms for the PAIRS system to incorporate space-based and other remote sensing geophysical parameters relevant to public health assessment and management, such as surface temperatures, precipitation, land cover/land use change, and humidity. This presentation will describe the PAIRS system and outline the Pennsylvania-NASA collaboration for integration of space-based data into the PAIRS system.

  7. Tools for the automatic identification and classification of RNA base pairs

    PubMed Central

    Yang, Huanwang; Jossinet, Fabrice; Leontis, Neocles; Chen, Li; Westbrook, John; Berman, Helen; Westhof, Eric

    2003-01-01

    Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson–Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/. PMID:12824344

  8. CARNA--alignment of RNA structure ensembles.

    PubMed

    Sorescu, Dragos Alexandru; Möhl, Mathias; Mann, Martin; Backofen, Rolf; Will, Sebastian

    2012-07-01

    Due to recent algorithmic progress, tools for the gold standard of comparative RNA analysis, namely Sankoff-style simultaneous alignment and folding, are now readily applicable. Such approaches, however, compare RNAs with respect to a simultaneously predicted, single, nested consensus structure. To make multiple alignment of RNAs available in cases, where this limitation of the standard approach is critical, we introduce a web server that provides a complete and convenient interface to the RNA structure alignment tool 'CARNA'. This tool uniquely supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically; these features are highly desirable for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots. We represent structural input and output information as base pair probability dot plots; this provides large flexibility in the input, ranging from fixed structures to structure ensembles, and enables immediate visual analysis of the results. In contrast to conventional Sankoff-style approaches, 'CARNA' optimizes all structural similarities in the input simultaneously, for example across an entire RNA structure ensemble. Even compared with already costly Sankoff-style alignment, 'CARNA' solves an intrinsically much harder problem by applying advanced, constraint-based, algorithmic techniques. Although 'CARNA' is specialized to the alignment of RNAs with several conserved structures, its performance on RNAs in general is on par with state-of-the-art general-purpose RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server is freely available at http://rna.informatik.uni-freiburg.de/CARNA. PMID:22689637

  9. Discrimination of Single Base Pair Differences Among Individual DNA Molecules Using a Nanopore

    NASA Technical Reports Server (NTRS)

    Vercoutere, Wenonah; DeGuzman, Veronica

    2003-01-01

    The protein toxin alpha-hemolysin form nanometer scale channels across lipid membranes. Our lab uses a single channel in an artificial lipid bilayer in a patch clamp device to capture and examine individual DNA molecules. This nanopore detector used with a support vector machine (SVM) can analyze DNA hairpin molecules on the millisecond time scale. We distinguish duplex stem length, base pair mismatches, loop length, and single base pair differences. The residual current fluxes also reveal structural molecular dynamics elements. DNA end-fraying (terminal base pair dissociation) can be observed as near full blockades, or spikes, in current. This technique can be used to investigate other biological processes dependent on DNA end-fraying, such as the processing of HIV DNA by HIV integrase.

  10. Nearest Alignment Space Termination

    2006-07-13

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

  11. Formation of Silver Nanoclusters from a DNA Template Containing Ag(I)-Mediated Base Pairs

    PubMed Central

    Léon, J. Christian; Stegemann, Linda; Peterlechner, Martin; Litau, Stefanie; Wilde, Gerhard; Strassert, Cristian A.; Müller, Jens

    2016-01-01

    A series of DNA double helices containing different numbers of silver(I)-mediated base pairs involving the artificial nucleobases imidazole or 2-methylimidazole has been applied for the generation of DNA-templated silver nanoclusters. The original Ag(I)-containing nucleic acids as well as the resulting nanoclusters and nanoparticles have been characterized by means of UV/Vis spectroscopy, circular dichroism (CD) spectroscopy, fluorescence spectroscopy, and transmission electron microscopy (TEM). The results show for the first time that metal-mediated base pairs can be used for the templated growth of metal nanoclusters. PMID:27034627

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    SciTech Connect

    Seletskiy, S. M.; Tupikov, V.

    2006-03-20

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

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

    NASA Astrophysics Data System (ADS)

    Eggert, D.; Dalyot, S.

    2012-07-01

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

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

    PubMed Central

    2013-01-01

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

  16. Discrimination of environmental background noise in presence of speech using sample-pairs statistics based features

    NASA Astrophysics Data System (ADS)

    Jhanwar, D.; Sharma, Kamlesh K.; Modani, S. G.

    2015-09-01

    A methodology to discriminate the different classes of background noise using new features based on samples of the signal is presented here. Two consecutive samples of different amplitude of the discretetime signals are termed as sample-pair and 14 types of sample-pairs are considered here as fundamental features. Results of simulation work proves that count of some of such type of sample-pairs as well as count of few combinations of two, three and four such sample-pairs are useful to detect and discriminate the different acoustic noise mixed with speech signals. On the basis of simulation results, the performance of proposed features have proved better than other spectral features like Mel Frequency Cepstral Coefficients (MFCC), Spectral Centroid, Spectral Flux and Spectral Roll-off regarding discrimination capabilities, simplicity of extraction process and lesser dependency over speech utterances mixed with noise. These sample-pairs based features having advantage of not requiring frame-decomposition and silence period removal. Their discrimination capabilities are shown by Fisher's F-ratio as performance index. The multiclass Support Vector Machine (SVM) is used as a classifier.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Salahuddin, Parveen; Khan, Asad U

    2014-01-01

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

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

    PubMed Central

    Salahuddin, Parveen; Khan, Asad U

    2014-01-01

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

  20. Single-molecule derivation of salt dependent base-pair free energies in DNA.

    PubMed

    Huguet, Josep M; Bizarro, Cristiano V; Forns, Núria; Smith, Steven B; Bustamante, Carlos; Ritort, Felix

    2010-08-31

    Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol(-1) precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our unique energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melting temperatures for oligos. The method should make it possible to obtain free energies, enthalpies, and entropies in conditions not accessible by bulk methodologies. PMID:20716688

  1. Triple helical DNA in a duplex context and base pair opening

    PubMed Central

    Esguerra, Mauricio; Nilsson, Lennart; Villa, Alessandra

    2014-01-01

    It is fundamental to explore in atomic detail the behavior of DNA triple helices as a means to understand the role they might play in vivo and to better engineer their use in genetic technologies, such as antigene therapy. To this aim we have performed atomistic simulations of a purine-rich antiparallel triple helix stretch of 10 base triplets flanked by canonical Watson–Crick double helices. At the same time we have explored the thermodynamic behavior of a flipping Watson–Crick base pair in the context of the triple and double helix. The third strand can be accommodated in a B-like duplex conformation. Upon binding, the double helix changes shape, and becomes more rigid. The triple-helical region increases its major groove width mainly by oversliding in the negative direction. The resulting conformations are somewhere between the A and B conformations with base pairs remaining almost perpendicular to the helical axis. The neighboring duplex regions maintain a B DNA conformation. Base pair opening in the duplex regions is more probable than in the triplex and binding of the Hoogsteen strand does not influence base pair breathing in the neighboring duplex region. PMID:25228466

  2. Single-molecule derivation of salt dependent base-pair free energies in DNA

    PubMed Central

    Huguet, Josep M.; Bizarro, Cristiano V.; Forns, Núria; Smith, Steven B.; Bustamante, Carlos; Ritort, Felix

    2010-01-01

    Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol-1 precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our unique energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melting temperatures for oligos. The method should make it possible to obtain free energies, enthalpies, and entropies in conditions not accessible by bulk methodologies. PMID:20716688

  3. A Bayesian-based Method for Particle Track Identification in Low-energy Pair-creation Telescopes

    SciTech Connect

    Zoglauer, Andreas; Andritschke, Robert; Kanbach, Gottfried; Boggs, Steven E.

    2007-07-12

    A critical step during the data analysis of pair creation telescopes is the correct identification of the electron and positron tracks. For MEGA, an electron-tracking Compton and pair telescope optimized for energies up to 50 MeV, we describe a low-energy pair event reconstruction approach partly based on Bayesian statistics.

  4. On comparing two structured RNA multiple alignments.

    PubMed

    Patel, Vandanaben; Wang, Jason T L; Setia, Shefali; Verma, Anurag; Warden, Charles D; Zhang, Kaizhong

    2010-12-01

    We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at http://bioinformatics.njit.edu/blockmatch. A jar file of the program is also available for download from the web server. PMID:21121021

  5. Concealed d-wave pairs in the s± condensate of iron-based superconductors.

    PubMed

    Ong, Tzen; Coleman, Piers; Schmalian, Jörg

    2016-05-17

    A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave ([Formula: see text]) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. Here, we propose a new class of [Formula: see text] state containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave ([Formula: see text]) motion of the pairs with the internal angular momenta [Formula: see text] of the iron orbitals to make a singlet ([Formula: see text]), an [Formula: see text] superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba1-x KXFe2As2 as a reconfiguration of the orbital and internal angular momentum into a high spin ([Formula: see text]) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. The formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy. PMID:27140626

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

    PubMed

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

    2015-08-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  8. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes

    PubMed Central

    Léon, J. Christian; Sinha, Indranil; Müller, Jens

    2016-01-01

    The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase. PMID:27089326

  9. Genome filtering using methylation-sensitive restriction enzymes with six-base pair recognition sites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large fraction of repetitive DNA in many plant genomes has complicated all aspects of DNA sequencing and assembly, and thus techniques that enrich for genes and low-copy sequences have been employed to isolate gene space. Methyl sensitive restriction enzymes with six base pair recognition sites...

  10. Free energy analysis and mechanism of base pair stacking in nicked DNA.

    PubMed

    Häse, Florian; Zacharias, Martin

    2016-09-01

    The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparison to experimental studies indicates qualitative agreement of the stability order but a general overestimation of base pair stacking interactions in the simulations. A significant dependence of calculated nucleobase stacking free energies on the employed water model was observed with the tendency of stacking free energies being more accurately reproduced by more complex water models. The simulation studies also suggest a mechanism of stacking/unstacking that involves significant motions perpendicular to the reaction coordinate and indicate that the equilibrium nicked base pair step may slightly differ from regular B-DNA geometry in a sequence-dependent manner. PMID:27407106

  11. Free energy analysis and mechanism of base pair stacking in nicked DNA

    PubMed Central

    Häse, Florian; Zacharias, Martin

    2016-01-01

    The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparison to experimental studies indicates qualitative agreement of the stability order but a general overestimation of base pair stacking interactions in the simulations. A significant dependence of calculated nucleobase stacking free energies on the employed water model was observed with the tendency of stacking free energies being more accurately reproduced by more complex water models. The simulation studies also suggest a mechanism of stacking/unstacking that involves significant motions perpendicular to the reaction coordinate and indicate that the equilibrium nicked base pair step may slightly differ from regular B-DNA geometry in a sequence-dependent manner. PMID:27407106

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

    NASA Astrophysics Data System (ADS)

    Ye, Lei; Hu, Huayong; He, Weiming

    2016-03-01

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

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

    PubMed

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

    2008-07-01

    This paper addresses the construction of a novel efficient rotation-invariant texture retrieval method that is based on the alignment in angle of signatures obtained via a steerable sub-Gaussian model. In our proposed scheme, we first construct a steerable multivariate sub-Gaussian model, where the fractional lower-order moments of a given image are associated with those of its rotated versions. The feature extraction step consists of estimating the so-called covariations between the orientation subbands of the corresponding steerable pyramid at the same or at adjacent decomposition levels and building an appropriate signature that can be rotated directly without the need of rotating the image and recalculating the signature. The similarity measurement between two images is performed using a matrix-based norm that includes a signature alignment in angle between the images being compared, achieving in this way the desired rotation-invariance property. Our experimental results show how this retrieval scheme achieves a lower average retrieval error, as compared to previously proposed methods having a similar computational complexity, while at the same time being competitive with the best currently known state-of-the-art retrieval system. In conclusion, our retrieval method provides the best compromise between complexity and average retrieval performance. PMID:18586628

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

    NASA Technical Reports Server (NTRS)

    Taylor, Jaime R.

    2003-01-01

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

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

    PubMed

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

    2015-08-01

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

  16. The conformational flexibility of nucleic acid bases paired in gas phase: A Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Xiao, Shiyan; Liang, Haojun

    2012-05-01

    The flexibilities of pyrimidine and imidazole rings in the paired nucleobases are investigated using Car-Parrinello molecular dynamics simulation in gas phase. The pairing influence on the stiffness of rings is analyzed based on the molecular structure of the nucleobases and constraints caused by pairing. We prove that the flexibilities of pyrimidine rings in isolated state have subtle correlation with the degree of aromaticity of the rings. The pairings in nucleic base pairs cause the rings to be more rigid for G, T, and U but more flexible for A and the same for C.

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

    PubMed

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

    2015-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  19. Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding.

    PubMed

    Chou, Shan-Ho; Chin, Ko-Hsin; Chen, Fu-Ming

    2002-05-14

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5'-GXC/CYG-5' complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson-Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition. PMID:12011426

  20. Looped out and perpendicular: Deformation of Watson–Crick base pair associated with actinomycin D binding

    PubMed Central

    Chou, Shan-Ho; Chin, Ko-Hsin; Chen, Fu-Ming

    2002-01-01

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5′-GXC/CYG-5′ complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson–Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition. PMID:12011426

  1. Tuning Locality of Pair Coherence in Graphene-based Andreev Interferometers

    PubMed Central

    Kim, Minsoo; Jeong, Dongchan; Lee, Gil-Ho; Shin, Yun-Sok; Lee, Hyun-Woo; Lee, Hu-Jong

    2015-01-01

    We report on gate-tuned locality of superconductivity-induced phase-coherent magnetoconductance oscillations in a graphene-based Andreev interferometer, consisting of a T-shaped graphene bar in contact with a superconducting Al loop. The conductance oscillations arose from the flux change through the superconducting Al loop, with gate-dependent Fraunhofer-type modulation of the envelope. We confirm a transitional change in the character of the pair coherence, between local and nonlocal, in the same device as the effective length-to-width ratio of the device was modulated by tuning the pair-coherence length ξT in the graphene layer. PMID:25737106

  2. Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

    NASA Astrophysics Data System (ADS)

    Yang, Bo; Rodgers, M. T.

    2015-08-01

    Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

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

    PubMed

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

    2015-01-01

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

  4. The characteristics of gamma-prime dislocation pairs in a nickel-base superalloy

    NASA Technical Reports Server (NTRS)

    Gabb, T. P.; Miner, R. V.; Welsch, G.

    1987-01-01

    The gamma-prime dislocation pairs of a single crystal nickel-base superalloy, PWA 1480, after tensile and fatigue loading at 650 C are analyzed. The existence and extent of cube cross slip in octahedral slip, and the nature of gamma-prime dislocation pairs in primary cube slip are investigated. It is observed that the PWA 1480 specimens oriented near (001) and (-3 6 10) line directions deform by octahedral slip and specimens oriented near (-1 1 1) and (-2 3 4) lines deform by primary cube slip. It is determined that the overall dislocation distributions are more homogeneous in low cycle fatigue (LCF) loading than in monotonic tensile loading; however, the gamma-prime dislocation pair characteristics are similar for tensile and LCF test specimens. The data reveal that the gamma-prime dislocation pairs of octahedral slip specimens are near-screw and on the cube cross slip plane and for the cube slip specimens, the dislocation pairs are of various characters and on the primary cube slip plane.

  5. Nearest-neighbor parameters for 7-deaza-adenosine·uridine base pairs in RNA duplexes.

    PubMed

    Richardson, Katherine E; Znosko, Brent M

    2016-06-01

    One of the major limitations in RNA structure prediction is the lack of information about the effect of nonstandard nucleotides on stability. The nonstandard nucleotide 7-deaza-adenosine (7DA) is a naturally occurring analog of adenosine that has been studied for medicinal purposes and is commonly referred to as tubercidin. In 7DA, the nitrogen in the 7 position of adenosine is replaced by a carbon. Differences in RNA duplex stability due to the removal of this nitrogen can be attributed to a possible change in hydration and a difference in base stacking interactions resulting from changes in the electrostatics of the ring. In order to determine how 7DA affects the stability of RNA, optical melting experiments were conducted on RNA duplexes that contain either internal or terminal 7DA·U pairs with all possible nearest-neighbor combinations. On average, duplexes containing 7DA·U pairs are 0.43 and 0.07 kcal/mol less stable than what is predicted for the same duplex containing internal and terminal A-U pairs, respectively. Thermodynamic parameters for all nearest-neighbor combinations of 7DA·U pairs were derived from the data. These parameters can be used to more accurately predict the secondary structure and stability of RNA duplexes containing 7DA·U pairs. PMID:27099368

  6. Double proton transfer dynamics of model DNA base pairs in the condensed phase

    PubMed Central

    Kwon, Oh-Hoon; Zewail, Ahmed H.

    2007-01-01

    The dynamics of excited-state double proton transfer of model DNA base pairs, 7-azaindole dimers, is reported using femtosecond fluorescence spectroscopy. To elucidate the nature of the transfer in the condensed phase, here we examine variation of solvent polarity and viscosity, solute concentration, and isotopic fractionation. The rate of proton transfer is found to be significantly dependent on polarity and on the isotopic composition in the pair. Consistent with a stepwise mechanism, the results support the presence of an ionic intermediate species which forms on the femtosecond time scale and decays to the final tautomeric form on the picosecond time scale. We discuss the results in relation to the molecular motions involved and comment on recent claims of concerted transfer in the condensed phase. The nonconcerted mechanism is in agreement with previous isolated-molecule femtosecond dynamics and is also consistent with the most-recent high-level theoretical study on the same pair. PMID:17502610

  7. N-H stretching excitations in adenosine-thymidine base pairs in solution: pair geometries, infrared line shapes, and ultrafast vibrational dynamics.

    PubMed

    Greve, Christian; Preketes, Nicholas K; Fidder, Henk; Costard, Rene; Koeppe, Benjamin; Heisler, Ismael A; Mukamel, Shaul; Temps, Friedrich; Nibbering, Erik T J; Elsaesser, Thomas

    2013-01-24

    We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen configurations with similar probability. Steady-state concentration and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH(2) bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes. PMID:23234439

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

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

    PubMed

    Menke, Matthew; Berger, Bonnie; Cowen, Lenore

    2008-01-01

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

  10. Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints

    PubMed Central

    2012-01-01

    Abstract A base-pairing probability matrix (BPPM) stores the probabilities for every possible base pair in an RNA sequence and has been used in many algorithms in RNA informatics (e.g., RNA secondary structure prediction and motif search). In this study, we propose a novel algorithm to perform iterative updates of a given BPPM, satisfying marginal probability constraints that are (approximately) given by recently developed biochemical experiments, such as SHAPE, PAR, and FragSeq. The method is easily implemented and is applicable to common models for RNA secondary structures, such as energy-based or machine-learning–based models. In this article, we focus mainly on the details of the algorithms, although preliminary computational experiments will also be presented. PMID:23210474

  11. Electron pairing in the presence of incipient bands in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Chen, Xiao; Maiti, S.; Linscheid, A.; Hirschfeld, P. J.

    2015-12-01

    Recent experiments on certain Fe-based superconductors have hinted at a role for paired electrons in "incipient" bands that are close to, but do not cross, the Fermi level. Related theoretical works disagree on whether or not strong-coupling superconductivity is required to explain such effects, and whether a critical interaction strength exists. In this work, we consider various versions of the model problem of pairing of electrons in the presence of an incipient band, within a simple multiband weak-coupling BCS approximation. We categorize the problem into two cases: case (i), where superconductivity arises from the "incipient band pairing" alone, and case (ii), where it is induced on an incipient band by pairing due to Fermi-surface-based interactions. Negative conclusions regarding the importance of incipient bands have been drawn so far largely based on case (i), but we show explicitly that models under case (ii) are qualitatively different, and can explain the nonexponential suppression of Tc, as well as robust large gaps on an incipient band. In the latter situation, large gaps on the incipient band do not require a critical interaction strength. We also model the interplay between phonon and spin fluctuation driven superconductivity and describe situations in which they can enhance each other rather than compete. Finally, we discuss the effect of the dimensionality of the incipient band on our results. We argue that pairing on incipient bands may be significant and important in several Fe-based materials, including LiFeAs, FeSe intercalates, and FeSe monolayers on strontium titanate, and indeed may contribute to high critical temperatures in some cases.

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

    PubMed

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

    2011-09-30

    Structural health monitoring of porous materials such as concrete is becoming a major component in our resource-limited economy, as it conditions durable exploitation of existing facilities. Durability in porous materials depends on nanoscale features which need to be monitored in situ with nanometric resolution. To address this problem, we put forward an approach based on the development of a new nanosensor, namely a capacitive micrometric ultrasonic transducer whose vibrating membrane is made of aligned single-walled carbon nanotubes (SWNT). Such sensors are meant to be embedded in large numbers within a porous material in order to provide information on its durability by monitoring in situ neighboring individual micropores. In the present paper, we report on the feasibility of the key building block of the proposed sensor: we have fabricated well-aligned, ultra-thin, dense SWNT membranes that show above-nanometer amplitudes of vibration over a large range of frequencies spanning from 100 kHz to 5 MHz. PMID:21891837

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

    PubMed

    Cawthon, Stephanie W

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  15. Acid-Base Pairs in Lewis Acidic Zeolites Promote Direct Aldol Reactions by Soft Enolization.

    PubMed

    Lewis, Jennifer D; Van de Vyver, Stijn; Román-Leshkov, Yuriy

    2015-08-17

    Hf-, Sn-, and Zr-Beta zeolites catalyze the cross-aldol condensation of aromatic aldehydes with acetone under mild reaction conditions with near quantitative yields. NMR studies with isotopically labeled molecules confirm that acid-base pairs in the Si-O-M framework ensemble promote soft enolization through α-proton abstraction. The Lewis acidic zeolites maintain activity in the presence of water and, unlike traditional base catalysts, in acidic solutions. PMID:26138135

  16. ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets

    PubMed Central

    2014-01-01

    Background We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end sequencing can achieve complete overlap of read pairs. Variant calling from Hi-Plex-derived datasets can thus rely on the identification of variants appearing in both reads of read-pairs, permitting stringent filtering of sequencing chemistry-induced errors. These principles underly ROVER software (derived from Read Overlap PCR-MPS variant caller), which we have recently used to report the screening for genetic mutations in the breast cancer predisposition gene PALB2. Here, we describe the algorithms underlying ROVER and its usage. Results ROVER enables users to quickly and accurately identify genetic variants from PCR-targeted, overlapping paired-end MPS datasets. The open-source availability of the software and threshold tailorability enables broad access for a range of PCR-MPS users. Methods ROVER is implemented in Python and runs on all popular POSIX-like operating systems (Linux, OS X). The software accepts a tab-delimited text file listing the coordinates of the target-specific primers used for targeted enrichment based on a specified genome-build. It also accepts aligned sequence files resulting from mapping to the same genome-build. ROVER identifies the amplicon a given read-pair represents and removes the primer sequences by using the mapping co-ordinates and primer co-ordinates. It considers overlapping read-pairs with respect to primer-intervening sequence. Only when a variant is observed in both reads of a read-pair does the signal contribute to a tally of read-pairs containing or not containing the variant. A user-defined threshold informs the minimum number of, and proportion of, read-pairs a variant must be observed in for a ‘call’ to be made. ROVER also reports the depth of coverage across amplicons to facilitate the

  17. Orientation and Alignment Echoes

    NASA Astrophysics Data System (ADS)

    Karras, G.; Hertz, E.; Billard, F.; Lavorel, B.; Hartmann, J.-M.; Faucher, O.; Gershnabel, Erez; Prior, Yehiam; Averbukh, Ilya Sh.

    2015-04-01

    We present one of the simplest classical systems featuring the echo phenomenon—a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation or alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by the kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO2 molecules excited by a pair of femtosecond laser pulses.

  18. Evidence of competing s and d-wave pairing channels in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Kretzschmar, Florian; Muschler, Bernhard; Böhm, Thomas; Baum, Andreas; Hackl, Rudi; Wen, Hai-Hu; Tsurkan, Vladimir; Deisenhofer, Joachim; Loidl, Alois

    2013-03-01

    Superconductivity is determined by the interactions that drive Cooper pairing. However, experimental access to the pairing potential Vk ,k' becomes increasingly complicated upon going from conventional metals to complex systems such as the cuprates, some heavy fermion compounds or the iron-based superconductors. We show that electronic Raman scattering affords a window into the essential properties of Vk ,k' of iron-based superconductors. In Ba0 . 6K0 . 4Fe2As2 we observe band dependent energy gaps along with excitonic Bardasis-Schrieffer modes characterizing, respectively, the dominant and subdominant pairing channel. The dx2 -y2 symmetry of all excitons allows us to identify the subdominant channel to originate from the interaction between the electron bands. Consequently, the dominant channel driving superconductivity results from the interaction between the electron and hole bands and has the full lattice symmetry. The results in Rb0 . 8Fe1 . 6Se2 along with earlier ones in Ba(Fe0.939Co0 . 061) 2As2 highlight the influence of the Fermi surface topology on the pairing interactions.

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

    PubMed Central

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

    2016-01-01

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

  20. DNA Aptamer Generation by Genetic Alphabet Expansion SELEX (ExSELEX) Using an Unnatural Base Pair System.

    PubMed

    Kimoto, Michiko; Matsunaga, Ken-ichiro; Hirao, Ichiro

    2016-01-01

    Genetic alphabet expansion of DNA using unnatural base pair systems is expected to provide a wide variety of novel tools and methods. Recent rapid progress in this area has enabled the creation of several types of unnatural base pairs that function as a third base pair in polymerase reactions. Presently, a major topic is whether the genetic alphabet expansion system actually increases nucleic acid functionalities. We recently applied our unnatural base pair system to in vitro selection (SELEX), using a DNA library containing four natural bases and an unnatural base, and succeeded in the generation of high-affinity DNA aptamers that specifically bind to target proteins. Only a few hydrophobic unnatural bases greatly augmented the affinity of the aptamers. Here, we describe a new approach (genetic alphabet Expansion SELEX, ExSELEX), using our hydrophobic unnatural base pair system for high affinity DNA aptamer generation. PMID:26552815

  1. A quantum theoretical study of reactions of methyldiazonium ion with DNA base pairs

    NASA Astrophysics Data System (ADS)

    Shukla, P. K.; Ganapathy, Vinay; Mishra, P. C.

    2011-09-01

    Methylation of the DNA bases in the Watson-Crick GC and AT base pairs by the methyldiazonium ion was investigated employing density functional and second order Møller-Plesset (MP2) perturbation theories. Methylation at the N3, N7 and O6 sites of guanine, N1, N3 and N7 sites of adenine, O2 and N3 sites of cytosine and the O2 and O4 sites of thymine were considered. The computed reactivities for methylation follow the order N7(guanine) > N3(adenine) > O6(guanine) which is in agreement with experiment. The base pairing in DNA is found to play a significant role with regard to reactivities of the different sites.

  2. Theoretical investigation of the molecular structure of the pi kappa DNA base pair.

    PubMed

    Florián, J; Leszczyński, J

    1995-04-01

    The structure of the nonclassical pi kappa base pair (7-methyl-oxoformycin B. . .2,4-diaminopyrimidine) was studied at the ab initio Hartree-Fock (HF) and MP2 levels using the 6-31G* and 6-31G** basis sets. The pi kappa base pair is bound by three parallel hydrogen bonds with the donor-acceptor-donor recognition pattern. Recently, these bases were proposed as an extension of the genetic alphabet from four to six letters (Piccirilli et al, Nature 343,33 (1990)). By the HF/6-31G* method with full geometry optimization we calculated the 12 degree propeller twist for the minimum energy structure of this complex. The linearity of hydrogen bonds is preserved in the twisted structure by virtue of the pyramidal arrangement of the kappa-base amino groups. The rings of both the pi and kappa molecules remain nearly planar. This nonplanar structure of the pi kappa base pair is only 0.1 kcal/mol more stable than the planar (Cs) conformation. The HF/6-31G* level gas-phase interaction energy of pi kappa (-13.5 kcal/mol) calculated by us turned out to be nearly the same as the interaction energy obtained previously for the adenine-thymine base pair (-13.4 kcal/mol) at the same computational level. The inclusion of p-polarization functions on hydrogens, electron correlation effects (MP2/6-31G** level), and the correction for the basis set superposition error (BSSE) increase this energy to -14.0 kcal/mol. PMID:7626240

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Xu, Liang; Du, Junping; Zhang, Zhenhong

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2014-04-01

    We report on a quasi-planar quantum-dot-based single-photon source that shows an unprecedented high extraction efficiency of 42% without complex photonic resonator geometries or post-growth nanofabrication. This very high efficiency originates from the coupling of the photons emitted by a quantum dot to a Gaussian shaped nanohill defect that naturally arises during epitaxial growth in a self-aligned manner. We investigate the morphology of these defects and characterize the photonic operation mechanism. Our results show that these naturally arising coupled quantum dot-defects provide a new avenue for efficient (up to 42% demonstrated) and pure (g(2)(0) value of 0.023) single-photon emission. PMID:24718190

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

    PubMed

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

    2015-08-24

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

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

    PubMed Central

    2013-01-01

    Highly uniform hole spacing micro brushes were fabricated based on aligned carbon nanotube (CNT) arrays synthesized by chemical vapor deposition method with the assistance of anodic aluminum oxide (AAO) template. Different micro brushes from CNT arrays were constructed on silicon, glass, and polyimide substrates, respectively. The micro brushes had highly uniform hole spacing originating from the regularly periodic pore structure of AAO template. The CNT arrays, serving as bristles, were firmly grafted on the substrates. The brushes can easily clean particles with scale of micrometer on the surface of silicon wafer and from the narrow spaces between the electrodes in a series of cleaning experiments. The results show the potential application of the CNT micro brushes as a cleaning tool in microelectronics manufacture field. PMID:24274897

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

    NASA Astrophysics Data System (ADS)

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

    2006-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Taylor, Jaime; Rakoczy, John; Steincamp, James

    2003-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  14. DNA separation and fluorescent detection in an optofluidic chip with sub-base-pair resolution

    NASA Astrophysics Data System (ADS)

    Pollnau, Markus; Hammer, Manfred; Dongre, Chaitanya; Hoekstra, Hugo J.

    2015-03-01

    DNA sequencing in a lab-on-a-chip aims at providing cheap, high-speed analysis of low reagent volumes to, e.g., identify genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions/deletions from DNA fragments in the diagnostically relevant range of 150-1000 base-pairs requires a sizing accuracy of S < 10-3. Here we demonstrate S = 4×10-4. A microfluidic chip was post-processed by femtosecond-laser writing of an optical waveguide. 12 blue-labeled and 23 red-labeled DNA fragments were separated in size by capillary electrophoresis, each set excited by either of two lasers power-modulated at different frequencies, their fluorescence detected by a photomultiplier, and blue/red signals distinguished by Fourier analysis. Different calibration strategies were tested: a) use either set of DNA molecules as reference to calibrate the set-up and identify the base-pair sizes of the other set in the same flow experiment, thereby eliminating variations in temperature, wall-coating and sieving-gel conditions, and actuation voltages; b) use the same molecular set as reference and sample with the same fluorescence label, flown in consecutive experiments; c) perform cross-experiments based on different molecular sets with different labels, flown in consecutive experiments. From the results we conclude: Applying quadratic instead of linear fit functions improves the calibration accuracy. Blue-labeled molecules are separated with higher accuracy. The influence of dye label is higher than fluctuations between two experiments. Choosing a single, suitable dye label combined with reference calibration and sample investigation in consecutive experiments results in S = 4×10-4, enabling detection of single base-pair insertion/deletion in a lab-on-a-chip.

  15. Comparison of NIR FRET pairs for quantitative transferrin-based assay

    NASA Astrophysics Data System (ADS)

    Sinsuebphon, Nattawut; Bevington, Travis; Zhao, Lingling; Ken, Abe; Barroso, Margarida; Intes, Xavier

    2014-02-01

    Transferrin (Tfn) is commonly used as a drug delivery carrier for cancer treatment. Tfn cellular internalization can be observed by Förster resonance energy transfer (FRET), which occurs when two fluorophores - donor and acceptor - are a few nanometers apart. Donor fluorescence lifetime can be used to sense and quantify FRET occurrence. In FRET state, the donor is quenched leading to a significant reduction in its lifetime. In this study, donor and acceptor near-infrared (NIR) fluorophore-labeled Tfn were used to quantify cellular internalization in breast cancer cell line (T47D). Based on donor lifetime, quantum yield and spectral data, seven NIR FRET pairs were chosen for this comparison. Performance of the different NIR FRET pairs was evaluated in vitro in multiwell plate settings and by analyzing the relationship between quenched donor fraction and acceptor:donor ratio. Additionally, we performed brightness comparison between each pairs. Several parameters, such as brightness, lifetime, R0 and FRET donor population values are used to identify the most suitable NIR FRET pair for in vivo studies in preclinical settings.

  16. Modulation of Pairing Symmetry with Bond Disorder in Iron-based Superconductors

    NASA Astrophysics Data System (ADS)

    Yao, Dao-Xin; Kang, Yao-Tai; Tsai, Wei-Feng

    2015-03-01

    We study a simple two-orbital t-J1-J2 model for iron-based superconductors in the presence of a bond disorder (via nearest-neighbor bond-dilution). By using Bogoliubov-de Gennes approach, we self-consistently calculate the local pairing amplitudes and the corresponding density of states, which demonstrate a change of dominant pairing symmetry from the s+- wave to d-wave as long as J2 J1. Although the system exhibits spatially inhomogeneous pairing in weak correlations with a given realization of disorder, it is still in sharp contrast to the case with potential disorder, where the superconducting islands and the insulating sea are both present in the strong disorder regime. Moreover, from the detailed examination of the pairing gap as well as the superfluid density, the superconducting transition here is suggested to be beyond the conventional Abrikosov-Gorkov consideration. Supported by NBRPC-2012CB821400, NSFC-11074310, NSFC-11275279, Fundamental Research Funds for the Central Universities, and the NSC in Taiwan under Grant No.102-2112-M-110-009.

  17. Thermodynamic and structural properties of the specific binding between Ag⁺ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair.

    PubMed

    Torigoe, Hidetaka; Okamoto, Itaru; Dairaku, Takenori; Tanaka, Yoshiyuki; Ono, Akira; Kozasa, Tetsuo

    2012-11-01

    Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag(+) ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag(+) ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag(+) ion. Isothermal titration calorimetry demonstrated that the Ag(+) ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10(6) M(-1), which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag(+) ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag(+) ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences. PMID:22766014

  18. Hoogsteen base-pairing revisited: Resolving a role in normal biological processes and human diseases

    SciTech Connect

    Ghosal, Gargi; Muniyappa, K. . E-mail: kmbc@biochem.iisc.ernet.in

    2006-04-28

    For a long time since the discovery of an alternative type of hydrogen bonding between adenine and thymidine, termed Hoogsteen base-pairing, its biological role remained elusive. Recent experiments provide compelling evidence that Hoogsteen base pairs manifest in a gamut of nuclear processes encompassing gene expression, replication, recombination, and telomere length maintenance. An increasing number of proteins that have been shown to bind, unwind or cleave G-quadruplexes or triplexes with high specificity underscore their biological significance. In humans, the absence of these cellular factors or their dysfunction leads to a wide spectrum of genetic diseases including cancer, neurodegenerative syndromes, and a myriad of other disorders. Thus, development of clinically useful compounds that target G-quadruplexes or triplexes, and interfere with specific cellular processes, provides considerable promise for successful and improved treatment of human diseases.

  19. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water.

    PubMed

    Cafferty, Brian J; Fialho, David M; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

    2016-01-01

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life. PMID:27108699

  20. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

    PubMed Central

    Cafferty, Brian J.; Fialho, David M.; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V.

    2016-01-01

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life. PMID:27108699

  1. Low-energy electron scattering from DNA including structural water and base-pair irregularities

    SciTech Connect

    Caron, Laurent; Sanche, Leon; Tonzani, Stefano; Greene, Chris H.

    2009-07-15

    Elastic scattering of low-energy (0-13 eV) electrons from more realistic models of a DNA base-pair decamer is studied using multiple-scattering theory and T matrices obtained from ab initio R-matrix calculations. The models include two types of irregularities usually found in cellular DNA: base-pair mismatch and structural water molecules. Furthermore, we include in our calculation inelastic collisions. It is found that the basic interference patterns observed in the ideal and nonideal (i.e., more realistic) decamers are similar but have different amplitudes and are shifted in energy. Substantial inelastic losses, interestingly, cause pronounced local resonances, which could have an important influence in DNA strand breaks.

  2. Hydrogen bond disruption in DNA base pairs from (14)C transmutation.

    PubMed

    Sassi, Michel; Carter, Damien J; Uberuaga, Blas P; Stanek, Christopher R; Mancera, Ricardo L; Marks, Nigel A

    2014-09-01

    Recent ab initio molecular dynamics simulations have shown that radioactive carbon does not normally fragment DNA bases when it decays. Motivated by this finding, density functional theory and Bader analysis have been used to quantify the effect of C → N transmutation on hydrogen bonding in DNA base pairs. We find that (14)C decay has the potential to significantly alter hydrogen bonds in a variety of ways including direct proton shuttling (thymine and cytosine), thermally activated proton shuttling (guanine), and hydrogen bond breaking (cytosine). Transmutation substantially modifies both the absolute and relative strengths of the hydrogen bonding pattern, and in two instances (adenine and cytosine), the density at the critical point indicates development of mild covalent character. Since hydrogen bonding is an important component of Watson-Crick pairing, these (14)C-induced modifications, while infrequent, may trigger errors in DNA transcription and replication. PMID:25127298

  3. Single-Base Pair Genome Editing in Human Cells by Using Site-Specific Endonucleases

    PubMed Central

    Ochiai, Hiroshi

    2015-01-01

    Genome-wide association studies have identified numerous single-nucleotide polymorphisms (SNPs) associated with human diseases or phenotypes. However, causal relationships between most SNPs and the associated disease have not been established, owing to technical challenges such as unavailability of suitable cell lines. Recently, efficient editing of a single base pair in the genome was achieved using programmable site-specific nucleases. This technique enables experimental confirmation of the causality between SNPs and disease, and is potentially valuable in clinical applications. In this review, I introduce the molecular basis and describe examples of single-base pair editing in human cells. I also discuss the challenges associated with the technique, as well as possible solutions. PMID:26404258

  4. Electric-field induced mutation of DNA: a theoretical investigation of the GC base pair.

    PubMed

    Cerón-Carrasco, José P; Jacquemin, Denis

    2013-04-01

    It is known that intense external electric fields affect the proton transfer (PT) reactions in simple chemical systems, such as hydrated chlorhydric acid or formic acid dimer. Accordingly, electric fields might be used to modulate the PT reactions responsible for the spontaneous mutation mechanism in DNA. In this contribution, we investigate the effect of these fields on the tautomeric equilibria of the guanine-cytosine (GC) base pair in order to gain further insight into this hypothesis. This task is performed with both density functional theory (DFT) and second-order Møller-Plesset (MP2) approaches. Our results demonstrate that electric fields not only drastically alter the rate constants of PT but also tune the mechanism of the PT reactions in the GC base pair. PMID:23338206

  5. Meiotic cohesin-based chromosome structure is essential for homologous chromosome pairing in Schizosaccharomyces pombe.

    PubMed

    Ding, Da-Qiao; Matsuda, Atsushi; Okamasa, Kasumi; Nagahama, Yuki; Haraguchi, Tokuko; Hiraoka, Yasushi

    2016-06-01

    Chromosome structure is dramatically altered upon entering meiosis to establish chromosomal architectures necessary for the successful progression of meiosis-specific events. An early meiotic event involves the replacement of the non-SMC mitotic cohesins with their meiotic equivalents in most part of the chromosome, forming an axis on meiotic chromosomes. We previously demonstrated that the meiotic cohesin complex is required for chromosome compaction during meiotic prophase in the fission yeast Schizosaccharomyces pombe. These studies revealed that chromosomes are elongated in the absence of the meiotic cohesin subunit Rec8 and shortened in the absence of the cohesin-associated protein Pds5. In this study, using super-resolution structured illumination microscopy, we found that Rec8 forms a linear axis on chromosomes, which is required for the organized axial structure of chromatin during meiotic prophase. In the absence of Pds5, the Rec8 axis is shortened whereas chromosomes are widened. In rec8 or pds5 mutants, the frequency of homologous chromosome pairing is reduced. Thus, Rec8 and Pds5 play an essential role in building a platform to support the chromosome architecture necessary for the spatial alignment of homologous chromosomes. PMID:26511279

  6. Electron pairing in the presence of incipient bands in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Linscheid, Andy; Chen, Xiao; Maiti, Saurabh; Hirschfeld, Peter

    Recent experiments on certain Fe-based superconductors (SC) have hinted at a role for paired electrons in ``incipient'' bands that are close to, but do not cross the Fermi level. Within a simple multiband weak-coupling BCS approximation, we categorize the problem into two cases: case(I) where SC arises from the incipient band pairing alone, and case(II) where it is induced on an incipient band by pairing due to Fermi-surface based interactions. Negative conclusions regarding the importance of incipient bands are largely based on case(I). However, we show explicitly that models under case(II) can explain the mild suppression of Tc, as well as robust large gaps on an incipient band. We also model the interplay between phonon and spin fluctuation (SF) driven SC and describe the bootstrap of electron-phonon SC by SF coupling the incipient and the regular bands. We argue that pairing on incipient bands may be important in several Fe-based materials, including LiFeAs, FeSe intercalates and FeSe monolayers on SrTiO3, and indeed may contribute to high Tc in some cases. In addition, we address the question whether this conclusion holds if the SF interaction is derived explicitly in the incipient band scenario and retardation effects are included on the level of the Eliashberg equations. SM was supported by NHMFL through NSF-DMR-1157490, AL and PJH were supported in part by DOE DE-FG02-05ER46236.

  7. Does base-pairing strength play a role in microRNA repression?

    PubMed

    Carmel, Ido; Shomron, Noam; Heifetz, Yael

    2012-11-01

    MicroRNAs (miRNAs) are short, single-stranded RNAs that silence gene expression by either degrading mRNA or repressing translation. Each miRNA regulates a specific set of mRNA "targets" by binding to complementary sequences in their 3' untranslated region. In this study, we examined the importance of the base-pairing strength of the miRNA-target duplex to repression. We hypothesized that if base-pairing strength affects the functionality of miRNA repression, organisms with higher body temperature or that live at higher temperatures will have miRNAs with higher G/C content so that the miRNA-target complex will remain stable. In the nine model organisms examined, we found a significant correlation between the average G/C content of miRNAs and physiological temperature, supporting our hypothesis. Next, for each organism examined, we compared the average G/C content of miRNAs that are conserved among distant organisms and that of miRNAs that are evolutionarily recent. We found that the average G/C content of ancient miRNAs is lower than recent miRNAs in homeotherms, whereas the trend was inversed in poikilotherms, suggesting that G/C content is associated with temperature, thus further supporting our hypothesis. In the organisms examined, the average G/C content of miRNA "seed" sequences was higher than that of mature miRNAs, which was higher than pre-miRNA loops, suggesting an association between the degree of functionality of the sequence and its average G/C content. Our analyses show a possible association between the base-pairing strength of miRNA-targets and the temperature of an organism, suggesting that base-pairing strength plays a role in repression by miRNAs. PMID:23019592

  8. Recognition of base pair inversions in duplex by chimeric (alpha,beta) triplex-forming oligonucleotides.

    PubMed

    Timofeev, Edward N; Goryaeva, Baira V; Florentiev, Vladimir L

    2006-10-01

    DNA recognition by triplex-forming oligonucleotides (TFOs) is usually limited by homopurine-homopyrimidine sequence in duplexes. Modifications of the third strand may overcome this limitation. Chimeric alpha-beta TFOs are expected to form triplex DNA upon binding to non-regular sequence duplexes. In the present study we describe binding properties of chimeric alpha-beta oligodeoxynucleotides in the respect to short DNA duplexes with one, three, and five base pair inversions. Non-natural chimeric TFO's contained alpha-thymidine residues inside (GT) or (GA) core sequences. Modified residues were addressed to AT/TA inversions in duplexes. It was found in the non-denaturing gel-electrophoresis experiments that single or five adjacent base pair inversions in duplexes may be recognized by chimeric alpha-beta TFO's at 10 degrees C and pH 7.8. Three dispersed base pair inversions in the double stranded DNA prevented triplex formation by either (GT) or (GA) chimeras. Estimation of thermal stability of chimeric alpha-beta triplexes showed decrease in T(m) values as compared with unmodified complexes. PMID:16928141

  9. Noncanonical registers and base pairs in human 5′ splice-site selection

    PubMed Central

    Tan, Jiazi; Ho, Jia Xin Jessie; Zhong, Zhensheng; Luo, Shufang; Chen, Gang; Roca, Xavier

    2016-01-01

    Accurate recognition of splice sites is essential for pre-messenger RNA splicing. Mammalian 5′ splice sites are mainly recognized by canonical base-pairing to the 5′ end of U1 small nuclear RNA, yet we described multiple noncanonical base-pairing registers by shifting base-pair positions or allowing one-nucleotide bulges. By systematic mutational and suppressor U1 analyses, we prove three registers involving asymmetric loops and show that two-nucleotide bulges but not longer can form in this context. Importantly, we established that a noncanonical uridine-pseudouridine interaction in the 5′ splice site/U1 helix contributes to the recognition of certain 5′ splice sites. Thermal melting experiments support the formation of noncanonical registers and uridine-pseudouridine interactions. Overall, we experimentally validated or discarded the majority of predicted noncanonical registers, to derive a list of 5′ splice sites using such alternative mechanisms that is much different from the original. This study allows not only the mechanistic understanding of the recognition of a wide diversity of mammalian 5′ splice sites, but also the future development of better splice-site scoring methods that reliably predict the effects of disease-causing mutations at these sequences. PMID:26969736

  10. Noncanonical registers and base pairs in human 5' splice-site selection.

    PubMed

    Tan, Jiazi; Ho, Jia Xin Jessie; Zhong, Zhensheng; Luo, Shufang; Chen, Gang; Roca, Xavier

    2016-05-01

    Accurate recognition of splice sites is essential for pre-messenger RNA splicing. Mammalian 5' splice sites are mainly recognized by canonical base-pairing to the 5' end of U1 small nuclear RNA, yet we described multiple noncanonical base-pairing registers by shifting base-pair positions or allowing one-nucleotide bulges. By systematic mutational and suppressor U1 analyses, we prove three registers involving asymmetric loops and show that two-nucleotide bulges but not longer can form in this context. Importantly, we established that a noncanonical uridine-pseudouridine interaction in the 5' splice site/U1 helix contributes to the recognition of certain 5' splice sites. Thermal melting experiments support the formation of noncanonical registers and uridine-pseudouridine interactions. Overall, we experimentally validated or discarded the majority of predicted noncanonical registers, to derive a list of 5' splice sites using such alternative mechanisms that is much different from the original. This study allows not only the mechanistic understanding of the recognition of a wide diversity of mammalian 5' splice sites, but also the future development of better splice-site scoring methods that reliably predict the effects of disease-causing mutations at these sequences. PMID:26969736

  11. Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

    NASA Astrophysics Data System (ADS)

    Swasey, Steven M.; Gwinn, Elisabeth G.

    2016-04-01

    The thermal and chemical fragility of DNA nanomaterials assembled by Watson–Crick (WC) pairing constrain the settings in which these materials can be used and how they can be functionalized. Here we investigate use of the silver cation, Ag+, as an agent for more robust, metal-mediated self-assembly, focusing on the simplest duplex building blocks that would be required for more elaborate Ag+–DNA nanostructures. Our studies of Ag+-induced assembly of non-complementary DNA oligomers employ strands of 2–24 bases, with varied base compositions, and use electrospray ionization mass spectrometry to determine product compositions. High yields of duplex products containing narrowly distributed numbers of Ag+ can be achieved by optimizing solution conditions. These Ag+-mediated duplexes are stable to at least 60 mM Mg2+, higher than is necessary for WC nanotechnology schemes such as tile assemblies and DNA origami, indicating that sequential stages of Ag+-mediated and WC-mediated assembly may be feasible. Circular dichroism spectroscopy suggests simple helical structures for Ag+-mediated duplexes with lengths to at least 20 base pairs, and further indicates that the structure of cytosine-rich duplexes is preserved at high urea concentrations. We therefore propose an approach towards dynamic DNA nanomaterials with enhanced thermal and chemical stability through designs that combine sturdy silver-mediated ‘frames’ with WC paired ‘pictures’.

  12. Membrane protein crystallization in micelles conjugated by nucleoside base-pairing: A different concept.

    PubMed

    Hosamani, Basavaprabhu; Kale, Raju R; Sharma, Hemlata; Wachtel, Ellen; Kesselman, Ellina; Danino, Dganit; Friedman, Noga; Sheves, Mordechai; Namboothiri, Irishi N N; Patchornik, Guy

    2016-09-01

    The dearth of high quality, three dimensional crystals of membrane proteins, suitable for X-ray diffraction analysis, constitutes a serious barrier to progress in structural biology. To address this challenge, we have developed a new crystallization medium that relies on the conjugation of surfactant micelles via base-pairing of complementary hydrophobic nucleosides. Base-pairs formed at the interface between micelles bring them into proximity with each other; and when the conjugated micelles contain a membrane protein, crystal nucleation centers can be stabilized, thereby promoting crystal growth. Accordingly, two hydrophobic nucleoside derivatives - deoxyguanosine (G) and deoxycytidine (C), each covalently bonded to a 10 carbon chain were synthesized and added to an aqueous solution containing octyl β-d-thioglucopyranoside micelles. These hydrophobic nucleosides induced the formation of oil-rich globules after 2days incubation at 19°C or after a few hours in the presence of ammonium sulfate; however, phase separation was inhibited by 100mM GMP. The presence of the membrane protein bacteriorhodopsin in the conjugated - micellar dispersion resulted in the growth within the colorless globules of a variety of purple crystals, the color indicating a functional protein. On this basis, we suggest that conjugation of micelles via base-pair complementarity may provide significant assistance to the structural determination of integral membrane proteins. PMID:27368128

  13. B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

    SciTech Connect

    Maehigashi, Tatsuya; Hsiao, Chiaolong; Woods, Kristen Kruger; Moulaei, Tinoush; Hud, Nicholas V.; Williams, Loren Dean

    2012-10-23

    Increasingly exact measurement of single crystal X-ray diffraction data offers detailed characterization of DNA conformation, hydration and electrostatics. However, instead of providing a more clear and unambiguous image of DNA, highly accurate diffraction data reveal polymorphism of the DNA atomic positions and conformation and hydration. Here we describe an accurate X-ray structure of B-DNA, painstakingly fit to a multistate model that contains multiple competing positions of most of the backbone and of entire base pairs. Two of ten base-pairs of CCAGGCCTGG are in multiple states distinguished primarily by differences in slide. Similarly, all the surrounding ions are seen to fractionally occupy discrete competing and overlapping sites. And finally, the vast majority of water molecules show strong evidence of multiple competing sites. Conventional resolution appears to give a false sense of homogeneity in conformation and interactions of DNA. In addition, conventional resolution yields an average structure that is not accurate, in that it is different from any of the multiple discrete structures observed at high resolution. Because base pair positional heterogeneity has not always been incorporated into model-building, even some high and ultrahigh-resolution structures of DNA do not indicate the full extent of conformational polymorphism.

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

    ERIC Educational Resources Information Center

    Vanfretti, Luigi; Farrokhabadi, Mostafa

    2015-01-01

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

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

    PubMed

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

    2015-03-25

    Photoresponsive carbohydrate-based giant surfactants (abbreviated as CELAnD-OH) were specifically designed and synthesized for the automatic vertical alignment (VA) layer of nematic (N) liquid crystal (LC), which can be applied for the fabrication of remote-controllable optical devices. Without the conventional polymer-based LC alignment process, a perfect VA layer was automatically constructed by directly adding the 0.1 wt % CELA1D-OH in the N-LC media. The programmed CELA1D-OH giant surfactants in the N-LC media gradually diffused onto the substrates of LC cell and self-assembled to the expanded monolayer structure, which can provide enough empty spaces for N-LC molecules to crawl into the empty zones for the construction of VA layer. On the other hand, the CELA3D-OH giant surfactants forming the condensed monolayer structure on the substrates exhibited a planar alignment (PA) rather than a VA. Upon tuning the wavelength of light, the N-LC alignments were reversibly switched between VA and PA in the remote-controllable LC optical devices. Based on the experimental results, it was realized that understanding the interactions between N-LC molecules and amphiphilic giant surfactants is critical to design the suitable materials for the automatic LC alignment. PMID:25738306

  16. Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.

    PubMed

    Zgarbová, Marie; Otyepka, Michal; Šponer, Jiří; Lankaš, Filip; Jurečka, Petr

    2014-08-12

    Terminal base pairs of DNA and RNA molecules in solution are known to undergo frequent transient opening events (fraying). Accurate modeling of this process is important because of its involvement in nucleic acid end recognition and enzymatic catalysis. In this article, we describe fraying in molecular dynamics simulations with the ff99bsc0, ff99bsc0χOL3, and ff99bsc0χOL4 force fields, both for DNA and RNA molecules. Comparison with the experiment showed that while some features of fraying are consistent with the available data, others indicate potential problems with the force field description. In particular, multiple noncanonical structures are formed at the ends of the DNA and RNA duplexes. Among them are tWC/sugar edge pair, C-H edge/Watson-Crick pair, and stacked geometries, in which the terminal bases are stacked above each other. These structures usually appear within the first tens to hundreds of nanoseconds and substantially limit the usefulness of the remaining part of the simulation due to geometry distortions that are transferred to several neighboring base pairs ("end effects"). We show that stability of the noncanonical structures in ff99bsc0 may be partly linked to inaccurate glycosidic (χ) torsion potentials that overstabilize the syn region and allow for rapid anti to syn transitions. The RNA refined glycosidic torsion potential χOL3 provides an improved description and substantially more stable MD simulations of RNA molecules. In the case of DNA, the χOL4 correction gives only partial improvement. None of the tested force fields provide a satisfactory description of the terminal regions, indicating that further improvement is needed to achieve realistic modeling of fraying in DNA and RNA molecules. PMID:26588288

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

    NASA Astrophysics Data System (ADS)

    Straub, Jeremy

    2016-05-01

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

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

    ERIC Educational Resources Information Center

    Drost, Bryan R.; Levine, Anita C.

    2015-01-01

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

  19. Effect of base-pair stability of nearest-neighbor nucleotides on the fidelity of deoxyribonucleic acid synthesis.

    PubMed

    Patten, J E; So, A G; Downey, K M

    1984-04-10

    The influence of the stability of base pairs formed by nearest-neighbor nucleotides on misincorporation frequency has been studied with the large fragment of DNA polymerase I, the alternating DNA copolymers, poly(dI-dC) and poly-(dG-dC), as template-primers, and dGTP, dITP, and dCTP as substrates. We have utilized the difference in thermodynamic stability between the doubly H-bonded I X C base pair and triply H-bonded G X C base pair to examine the effects of base-pair stability of both the "preceding" and the "following" nucleotides on the frequency of insertion of a mismatched nucleotide, as well as on its stable incorporation into polynucleotide. The present studies demonstrate that the stability of the base pairs formed by nearest-neighbor nucleotides affects the frequency of incorporation of noncomplementary nucleotides. Misincorporation frequency is increased when the nearest-neighbor nucleotides form more stable base pairs with the corresponding nucleotides in the template and is decreased when they form less stable base pairs. The stability of the base pair formed by a nucleotide either preceding (5' to) or following (3' to) a misincorporated nucleotide influences misincorporation frequency, but by different mechanisms. The stability of base pairs formed by preceding nucleotides affects the rate of insertion of mismatched nucleotide but does not protect the mismatched nucleotide from removal by the 3' to 5' exonuclease activity. In contrast, the stability of a base pair formed by a following nucleotide determines whether a misincorporated nucleotide is extended or excised by affecting the ability of the enzyme to edit errors of incorporation. PMID:6722115

  20. High efficient key-insulated attribute based encryption scheme without bilinear pairing operations.

    PubMed

    Hong, Hanshu; Sun, Zhixin

    2016-01-01

    Attribute based encryption (ABE) has been widely applied for secure data protection in various data sharing systems. However, the efficiency of existing ABE schemes is not high enough since running encrypt and decrypt algorithms need frequent bilinear pairing operations, which may occupy too much computing resources on terminal devices. What's more, since different users may share the same attributes in the system, a single user's private key exposure will threaten the security and confidentiality of the whole system. Therefore, to further decrease the computation cost in attribute based cryptosystem as well as provide secure protection when key exposure happens, in this paper, we firstly propose a high efficient key-insulated ABE algorithm without pairings. The key-insulated mechanism guarantees both forward security and backward security when key exposure or user revocation happens. Besides, during the running of algorithms in our scheme, users and attribute authority needn't run any bilinear pairing operations, which will increase the efficiency to a large extent. The high efficiency and security analysis indicate that our scheme is more appropriate for secure protection in data sharing systems. PMID:26933630

  1. Increasing Occurrences and Functional Roles for High Energy Purine-Pyrimidine Base-Pairs in Nucleic Acids

    PubMed Central

    Kimsey, Isaac; Al-Hashimi, Hashim M.

    2014-01-01

    There are a growing number of studies reporting the observation of purine-pyrimidine base-pairs that are seldom observed in unmodified nucleic acids because they entail the loss of energetically favorable interactions or require energetically costly base ionization or tautomerization. These high energy purine-pyrimidine base-pairs include G•C+ and A•T Hoogsteen base-pairs, which entail ~180° rotation of the purine base in a Watson-Crick base-pair, protonation of cytosine N3, and constriction of the C1′–C1′ distance by ~2.5 Å. Other high energy pure-pyrimidine base-pairs include G•T, G•U, and A•C mispairs that adopt Watson-Crick like geometry through either base ionization or tautomerization. Although difficult to detect and characterize using biophysical methods, high energy purine-pyrimidine base-pairs appear to be more common than once thought. They further expand the structural and functional diversity of canonical and noncanonical nucleic acid base-pairs. PMID:24721455

  2. Using gap symmetry and structure to reveal the pairing mechanism in Fe-based superconductors

    NASA Astrophysics Data System (ADS)

    Hirschfeld, Peter J.

    2016-01-01

    I review theoretical ideas and implications of experiments for the gap structure and symmetry of the Fe-based superconductors. Unlike any other class of unconventional superconductors, one has in these systems the possibility to tune the interactions by small changes in pressure, doping or disorder. Thus, measurements of order parameter evolution with these parameters should enable a deeper understanding of the underlying interactions. I briefly review the "standard paradigm" for s-wave pairing in these systems, and then focus on developments in the past several years which have challenged this picture. I further discuss the reasons for the apparent close competition between pairing in s- and d-wave channels, particularly in those systems where one type of Fermi surface pocket - hole or electron - is missing. Observation of a transition between s- and d-wave symmetry, possibly via a time reversal symmetry breaking "s + id" state, would provide an important confirmation of these ideas. Several proposals for detecting these novel phases are discussed, including the appearance of order parameter collective modes in Raman and optical conductivities. Transitions between two different types of s-wave states, involving various combinations of signs on Fermi surface pockets, can also proceed through a T-breaking "s + is" state. I discuss recent work that suggests pairing may take place away from the Fermi level over a surprisingly large energy range, as well as the effect of glide plane symmetry of the Fe-based systems on the superconductivity, including various exotic, time and translational invariance breaking pair states that have been proposed. Finally, I address disorder issues, and the various ways systematic introduction of disorder can (and cannot) be used to extract information on gap symmetry and structure.

  3. Protein multiple sequence alignment by hybrid bio-inspired algorithms.

    PubMed

    Cutello, Vincenzo; Nicosia, Giuseppe; Pavone, Mario; Prizzi, Igor

    2011-03-01

    This article presents an immune inspired algorithm to tackle the Multiple Sequence Alignment (MSA) problem. MSA is one of the most important tasks in biological sequence analysis. Although this paper focuses on protein alignments, most of the discussion and methodology may also be applied to DNA alignments. The problem of finding the multiple alignment was investigated in the study by Bonizzoni and Vedova and Wang and Jiang, and proved to be a NP-hard (non-deterministic polynomial-time hard) problem. The presented algorithm, called Immunological Multiple Sequence Alignment Algorithm (IMSA), incorporates two new strategies to create the initial population and specific ad hoc mutation operators. It is based on the 'weighted sum of pairs' as objective function, to evaluate a given candidate alignment. IMSA was tested using both classical benchmarks of BAliBASE (versions 1.0, 2.0 and 3.0), and experimental results indicate that it is comparable with state-of-the-art multiple alignment algorithms, in terms of quality of alignments, weighted Sums-of-Pairs (SP) and Column Score (CS) values. The main novelty of IMSA is its ability to generate more than a single suboptimal alignment, for every MSA instance; this behaviour is due to the stochastic nature of the algorithm and of the populations evolved during the convergence process. This feature will help the decision maker to assess and select a biologically relevant multiple sequence alignment. Finally, the designed algorithm can be used as a local search procedure to properly explore promising alignments of the search space. PMID:21071394

  4. Aligning Biomolecular Networks Using Modular Graph Kernels

    NASA Astrophysics Data System (ADS)

    Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

    Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

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

    SciTech Connect

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

    2010-08-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-05-14

    A study on the development of high-power supercapacitor materials based on formation of thick mesoporous MnO2 shells on a highly conductive 3D template using vertically aligned carbon nanofibers (VACNFs). Coaxial manganese shells of 100 to 600 nm nominal thicknesses are sputter-coated on VACNFs and then electrochemically oxidized into rose-petal-like mesoporous MnO2 structure. Such a 3D MnO2/VACNF hybrid architecture provides enhanced ion diffusion throughout the whole MnO2 shell and yields excellent current collection capability through the VACNF electrode. These two effects collectively enable faster electrochemical reactions during charge-discharge of MnO2 in 1 M Na2SO4. Thick MnO2 shells (up to 200 nm in radial thickness) can be employed, giving a specific capacitance up to 437 F g(-1). More importantly, supercapacitors employing such a 3D MnO2/VACNF hybrid electrode illustrate more than one order of magnitude higher specific power than the state-of-the-art ones based on other MnO2 structures, reaching ∼240 kW kg(-1), while maintaining a comparable specific energy in the range of 1 to 10 Wh kg(-1). This hybrid approach demonstrates the potential of 3D core-shell architectures for high-power energy storage devices. PMID:25894255

  8. Girder Alignment Plan

    SciTech Connect

    Wolf, Zackary; Ruland, Robert; LeCocq, Catherine; Lundahl, Eric; Levashov, Yurii; Reese, Ed; Rago, Carl; Poling, Ben; Schafer, Donald; Nuhn, Heinz-Dieter; Wienands, Uli; /SLAC

    2010-11-18

    The girders for the LCLS undulator system contain components which must be aligned with high accuracy relative to each other. The alignment is one of the last steps before the girders go into the tunnel, so the alignment must be done efficiently, on a tight schedule. This note documents the alignment plan which includes efficiency and high accuracy. The motivation for girder alignment involves the following considerations. Using beam based alignment, the girder position will be adjusted until the beam goes through the center of the quadrupole and beam finder wire. For the machine to work properly, the undulator axis must be on this line and the center of the undulator beam pipe must be on this line. The physics reasons for the undulator axis and undulator beam pipe axis to be centered on the beam are different, but the alignment tolerance for both are similar. In addition, the beam position monitor must be centered on the beam to preserve its calibration. Thus, the undulator, undulator beam pipe, quadrupole, beam finder wire, and beam position monitor axes must all be aligned to a common line. All relative alignments are equally important, not just, for example, between quadrupole and undulator. We begin by making the common axis the nominal beam axis in the girder coordinate system. All components will be initially aligned to this axis. A more accurate alignment will then position the components relative to each other, without incorporating the girder itself.

  9. Base pairing and structural insights into the 5-formylcytosine in RNA duplex

    PubMed Central

    Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O.; Chen, Doris; Sheng, Jia

    2016-01-01

    5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5′-GUA(f5C)GUAC-3′]2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

  10. Base pairing and structural insights into the 5-formylcytosine in RNA duplex.

    PubMed

    Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O; Chen, Doris; Sheng, Jia

    2016-06-01

    5-Formylcytidine (f(5)C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m(5)C) through 5-hydroxymethylcytidine (hm(5)C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f(5)C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5'-GUA(f(5)C)GUAC-3']2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f(5)C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

  11. A convenient alignment approach for x-ray imaging experiments based on laser positioning devices

    SciTech Connect

    Zhang Da; Donovan, Molly; Wu Xizeng; Liu Hong

    2008-11-15

    This study presents a two-laser alignment approach for facilitating the precise alignment of various imaging and measuring components with respect to the x-ray beam. The first laser constantly pointed to the output window of the source, in a direction parallel to the path along which the components are placed. The second laser beam, originating from the opposite direction, was calibrated to coincide with the first laser beam. Thus, a visible indicator of the direction of the incident x-ray beam was established, and the various components could then be aligned conveniently and accurately with its help.

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

    NASA Technical Reports Server (NTRS)

    Coulter, Phillip; Ohl, Raymond G.; Blake, Peter N.; Bos, Brent J.; Casto, Gordon V.; Eichhorn, William L.; Gum, Jeffrey S.; Hadjimichael, Theodore J.; Hagopian, John G.; Hayden, Joseph E.; Hicks, Samantha L.; Kubalak, Dave; Mclean, Kyle F.; McMann, Joseph; Redman, Kevin; Wenzel, Greg; Young, Jerrod

    2016-01-01

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

  13. Enhanced s +/- pairing due to prioritized diagonal motion of electrons in the iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Kuroki, Kazuhiko; Suzuki, Katsuhiro; Usui, Hidetomo

    2015-03-01

    In the itinerant spin picture of the iron-based superconductors, the nesting between electron and hole Fermi surfaces is usually considered to be the origin of the spin fluctuation. However, there are now some experimental results suggesting that the nesting is not important for superconductivity. An example is the 1111 materials LnFeAsO1-xHx (Ln=La,Sm etc.), where over 50% of electron doping can be accomplished. Superconductivity not only survives, but is even enhanced in the largely electron doped regime, in contradition to the expectation from the bad nesting. In LaFeAsO1-xHx in particular, the x vs. Tc phase diagram exhibits a double dome feature, suggesting a possible difference in the pairing mechanism between the lightly doped and the heavily doped regimes. In the present study, we analyze the five orbital model of this system, and show that a peculiar relation among the real space hoppings is realized in the largely electron doped regime, namely, the next nearest neighbor hopping dominates over the nearest one within the dxy orbitals. We argue that this enhances the s +/- pairing, which is a next nearest neighbor pairing in real space, despite the degraded nesting. We also discuss about some other materials having similar real space hoppings.

  14. Characterizing a Wake-Free Safe Zone for the Simplified Aircraft-Based Paired Approach Concept

    NASA Technical Reports Server (NTRS)

    Guerreiro, Nelson M.; Neitzke, Kurt W.; Johnson, Sally C.; Stough, H. Paul, III; McKissick, Burnell T.; Syed, Hazari I.

    2010-01-01

    The Federal Aviation Administration (FAA) has proposed a concept of operations geared towards achieving increased arrival throughput at U.S. Airports, known as the Simplified Aircraft-based Paired Approach (SAPA) concept. In this study, a preliminary characterization of a wake-free safe zone (WFSZ) for the SAPA concept has been performed. The experiment employed Monte-Carlo simulations of varying approach profiles by aircraft pairs to closely-spaced parallel runways. Three different runway lateral spacings were investigated (750 ft, 1000 ft and 1400 ft), along with no stagger and 1500 ft stagger between runway thresholds. The paired aircraft were flown in a leader/trailer configuration with potential wake encounters detected using a wake detection surface translating with the trailing aircraft. The WFSZ is characterized in terms of the smallest observed initial in-trail distance leading to a wake encounter anywhere along the approach path of the aircraft. The results suggest that the WFSZ can be characterized in terms of two primary altitude regions, in ground-effect (IGE) and out of ground-effect (OGE), with the IGE region being the limiting case with a significantly smaller WFSZ. Runway stagger was observed to only modestly reduce the WFSZ size, predominantly in the OGE region.

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

    PubMed

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

    2011-03-22

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

  16. Origin of Asymmetry of Paired Nanogap Voltammograms Based on Scanning Electrochemical Microscopy: Contamination Not Adsorption.

    PubMed

    Chen, Ran; Balla, Ryan J; Li, Zhiting; Liu, Haitao; Amemiya, Shigeru

    2016-08-16

    Formation of a nanometer-wide gap between tip and substrate electrodes by scanning electrochemical microscopy (SECM) enables voltammetric measurement of ultrafast electron-transfer kinetics. Herein, we demonstrate the advantage of SECM-based nanogap voltammetry to assess the cleanness of the substrate surface in solution by confirming that airborne contamination of highly oriented pyrolytic graphite (HOPG) causes the nonideal asymmetry of paired nanogap voltammograms of (ferrocenylmethyl)trimethylammonium (Fc(+)). We hypothesize that the amperometric response of a 1 μm-diameter Pt tip is less enhanced in the feedback mode, where more hydrophilic Fc(2+) is generated from Fc(+) at the tip and reduced voltammetrically at the HOPG surface covered with airborne hydrophobic contaminants. The tip current is more enhanced in the substrate generation/tip collection mode, where less charged Fc(+) is oxidized at the contaminated HOPG surface. In fact, symmetric pairs of nanogap voltammograms are obtained with the cleaner HOPG surface that is exfoliated in humidified air and covered with a nanometer-thick water adlayer to suppress airborne contamination. This result disproves a misconception that the asymmetry of paired nanogap voltammograms is due to electron exchange mediated by Fc(2+) adsorbed on the glass sheath of the tip. Moreover, weak Fc(+) adsorption on the HOPG surface causes only the small hysteresis of each voltammogram upon forward and reverse sweeps of the HOPG potential. Significantly, no Fc(2+) adsorption on the HOPG surface ensures that the simple outer-sphere pathway mediates ultrafast electron transfer of the Fc(2+/+) couple with standard rate constants of ≥12 cm/s as estimated from symmetric pairs of reversible nanogap voltammograms. PMID:27426255

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  18. Ultrasound-driven preparation and pair distribution function-assisted structure solution of a copper-based layered coordination polymer.

    PubMed

    Mohideen, M Infas; Allan, Phoebe K; Chapman, Karena W; Hriljac, Joseph A; Morris, Russell E

    2014-07-21

    Nanoparticles of a copper-based layered coordination polymer, STAM-2, have been prepared via an ultrasound mediated transformation from a layered metal-organic framework, STAM-1. The structure of the material was then solved using pair distribution function analysis to identify the structural units present and the final structural model refined against the pair distribution function data. PMID:24310447

  19. Rearrangement or hydrogen-bonded ion pairs of protonated amines in solutions of bases

    SciTech Connect

    Nabiullin, A.A.; Mashkovskii, A.A.; Odinokov, S.E.

    1987-10-01

    Earlier the authors showed that the ion pairs of salts of protonated amines N/sup +/H...A/sup -/ (N/sup +/H is the triethylammonium, pyridinium, or 2,4,6-collidinium cation; A/sup -/ represents the anions SbCl/sub 6//sup -/, BF/sub 4//sup -/, ClO/sub 4//sup -/, I/sup -/) in binary or ternary (with inert solvent) solutions of bases are rearranged into ionic-molecular complexes (N/sup +/H...B) x A/sup -/. In these complexes the cation is bonded to a molecule of the solvating base by a H-bond N/sup +/H...B and to the anion by electrostatic forces, forming a contact ion pair. In this work, on the example of triethylammonium salts, they present the results of IR-spectroscopic investigations of the specific solvation by molecules of bases of systems in which the strength of the H-bond N/sup +/H...B is varied within wide limits. A large assortment of bases, from the weakest (nitromethane, acetonitrile) to the strongest (arsine and phosphine oxides, amines and their N-oxides), were used.

  20. Efficient and provable secure pairing-free security-mediated identity-based identification schemes.

    PubMed

    Chin, Ji-Jian; Tan, Syh-Yuan; Heng, Swee-Huay; Phan, Raphael C-W

    2014-01-01

    Security-mediated cryptography was first introduced by Boneh et al. in 2001. The main motivation behind security-mediated cryptography was the capability to allow instant revocation of a user's secret key by necessitating the cooperation of a security mediator in any given transaction. Subsequently in 2003, Boneh et al. showed how to convert a RSA-based security-mediated encryption scheme from a traditional public key setting to an identity-based one, where certificates would no longer be required. Following these two pioneering papers, other cryptographic primitives that utilize a security-mediated approach began to surface. However, the security-mediated identity-based identification scheme (SM-IBI) was not introduced until Chin et al. in 2013 with a scheme built on bilinear pairings. In this paper, we improve on the efficiency results for SM-IBI schemes by proposing two schemes that are pairing-free and are based on well-studied complexity assumptions: the RSA and discrete logarithm assumptions. PMID:25207333

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

    PubMed

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

    2009-10-01

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

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

    SciTech Connect

    Zwaska, R.; Bishai, M.; Childress, S.; Drake, G.; Escobar, C.; Gouffon, P.; Harris, D.A.; Hylen, J.; Indurthy, D.; Koizumi, G.; Kopp, S.; /Argonne /Brookhaven /Frascati /Sao Paulo U. /Campinas State U. /Texas U.

    2006-09-01

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

  3. Femtosecond decay dynamics of intact adenine and thymine base pairs in a supersonic jet.

    PubMed

    Kim, Nam Joon; Chang, Jinyoung; Kim, Hyung Min; Kang, Hyuk; Ahn, Tae Kyu; Heo, Jiyoung; Kim, Seong Keun

    2011-07-11

    We investigated the decay dynamics of the DNA base pairs adenine-adenine (A(2)), adenine-thymine (AT), and thymine-thymine (T(2)) produced in a supersonic jet by femtosecond (fs) time-resolved photoionization spectroscopy. The base pair was excited by a fs pump pulse at 267 nm and the population change of its excited state was monitored by non-resonant three-photon ionization using a fs probe pulse at 800 nm after a certain time delay. All of the transients recorded in the mass channel of the parent ion exhibited a tri-exponential decay, with time constants ranging from 100 fs to longer than 100 ps. Most of these time constants coincide well with the previous values deduced indirectly from the transients of protonated adenine (AH(+)) and thymine (TH(+)), which were assumed to be produced by fragmentation of the base-pair ions. Notably, for the transient of T(2), we observed a new decay component with a time constant of 2.3 ps, which was absent in the transient of TH(+). We suggest that the new decay component arises from the decay of stacked T(2) dimers that are mostly ionized to T(2)(+), whereas the decay signal recorded in the mass channel of TH(+) is merely from the relaxation of hydrogen-bonded T(2) dimers. From the amplitude of the new decay component, the population of the stacked T(2) dimers relative to the hydrogen-bonded dimers was estimated to be ∼2 % in the supersonic jet, which is about fifteen times higher than the theoretical value. PMID:21710523

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

    Frazier, Shane D; Srubar, Wil V

    2016-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  8. CMOS compatible on-chip decoupling capacitor based on vertically aligned carbon nanofibers

    NASA Astrophysics Data System (ADS)

    Saleem, A. M.; Göransson, G.; Desmaris, V.; Enoksson, P.

    2015-05-01

    On-chip decoupling capacitor of specific capacitance 55 pF/μm2 (footprint area) which is 10 times higher than the commercially available discrete and on-chip (65 nm technology node) decoupling capacitors is presented. The electrodes of the capacitor are based on vertically aligned carbon nanofibers (CNFs) capable of being integrated directly on CMOS chips. The carbon nanofibers employed in this study were grown on CMOS chips using direct current plasma enhanced chemical vapor deposition (DC-PECVD) technique at CMOS compatible temperature. The carbon nanofibers were grown at temperature from 390 °C to 550 °C. The capacitance of the carbon nanofibers was measured by cyclic voltammetry and thus compared. Futhermore the capacitance of decoupling capacitor was measured using different voltage scan rate to show their high charge storage capability and finally the cyclic voltammetry is run for 1000 cycles to assess their suitability as electrode material for decoupling capacitor. Our results show the high specific capacitance and long-term reliability of performance of the on-chip decoupling capacitors. Moreover, the specific capacitance shown is larger for carbon nanofibers grown at higher temperature.

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

    PubMed Central

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

    2016-01-01

    Dementia is a growing problem that affects elderly people worldwide. More accurate evaluation of dementia diagnosis can help during the medical examination. Several methods for computer-aided dementia diagnosis have been proposed using resonance imaging scans to discriminate between patients with Alzheimer's disease (AD) or mild cognitive impairment (MCI) and healthy controls (NC). Nonetheless, the computer-aided diagnosis is especially challenging because of the heterogeneous and intermediate nature of MCI. We address the automated dementia diagnosis by introducing a novel supervised pretraining approach that takes advantage of the artificial neural network (ANN) for complex classification tasks. The proposal initializes an ANN based on linear projections to achieve more discriminating spaces. Such projections are estimated by maximizing the centered kernel alignment criterion that assesses the affinity between the resonance imaging data kernel matrix and the label target matrix. As a result, the performed linear embedding allows accounting for features that contribute the most to the MCI class discrimination. We compare the supervised pretraining approach to two unsupervised initialization methods (autoencoders and Principal Component Analysis) and against the best four performing classification methods of the 2014 CADDementia challenge. As a result, our proposal outperforms all the baselines (7% of classification accuracy and area under the receiver-operating-characteristic curve) at the time it reduces the class biasing. PMID:27148392

  10. Ion Pair in Extreme Aqueous Environments, Molecular-Based and Electric Conductance Approaches

    SciTech Connect

    Chialvo, Ariel A; Gruszkiewicz, Miroslaw {Mirek} S; Simonson, J Michael {Mike}; Palmer, Donald; Cole, David R

    2009-01-01

    We determine by molecular-based simulation the density profiles of the Na+!Cl! ion-pair association constant in steam environments along three supercritical isotherms to interrogate the behavior of ion speciation in dilute aqueous solutions at extreme conditions. Moreover, we describe a new ultra-sensitive flow-through electric conductance apparatus designed to bridge the gap between the currently lowest steam-density conditions at which we are experimentally able to attain electric conductance measurements and the theoretically-reachable zero-density limit. Finally, we highlight important modeling challenges encountered near the zero-density limit and discuss ways to overcome them.

  11. A Multiparty Controlled Bidirectional Quantum Secure Direct Communication and Authentication Protocol Based on EPR Pairs

    NASA Astrophysics Data System (ADS)

    Chang, Yan; Zhang, Shi-Bin; Yan, Li-Li; Sheng, Zhi-Wei

    2013-06-01

    A multiparty controlled bidirectional quantum secure direct communication and authentication protocol is proposed based on EPR pair and entanglement swapping. The legitimate identities of communicating parties are encoded to Bell states which act as a detection sequence. Secret messages are transmitted by using the classical XOR operation, which serves as a one-time-pad. No photon with secret information transmits in the quantum channel. Compared with the protocols proposed by Wang et al. [Acta Phys. Sin. 56 (2007) 673; Opt. Commun. 266 (2006) 732], the protocol in this study implements bidirectional communication and authentication, which defends most attacks including the ‘man-in-the-middle’ attack efficiently.

  12. Superior coexistence: systematicALLY regulatING land subsidence BASED on set pair theory

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Gong, S.-L.

    2015-11-01

    Anthropogenic land subsidence is an environmental side effect of exploring and using natural resources in the process of economic development. The key points of the system for controlling land subsidence include cooperation and superior coexistence while the economy develops, exploring and using natural resources, and geological environmental safety. Using the theory and method of set pair analysis (SPA), this article anatomises the factors, effects, and transformation of land subsidence. Based on the principle of superior coexistence, this paper promotes a technical approach to the system for controlling land subsidence, in order to improve the prevention and control of geological hazards.

  13. Mass spectrometry based on a coupled Cooper-pair box and nanomechanical resonator system

    NASA Astrophysics Data System (ADS)

    Jiang, Cheng; Chen, Bin; Li, Jin-Jin; Zhu, Ka-Di

    2011-10-01

    Nanomechanical resonators (NRs) with very high frequency have a great potential for mass sensing with unprecedented sensitivity. In this study, we propose a scheme for mass sensing based on the NR capacitively coupled to a Cooper-pair box (CPB) driven by two microwave currents. The accreted mass landing on the resonator can be measured conveniently by tracking the resonance frequency shifts because of mass changes in the signal absorption spectrum. We demonstrate that frequency shifts induced by adsorption of ten 1587 bp DNA molecules can be well resolved in the absorption spectrum. Integration with the CPB enables capacitive readout of the mechanical resonance directly on the chip.

  14. How Does Guanine-Cytosine Base Pair Affect Excess-Electron Transfer in DNA?

    PubMed

    Lin, Shih-Hsun; Fujitsuka, Mamoru; Majima, Tetsuro

    2015-06-25

    Charge transfer and proton transfer in DNA have attracted wide attention due to their relevance in biological processes and so on. Especially, excess-electron transfer (EET) in DNA has strong relation to DNA repair. However, our understanding on EET in DNA still remains limited. Herein, by using a strongly electron-donating photosensitizer, trimer of 3,4-ethylenedioxythiophene (3E), and an electron acceptor, diphenylacetylene (DPA), two series of functionalized DNA oligomers were synthesized for investigation of EET dynamics in DNA. The transient absorption measurements during femtosecond laser flash photolysis showed that guanine:cytosine (G:C) base pair affects EET dynamics in DNA by two possible mechanisms: the excess-electron quenching by proton transfer with the complementary G after formation of C(•-) and the EET hindrance by inserting a G:C base pair as a potential barrier in consecutive thymines (T's). In the present paper, we provided useful information based on the direct kinetic measurements, which allowed us to discuss EET through oligonucleotides for the investigation of DNA damage/repair. PMID:26042867

  15. SRP-RNA sequence alignment and secondary structure.

    PubMed Central

    Larsen, N; Zwieb, C

    1991-01-01

    The secondary structures of the RNAs from the signal recognition particle, termed SRP-RNA, were derived buy comparative analyses of an alignment of 39 sequences. The models are minimal in that only base pairs are included for which there is comparative evidence. The structures represent refinements of earlier versions and include a new short helix. PMID:1707519

  16. CARNA—alignment of RNA structure ensembles

    PubMed Central

    Sorescu, Dragoş Alexandru; Möhl, Mathias; Mann, Martin; Backofen, Rolf; Will, Sebastian

    2012-01-01

    Due to recent algorithmic progress, tools for the gold standard of comparative RNA analysis, namely Sankoff-style simultaneous alignment and folding, are now readily applicable. Such approaches, however, compare RNAs with respect to a simultaneously predicted, single, nested consensus structure. To make multiple alignment of RNAs available in cases, where this limitation of the standard approach is critical, we introduce a web server that provides a complete and convenient interface to the RNA structure alignment tool ‘CARNA’. This tool uniquely supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically; these features are highly desirable for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots. We represent structural input and output information as base pair probability dot plots; this provides large flexibility in the input, ranging from fixed structures to structure ensembles, and enables immediate visual analysis of the results. In contrast to conventional Sankoff-style approaches, ‘CARNA’ optimizes all structural similarities in the input simultaneously, for example across an entire RNA structure ensemble. Even compared with already costly Sankoff-style alignment, ‘CARNA’ solves an intrinsically much harder problem by applying advanced, constraint-based, algorithmic techniques. Although ‘CARNA’ is specialized to the alignment of RNAs with several conserved structures, its performance on RNAs in general is on par with state-of-the-art general-purpose RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server is freely available at http://rna.informatik.uni-freiburg.de/CARNA. PMID:22689637

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    A study on the development of high-power supercapacitor materials based on formation of thick mesoporous MnO2 shells on a highly conductive 3D template using vertically aligned carbon nanofibers (VACNFs). Coaxial manganese shells of 100 to 600 nm nominal thicknesses are sputter-coated on VACNFs and then electrochemically oxidized into rose-petal-like mesoporous MnO2 structure. Such a 3D MnO2/VACNF hybrid architecture provides enhanced ion diffusion throughout the whole MnO2 shell and yields excellent current collection capability through the VACNF electrode. These two effects collectively enable faster electrochemical reactions during charge-discharge of MnO2 in 1 M Na2SO4. Thick MnO2 shells (up to 200 nm in radial thickness) can be employed, giving a specific capacitance up to 437 F g-1. More importantly, supercapacitors employing such a 3D MnO2/VACNF hybrid electrode illustrate more than one order of magnitude higher specific power than the state-of-the-art ones based on other MnO2 structures, reaching ~240 kW kg-1, while maintaining a comparable specific energy in the range of 1 to 10 Wh kg-1. This hybrid approach demonstrates the potential of 3D core-shell architectures for high-power energy storage devices.A study on the development of high-power supercapacitor materials based on formation of thick mesoporous MnO2 shells on a highly conductive 3D template using vertically aligned carbon nanofibers (VACNFs). Coaxial manganese shells of 100 to 600 nm nominal thicknesses are sputter-coated on VACNFs and then electrochemically oxidized into rose-petal-like mesoporous MnO2 structure. Such a 3D MnO2/VACNF hybrid architecture provides enhanced ion diffusion throughout the whole MnO2 shell and yields excellent current collection capability through the VACNF electrode. These two effects collectively enable faster electrochemical reactions during charge-discharge of MnO2 in 1 M Na2SO4. Thick MnO2 shells (up to 200 nm in radial thickness) can be employed, giving a

  18. Markov Random Field Based Automatic Image Alignment for ElectronTomography

    SciTech Connect

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

    2007-11-30

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

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

    NASA Astrophysics Data System (ADS)

    Zhu, Yongwei; Kankanhalli, Mohan S.

    2003-01-01

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

  20. Structural analysis of aligned RNAs.

    PubMed

    Voss, Björn

    2006-01-01

    The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de. PMID:17020924

  1. Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes

    PubMed Central

    Kondo, Jiro; Westhof, Eric

    2011-01-01

    Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide–protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson–Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson–Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues. PMID:21737431

  2. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

    NASA Technical Reports Server (NTRS)

    Urakawa, Hidetoshi; El Fantroussi, Said; Smidt, Hauke; Smoot, James C.; Tribou, Erik H.; Kelly, John J.; Noble, Peter A.; Stahl, David A.

    2003-01-01

    The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

  3. Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing

    PubMed Central

    Li, Sanshu; Breaker, Ronald R.

    2013-01-01

    Thiamin pyrophosphate (TPP) riboswitches are found in organisms from all three domains of life. Examples in bacteria commonly repress gene expression by terminating transcription or by blocking ribosome binding, whereas most eukaryotic TPP riboswitches are predicted to regulate gene expression by modulating RNA splicing. Given the widespread distribution of eukaryotic TPP riboswitches and the diversity of their locations in precursor messenger RNAs (pre-mRNAs), we sought to examine the mechanism of alternative splicing regulation by a fungal TPP riboswitch from Neurospora crassa, which is mostly located in a large intron separating protein-coding exons. Our data reveal that this riboswitch uses a long-distance (∼530-nt separation) base-pairing interaction to regulate alternative splicing. Specifically, a portion of the TPP-binding aptamer can form a base-paired structure with a conserved sequence element (α) located near a 5′ splice site, which greatly increases use of this 5′ splice site and promotes gene expression. Comparative sequence analyses indicate that many fungal species carry a TPP riboswitch with similar intron architecture, and therefore the homologous genes in these fungi are likely to use the same mechanism. Our findings expand the scope of genetic control mechanisms relying on long-range RNA interactions to include riboswitches. PMID:23376932

  4. Conserved arginines on the rim of Hfq catalyze base pair formation and exchange

    PubMed Central

    Panja, Subrata; Schu, Daniel J.; Woodson, Sarah A.

    2013-01-01

    The Sm-like protein Hfq is required for gene regulation by small RNAs (sRNAs) in bacteria and facilitates base pairing between sRNAs and their mRNA targets. The proximal and distal faces of the Hfq hexamer specifically bind sRNA and mRNA targets, but they do not explain how Hfq accelerates the formation and exchange of RNA base pairs. Here, we show that conserved arginines on the outer rim of the hexamer that are known to interact with sRNA bodies are required for Hfq’s chaperone activity. Mutations in the arginine patch lower the ability of Hfq to act in sRNA regulation of rpoS translation and eliminate annealing of natural sRNAs or unstructured oligonucleotides, without preventing binding to either the proximal or distal face. Stopped-flow FRET and fluorescence anisotropy show that complementary RNAs transiently form a ternary complex with Hfq, but the RNAs are not released as a double helix in the absence of rim arginines. RNAs bound to either face of Hfq quench the fluorescence of a tryptophan adjacent to the arginine patch, demonstrating that the rim can simultaneously engage two RNA strands. We propose that the arginine patch overcomes entropic and electrostatic barriers to helix nucleation and constitutes the active site for Hfq’s chaperone function. PMID:23771143

  5. Design and performance of an automated video-based laser beam alignment system

    SciTech Connect

    Rundle, W.J. ); Kartz, M.W. ); Bliss, E.S.; English, R.E. Jr.; Peterson, R.L.; Thompson, G.R.; Uhlich, D.M. )

    1992-07-14

    This paper describes the design and performance of an automated, closed-loop, laser beam alignment system. Its function is to sense a beam alignment error in a laser beam transport system and automatically steer mirrors preceding the sensor location as required to maintain beam alignment. The laser beam is sampled by an optomechanical package which uses video cameras to sense pointing and centering errors. The camera outputs are fed to an image processing module, which includes video digitizers and uses image storage and software to sense the centroid of the image. Signals are sent through a VMEbus to an optical device controller'' (ODC), which drives stepper-motor actuators on mirror mounts preceding the beam-sampling location to return the beam alignment to the prescribed condition. Photodiodes are also used to extend the control bandwidth beyond that which is achievable with video cameras. This system has been operated at LLNL in the Atomic Vapor Laser Isotope Separation (AVLIS) program to maintain the alignment of copper and dye laser beams, the latter to within [plus minus]2 [mu]r in pointing and less than 1 mm in centering. The optomechanical design of the instrumented package, which includes lens, mirror, and video mounts in a rigid housing, the automated control system architecture, and the performance of this equipment is described.

  6. Design and performance of an automated video-based laser beam alignment system

    SciTech Connect

    Rundle, W.J.; Kartz, M.W.; Bliss, E.S.; English, R.E. Jr.; Peterson, R.L.; Thompson, G.R.; Uhlich, D.M.

    1992-07-14

    This paper describes the design and performance of an automated, closed-loop, laser beam alignment system. Its function is to sense a beam alignment error in a laser beam transport system and automatically steer mirrors preceding the sensor location as required to maintain beam alignment. The laser beam is sampled by an optomechanical package which uses video cameras to sense pointing and centering errors. The camera outputs are fed to an image processing module, which includes video digitizers and uses image storage and software to sense the centroid of the image. Signals are sent through a VMEbus to an ``optical device controller`` (ODC), which drives stepper-motor actuators on mirror mounts preceding the beam-sampling location to return the beam alignment to the prescribed condition. Photodiodes are also used to extend the control bandwidth beyond that which is achievable with video cameras. This system has been operated at LLNL in the Atomic Vapor Laser Isotope Separation (AVLIS) program to maintain the alignment of copper and dye laser beams, the latter to within {plus_minus}2 {mu}r in pointing and less than 1 mm in centering. The optomechanical design of the instrumented package, which includes lens, mirror, and video mounts in a rigid housing, the automated control system architecture, and the performance of this equipment is described.

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

    SciTech Connect

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

    2007-07-21

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

  8. How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations.

    PubMed Central

    Levitt, M

    1978-01-01

    Calculations on a 20-base pair segment of DNA double helix using empirical energy functions show that DNA can be bent smoothly and uniformly into a superhelix with a small enough radius (45 A) to fit the dimensions of chromatin. The variation of energy with the twist of the base pairs about the helix axis shows the straight DNA free in solution is most stable with about 10 1/2 base pairs per turn rather than 10 as observed in the solid state, whereas superhelical DNA in chromatin is most stable with about 10 base pairs per turn. This result, which has a simple physical interpretation, explains the pattern of nuclease cuts and the linkage number changes observed for DNA arranged in chromatin. PMID:273227

  9. An efficient and near linear scaling pair natural orbital based local coupled cluster method

    NASA Astrophysics Data System (ADS)

    Riplinger, Christoph; Neese, Frank

    2013-01-01

    In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009), 10.1063/1.3173827]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 105-106 relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below <0.05%, which implies typically 15-20 but occasionally up to 30 atoms per domain on average. The new method has been given the acronym DLPNO-CCSD ("domain based LPNO-CCSD"). The method is nearly linear scaling with respect to system size. The original LPNO-CCSD method had three adjustable truncation thresholds that were chosen conservatively and do not need to be changed for actual applications. In the present treatment, no additional truncation parameters have been introduced. Any additional truncation

  10. Simulation Based on Negative ion pair Techniques of Electric propulsion In Satellite Mission Using Chlorine Gas

    NASA Astrophysics Data System (ADS)

    Bakkiyaraj, R.

    R.Bakkiyaraj,Assistant professor,Government college of Engineering ,Bargur,Tamilnadu. *C.Sathiyavel, PG Student and Department of Aeronautical Engineering/Branch of Avionics, PSN college of Engineering and Technology,Tirunelveli,India. Abstract: Ion propulsion rocket system is expected to become popular with the development of ion-ion pair techniques because of their stimulated of low propellant, Design of repulsive between negative ions with low electric power and high efficiency. A Negative ion pair of ion propulsion rocket system is proposed in this work .Negative Ion Based Rocket system consists of three parts 1.ionization chamber 2. Repulsion force and ion accelerator 3. Exhaust of Nozzle. The Negative ions from electro negatively gas are produced by attachment of the gas ,such as chlorine with electron emitted from a Electron gun ionization chamber. The formulate of large stable negative ion is achievable in chlorine gas with respect to electron affinity (∆E). When a neutral chlorine atom in the gaseous form picks up an electron to form a cl- ion, it releases energy of 349 kJ/mol or 3.6 eV/atom. It is said to have an electron affinity of -349 kJ/mol ,the negative sign indicating that energy is released during this process .The distance between negative ions pair is important for the evaluation of the rocket thrust and is also determined by the exhaust velocity of the propellant. The mass flow rate of ions is related to the ion beam current. Accelerate the Negative ions to a high velocity in the thrust vector direction with a significantly intense grids and the exhaust of negative ions through Nozzle. The simulation of the ion propulsion system has been carried out by MATLAB. By comparing the simulation results with the theoretical and previous results, we have found that the proposed method is achieved of thrust value with low electric power for simulating the ion propulsion rocket system

  11. Evaluating changes in matrix based, recovery-adjusted concentrations in paired data for pesticides in groundwater

    USGS Publications Warehouse

    Zimmerman, Tammy M.; Breen, Kevin J.

    2012-01-01

    Pesticide concentration data for waters from selected carbonate-rock aquifers in agricultural areas of Pennsylvania were collected in 1993–2009 for occurrence and distribution assessments. A set of 30 wells was visited once in 1993–1995 and again in 2008–2009 to assess concentration changes. The data include censored matched pairs (nondetections of a compound in one or both samples of a pair). A potentially improved approach for assessing concentration changes is presented where (i) concentrations are adjusted with models of matrix-spike recovery and (ii) area-wide temporal change is tested by use of the paired Prentice-Wilcoxon (PPW) statistical test. The PPW results for atrazine, simazine, metolachlor, prometon, and an atrazine degradate, deethylatrazine (DEA), are compared using recovery-adjusted and unadjusted concentrations. Results for adjusted compared with unadjusted concentrations in 2008–2009 compared with 1993–1995 were similar for atrazine and simazine (significant decrease; 95% confidence level) and metolachlor (no change) but differed for DEA (adjusted, decrease; unadjusted, increase) and prometon (adjusted, decrease; unadjusted, no change). The PPW results were different on recovery-adjusted compared with unadjusted concentrations. Not accounting for variability in recovery can mask a true change, misidentify a change when no true change exists, or assign a direction opposite of the true change in concentration that resulted from matrix influences on extraction and laboratory method performance. However, matrix-based models of recovery derived from a laboratory performance dataset from multiple studies for national assessment, as used herein, rather than time- and study-specific recoveries may introduce uncertainty in recovery adjustments for individual samples that should be considered in assessing change.

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

    PubMed

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

    2015-08-01

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

  13. Identification of DNA lesions using a third base pair for amplification and nanopore sequencing

    PubMed Central

    Riedl, Jan; Ding, Yun; Fleming, Aaron M.; Burrows, Cynthia J.

    2015-01-01

    Damage to the genome is implicated in the progression of cancer and stress-induced diseases. DNA lesions exist in low levels, and cannot be amplified by standard PCR because they are frequently strong blocks to polymerases. Here, we describe a method for PCR amplification of lesion-containing DNA in which the site and identity could be marked, copied and sequenced. Critical for this method is installation of either the dNaM or d5SICS nucleotides at the lesion site after processing via the base excision repair process. These marker nucleotides constitute an unnatural base pair, allowing large quantities of marked DNA to be made by PCR amplification. Sanger sequencing confirms the potential for this method to locate lesions by marking, amplifying and sequencing a lesion in the KRAS gene. Detection using the α-hemolysin nanopore is also developed to analyse the markers in individual DNA strands with the potential to identify multiple lesions per strand. PMID:26542210

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

    SciTech Connect

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

    2005-11-10

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

  15. Sheared-type G(anti).C(syn) base-pair: a unique d(GXC) loop closure motif.

    PubMed

    Chin, Ko-Hsin; Chou, Shan-Ho

    2003-05-30

    Stable DNA loop structures closed by a novel G.C base-pair have been determined for the single-residue d(GXC) loops (X=A, T, G or C) in low-salt solution by high-resolution nuclear magnetic resonance (NMR) techniques. The closing G.C base-pair in these loops is not of the canonical Watson-Crick type, but adopts instead a unique sheared-type (trans Watson-Crick/sugar-edge) pairing, like those occurring in the sheared mismatched G.A or A.C base-pair, to draw the two opposite strands together. The cytidine residue in the closing base-pair is transformed into the rare syn domain to form two H-bonds with the guanine base and to prevent the steric clash between the G 2NH(2) and the C H-5 protons. Besides, the sugar pucker of the syn cytidine is still located in the regular C2'-endo domain, unlike the C3'-endo domain adopted for the pyrimidines of the out-of-alternation left-handed Z-DNA structure. The facile formation of the compact d(GXC) loops closed by a unique sheared-type G(anti).C(syn) base-pair demonstrates the great potential of the single-stranded d(GXC) triplet repeats to fold into stable hairpins. PMID:12758081

  16. A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA

    PubMed Central

    Kladwang, Wipapat; Cordero, Pablo; Das, Rhiju

    2011-01-01

    We present a rapid experimental strategy for inferring base pairs in structured RNAs via an information-rich extension of classic chemical mapping approaches. The mutate-and-map method, previously applied to a DNA/RNA helix, systematically searches for single mutations that enhance the chemical accessibility of base-pairing partners distant in sequence. To test this strategy for structured RNAs, we have carried out mutate-and-map measurements for a 35-nt hairpin, called the MedLoop RNA, embedded within an 80-nt sequence. We demonstrate the synthesis of all 105 single mutants of the MedLoop RNA sequence and present high-throughput DMS, CMCT, and SHAPE modification measurements for this library at single-nucleotide resolution. The resulting two-dimensional data reveal visually clear, punctate features corresponding to RNA base pair interactions as well as more complex features; these signals can be qualitatively rationalized by comparison to secondary structure predictions. Finally, we present an automated, sequence-blind analysis that permits the confident identification of nine of the 10 MedLoop RNA base pairs at single-nucleotide resolution, while discriminating against all 1460 false-positive base pairs. These results establish the accuracy and information content of the mutate-and-map strategy and support its feasibility for rapidly characterizing the base-pairing patterns of larger and more complex RNA systems. PMID:21239468

  17. Role of the Closing Base Pair for d(GCA) Hairpin Stability: Free Energy Analysis and Folding Simulations

    SciTech Connect

    Kannan, Srinivasaraghavan; Zacharias, Martin W.

    2011-06-30

    Hairpin loops belong to the most important structural motifs in folded nucleic acids. The d(GNA) sequence in DNA can form very stable trinucleotide hairpin loops depending, however, strongly on the closing base pair. Replica-exchange molecular dynamics (REMD) were employed to study hairpin folding of two DNA sequences, d(gcGCAgc) and d(cgGCAcg), with the same central loop motif but different closing base pairs starting from singlestranded structures. In both cases, conformations of the most populated conformational cluster at the lowest temperature showed close agreement with available experimental structures. For the loop sequence with the less stable G:C closing base pair, an alternative loop topology accumulated as second most populated conformational state indicating a possible loop structural heterogeneity. Comparative-free energy simulations on induced loop unfolding indicated higher stability of the loop with a C:G closing base pair by 3 kcal mol1 (compared to a G:C closing base pair) in very good agreement with experiment. The comparative energetic analysis of sampled unfolded, intermediate and folded conformational states identified electrostatic and packing interactions as the main contributions to the closing base pair dependence of the d(GCA) loop stability.

  18. Synthesis of Vertically Aligned ZnO Nanorods on Ni-Based Buffer Layers Using a Thermal Evaporation Process

    NASA Astrophysics Data System (ADS)

    Kuo, Dong-Hau; He, Jheng-Yu; Huang, Ying-Sheng

    2012-03-01

    Uniform, vertically aligned ZnO nanorods have been grown mainly on Au-coated and ZnO-coated sapphire substrates, ZnO- and GaN-coated substrates, or self-catalyzing substrates. Conventionally, Ni-coated substrates have resulted in thick rods with diameter more than 250 nm, rods with nonuniform distribution in diameter, or rods with an alignment problem. In the best result in this paper, slender, uniform, vertically aligned, solely UV-emitting ZnO nanorods with diameter of 110 ± 25 nm and length of 30 ± 10 μm have been successfully grown at 700°C for 2 h on sapphire substrates covered with Ni-based buffer layers by using metallic zinc and oxygen as reactants. Scanning electron microscopy and room-temperature photoluminescence have been used to investigate the effects of process conditions on the slenderness and vertical alignment of the ZnO rods. To develop the desired ZnO nanorods, etched sapphire substrates, a second metallic Sn buffer layer on top of a spin-coated nickel oxide layer, polyvinyl alcohol binder at 10% concentration in solution of iron nitrate, and pyrolysis and reduction reactions were involved. Defect photoemission for thick ZnO rods is attributed to insufficient oxygen supply during the growth process with fixed oxygen flow rate.

  19. STAR: ultrafast universal RNA-seq aligner

    PubMed Central

    Dobin, Alexander; Davis, Carrie A.; Schlesinger, Felix; Drenkow, Jorg; Zaleski, Chris; Jha, Sonali; Batut, Philippe; Chaisson, Mark; Gingeras, Thomas R.

    2013-01-01

    Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. Results: To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80–90% success rate, corroborating the high precision of the STAR mapping strategy. Availability and implementation: STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/. Contact: dobin@cshl.edu. PMID:23104886

  20. Ion-Pairing Assemblies Based on Pentacyano-Substituted Cyclopentadienide as a π-Electronic Anion.

    PubMed

    Bando, Yuya; Haketa, Yohei; Sakurai, Tsuneaki; Matsuda, Wakana; Seki, Shu; Takaya, Hikaru; Maeda, Hiromitsu

    2016-06-01

    Pentacyanocyclopentadienide (PCCp(-) ), a stable π-electronic anion, provided various ion-pairing assemblies in combination with various cations. PCCp(-) -based assemblies exist as single crystals and mesophases owing to interionic interactions with π-electronic and aliphatic cations with a variety of geometries, substituents, and electronic structures. Single-crystal X-ray analysis revealed that PCCp(-) formed cation-dependent arrangements with contributions from charge-by-charge and charge-segregated assembly modes for ion pairs with π-electronic and aliphatic cations, respectively. Furthermore, some aliphatic cations gave dimension-controlled organized structures with PCCp(-) , as observed in the mesophases, for which synchrotron XRD analysis suggested the formation of charge-segregated modes. Noncontact evaluation of conductivity for (C12 H25 )3 MeN(+) ⋅PCCp(-) films revealed potential hole-transporting properties, yielding a local-scale hole mobility of 0.4 cm(2)  V(-1)  s(-1) at semiconductor-insulator interfaces. PMID:27120581

  1. Extruded polymer films pigmented with a heterogeneous ion-pair based lumophore for O2 sensing.

    PubMed

    Mills, Andrew; Graham, Ashleigh

    2013-11-01

    A novel approach to polymeric Ru(II)-diimine luminescent O2 sensors is described. The Ru(II)-diimine, tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride ([Ru(dpp)3](2+)), is first ion-paired to the surface of heterogeneous TiO2 particles, rendered negatively charged due to the alkali nature of the aqueous solution, to produce an O2 sensitive pigment with a strikingly high oxygen sensitivity (i.e. PO2 (S = 1/2) = 0.002 atm, where PO2 (S = 1/2) is defined as the amount of oxygen required to reduce the initial, oxygen free luminescence by 50%), and a rapid response to oxygen. The pigment is extruded in low density polyethylene (LDPE) to produce a thin (60 μm), flexible, O2 sensing plastic film, with an O2 sensitivity (PO2 (S = 1/2) = 0.84 atm) comparable to the more traditional homogeneous lumophore ion-pair based O2 sensor ink films reported in the literature. PMID:24040643

  2. GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

    PubMed

    Nemoto, Wataru; Yamanishi, Yoshihiro; Limviphuvadh, Vachiranee; Saito, Akira; Toh, Hiroyuki

    2016-09-01

    G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-dimers or higher-order molecular complexes. Many GPCRs exert a wide variety of molecular functions by forming specific combinations of GPCR subtypes. In addition, some GPCRs are reportedly associated with diseases. GPCR oligomerization is now recognized as an important event in various biological phenomena, and many researchers are investigating this subject. We have developed a support vector machine (SVM)-based method to predict interacting pairs for GPCR oligomerization, by integrating the structure and sequence information of GPCRs. The performance of our method was evaluated by the Receiver Operating Characteristic (ROC) curve. The corresponding area under the curve was 0.938. As far as we know, this is the only prediction method for interacting pairs among GPCRs. Our method could accelerate the analyses of these interactions, and contribute to the elucidation of the global structures of the GPCR networks in membranes. Proteins 2016; 84:1224-1233. © 2016 Wiley Periodicals, Inc. PMID:27191053

  3. Critical Alignment in Inquiry-Based Practice in Developing Mathematics Teaching

    ERIC Educational Resources Information Center

    Goodchild, Simon; Fuglestad, Anne Berit; Jaworski, Barbara

    2013-01-01

    This paper reports a case study from a mathematics teaching developmental research project. The theoretical foundation for the research comprises "communities of inquiry" and "critical alignment," with which the developmental methodology has a particular synergy. This synergy is the main focus of the paper. The paper elaborates…

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

    PubMed Central

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

    2015-01-01

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

  5. Image correlation method for DNA sequence alignment.

    PubMed

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

    2012-01-01

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

  6. Tidal alignment of galaxies

    NASA Astrophysics Data System (ADS)

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    2015-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  8. Fingerprint identification using SIFT-based minutia descriptors and improved all descriptor-pair matching.

    PubMed

    Zhou, Ru; Zhong, Dexing; Han, Jiuqiang

    2013-01-01

    The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT) descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1) the similar patterns of parallel ridges; and (2) high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD) to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM), is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA) achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements. PMID:23467056

  9. Fingerprint Identification Using SIFT-Based Minutia Descriptors and Improved All Descriptor-Pair Matching

    PubMed Central

    Zhou, Ru; Zhong, Dexing; Han, Jiuqiang

    2013-01-01

    The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT) descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1) the similar patterns of parallel ridges; and (2) high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD) to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM), is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA) achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements. PMID:23467056

  10. Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition

    PubMed Central

    Kuznetsov, Nikita A.; Bergonzo, Christina; Campbell, Arthur J.; Li, Haoquan; Mechetin, Grigory V.; de los Santos, Carlos; Grollman, Arthur P.; Fedorova, Olga S.; Zharkov, Dmitry O.; Simmerling, Carlos

    2015-01-01

    Formamidopyrimidine-DNA glycosylase (Fpg) excises 8-oxoguanine (oxoG) from DNA but ignores normal guanine. We combined molecular dynamics simulation and stopped-flow kinetics with fluorescence detection to track the events in the recognition of oxoG by Fpg and its mutants with a key phenylalanine residue, which intercalates next to the damaged base, changed to either alanine (F110A) or fluorescent reporter tryptophan (F110W). Guanine was sampled by Fpg, as evident from the F110W stopped-flow traces, but less extensively than oxoG. The wedgeless F110A enzyme could bend DNA but failed to proceed further in oxoG recognition. Modeling of the base eversion with energy decomposition suggested that the wedge destabilizes the intrahelical base primarily through buckling both surrounding base pairs. Replacement of oxoG with abasic (AP) site rescued the activity, and calculations suggested that wedge insertion is not required for AP site destabilization and eversion. Our results suggest that Fpg, and possibly other DNA glycosylases, convert part of the binding energy into active destabilization of their substrates, using the energy differences between normal and damaged bases for fast substrate discrimination. PMID:25520195

  11. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs.

    PubMed

    Fang, Wei; Chen, Ji; Rossi, Mariana; Feng, Yexin; Li, Xin-Zheng; Michaelides, Angelos

    2016-06-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  12. Pair normalized channel feature and statistics-based learning for high-performance pedestrian detection

    NASA Astrophysics Data System (ADS)

    Zeng, Bobo; Wang, Guijin; Ruan, Zhiwei; Lin, Xinggang; Meng, Long

    2012-07-01

    High-performance pedestrian detection with good accuracy and fast speed is an important yet challenging task in computer vision. We design a novel feature named pair normalized channel feature (PNCF), which simultaneously combines and normalizes two channel features in image channels, achieving a highly discriminative power and computational efficiency. PNCF applies to both gradient channels and color channels so that shape and appearance information are described and integrated in the same feature. To efficiently explore the formidably large PNCF feature space, we propose a statistics-based feature learning method to select a small number of potentially discriminative candidate features, which are fed into the boosting algorithm. In addition, channel compression and a hybrid pyramid are employed to speed up the multiscale detection. Experiments illustrate the effectiveness of PNCF and its learning method. Our proposed detector outperforms the state-of-the-art on several benchmark datasets in both detection accuracy and efficiency.

  13. The influence of arene-ring size on stacking interaction with canonical base pairs

    NASA Astrophysics Data System (ADS)

    Formánek, Martin; Burda, Jaroslav V.

    2014-04-01

    Stacking interactions between aromatic molecules (benzene, p-cymene, biphenyl, and di- and tetra-hydrogen anthracene) and G.C and A.T canonical Watson-Crick (WC) base pairs are explored. Two functionals with dispersion corrections: ω-B97XD and B3LYP-D3 are used. For a comparison also the MP2 and B3LYP-D3/PCM methods were used for the most stable p-cymene…WC geometries. It was found that the stacking interaction increases with the size of π-conjugation system. Its extent is in agreement with experimental finding on anticancer activity of Ru(II) piano-stool complexes where intercalation of these aromatic molecules should play an important role. The explored structures are considered as ternary system so that decomposition of the interaction energy to pairwise and non-additivity contributions is also examined.

  14. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

    PubMed Central

    2016-01-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  15. A 26-base-pair repetitive sequence specific for Neisseria gonorrhoeae and Neisseria meningitidis genomic DNA.

    PubMed Central

    Correia, F F; Inouye, S; Inouye, M

    1986-01-01

    Two-dimensional heteroduplex mapping of Neisseria gonorrhoeae genomic DNA revealed a number of spots, indicating the existence of repetitive sequences. When one of the spots was extracted and used as a probe for Southern blot analysis, two HindIII bands (11.0 and 3.6 kilobases [kb]) of the genomic digest hybridized with approximately equal intensity. The 3.6-kb fragment was cloned and found to contain two different types of repeated sequence. One type was approximately 1.1 kb in length and was found at least twice in the entire genome. The other consisted of a 26-base-pair family GT(C/A)C(Py)G(Pu)TTTTTGTTAAT(Py)C(Pu)CTATA (Py, pyrimidine; Pu, purine) that was repeated at least 20 times in the entire genome. This repetitive sequence was found also in Neisseria meningitidis but not in various other gram-negative bacteria. Images PMID:3091577

  16. Single base pair differences in a shared motif determine differential Rhodopsin expression

    PubMed Central

    Rister, Jens; Razzaq, Ansa; Boodram, Pamela; Desai, Nisha; Tsanis, Cleopatra; Chen, Hongtao; Jukam, David; Desplan, Claude

    2016-01-01

    The final identity and functional properties of a neuron are specified by terminal differentiation genes, which are controlled by specific motifs in compact regulatory regions. To determine how these sequences integrate inputs from transcription factors that specify cell types, we compared the regulatory mechanism of Drosophila Rhodopsin genes that are expressed in subsets of photoreceptors to that of phototransduction genes that are expressed broadly, in all photoreceptors. Both sets of genes share an 11bp activator motif. Broadly expressed genes contain a palindromic version that mediates expression in all photoreceptors. In contrast, each Rhodopsin exhibits unique single bp substitutions that break the symmetry of the palindrome and generate activator or repressor motifs critical for restricting expression to photoreceptor subsets. Novel sensory neuron subtypes can therefore evolve through single base pair changes in short regulatory motifs, allowing the discrimination of a wide spectrum of stimuli. PMID:26785491

  17. Wavelet transform based on the optimal wavelet pairs for tunable diode laser absorption spectroscopy signal processing.

    PubMed

    Li, Jingsong; Yu, Benli; Fischer, Horst

    2015-04-01

    This paper presents a novel methodology-based discrete wavelet transform (DWT) and the choice of the optimal wavelet pairs to adaptively process tunable diode laser absorption spectroscopy (TDLAS) spectra for quantitative analysis, such as molecular spectroscopy and trace gas detection. The proposed methodology aims to construct an optimal calibration model for a TDLAS spectrum, regardless of its background structural characteristics, thus facilitating the application of TDLAS as a powerful tool for analytical chemistry. The performance of the proposed method is verified using analysis of both synthetic and observed signals, characterized with different noise levels and baseline drift. In terms of fitting precision and signal-to-noise ratio, both have been improved significantly using the proposed method. PMID:25741689

  18. Gapped graphene-based Josephson junction with d-wave pair coupling

    NASA Astrophysics Data System (ADS)

    Goudarzi, H.; Khezerlou, M.; Dezhaloud, T.

    2013-06-01

    The Josephson current passing through a S/I/S gapped graphene-based junction, where superconductivity in the S region is induced by depositing unconventional d-wave superconductor is investigated. The energy levels of massive Dirac fermions are exactly found for Andreev bound states. We illustrate the effect of characteristic of d-wave pairing symmetry on the Andreev bound states and the Josephson current. It is shown that the Josephson current vanishes for special range of superconductivity phase, φ = φ1 - φ2 and the position of the maximum current depends on the mass gap of graphene. The critical supercurrent varies in an oscillatory manner as function of the barrier strength, so that the period of oscillations does not change by increasing the effective mass of quasiparticles.

  19. Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses

    NASA Technical Reports Server (NTRS)

    Urakawa, Hidetoshi; Noble, Peter A.; El Fantroussi, Said; Kelly, John J.; Stahl, David A.

    2002-01-01

    The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T(d)) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5' terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T(d) and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T(d) and signal intensity, and it decreased the variability of the signal. Although T(d)s of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T(d)s than those with mismatches in the first or second position. The trained NNs predicted the T(d) with high accuracies (R(2) = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R(2) = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T(d)s, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5' terminus plays a greater role in determining the T(d) and signal intensity of duplexes than the type of mismatch.

  20. Hydrogen-bonding studies of amino acid side-chains with DNA base pairs

    NASA Astrophysics Data System (ADS)

    Deepa, P.; Kolandaivel, P.; Senthilkumar, K.

    2011-08-01

    The interactions of the amino acid side-chains arginine (ARG), aspartic acid (ASP), asparagine (ASN), lysine (LYS) and serine (SER) with nucleic acid base pairs have been investigated using theoretical methods. The interaction energy of the short intermolecular N-H ... N, N-H ... O, O-H ... O, O-H ... N, C-H ... O and C-H ... N hydrogen bonds present in both isolated base pairs and complexes and its role in providing stability to the complexes have been explored. The homonuclear interactions are found to be stronger than the heteronuclear interactions. An improper hydrogen bond has been observed for some of the N-H ... O and N-H ... N hydrogen-bond interactions with the contraction of the N-H bond varying from 0.001 to 0.0260 Å and the corresponding blue shift of the stretching frequency by 4-291 cm-1. Localized molecular orbital energy decomposition analysis (LMOEDA) reveals that the major contributions to the energetics are from the long-range polarization (PL) interaction, and the short-range attractive (ES, EX) and repulsive (REP) interactions. The Bader's atoms in molecules (AIM) theory shows good correlation for the electron density and its Laplacian at the bond critical points (BCP) with the N-H ... N and N-H ... O hydrogen-bond lengths in the complexes, and gives a proper explanation for the stability of the structure. The charge-transfer from the proton acceptor to the antibonding orbital of the X-H bond in the complexes was studied using natural bond orbital (NBO) analysis.

  1. Genetic association mapping based on discordant sib pairs: the discordant-alleles test.

    PubMed

    Boehnke, M; Langefeld, C D

    1998-04-01

    Family-based tests of association provide the opportunity to test for an association between a disease and a genetic marker. Such tests avoid false-positive results produced by population stratification, so that evidence for association may be interpreted as evidence for linkage or causation. Several methods that use family-based controls have been proposed, including the haplotype relative risk, the transmission-disequilibrium test, and affected family-based controls. However, because these methods require genotypes on affected individuals and their parents, they are not ideally suited to the study of late-onset diseases. In this paper, we develop several family-based tests of association that use discordant sib pairs (DSPs) in which one sib is affected with a disease and the other sib is not. These tests are based on statistics that compare counts of alleles or genotypes or that test for symmetry in tables of alleles or genotypes. We describe the use of a permutation framework to assess the significance of these statistics. These DSP-based tests provide the same general advantages as parent-offspring trio-based tests, while being applicable to essentially any disease; they may also be tailored to particular hypotheses regarding the genetic model. We compare the statistical properties of our DSP-based tests by computer simulation and illustrate their use with an application to Alzheimer disease and the apolipoprotein E polymorphism. Our results suggest that the discordant-alleles test, which compares the numbers of nonmatching alleles in DSPs, is the most powerful of the tests we considered, for a wide class of disease models and marker types. Finally, we discuss advantages and disadvantages of the DSP design for genetic association mapping. PMID:9529345

  2. A Case Study of the Alignment between Curriculum and Assessment in the New York State Earth Science Standards-Based System

    ERIC Educational Resources Information Center

    Contino, Julie

    2013-01-01

    In a standards-based system, it is important for all components of the system to align in order to achieve the intended goals. No Child Left Behind law mandates that assessments be fully aligned with state standards, be valid, reliable and fair, be reported to all stakeholders, and provide evidence that all students in the state are meeting the…

  3. Characterization of the Trans Watson-Crick GU Base Pair Located in the Catalytic Core of the Antigenomic HDV Ribozyme

    PubMed Central

    Lévesque, Dominique; Reymond, Cédric; Perreault, Jean-Pierre

    2012-01-01

    The HDV ribozyme’s folding pathway is, by far, the most complex folding pathway elucidated to date for a small ribozyme. It includes 6 different steps that have been shown to occur before the chemical cleavage. It is likely that other steps remain to be discovered. One of the most critical of these unknown steps is the formation of the trans Watson-Crick GU base pair within loop III. The U23 and G28 nucleotides that form this base pair are perfectly conserved in all natural variants of the HDV ribozyme, and therefore are considered as being part of the signature of HDV-like ribozymes. Both the formation and the transformation of this base pair have been studied mainly by crystal structure and by molecular dynamic simulations. In order to obtain physical support for the formation of this base pair in solution, a set of experiments, including direct mutagenesis, the site-specific substitution of chemical groups, kinetic studies, chemical probing and magnesium-induced cleavage, were performed with the specific goal of characterizing this trans Watson-Crick GU base pair in an antigenomic HDV ribozyme. Both U23 and G28 can be substituted for nucleotides that likely preserve some of the H-bond interactions present before and after the cleavage step. The formation of the more stable trans Watson-Crick base pair is shown to be a post-cleavage event, while a possibly weaker trans Watson-Crick/Hoogsteen interaction seems to form before the cleavage step. The formation of this unusually stable post-cleavage base pair may act as a driving force on the chemical cleavage by favouring the formation of a more stable ground state of the product-ribozyme complex. To our knowledge, this represents the first demonstration of a potential stabilising role of a post-cleavage conformational switch event in a ribozyme-catalyzed reaction. PMID:22768274

  4. In silico studies toward understanding the interactions of DNA base pairs with protonated linear/cyclic diamines.

    PubMed

    Sen, Anik; Sahu, Debashis; Ganguly, Bishwajit

    2013-08-29

    Protonated amino groups are ubiquitous in nature and important in the fields of chemistry and biology. In search of efficient polyamine analogues, we have performed DFT calculations on the interactions of some simple cyclic and constrained protonated diamines with the DNA base pairs and compared the results with those obtained for the corresponding interactions involving linear diamines, which mimic biogenic polyamines such as spermine. The interactions are mainly governed by the strong hydrogen bonding between the ligand and the DNA base pairs. The DFT calculations suggest that the major-groove N7 interaction (GC base pair) with linear diamine is energetically more favored than other possible interactions, as reported with spermine. The cyclic diamines exhibited better interactions with the N7 site of the AT and GC base pairs of DNA than the linear diamines. The net atomic charges calculated for the protonated amine hydrogens were higher for the cyclic systems than for the linear diamines, inducing better binding affinity with the DNA base pairs. The stable conformers of cyclic diamines were predicted using the MP2/aug-cc-pVDZ level of theory. The positions of the protonated diamine groups in these cyclic systems are crucial for effective binding with the DNA base pairs. The DFT-calculated results show that diequatorial (ee) 1,2-cyclohexadiamine (CHDA) is a promising candidate as a polyamine analogue for biogenic polyamines. Molecular dynamics simulations were performed using explicit water molecules for the interaction of representative ligands with the DNA base pairs to examine the influence of solvent molecules on such interactions. PMID:23909683

  5. Predicting and improving the protein sequence alignment quality by support vector regression

    PubMed Central

    Lee, Minho; Jeong, Chan-seok; Kim, Dongsup

    2007-01-01

    Background For successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significantly depending on our choice of various alignment parameters such as gap opening penalty and gap extension penalty. Because the accuracy of sequence alignment is typically measured by comparing it with its corresponding structure alignment, there is no good way of evaluating alignment accuracy without knowing the structure of a query protein, which is obviously not available at the time of structure prediction. Moreover, there is no universal alignment parameter option that would always yield the optimal alignment. Results In this work, we develop a method to predict the quality of the alignment between a query and a template. We train the support vector regression (SVR) models to predict the MaxSub scores as a measure of alignment quality. The alignment between a query protein and a template of length n is transformed into a (n + 1)-dimensional feature vector, then it is used as an input to predict the alignment quality by the trained SVR model. Performance of our work is evaluated by various measures including Pearson correlation coefficient between the observed and predicted MaxSub scores. Result shows high correlation coefficient of 0.945. For a pair of query and template, 48 alignments are generated by changing alignment options. Trained SVR models are then applied to predict the MaxSub scores of those and to select the best alignment option which is chosen specifically to the query-template pair. This adaptive selection procedure results in 7.4% improvement of MaxSub scores, compared to those when the single best parameter option is used for all query-template pairs. Conclusion The present work demonstrates that the alignment quality can be

  6. Chip electrochromatographic systems: Novel vertically aligned carbon nanotube and silica monoliths based separations

    NASA Astrophysics Data System (ADS)

    Goswami, Shubhodeep

    2009-12-01

    Miniaturized chemical analysis systems, also know as 'lab-on-a-chip' devices have been rapidly developing over the last decade. Capillary electrochromatography (CEC), a multidimensional separation technique combining capillary electrophoresis (CE) and liquid chromatography (LC) has been of great interest for chip based applications. Preliminary work has been undertaken to develop vertically aligned carbon nanotubes and photopolymerizable silica solgel as novel stationary phase materials for 'chip CEC' separations. Patterned growth of CNTs in a specific location of the channel has been carried out using a solid phase Fe-Al catalyst as well as a vapor deposited ferrocene catalyst. Characterization of the CNT "forests" was achieved using optical microscopy, secondary electron microscopy, high resolution tunneling electron microscopy and Raman spectroscopy. Proof-of-concept applications were demonstrated using reversed phase CEC separations as well as solid phase extraction of a glycosylated protein using concanavilin A immobilized onto the CNT bed. Photopolymerizable silica solgel materials were developed as stationary phase for microfluidic electrochromatographic separations in disposable polydimethylsiloxane (PDMS) chip devices. Effect on morphology and pore size of gels were studied as function of UV and solgel polymerization conditions, porogen, salt additives, geometry and hydrolyzable methoxy-ies. Structural morphologies were studied with Secondary Electron Microscopy (SEM). Pore size and pore volumes were characterized by thermal porometry, nitrogen BET adsorptions and differential scanning calorimetry. Computational fluid dynamics and confocal microscopy tools were employed to study the transport of fluids and model analytes. These investigations were directed towards evolving improved strategies for rinsing of uncrosslinked monomers to form porous monoliths as well as to effect a desired separation under a set of electrochromatograhic conditions

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

    PubMed Central

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

    2016-01-01

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

  8. Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads

    PubMed Central

    Song, Kai; Ren, Jie; Zhai, Zhiyuan; Liu, Xuemei

    2013-01-01

    Abstract Next-generation sequencing (NGS) technologies have generated enormous amounts of shotgun read data, and assembly of the reads can be challenging, especially for organisms without template sequences. We study the power of genome comparison based on shotgun read data without assembly using three alignment-free sequence comparison statistics, D2, \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin{document} $$\\textbf{\\textit{D}}_{\\bf 2}^{\\bf *}$$ \\end{document}, and \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin{document} $$\\textbf{\\textit{D}}_{\\bf 2}^S$$ \\end{document}, both theoretically and by simulations. Theoretical formulas for the power of detecting the relationship between two sequences related through a common motif model are derived. It is shown that both \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin{document} $$\\textbf{\\textit{D}}_{\\bf 2}^{\\bf *}$$ \\end{document} and \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin

  9. KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins

    PubMed Central

    Lange, Joanna; Wyrwicz, Lucjan S.; Vriend, Gert

    2016-01-01

    Summary: Intrinsically disordered proteins (IDPs) lack tertiary structure and thus differ from globular proteins in terms of their sequence–structure–function relations. IDPs have lower sequence conservation, different types of active sites and a different distribution of functionally important regions, which altogether make their multiple sequence alignment (MSA) difficult. The KMAD MSA software has been written specifically for the alignment and annotation of IDPs. It augments the substitution matrix with knowledge about post-translational modifications, functional domains and short linear motifs. Results: MSAs produced with KMAD describe well-conserved features among IDPs, tend to agree well with biological intuition, and are a good basis for designing new experiments to shed light on this large, understudied class of proteins. Availability and implementation: KMAD web server is accessible at http://www.cmbi.ru.nl/kmad/. A standalone version is freely available. Contact: vriend@cmbi.ru.nl PMID:26568635

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

    NASA Astrophysics Data System (ADS)

    Li, Lian; Ma, TianMeng

    2014-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

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

    2016-01-01

    In bioinformatics, sequence alignment is one of the most common problems. Multiple sequence alignment is an NP (nondeterministic polynomial time) problem, which requires further study and exploration. The chaos optimization algorithm is a type of chaos theory, and a procedure for combining the genetic algorithm (GA), which uses ergodicity, and inherent randomness of chaotic iteration. It is an efficient method to solve the basic premature phenomenon of the GA. Applying the Logistic map to the GA and using chaotic sequences to carry out the chaotic perturbation can improve the convergence of the basic GA. In addition, the random tournament selection and optimal preservation strategy are used in the GA. Experimental evidence indicates good results for this process. PMID:27420977

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

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

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

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

    PubMed Central

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

    2014-01-01

    Optical phase conjugation (OPC) has enabled many optical applications such as aberration correction and image transmission through fiber. In recent years, implementation of digital optical phase conjugation (DOPC) has opened up the possibility of its use in biomedical optics (e.g. deep-tissue optical focusing) due to its ability to provide greater-than-unity OPC reflectivity (the power ratio of the phase conjugated beam and input beam to the OPC system) and its flexibility to accommodate additional wavefront manipulations. However, the requirement for precise (pixel-to-pixel matching) alignment of the wavefront sensor and the spatial light modulator (SLM) limits the practical usability of DOPC systems. Here, we report a method for auto-alignment of a DOPC system by which the misalignment between the sensor and the SLM is auto-corrected through digital light propagation. With this method, we were able to accomplish OPC playback with a DOPC system with gross sensor-SLM misalignment by an axial displacement of up to~1.5 cm, rotation and tip/tilt of ~5∘, and in-plane displacement of ~5 mm (dependent on the physical size of the sensor and the SLM). Our auto-alignment method robustly achieved a DOPC playback peak-to-background ratio (PBR) corresponding to more than ~30 % of the theoretical maximum. As an additional advantage, the auto-alignment procedure can be easily performed at will and, as such, allows us to correct for small mechanical drifts within the DOPC systems, thus overcoming a previously major DOPC system vulnerability. We believe that this reported method for implementing robust DOPC systems will broaden the practical utility of DOPC systems. PMID:24977504

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

    PubMed

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

    2014-06-16

    Optical phase conjugation (OPC) has enabled many optical applications such as aberration correction and image transmission through fiber. In recent years, implementation of digital optical phase conjugation (DOPC) has opened up the possibility of its use in biomedical optics (e.g. deep-tissue optical focusing) due to its ability to provide greater-than-unity OPC reflectivity (the power ratio of the phase conjugated beam and input beam to the OPC system) and its flexibility to accommodate additional wavefront manipulations. However, the requirement for precise (pixel-to-pixel matching) alignment of the wavefront sensor and the spatial light modulator (SLM) limits the practical usability of DOPC systems. Here, we report a method for auto-alignment of a DOPC system by which the misalignment between the sensor and the SLM is auto-corrected through digital light propagation. With this method, we were able to accomplish OPC playback with a DOPC system with gross sensor-SLM misalignment by an axial displacement of up to~1.5 cm, rotation and tip/tilt of ~5° and in-plane displacement of ~5 mm (dependent on the physical size of the sensor and the SLM). Our auto-alignment method robustly achieved a DOPC playback peak-to-background ratio (PBR) corresponding to more than ~30 % of the theoretical maximum. As an additional advantage, the auto-alignment procedure can be easily performed at will and, as such, allows us to correct for small mechanical drifts within the DOPC systems, thus overcoming a previously major DOPC system vulnerability. We believe that this reported method for implementing robust DOPC systems will broaden the practical utility of DOPC systems. PMID:24977504

  16. Heterogeneous Data Fusion via Space Alignment Using Nonmetric Multidimensional Scaling

    SciTech Connect

    Choo, Jaegul; Bohn, Shawn J.; Nakamura, Grant C.; White, Amanda M.; Park, Haesun

    2012-04-26

    Heterogeneous data sets are typically represented in different feature spaces, making it difficult to analyze relationships spanning different data sets even when they are semantically related. Data fusion via space alignment can remedy this task by integrating multiple data sets lying in different spaces into one common space. Given a set of reference correspondence data that share the same semantic meaning across different spaces, space alignment attempts to place the corresponding reference data as close together as possible, and accordingly, the entire data are aligned in a common space. Space alignment involves optimizing two potentially conflicting criteria: minimum deformation of the original relationships and maximum alignment between the different spaces. To solve this problem, we provide a novel graph embedding framework for space alignment, which converts each data set into a graph and assigns zero distance between reference correspondence pairs resulting in a single graph. We propose a graph embedding method for fusion based on nonmetric multidimensional scaling (MDS). Its criteria using the rank order rather than the distance allows nonmetric MDS to effectively handle both deformation and alignment. Experiments using parallel data sets demonstrate that our approach works well in comparison to existing methods such as constrained Laplacian eigenmaps, Procrustes analysis, and tensor decomposition. We also present standard cross-domain information retrieval tests as well as interesting visualization examples using space alignment.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2015-10-19

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

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

    PubMed

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

    2016-06-01

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

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

    SciTech Connect

    Gu, Tingkun

    2014-05-28

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

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

    NASA Astrophysics Data System (ADS)

    Gu, Tingkun

    2014-05-01

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

  3. miRNA-dis: microRNA precursor identification based on distance structure status pairs.

    PubMed

    Liu, Bin; Fang, Longyun; Chen, Junjie; Liu, Fule; Wang, Xiaolong

    2015-04-01

    MicroRNA precursor identification is an important task in bioinformatics. Support Vector Machine (SVM) is one of the most effective machine learning methods used in this field. The performance of SVM-based methods depends on the vector representations of RNAs. However, the discriminative power of the existing feature vectors is limited, and many methods lack an interpretable model for analysis of characteristic sequence features. Prior studies have demonstrated that sequence or structure order effects were relevant for discrimination, but little work has explored how to use this kind of information for human pre-microRNA identification. In this study, in order to incorporate the structure-order information into the prediction, a method called "miRNA-dis" was proposed, in which the feature vector was constructed by the occurrence frequency of the "distance structure status pair" or just the "distance-pair". Rigorous cross-validations on a much larger and more stringent newly constructed benchmark dataset showed that the miRNA-dis outperformed some state-of-the-art predictors in this area. Remarkably, miRNA-dis trained with human data can correctly predict 87.02% of the 4022 pre-miRNAs from 11 different species ranging from animals, plants and viruses. miRNA-dis would be a useful high throughput tool for large-scale analysis of microRNA precursors. In addition, the learnt model can be easily analyzed in terms of discriminative features, and some interesting patterns were discovered, which could reflect the characteristics of microRNAs. A user-friendly web-server of miRNA-dis was constructed, which is freely accessible to the public at the web-site on http://bioinformatics.hitsz.edu.cn/miRNA-dis/. PMID:25715848

  4. Novel H⁺-Ion Sensor Based on a Gated Lateral BJT Pair.

    PubMed

    Yuan, Heng; Zhang, Jixing; Cao, Chuangui; Zhang, Gangyuan; Zhang, Shaoda

    2015-01-01

    An H⁺-ion sensor based on a gated lateral bipolar junction transistor (BJT) pair that can operate without the classical reference electrode is proposed. The device is a special type of ion-sensitive field-effect transistor (ISFET). Classical ISFETs have the advantage of miniaturization, but  they are difficult to fabricate by a single fabrication process because of the bulky and brittle reference electrode materials. Moreover, the reference electrodes need to be separated from the sensor device in some cases. The proposed device is composed of two gated lateral BJT components, one of which had a silicide layer while the other was without the layer. The two components were operated under the metal-oxide semiconductor field-effect transistor (MOSFET)-BJT hybrid mode, which can be controlled by emitter voltage and base current. Buffer solutions with different pH values were used as the sensing targets to verify the characteristics of the proposed device. Owing to their different sensitivities, both components could simultaneously detect the H⁺-ion concentration and function as a reference to each other. Per the experimental results, the sensitivity of the proposed device was found to be approximately 0.175 μA/pH. This experiment demonstrates enormous potential to lower the cost of the ISFET-based sensor technology. PMID:26703625

  5. Novel H+-Ion Sensor Based on a Gated Lateral BJT Pair

    PubMed Central

    Yuan, Heng; Zhang, Jixing; Cao, Chuangui; Zhang, Gangyuan; Zhang, Shaoda

    2015-01-01

    An H+-ion sensor based on a gated lateral bipolar junction transistor (BJT) pair that can operate without the classical reference electrode is proposed. The device is a special type of ion-sensitive field-effect transistor (ISFET). Classical ISFETs have the advantage of miniaturization, but  they are difficult to fabricate by a single fabrication process because of the bulky and brittle reference electrode materials. Moreover, the reference electrodes need to be separated from the sensor device in some cases. The proposed device is composed of two gated lateral BJT components, one of which had a silicide layer while the other was without the layer. The two components were operated under the metal-oxide semiconductor field-effect transistor (MOSFET)-BJT hybrid mode, which can be controlled by emitter voltage and base current. Buffer solutions with different pH values were used as the sensing targets to verify the characteristics of the proposed device. Owing to their different sensitivities, both components could simultaneously detect the H+-ion concentration and function as a reference to each other. Per the experimental results, the sensitivity of the proposed device was found to be approximately 0.175 μA/pH. This experiment demonstrates enormous potential to lower the cost of the ISFET-based sensor technology. PMID:26703625

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

    PubMed

    Yan, Jing; Jeong, Young Gyu

    2016-06-22

    Piezoelectric nanogenerators, harvesting energy from mechanical stimuli in our living environments, hold great promise to power sustainable self-sufficient micro/nanosystems and mobile/portable electronics. BaTiO3 as a lead-free material with high piezoelectric coefficient and dielectric constant has been widely examined to realize nanogenerators, capacitors, sensors, etc. In this study, polydimethylsiloxane (PDMS)-based flexible composites including BaTiO3 nanofibers with different alignment modes were manufactured and their piezoelectric performance was examined. For the study, BaTiO3 nanofibers were prepared by an electrospinning technique utilizing a sol-gel precursor and following calcination process, and they were then aligned vertically or horizontally or randomly in PDMS matrix-based nanogenerators. The morphological structures of BaTiO3 nanofibers and their nanogenerators were analyzed by using SEM images. The crystal structures of the nanogenerators before and after poling were characterized by X-ray diffraction. The dielectric and piezoelectric properties of the nanogenerators were investigated as a function of the nanofiber alignment mode. The nanogenerator with BaTiO3 nanofibers aligned vertically in the PDMS matrix sheet achieved high piezoelectric performance of an output power of 0.1841 μW with maximum voltage of 2.67 V and current of 261.40 nA under a low mechanical stress of 0.002 MPa, in addition to a high dielectric constant of 40.23 at 100 Hz. The harvested energy could thus power a commercial LED directly or be stored into capacitors after rectification. PMID:27237223

  7. Future hospital care in a population-based series of twin pairs discordant for physical activity behavior.

    PubMed Central

    Kujala, U M; Kaprio, J; Sarna, S; Koskenvuo, M

    1999-01-01

    OBJECTIVES: This study investigated the association between physical activity behavior and morbidity, taking into account genetic selection. METHODS: Hospitalizations were followed from the beginning of 1977 to the end of 1986 in 710 same-sex healthy twin pairs discordant for leisure-time physical activity and in 151 pairs discordant for all physical activity at base-line in 1975. RESULTS: During the follow-up, among twin pairs discordant for leisure activity, the active member spent, on average, 43% fewer days in the hospital than the inactive member; the corresponding percentage was 55% among pairs discordant for all activity. CONCLUSIONS: Physically inactive behavior is associated with increased need for hospital treatments, even after genetic and other confounding factors are taken into account. PMID:10589321

  8. Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs.

    PubMed

    Mondal, Manas; Halder, Sukanya; Chakrabarti, Jaydeb; Bhattacharyya, Dhananjay

    2016-04-01

    Stacking interaction between the aromatic heterocyclic bases plays an important role in the double helical structures of nucleic acids. Considering the base as rigid body, there are total of 18 degrees of freedom of a dinucleotide step. Some of these parameters show sequence preferences, indicating that the detailed atomic interactions are important in the stacking. Large variants of non-canonical base pairs have been seen in the crystallographic structures of RNA. However, their stacking preferences are not thoroughly deciphered yet from experimental results. The current theoretical approaches use either the rigid body degrees of freedom where the atomic information are lost or computationally expensive all atom simulations. We have used a hybrid simulation approach incorporating Monte-Carlo Metropolis sampling in the hyperspace of 18 stacking parameters where the interaction energies using AMBER-parm99bsc0 and CHARMM-36 force-fields were calculated from atomic positions. We have also performed stacking energy calculations for structures from Monte-Carlo ensemble by Dispersion corrected density functional theory. The available experimental data with Watson-Crick base pairs are compared to establish the validity of the method. Stacking interaction involving A:U and G:C base pairs with non-canonical G:U base pairs also were calculated and showed that these structures were also sequence dependent. This approach could be useful to generate multiscale modeling of nucleic acids in terms of coarse-grained parameters where the atomic interactions are preserved. This method would also be useful to predict structure and dynamics of different base pair steps containing non Watson-Crick base pairs, as found often in the non-coding RNA structures. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 212-226, 2016. PMID:26600167

  9. Alignment validation

    SciTech Connect

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

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

  10. Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs.

    PubMed Central

    Coll, M; Fita, I; Lloveras, J; Subirana, J A; Bardella, F; Huynh-Dinh, T; Igolen, J

    1988-01-01

    The left-handed Z-DNA conformation has been observed in crystals made from the self-complementary DNA hexamer d(CACGTG). This is the first time that a non disordered Z form is found in the crystal structure of an alternating sequence containing AT base pairs without methylated or brominated cytosines. The structure has been determined and refined to an agreement factor R = 22.9% using 746 reflections in the resolution in the resolution shell 7 to 2.5 A. The overall shape of the molecule is very similar to the Z-structure of the related hexamer d(CG)3 confirming the rigidity of the Z form. No solvent molecules were detected in the minor groove of the helix near the A bases. The disruption of the spine of hydration in the AT step appears to be a general fact in the Z form in contrast with the B form. The biological relevance of the structure in relation to the CA genome repeats is discussed. PMID:3419929

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

    PubMed Central

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

    2016-01-01

    Axial alignment is one of the main objectives in total knee arthroplasty (TKA). Computer-assisted surgery (CAS) is more accurate regarding limb alignment reconstruction compared to the conventional technique. The aim of this study was to analyse the precision of the innovative navigation system DASH® by Brainlab and to evaluate the reliability of intraoperatively acquired data. A retrospective analysis of 40 patients was performed, who underwent CAS TKA using the iPod-based navigation system DASH. Pre- and postoperative axial alignment were measured on standardized radiographs by two independent observers. These data were compared with the navigation data. Furthermore, interobserver reliability was measured. The duration of surgery was monitored. The mean difference between the preoperative mechanical axis by X-ray and the first intraoperatively measured limb axis by the navigation system was 2.4°. The postoperative X-rays showed a mean difference of 1.3° compared to the final navigation measurement. According to radiographic measurements, 88% of arthroplasties had a postoperative limb axis within ±3°. The mean additional time needed for navigation was 5 minutes. We could prove very good precision for the DASH system, which is comparable to established navigation devices with only negligible expenditure of time compared to conventional TKA. PMID:27313898

  12. 2',4'-BNA bearing a 2-pyridine nucleobase for CG base pair recognition in the parallel motif triplex DNA.

    PubMed

    Hari, Yoshiyuki; Matsugu, Sachiko; Inohara, Hiroyasu; Hatanaka, Yuri; Akabane, Masaaki; Imanishi, Takeshi; Obika, Satoshi

    2010-09-21

    We succeeded in the synthesis of triplex-forming oligonucleotides (TFOs) that contain a deoxyribonucleotide (Py) bearing a 2-pyridine nucleobase or the 2',4'-BNA congener (Py(B)). By UV melting experiments, it was found that 2-pyridine was a very promising nucleobase for the sequence-selective recognition of a CG base pair within double-stranded DNA (dsDNA) in a parallel motif triplex. Moreover, Py(B) in TFOs showed stronger affinity to a CG base pair than Py with further increase in the selectivity. Using TFO including multiple Py(B) units, triplex formation with dsDNA containing three CG base pairs was observed. PMID:20648389

  13. Evidence for tautomerism in nucleic acid base pairs. 1H NMR study of 15N labeled tRNA.

    PubMed Central

    Rüterjans, H; Kaun, E; Hull, W E; Limbach, H H

    1982-01-01

    The imino proton resonances of 15N labeled tRNA appear as asymmetric doublet signals, the asymmetry being dependent on the applied magnetic field strength. Assuming a tautomerism of the type N-H...N not equal to N...H-N in the base pairs the line shapes can be simulated. The most important parameters fitted in the simulation are the rate constants of the proton transfer and the mole fractions of either tautomeric state. The rate constants are of the order of 100s-1 and the mole fractions of the non dominant tautomer about 0.1 depending on the temperature and on the nature of the base pairing. The observations are attributed to a double proton transfer in the base pairs. The unexpectedly slow rates of the double proton transfer process may be connected with a concomitant conformational change of the duplex structure. PMID:7177856

  14. High Levels of Transcription Stimulate Transversions at GC Base Pairs in Yeast

    PubMed Central

    Alexander, Matthew P.; Begins, Kaitlyn J.; Crall, William C.; Holmes, Margaret P.; Lippert, Malcolm J.

    2016-01-01

    High-levels of transcription through a gene stimulate spontaneous mutation rate, a phenomenon termed transcription-associated mutation (TAM). While transcriptional effects on specific mutation classes have been identified using forward mutation and frameshift-reversion assays, little is yet known about transcription-associated base substitutions in yeast. To address this issue, we developed a new base substitution reversion assay (the lys2-TAG allele). We report a 22-fold increase in overall reversion rate in the high- relative to the low-transcription strain (from 2.1- to 47- × 10−9). While all detectable base substitution types increased in the high-transcription strain, G→T and G→C transversions increased disproportionately by 58- and 52-fold, respectively. To assess a potential role of DNA damage in the TAM events, we measured mutation rates and spectra in individual strains defective in the repair of specific DNA lesions or null for the error-prone translesion DNA polymerase zeta (Pol zeta). Results exclude a role of 8-oxoGuanine, general oxidative damage, or apurinic/apyrimidinic sites in the generation of TAM G→T and G→C transversions. In contrast, the TAM transversions at GC base pairs depend on Pol zeta for occurrence implicating DNA damage, other than oxidative lesions or AP sites, in the TAM mechanism. Results further indicate that transcription-dependent G→T transversions in yeast differ mechanistically from equivalent events in E. coli reported by others. Given their occurrences in repair-proficient cells, transcription-associated G→T and G→C events represent a novel type of transcription-associated mutagenesis in normal cells with potentially important implications for evolution and genetic disease. PMID:23055242

  15. Sentence alignment using feed forward neural network.

    PubMed

    Fattah, Mohamed Abdel; Ren, Fuji; Kuroiwa, Shingo

    2006-12-01

    Parallel corpora have become an essential resource for work in multi lingual natural language processing. However, sentence aligned parallel corpora are more efficient than non-aligned parallel corpora for cross language information retrieval and machine translation applications. In this paper, we present a new approach to align sentences in bilingual parallel corpora based on feed forward neural network classifier. A feature parameter vector is extracted from the text pair under consideration. This vector contains text features such as length, punctuate score, and cognate score values. A set of manually prepared training data has been assigned to train the feed forward neural network. Another set of data was used for testing. Using this new approach, we could achieve an error reduction of 60% over length based approach when applied on English-Arabic parallel documents. Moreover this new approach is valid for any language pair and it is quite flexible approach since the feature parameter vector may contain more/less or different features than that we used in our system such as lexical match feature. PMID:17285688

  16. Experimental study of laser-detected magnetic resonance based on atomic alignment

    SciTech Connect

    Di Domenico, Gianni; Bison, Georg; Groeger, Stephan; Knowles, Paul; Pazgalev, Anatoly S.; Rebetez, Martin; Saudan, Herve; Weis, Antoine

    2006-12-15

    We present an experimental study of the spectra produced by optical-radio-frequency double resonance in which resonant linearly polarized laser light is used in the optical pumping and detection processes. We show that the experimental spectra obtained for cesium are in excellent agreement with a very general theoretical model developed in our group [Weis, Bison, and Pazgalev, Phys. Rev. A 74, 033401 (2006)] and we investigate the limitations of this model. Finally, the results are discussed in view of their use in the study of relaxation processes in aligned alkali-metal vapors.

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

    SciTech Connect

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

    1989-03-01

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

  18. Testing and alignment of freeform-based multi-mirror telescopes

    NASA Astrophysics Data System (ADS)

    Zhang, Xue-jun; Hu, Hai-xiang; Xue, Dong-lin; Li, Ming

    2015-09-01

    Three Mirror Anastigmat (TMA) systems including both on-axis and off-axis configurations have been widely used in space applications. In some designs, to correct for high order aberrations and realize large FOV, freeform surfaces are used to provide more design freedoms. This trend brings challenges to optical manufacturing and testing community. Since testing is critical to make high accurate aspheres and freeform surfaces, the paper addressed Computer Generated Hologram (CGH) design and implement to measure large freeform mirrors. In particular, CGH assisted alignment procedure for TMA telescopes were discussed in detail.

  19. Identification of Anoectochilus based on rDNA ITS sequences alignment and SELDI-TOF-MS.

    PubMed

    Gao, Chuan; Zhang, Fusheng; Zhang, Jun; Guo, Shunxing; Shao, Hongbo

    2009-01-01

    The internal transcribed spacer (ITS) sequences alignment and proteomic difference of Anoectochilus interspecies have been studied by means of ITS molecular identification and surface enhanced laser desorption ionization time of flight mass spectrography. Results showed that variety certification on Anoectochilus by ITS sequences can not determine species, and there is proteomic difference among Anoectochilus interspecies. Moreover, proteomic finger printings of five Anoectochilus species have been established for identifying species, and genetic relationships of five species within Anoectochilus have been deduced according to proteomic differences among five species. PMID:20016748

  20. Identification of Anoectochilus based on rDNA ITS sequences alignment and SELDI-TOF-MS

    PubMed Central

    Gao, Chuan; Zhang, Fusheng; Zhang, Jun; Guo, Shunxing; Shao, Hongbo

    2009-01-01

    The internal transcribed spacer (ITS) sequences alignment and proteomic difference of Anoectochilus interspecies have been studied by means of ITS molecular identification and surface enhanced laser desorption ionization time of flight mass spectrography. Results showed that variety certification on Anoectochilus by ITS sequences can not determine species, and there is proteomic difference among Anoectochilus interspecies. Moreover, proteomic finger printings of five Anoectochilus species have been established for identifying species, and genetic relationships of five species within Anoectochilus have been deduced according to proteomic differences among five species. PMID:20016748

  1. Nucleon-pair states of even-even Sn isotopes based on realistic effective interactions

    NASA Astrophysics Data System (ADS)

    Cheng, Y. Y.; Qi, C.; Zhao, Y. M.; Arima, A.

    2016-08-01

    In this paper we study yrast states of 128,126,124Sn and 104,106,108Sn by using the monopole-optimized realistic interactions in terms of both the shell model (SM) and the nucleon-pair approximation (NPA). For yrast states of 128,126Sn and 104,106Sn, we calculate the overlaps between the wave functions obtained in the full SM space and those obtained in the truncated NPA space, and find that most of these overlaps are very close to 1. Very interestingly, for most of these states with positive parity and even spin or with negative parity and odd spin, the SM wave function is found to be well represented by one nucleon-pair basis state, viz., a simple picture of "nucleon-pair states" (nucleon-pair configuration without mixings) emerges. In 128,126Sn, the positive-parity (or negative-parity) yrast states with spin J >10 (or J >7 ) are found to be well described by breaking one or two S pairs in the 101+ (or 71-) state, i.e., the yrast state of seniority-two, spin-maximum, and positive-parity (or negative-parity), into non-S pair(s). Similar regularity is also pointed out for 104,106Sn. The evolution of E 2 transition rates between low-lying states in 128,126,124Sn is discussed in terms of the seniority scheme.

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

    PubMed

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

    2015-05-15

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

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

    PubMed Central

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

    2015-01-01

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

  4. Base pairing enhances fluorescence and favors cyclobutane dimer formation induced upon absorption of UVA radiation by DNA.

    PubMed

    Banyasz, Akos; Vayá, Ignacio; Changenet-Barret, Pascale; Gustavsson, Thomas; Douki, Thierry; Markovitsi, Dimitra

    2011-04-13

    The photochemical properties of the DNA duplex (dA)(20)·(dT)(20) are compared with those of the parent single strands. It is shown that base pairing increases the probability of absorbing UVA photons, probably due to the formation of charge-transfer states. UVA excitation induces fluorescence peaking at ∼420 nm and decaying on the nanosecond time scale. The fluorescence quantum yield, the fluorescence lifetime, and the quantum yield for cyclobutane dimer formation increase upon base pairing. Such behavior contrasts with that of the UVC-induced processes. PMID:21417388

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

    PubMed

    Fieth, Pascal; Hartmann, Alexander K

    2016-08-01

    Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small. For gapless local alignments of infinitely long sequences this distribution is known analytically to follow a Gumbel distribution. Distributions for gapped local alignments and global alignments of finite lengths can only be obtained numerically. To obtain result for the small-probability region, specific statistical mechanics-based rare-event algorithms can be applied. In previous studies, this was achieved for pairwise alignments. They showed that, contrary to results from previous simple sampling studies, strong deviations from the Gumbel distribution occur in case of finite sequence lengths. Here we extend the studies to multiple sequence alignments with gaps, which are much more relevant for practical applications in molecular biology. We study the distributions of scores over a large range of the support, reaching probabilities as small as 10^{-160}, for global and local (sum-of-pair scores) multiple alignments. We find that even after suitable rescaling, eliminating the sequence-length dependence, the distributions for multiple alignment differ from the pairwise alignment case. Furthermore, we also show that the previously discussed Gaussian correction to the Gumbel distribution needs to be refined, also for the case of pairwise alignments. PMID:27627266

  6. Remarkably enhanced thermal transport based on a flexible horizontally-aligned carbon nanotube array film

    NASA Astrophysics Data System (ADS)

    Qiu, Lin; Wang, Xiaotian; Su, Guoping; Tang, Dawei; Zheng, Xinghua; Zhu, Jie; Wang, Zhiguo; Norris, Pamela M.; Bradford, Philip D.; Zhu, Yuntian

    2016-02-01

    It has been more than a decade since the thermal conductivity of vertically aligned carbon nanotube (VACNT) arrays was reported possible to exceed that of the best thermal greases or phase change materials by an order of magnitude. Despite tremendous prospects as a thermal interface material (TIM), results were discouraging for practical applications. The primary reason is the large thermal contact resistance between the CNT tips and the heat sink. Here we report a simultaneous sevenfold increase in in-plane thermal conductivity and a fourfold reduction in the thermal contact resistance at the flexible CNT-SiO2 coated heat sink interface by coupling the CNTs with orderly physical overlapping along the horizontal direction through an engineering approach (shear pressing). The removal of empty space rapidly increases the density of transport channels, and the replacement of the fine CNT tips with their cylindrical surface insures intimate contact at CNT-SiO2 interface. Our results suggest horizontally aligned CNT arrays exhibit remarkably enhanced in-plane thermal conductivity and reduced out-of-plane thermal conductivity and thermal contact resistance. This novel structure makes CNT film promising for applications in chip-level heat dissipation. Besides TIM, it also provides for a solution to anisotropic heat spreader which is significant for eliminating hot spots.

  7. Alignment based on a no adjustment philosophy for the Immersion Grating Infrared Spectrometer (IGRINS)

    NASA Astrophysics Data System (ADS)

    Han, Jeong-Yeol; Yuk, In-Soo; Ko, Kyeongyeon; Oh, Heeyoung; Nah, Jakyoung; Oh, Jae Sok; Park, Chan; Lee, Sungho; Kim, Kang-Min; Chun, Moo-Young; Jaffe, Daniel T.; Pak, Soojong; Gully-Santiago, Michael

    2012-12-01

    IGRINS, the Immersion GRating INfrared Spectrometer includes an immersion grating made of silicon and observes both H-band (1.49~1.80 μm) and K-band (1.96~2.46 μm), simultaneously. In order to align such an infrared optical system, the compensator in its optical components has been adjusted within tolerances at room temperature without vacuum environment. However, such a system will ultimately operate at low temperature and vacuum with no adjustment mechanism. Therefore a reasonable relationship between different environmental variations such as room and low temperature might provide useful knowledge to align the system properly. We are attempting to develop a new process to predict the Wave Front Error (WFE), and to produce correct mechanical control values when the optical system is perturbed by moving the lens at room temperature. The purpose is to provide adequate optical performance without making changes at operating temperature. In other words, WFE was measured at operating temperature without any modification but a compensator was altered correctly at room temperature to meet target performance. The `no adjustment' philosophy was achieved by deterministic mechanical adjustment at room temperature from a simulation that we developed. In this study, an achromatic doublet lens was used to substitute for the H and K band camera of IGRINS. This novel process exhibits accuracy predictability of about 0.002 λ rms WFE and can be applied to a cooled infrared optical systems.

  8. Remarkably enhanced thermal transport based on a flexible horizontally-aligned carbon nanotube array film.

    PubMed

    Qiu, Lin; Wang, Xiaotian; Su, Guoping; Tang, Dawei; Zheng, Xinghua; Zhu, Jie; Wang, Zhiguo; Norris, Pamela M; Bradford, Philip D; Zhu, Yuntian

    2016-01-01

    It has been more than a decade since the thermal conductivity of vertically aligned carbon nanotube (VACNT) arrays was reported possible to exceed that of the best thermal greases or phase change materials by an order of magnitude. Despite tremendous prospects as a thermal interface material (TIM), results were discouraging for practical applications. The primary reason is the large thermal contact resistance between the CNT tips and the heat sink. Here we report a simultaneous sevenfold increase in in-plane thermal conductivity and a fourfold reduction in the thermal contact resistance at the flexible CNT-SiO2 coated heat sink interface by coupling the CNTs with orderly physical overlapping along the horizontal direction through an engineering approach (shear pressing). The removal of empty space rapidly increases the density of transport channels, and the replacement of the fine CNT tips with their cylindrical surface insures intimate contact at CNT-SiO2 interface. Our results suggest horizontally aligned CNT arrays exhibit remarkably enhanced in-plane thermal conductivity and reduced out-of-plane thermal conductivity and thermal contact resistance. This novel structure makes CNT film promising for applications in chip-level heat dissipation. Besides TIM, it also provides for a solution to anisotropic heat spreader which is significant for eliminating hot spots. PMID:26880221

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

    PubMed Central

    Ashida, Hiroki; Asai, Kiyoshi; Hamada, Michiaki

    2012-01-01

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

  10. Remarkably enhanced thermal transport based on a flexible horizontally-aligned carbon nanotube array film

    PubMed Central

    Qiu, Lin; Wang, Xiaotian; Su, Guoping; Tang, Dawei; Zheng, Xinghua; Zhu, Jie; Wang, Zhiguo; Norris, Pamela M.; Bradford, Philip D.; Zhu, Yuntian

    2016-01-01

    It has been more than a decade since the thermal conductivity of vertically aligned carbon nanotube (VACNT) arrays was reported possible to exceed that of the best thermal greases or phase change materials by an order of magnitude. Despite tremendous prospects as a thermal interface material (TIM), results were discouraging for practical applications. The primary reason is the large thermal contact resistance between the CNT tips and the heat sink. Here we report a simultaneous sevenfold increase in in-plane thermal conductivity and a fourfold reduction in the thermal contact resistance at the flexible CNT-SiO2 coated heat sink interface by coupling the CNTs with orderly physical overlapping along the horizontal direction through an engineering approach (shear pressing). The removal of empty space rapidly increases the density of transport channels, and the replacement of the fine CNT tips with their cylindrical surface insures intimate contact at CNT-SiO2 interface. Our results suggest horizontally aligned CNT arrays exhibit remarkably enhanced in-plane thermal conductivity and reduced out-of-plane thermal conductivity and thermal contact resistance. This novel structure makes CNT film promising for applications in chip-level heat dissipation. Besides TIM, it also provides for a solution to anisotropic heat spreader which is significant for eliminating hot spots. PMID:26880221

  11. Amino acid sequence alignment of bacterial and mammalian pancreatic serine proteases based on topological equivalences.

    PubMed

    James, M N; Delbaere, L T; Brayer, G D

    1978-06-01

    The three-dimensional structures of the bacterial serine proteases SGPA, SGPB, and alpha-lytic protease have been compared with those of the pancreatic enzymes alpha-chymotrypsin and elastase. This comparison shows that approximately 60% (55-64%) of the alpha-carbon atom positions of the bacterial serine proteases are topologically equivalent to the alpha-carbon atom positions of the pancreatic enzymes. The corresponding value for a comparison of the bacterial enzymes among themselves is approximately 84%. The results of these topological comparisons have been used to deduce an experimentally sound sequence alignment for these several enzymes. This alignment shows that there is extensive tertiary structural homology among the bacteria and pancreatic enzymes without significant primary sequence identity (less than 21%). The acquisition of a zymogen function by the pancreatic enzymes is accompanied by two major changes to the bacterial enzymes' architecture: an insertion of 9 residues to increase the length of the N-terminal loop, and one of 12 residues to a loop near the activation salt bridge. In addition, in these two enzyme families, the methionine loop (residues 164-182) adopts very different comformations which are associated with their altered substrate specificities. PMID:96920

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

    PubMed

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

    2015-05-26

    Monodisperse, nonmagnetic, asymmetrical composite dumbbells in a suspension of magnetic nanoparticles (ferrofluid) were aligned by application of an external magnetic field to the ferrofluid. The asymmetrical composite dumbbells were prepared by two-step soap-free emulsion polymerization consisting of the first polymerization to coat spherical silica cores with cross-linked poly(methyl methacrylate) (PMMA) shell and the second polymerization to protrude a polystyrene (PSt) lobe from the core-shell particles. A chain structure of nonmagnetic dumbbells oriented to the applied magnetic field was observed at nanoparticle content of 2.0 vol % and field strengths higher than 1.0 mT. A similar chain structure of the dumbbells was observed under application of alternating electric field at strengths higher than 50 V/mm. Parallel and orthogonally combined applications of the electric and magnetic fields were also conducted to examine independence of the electric and magnetic applications as operational factors in the dumbbell assembling. Dumbbell chains stiffer than those in a single application of external field were formed in the parallel combined application of electric and magnetic fields. The orthogonal combination of the different applied fields could form a magnetically aligned chain structure of the nonmagnetic dumbbells oriented to the electric field. The present work experimentally indicated that the employment of inverse magnetorheological effect for nonmagnetic, anisotropic particles can be a useful method for the simultaneous controls over the orientation and the positon of anisotropic particles in their assembling. PMID:25927488

  13. Triple-layered QSAR studies on substituted 1,2,4-trioxanes as potential antimalarial agents: superiority of the quantitative pharmacophore-based alignment over common substructure-based alignment.

    PubMed

    Gupta, A K; Saxena, A K

    2013-01-01

    This study reports the utilization of three approaches - pharmacophore, CoMFA/CoMSIA and HQSAR studies - to identify the essential structural requirements in 3D chemical space for the modulation of the antimalarial activity of substituted 1,2,4-trioxanes. The superiority of quantitative pharmacophore-based alignment (QuantitativePBA) over global minima energy conformer-based alignment (GMCBA) has been reported in CoMFA and CoMSIA studies. The developed models showed good statistical significance in internal validation (q(2), group cross-validation and bootstrapping) and performed very well in predicting the antimalarial activity of test set compounds. Structural features in terms of their steric, electrostatic and hydrophobic interactions in 3D space have been found to be important for the antimalarial activity of substituted 1,2,4-trioxanes. Further, the HQSAR studies based on the same training and test set acted as an additional tool to find the sub-structural fingerprints of substituted 1,2,4-trioxanes for their antimalarial activity. Together, these studies may facilitate the design and discovery of new substituted 1,2,4-trioxanes with potent antimalarial activity. PMID:23194465

  14. A 145-base pair DNA sequence that positions itself precisely and asymmetrically on the nucleosome core.

    PubMed Central

    Ramsay, N; Felsenfeld, G; Rushton, B M; McGhee, J D

    1984-01-01

    A 145-bp DNA sequence, cloned from Escherichia coli, was reconstituted into nucleosome core particles by a number of methods. The behaviour of the resulting complex upon sucrose gradient sedimentation and nucleoprotein gel electrophoresis closely resembled that of control bulk nucleosome core particles. DNase I digestion of the 32P-end-labelled complex revealed the 10-bp periodicity of cleavages expected for DNA bound on a histone surface. The narrow cleavage sites observed (1 bp wide) imply that the sequence occupies a single preferred position on the nucleosome core, accurate to the level of single base pairs. By relating the digestion pattern observed to the pattern of site protection found for random sequence nucleosomes, the DNA position was found to be offset by 17 bp from that in the normal core particle. A number of experiments argue against the involvement of length or end effects and suggest that it is some feature of the DNA sequence itself that determines this precise positioning of DNA on the nucleosome. Images Fig. 3. Fig. 4. Fig. 5. PMID:6096135

  15. Paired-Associate and Feedback-Based Weather Prediction Tasks Support Multiple Category Learning Systems.

    PubMed

    Li, Kaiyun; Fu, Qiufang; Sun, Xunwei; Zhou, Xiaoyan; Fu, Xiaolan

    2016-01-01

    It remains unclear whether probabilistic category learning in the feedback-based weather prediction task (FB-WPT) can be mediated by a non-declarative or procedural learning system. To address this issue, we compared the effects of training time and verbal working memory, which influence the declarative learning system but not the non-declarative learning system, in the FB and paired-associate (PA) WPTs, as the PA task recruits a declarative learning system. The results of Experiment 1 showed that the optimal accuracy in the PA condition was significantly decreased when the training time was reduced from 7 to 3 s, but this did not occur in the FB condition, although shortened training time impaired the acquisition of explicit knowledge in both conditions. The results of Experiment 2 showed that the concurrent working memory task impaired the optimal accuracy and the acquisition of explicit knowledge in the PA condition but did not influence the optimal accuracy or the acquisition of self-insight knowledge in the FB condition. The apparent dissociation results between the FB and PA conditions suggested that a non-declarative or procedural learning system is involved in the FB-WPT and provided new evidence for the multiple-systems theory of human category learning. PMID:27445958

  16. Locations of Joint Physical Activity in Parent-Child Pairs Based on Accelerometer and GPS Monitoring

    PubMed Central

    Dunton, Genevieve Fridlund; Liao, Yue; Almanza, Estela; Jerrett, Micheal; Spruijt-Metz, Donna; Pentz, Mary Ann

    2012-01-01

    Background Parental factors may play an important role in influencing children’s physical activity levels. Purpose This cross-sectional study sought to describe the locations of joint physical activity among parents and children. Methods Parent-child pairs (N = 291) wore an Actigraph GT2M accelerometer and GlobalSat BT-335 Global Positioning Systems (GPS) device over the same 7-day period. Children were ages 8–14 years. Joint behavior was defined by a linear separation distance of less than 50m between parent and child. Land use classifications were assigned to GPS data points. Results Joint physical activity was spread across residential locations (35%), and commercial venues (24%), and open spaces/parks (20%). Obese children and parents performed less joint physical activity in open spaces/parks than under/normal weight children and parents (p’s < .01). Conclusions Understanding where joint parent-child physical activity naturally occurs may inform location-based interventions to promote these behaviors. PMID:23011914

  17. Paired-Associate and Feedback-Based Weather Prediction Tasks Support Multiple Category Learning Systems

    PubMed Central

    Li, Kaiyun; Fu, Qiufang; Sun, Xunwei; Zhou, Xiaoyan; Fu, Xiaolan

    2016-01-01

    It remains unclear whether probabilistic category learning in the feedback-based weather prediction task (FB-WPT) can be mediated by a non-declarative or procedural learning system. To address this issue, we compared the effects of training time and verbal working memory, which influence the declarative learning system but not the non-declarative learning system, in the FB and paired-associate (PA) WPTs, as the PA task recruits a declarative learning system. The results of Experiment 1 showed that the optimal accuracy in the PA condition was significantly decreased when the training time was reduced from 7 to 3 s, but this did not occur in the FB condition, although shortened training time impaired the acquisition of explicit knowledge in both conditions. The results of Experiment 2 showed that the concurrent working memory task impaired the optimal accuracy and the acquisition of explicit knowledge in the PA condition but did not influence the optimal accuracy or the acquisition of self-insight knowledge in the FB condition. The apparent dissociation results between the FB and PA conditions suggested that a non-declarative or procedural learning system is involved in the FB-WPT and provided new evidence for the multiple-systems theory of human category learning. PMID:27445958

  18. Biomolecule Analogues 2-Hydroxypyridine and 2-Pyridone Base Pairing on Ice Nanoparticles.

    PubMed

    Rubovič, Peter; Pysanenko, Andriy; Lengyel, Jozef; Nachtigallová, Dana; Fárník, Michal

    2016-07-14

    Ice nanoparticles (H2O)N, N ≈ 450 generated in a molecular beam experiment pick up individual gas phase molecules of 2-hydroxypyridine and 2-pyridone (HP) evaporated in a pickup cell at temperatures between 298 and 343 K. The mass spectra of the doped nanoparticles show evidence for generation of clusters of adsorbed molecules (HP)n up to n = 8. The clusters are ionized either by 70 eV electrons or by two photons at 315 nm (3.94 eV). The two ionization methods yield different spectra, and their comparison provides an insight into the neutral cluster composition, ionization and intracluster ion-molecule reactions, and cluster fragmentation. Quite a few molecules were reported not to coagulate on ice nanoparticles previously. The (HP)n cluster generation on ice nanoparticles represents the first evidence for coagulating of molecules and cluster formation on free ice nanoparticles. For comparison, we investigate the coagulation of HP molecules picked up on large clusters ArN, N ≈ 205, and also (HP)n clusters generated in supersonic expansions with Ar buffer gas. This comparison points to a propensity for the (HP)2 dimer generation on ice nanoparticles. This shows the feasibility of base pairing for model of biological molecules on free ice nanoparticles. This result is important for hypotheses of the biomolecule synthesis on ice grains in the space. We support our findings by theoretical calculations that show, among others, the HP dimer structures on water clusters. PMID:26785038

  19. X-ray Pair Distribution Function Analysis of Potassium Based Geopolymer

    SciTech Connect

    Bell, J.; Sarin, P; Driemeyer, P; Haggerty, R; Chupas, P; Kriven, W

    2008-01-01

    The atomic structure of geopolymers is often described as amorphous with a local structure that is equivalent to that of crystalline zeolites. However, this structural relationship has never been quantified beyond a first-nearest-neighbor bonding environment. In this study, the short to medium range (1 nm) structural order of metakaolin-based KAlSi{sub 2}O{sub 6}{center_dot}5.5H{sub 2}O geopolymer was quantified and compared to zeolitic tetragonal leucite (KAlSi2O6) using the X-ray atomic pair distribution function technique. Unheated KAlSi{sub 2}O{sub 6}{center_dot}5.5H{sub 2}O was found to be structurally similar to leucite out to a length of 8 {angstrom}, but had increased medium range disorder over the 4.5 {angstrom} < r < 8 {angstrom} range. On heating to >300 C, changes in the short to medium range structure were observed due to dehydration and removal of chemically bound water. Crystallization of leucite occurred in samples heated beyond 1050 C. Refinements of a leucite model against the PDF data for geopolymer heated to 1100 C for 24 h yielded a good fit.

  20. The Common Prescription Patterns Based on the Hierarchical Clustering of Herb-Pairs Efficacies

    PubMed Central

    2016-01-01

    Prescription patterns are rules or regularities used to generate, recognize, or judge a prescription. Most of existing studies focused on the specific prescription patterns for diverse diseases or syndromes, while little attention was paid to the common patterns, which reflect the global view of the regularities of prescriptions. In this paper, we designed a method CPPM to find the common prescription patterns. The CPPM is based on the hierarchical clustering of herb-pair efficacies (HPEs). Firstly, HPEs were hierarchically clustered; secondly, the individual herbs are labeled by the HPEC (the clusters of HPEs); and then the prescription patterns were extracted from the combinations of HPEC; finally the common patterns are recognized statistically. The results showed that HPEs have hierarchical clustering structure. When the clustering level is 2 and the HPEs were classified into two clusters, the common prescription patterns are obvious. Among 332 candidate prescriptions, 319 prescriptions follow the common patterns. The description of the patterns is that if a prescription contains the herbs of the cluster (C 1), it is very likely to have other herbs of another cluster (C 2); while a prescription has the herbs of C 2, it may have no herbs of C 1. Finally, we discussed that the common patterns are mathematically coincident with the Blood-Qi theory. PMID:27190534

  1. Doppler Broadening Analysis of Steel Specimens Using Accelerator Based In Situ Pair Production

    SciTech Connect

    Makarashvili, V.; Wells, D. P.; Roy, A. K.

    2009-03-10

    Positron Annihilation Spectroscopy (PAS) techniques can be utilized as a sensitive probe of defects in materials. Studying these microscopic defects is very important for a number of industries in order to predict material failure or structural integrity. We have been developing gamma-induced pair-production techniques to produce positrons in thick samples ({approx}4-40 g/cm{sup 2}, or {approx}0.5-5 cm in steel). These techniques are called 'Accelerator-based Gamma-induced Positron Annihilation Spectroscopy'(AG-PAS). We have begun testing the capabilities of this technique for imaging of defect densities in thick structural materials. As a first step, a linear accelerator (LINAC) was employed to produce photon beams by stopping 15 MeV electrons in a 1 mm thick tungsten converter. The accelerator is capable of operating with 30-60 ns pulse width, up to 200 mA peak current at 1 kHz repetition rate. The highly collimated bremsstrahlung beam impinged upon our steel tensile specimens, after traveling through a 1.2 m thick concrete wall. Annihilation radiation was detected by a well-shielded and collimated high-purity germanium detector (HPGe). Conventional Doppler broadening spectrometry (DBS) was performed to determine S, W and T parameters for our samples.

  2. Simplified Aircraft-Based Paired Approach: Concept Definition and Initial Analysis

    NASA Technical Reports Server (NTRS)

    Johnson, Sally C.; Lohr, Gary W.; McKissick, Burnell T.; Abbott, Terence S.; Geurreiro, Nelson M.; Volk, Paul

    2013-01-01

    Simplified Aircraft-based Parallel Approach (SAPA) is an advanced concept proposed by the Federal Aviation Administration (FAA) to support dependent parallel approach operations to runways with lateral spacing closer than 2500 ft. At the request of the FAA, NASA performed an initial assessment of the potential performance and feasibility of the SAPA concept, including developing and assessing an operational implementation of the concept and conducting a Monte Carlo wake simulation study to examine the longitudinal spacing requirements. The SAPA concept was shown to have significant operational advantages in supporting the pairing of aircraft with dissimilar final approach speeds. The wake simulation study showed that support for dissimilar final approach speeds could be significantly enhanced through the use of a two-phased altitudebased longitudinal positioning requirement, with larger longitudinal positioning allowed for higher altitudes out of ground effect and tighter longitudinal positioning defined for altitudes near and in ground effect. While this assessment is preliminary and there are a number of operational issues still to be examined, it has shown the basic SAPA concept to be technically and operationally feasible.

  3. The Simplified Aircraft-Based Paired Approach With the ALAS Alerting Algorithm

    NASA Technical Reports Server (NTRS)

    Perry, Raleigh B.; Madden, Michael M.; Torres-Pomales, Wilfredo; Butler, Ricky W.

    2013-01-01

    This paper presents the results of an investigation of a proposed concept for closely spaced parallel runways called the Simplified Aircraft-based Paired Approach (SAPA). This procedure depends upon a new alerting algorithm called the Adjacent Landing Alerting System (ALAS). This study used both low fidelity and high fidelity simulations to validate the SAPA procedure and test the performance of the new alerting algorithm. The low fidelity simulation enabled a determination of minimum approach distance for the worst case over millions of scenarios. The high fidelity simulation enabled an accurate determination of timings and minimum approach distance in the presence of realistic trajectories, communication latencies, and total system error for 108 test cases. The SAPA procedure and the ALAS alerting algorithm were applied to the 750-ft parallel spacing (e.g., SFO 28L/28R) approach problem. With the SAPA procedure as defined in this paper, this study concludes that a 750-ft application does not appear to be feasible, but preliminary results for 1000-ft parallel runways look promising.

  4. Decentralized supervisory based switching control for uncertain multivariable plants with variable input-output pairing.

    PubMed

    Namaki-Shoushtari, Omid; Khaki-Sedigh, Ali

    2012-01-01

    In this paper, the design of decentralized switching control for uncertain multivariable plants is considered. In the proposed strategy, the uncertainty region is divided into smaller regions with a nominal model and specific control structure. The underlying design is based on the quantitative feedback theory (QFT). It is assumed that a MIMO-QFT controller exists for robust stability and performance of the individual uncertain sets. The proposed control structure is made up by these local decentralized controllers, which commute among themselves in accordance with the decision of a high level decision maker called the supervisor. The supervisor makes the decision by comparing the local models' behaviors with the one of the plant and selects the controller corresponding to the best fitted model. A hysteresis switching logic is used to slow down the switching to guarantee the overall closed loop stability. It is shown that this strategy provides a stable and robust adaptive controller to deal with complex multivariable plants with input-output pairing changes during the plant operation, which can facilitate the development of a reconfigurable decentralized control. Also, the multirealization technique is used to implement a family of controllers to achieve bumpless transfer. Simulation results are employed to show the effectiveness of the proposed method. PMID:21999896

  5. Enhanced spin fluctuations and s +/- pairing by diagonal electron hopping in Fe-based superconductors

    NASA Astrophysics Data System (ADS)

    Kuroki, Kazuhiko

    2015-03-01

    In the itinerant spin picture of the iron-based superconductors, the nesting between electron and hole Fermi surfaces is usually considered to be the origin of the spin fluctuation and thus the pairing glue. However, there have appeared some experimental observations suggesting absence of Fermi surface nesting. For instance, in the 1111 materials Ln FeAsO1-xHx (Ln =La,Sm, etc.), electron doping rate x reaches up to 50%, which in a rigid band picture would wipe out the hole Fermi surfaces. Still, superconductivity not only survives, but is even enhanced in the largely doped regime, in contradiction to the expectation from the bad nesting. Another example is KxFe2-ySe2, where the ARPES experiments show the absence of hole Fermi surfaces. In the present talk, we first focus on Ln FeAsO1-xHx, where the band structure is actually not rigid against doping, and the hole Fermi surface originating from the dxy orbital remains nearly unchanged. The origin of this can be traced back to real space, where the nearest neighbor hopping t1 within the dxy orbital is found to be strongly suppressed with doping. Although the nesting itself is degraded, the spin fluctuation in the largely electron doped regime is enhanced due to t2 >t1 , where t2 is the 2nd neighbor diagonal hopping. This re-enhances s +/- pairing superconductivity, and explains the double dome x-Tc phase diagram of LaFeAsO1-xHx. From this viewpoint, it is also interesting to look into the relation between t1 and t2 in other materials. For instance, our first principles estimation for KFe2Se2givest1 = - 0 . 008 eV and t2 = 0 . 056 eV, and from this strong reduction of t1, both electron and hole Fermi surfaces are expected to be present around the Γ point, in contradiction to previous experimental observations. Results of a recent ARPES experiment will be discussed from this viewpoint.

  6. Simulation Based on Ion Propulsion Rocket System with Using Negative ion - Negative Ion Pair Techniques

    NASA Astrophysics Data System (ADS)

    Sathiyavel, C.

    2016-07-01

    Ion propulsion rocket system is expected to become popular with the development of ion-ion pair techniques because of their stimulated of low propellant, Design of Thrust range is 1N with low electric power and high efficiency. A Negative ion-Negative ion pair of ion propulsion rocket system is proposed in this work .Negative Ion Based Rocket system consists of three parts 1.ionization chamber 2. Repulsion force and ion accelerator 3. Exhaust of Nozzle. The Negative ions from electro negatively gas are produced by attachment of the gas ,such as chlorine with electron emitted from a Electron gun ionization chamber. The formulate of large stable negative ion is achievable in chlorine gas with respect to electron affinity (∆E). The electron affinity is a measure of the energy change when an electron is added to a neutral atom to form a negative ion. When a neutral chlorine atom in the gaseous form picks up an electron to form a Cl- ion, it releases energy of 349 kJ/mol or 3.6 ev/atom. It is said to have an electron affinity of -349 kJ/mol ,the negative sign indicating that energy is released during this process .The mechanisms of attachment involve the formation of intermediate states. In that reason for , the highly repulsive force created between the same negative ions. The distance between same negative ions is important for the evaluate of the rocket thrust and is also determined by the exhaust velocity of the propellant. The mass flow rate of propellant is achieved by the ratio of total mass of the propellant (Kg) needed for operation to time period(s). Accelerate the Negative ions to a high velocity in the thrust vector direction with a significantly intense Magnetic field and the exhaust of negative ions through Nozzle. The simulation of the ion propulsion system has been carried out by MATLAB. By comparing the simulation results with the theoretical and previous results, we have found that the proposed method is achieved of thrust value with estimated

  7. Fusion bonding and alignment fixture

    DOEpatents

    Ackler, Harold D.; Swierkowski, Stefan P.; Tarte, Lisa A.; Hicks, Randall K.

    2000-01-01

    An improved vacuum fusion bonding structure and process for aligned bonding of large area glass plates, patterned with microchannels and access holes and slots, for elevated glass fusion temperatures. Vacuum pumpout of all the components is through the bottom platform which yields an untouched, defect free top surface which greatly improves optical access through this smooth surface. Also, a completely non-adherent interlayer, such as graphite, with alignment and location features is located between the main steel platform and the glass plate pair, which makes large improvements in quality, yield, and ease of use, and enables aligned bonding of very large glass structures.

  8. System for DNA sequencing with resolution of up to 600 base pairs.

    PubMed

    Ansorge, W; Barker, R

    1984-03-01

    A system capable of resolving about 500 bases is of interest for sequencing of longer DNA molecules. Studies on further optimization of resolution on DNA sequencing gels were carried out. The effect of physico-chemical properties of gels and buffers on resolution were tested, e.g. ionic strength and pH of buffers, different buffer systems, acrylamide concentration, crosslinker concentration, type of crosslinker, temperature of polymerization, denaturing conditions, gel length and thickness. Tested were as well different running conditions like electric field, gel temperature, dimension of sample slots. Gels 0.1-0.2 mm thick and up to 1.2 m long were cast and tested routinely. Gel lengths of 60-70 cm (for sequencing up to 350-400 bases) to about 100 cm (above 400 bases) are practicable. Little is gained in resolution by increasing the gel length from 1 to 1.2 m. Resolution was improved using 0.1 mm thick gels, at a higher pH value of 8.6-8.8, and molarity increased to 0.2 M. The sequencing pattern in the region of higher bases could be better resolved on a twice-magnified picture of that region on the autoradiogram. With the long gels (70-120 cm), it is advantageous to obtain the sequence overlap by running in parallel gels of different concentrations, without re-application of samples, all loaded at the same time. Buffer chamber for running of two of three gels and thermostating plates up to 1.2 m long were designed. In this way four to six thermostated gels can be run from a power supply with two inputs. Three 1 m long gels (concentrations: 4%, 6%, 12-16%) are loaded with several samples of DNA to be sequenced and run in parallel without re-application of the samples. With good samples, the sequence overlap from the gels could be counted up to 500 base pairs, with exceptionally good samples closer to 600 bases. At present this number seems to be near the limit of the resolving power of the polyacrylamide gels. PMID:6725850

  9. Universal quantum gates for Single Cooper Pair Box based quantum computing

    NASA Technical Reports Server (NTRS)

    Echternach, P.; Williams, C. P.; Dultz, S. C.; Braunstein, S.; Dowling, J. P.

    2000-01-01

    We describe a method for achieving arbitrary 1-qubit gates and controlled-NOT gates within the context of the Single Cooper Pair Box (SCB) approach to quantum computing. Such gates are sufficient to support universal quantum computation.

  10. DAPS: Database of Aligned Protein Structures

    DOE Data Explorer

    Mallick, Parag; Rice, Danny; Eisenberg, David

    DAPS is based on the FSSP, DSSP, PDB and CATH databases. There also exists a subset of DAPS known as DDAPS (also pronounced DAPS) - Database of Distant Aligned Protein Structures. It is a database of structures that have low sequence similarity but share a similar fold. There are a number of filters used to make the DDAPS list more useful. The algorithm requires that an FSSP file exists for one of the members of a pair and that the other member is listed in that FSSP file. It requires that each member of the pair be within the CATH database and share a common CAT classification. It also requires that the secondary structure can be determined by DSSP. How is DAPS constructed? We begin with the set of all chains from the current release of the PDB. An all on all search is done on the list to find pairs that have the same fold acoording to both the FSSP and CATH databases and clustered into groups by a representative structure (representative structures have less than 25% sequence identity to each other). For each protein pair, regions aligned by the DALI program are extracted from the corresponding FSSP file, or recomputed using DALI-lite. In domain DAPS, only regions that are called "domains" by CATH are included in the alignment. The amino acid type, secondary structure type, and solvent accessibility are extracted from the DSSP file and written pairwise into the database. DAPS is updated with updates of CATH.[Taken from http://nihserver.mbi.ucla.edu/DAPS/daps_help.html

  11. Recombination-aware alignment of diploid individuals

    PubMed Central

    2014-01-01

    Background Traditionally biological similarity search has been studied under the abstraction of a single string to represent each genome. The more realistic representation of diploid genomes, with two strings defining the genome, has so far been largely omitted in this context. With the development of sequencing techniques and better phasing routines through haplotype assembly algorithms, we are not far from the situation when individual diploid genomes could be represented in their full complexity with a pair-wise alignment defining the genome. Results We propose a generalization of global alignment that is designed to measure similarity between phased predictions of individual diploid genomes. This generalization takes into account that individual diploid genomes evolve through a mutation and recombination process, and that predictions may be erroneous in both dimensions. Even though our model is generic, we focus on the case where one wants to measure only the similarity of genome content allowing free recombination. This results into efficient algorithms for direct application in (i) evaluation of variation calling predictions and (ii) progressive multiple alignments based on labeled directed acyclic graphs (DAGs) to represent profiles. The latter may be of more general interest, in connection to covering alignment of DAGs. Extensions of our model and algorithms can be foreseen to have applications in evaluating phasing algorithms, as well as more fundamental role in phasing child genome based on parent genomes. PMID:25572943

  12. Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair.

    PubMed Central

    Beuning, Penny J; Nagan, Maria C; Cramer, Christopher J; Musier-Forsyth, Karin; Gelpí, Josep-Lluis; Bashford, Donald

    2002-01-01

    Specific aminoacylation by aminoacyl-tRNA synthetases requires accurate recognition of cognate tRNA substrates. In the case of alanyl-tRNA synthetase (AlaRS), RNA duplexes that mimic the acceptor stem of the tRNA are efficient substrates for aminoacylation in vitro. It was previously shown that recognition by AlaRS is severely affected by a simple base pair transversion of the G2:C71 pair at the second position in the RNA helix. In this study, we determined the aminoacylation efficiencies of 50 variants of the tRNA(Ala) acceptor stem containing substitutions at the 2:71 position. We find that there is not a single functional group of the wild-type G2:C71 base pair that is critical for positive recognition. Rather, we observed that base-pair orientation plays an important role in recognition. In particular, pyrimidine2:purine71 combinations generally resulted in decreased aminoacylation efficiency compared to the corresponding purine:pyrimidine pair. Moreover, the activity of a pyrimidine:purine variant could be partially restored by the presence of a major groove amino group at position 71. In an attempt to understand this result further, dielectric continuum electrostatic calculations were carried out, in some cases with additional inclusion of van der Waals interaction energies, to determine interaction potentials of the wild-type duplexAla and seven 2:71 variants. This analysis revealed a positive correlation between major groove negative electrostatic potential in the vicinity of the 3:70 base pair and measured aminoacylation efficiency. PMID:12022232

  13. Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs

    SciTech Connect

    Patra, Amritraj; Harp, Joel; Pallan, Pradeep S.; Zhao, Linlin; Abramov, Mikhail; Herdewijn, Piet; Egli, Martin

    2012-12-28

    The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2'-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marlière,P., Patrouix,J., Döring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium’s genome. Angew. Chem. Int. Ed., 50, 7109–7114]. The residual fraction of T in the DNA of adapted bacteria was <2% and the switch from T to ClU was accompanied by a massive number of mutations, including >1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T→ClU genome substitution.

  14. [Structural and energetic properties of the four configurations of the A.T and G.C DNA base pairs].

    PubMed

    Brovarets', O O

    2013-01-01

    Using the methods of non-empirical quantum chemistry at the MP2/6-311++G(2df,pd)// B3LYP/6-311++G(d,p) level of theory it was established for the first time, that Hoogsteen, reverse Hoogsteen, Watson-Crick and reverse Watson-Crick configurations of the A.T and G.C DNA base pairs are isoelectronic and isomorphic structures with similar dynamic properties. Based on these results, non-ionisation mechanism of the Hoogsteen <"breathing" of the G*.C* DNA base pair, namely transformation of the tautomerised (Lowdin's) G-C base pair with Watson-Crick geometry into the Hoogsteen electroneutral G*.C* H base pair stabilized by the three O6H...N4, N3H...N7 and C8H...02 H-bonds, was postulated. It is suggested that such scenario activates only in those cases, when DNA is not located in aqueous solution, but works together with proteins and cytosine protonation at the N3 atom is precluded. PMID:24319980

  15. Role of interaction energy in the specificity of transcription. I-The Watson Crick G-C base pair template.

    PubMed Central

    Sanyal, N K; Kumar, U; Roychoudhury, M

    1980-01-01

    The purpose of this work is to show that the selectivity of the nucleotide bases in RNA transcription c an be inferred, in principle, from the DNA base pair - RNA base interaction. The catalytic role of enzymes in this process is, therefore, only to form the sugar - phosphate backbone. A systematic study for the evaluation of the interaction energy of the DNA base pair with the enterant RNA bases have been undertaken to elucidate the aforesaid mechanism. Electrostatic hard sphere approximation of Nash and Bradley 1 has been employed. Non bonded induced dipole and London dispersion forces are not taken into account. The present communication gives the results of computations of the interaction energy of the four RNA bases. The results have been discussed with reference to Stent's and Zubay's schemes of RNA transcription. PMID:7443519

  16. The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution.

    PubMed

    Cao, Hieu Xuan; Vu, Giang Thi Ha; Wang, Wenqin; Appenroth, Klaus J; Messing, Joachim; Schubert, Ingo

    2016-01-01

    Duckweeds are aquatic monocotyledonous plants of potential economic interest with fast vegetative propagation, comprising 37 species with variable genome sizes (0.158-1.88 Gbp). The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome, needs to be aligned to its chromosomes as a reference and prerequisite to study the genome and karyotype evolution of other duckweed species. We selected physically mapped bacterial artificial chromosomes (BACs) containing Spirodela DNA inserts with little or no repetitive elements as probes for multicolor fluorescence in situ hybridization (mcFISH), using an optimized BAC pooling strategy, to validate its physical map and correlate it with its chromosome complement. By consecutive mcFISH analyses, we assigned the originally assembled 32 pseudomolecules (supercontigs) of the genomic sequences to the 20 chromosomes of S. polyrhiza. A Spirodela cytogenetic map containing 96 BAC markers with an average distance of 0.89 Mbp was constructed. Using a cocktail of 41 BACs in three colors, all chromosome pairs could be individualized simultaneously. Seven ancestral blocks emerged from duplicated chromosome segments of 19 Spirodela chromosomes. The chromosomally integrated genome of S. polyrhiza and the established prerequisites for comparative chromosome painting enable future studies on the chromosome homoeology and karyotype evolution of duckweed species. PMID:26305472

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

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

  18. Highly Stretchable Supercapacitors Based on Aligned Carbon Nanotube/Molybdenum Disulfide Composites.

    PubMed

    Lv, Tian; Yao, Yao; Li, Ning; Chen, Tao

    2016-08-01

    Stretchable supercapacitors that can sustain their performance under unpredictable tensile force are important elements for practical applications of various portable and wearable electronics. However, the stretchability of most reported supercapacitors was often lower than 100 % because of the limitation of the electrodes used. Herein we developed all-solid-state supercapacitors with a stretchability as high as 240 % by using aligned carbon nanotube composites with compact structure as electrodes. By combined with pseudocapacitive molybdenum disulfide nanosheets, the newly developed supercapacitor showed a specific capacitance of 13.16 F cm(-3) , and also showed excellent cycling retention (98 %) after 10 000 charge-discharge cycles. This work also presents a general and effective approach in developing high-performance electrodes for flexible and stretchable electronics. PMID:27328623

  19. Mechanochromic photonic-crystal fibers based on continuous sheets of aligned carbon nanotubes.

    PubMed

    Sun, Xuemei; Zhang, Jing; Lu, Xin; Fang, Xin; Peng, Huisheng

    2015-03-16

    A new family of mechanochromic photonic-crystal fibers exhibits tunable structural colors under stretching. This novel mechanochromic fiber is prepared by depositing polymer microspheres onto a continuous aligned-carbon-nanotube sheet that has been wound on an elastic poly(dimethylsiloxane) fiber, followed by further embedding in poly(dimethylsiloxane). The color of the fiber can be tuned by varying the size and the center-to-center distance of the polymer spheres. It further experiences reversible and rapid multicolor changes during the stretch and release processes, for example, between red, green, and blue. Both the high sensitivity and stability were maintained after 1000 deformation cycles. These elastic photonic-crystal fibers were woven into patterns and smart fabrics for various display and sensing applications. PMID:25728690

  20. Energy-effective frost-free coatings based on superhydrophobic aligned nanocones.

    PubMed

    Xu, Qian; Li, Juan; Tian, Jian; Zhu, Jie; Gao, Xuefeng

    2014-06-25

    We demonstrate the feasibility of superhydrophobic aligned nanocones as energy-effective frost-free coatings. Exemplified by Co(OH)2 nanocone films with condensed microdrop self-removal ability, their edge and whole-surface frosting time can be delayed to about 10 and 150 min, respectively. By using a Teflon gasket to shield edges, the samples can keep frost-free state over 90 min. Further, the lasting frost-free state can be realized by intermittent weak airflow heating, which is energy-effective in contrast to usual high-power heating for defrosting flat surfaces. These findings are significant to develop antifrosting nanotechnologies for energy-effective heat exchangers such as heat pumps and refrigerators. PMID:24912381

  1. A vertically aligned carbon nanotube-based impedance sensing biosensor for rapid and high sensitive detection of cancer cells.

    PubMed

    Abdolahad, Mohammad; Taghinejad, Mohammad; Taghinejad, Hossein; Janmaleki, Mohsen; Mohajerzadeh, Shams

    2012-03-21

    A novel vertically aligned carbon nanotube based electrical cell impedance sensing biosensor (CNT-ECIS) was demonstrated for the first time as a more rapid, sensitive and specific device for the detection of cancer cells. This biosensor is based on the fast entrapment of cancer cells on vertically aligned carbon nanotube arrays and leads to mechanical and electrical interactions between CNT tips and entrapped cell membranes, changing the impedance of the biosensor. CNT-ECIS was fabricated through a photolithography process on Ni/SiO(2)/Si layers. Carbon nanotube arrays have been grown on 9 nm thick patterned Ni microelectrodes by DC-PECVD. SW48 colon cancer cells were passed over the surface of CNT covered electrodes to be specifically entrapped on elastic nanotube beams. CNT arrays act as both adhesive and conductive agents and impedance changes occurred as fast as 30 s (for whole entrapment and signaling processes). CNT-ECIS detected the cancer cells with the concentration as low as 4000 cells cm(-2) on its surface and a sensitivity of 1.7 × 10(-3)Ω cm(2). Time and cell efficiency factor (TEF and CEF) parameters were defined which describe the sensor's rapidness and resolution, respectively. TEF and CEF of CNT-ECIS were much higher than other cell based electrical biosensors which are compared in this paper. PMID:22294045

  2. ASH structure alignment package: Sensitivity and selectivity in domain classification

    PubMed Central

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

    2007-01-01

    Background Structure alignment methods offer the possibility of measuring distant evolutionary relationships between proteins that are not visible by sequence-based analysis. However, the question of how structural differences and similarities ought to be quantified in this regard remains open. In this study we construct a training set of sequence-unique CATH and SCOP domains, from which we develop a scoring function that can reliably identify domains with the same CATH topology and SCOP fold classification. The score is implemented in the ASH structure alignment package, for which the source code and a web service are freely available from the PDBj website . Results The new ASH score shows increased selectivity and sensitivity compared with values reported for several popular programs using the same test set of 4,298,905 structure pairs, yielding an area of .96 under the receiver operating characteristic (ROC) curve. In addition, weak sequence homologies between similar domains are revealed that could not be detected by BLAST sequence alignment. Also, a subset of domain pairs is identified that exhibit high similarity, even though their CATH and SCOP classification differs. Finally, we show that the ranking of alignment programs based solely on geometric measures depends on the choice of the quality measure. Conclusion ASH shows high selectivity and sensitivity with regard to domain classification, an important step in defining distantly related protein sequence families. Moreover, the CPU cost per alignment is competitive with the fastest programs, making ASH a practical option for large-scale structure classification studies. PMID:17407606

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

    SciTech Connect

    Druckmueller, M.

    2009-12-01

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

  4. Ultrafast IR pump-probe and 2D-IR photon echo spectroscopy of adenosine-thymidine base pairs

    NASA Astrophysics Data System (ADS)

    Greve, Christian; Preketes, Nicholas K.; Costard, Rene.; Koeppe, Benjamin; Fidder, Henk; Nibbering, Erik T. J.; Temps, Friedrich; Mukamel, Shaul; Elsaesser, Thomas

    2013-03-01

    We characterize diagonal and off-diagonal anharmonicities of N-H stretching vibrations in adenosine and thymidine monomers and in A•T-base pairs in chloroform solution, showing the important role of coupling between vibrationally excited N-H stretching states.

  5. Relationship between the 19 base pair deletion polymorphism in DHFR and unmetabolized folic and in plasma and RBC folate

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: A 19 base pair (bp) deletion allele of dihydrofolate reductase (DHFR), an enzyme that makes folic acid metabolically active and reduces dihydrofolate to tetrahydrofolate to stimulate folate turnover, has been implicated in folate related health outcomes. Objective: Examine the effect ...

  6. Lewis base activation of borane-dimethylsulfide into strongly reducing ion pairs for the transformation of carbon dioxide to methoxyboranes.

    PubMed

    Légaré, Marc-André; Courtemanche, Marc-André; Fontaine, Frédéric-Georges

    2014-10-01

    The hydroboration of carbon dioxide into methoxyboranes by borane-dimethylsulfide using different base catalysts is described. A non-nucleophilic proton sponge is found to be the most active catalyst, with TOF reaching 64 h(-1) at 80 °C, and is acting via the activation of BH3·SMe2 into a boronium-borohydride ion pair. PMID:25164269

  7. The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs.

    PubMed

    Halder, Antarip; Bhattacharya, Sohini; Datta, Ayan; Bhattacharyya, Dhananjay; Mitra, Abhijit

    2015-10-21

    The roles of protonated nucleobases in stabilizing different structural motifs and in facilitating catalytic functions of RNA are well known. Among different polar sites of all the nucleobases, N7 of guanine has the highest protonation propensity at physiological pH. However, unlike other easily protonable sites such as N1 and N3 of adenine or N3 of cytosine, N7 protonation of guanine does not lead to the stabilization of base pairs involving its protonated Hoogsteen edge. It also does not facilitate its participation in any acid-base catalysis process. To explore the possible roles of N7 protonated guanine, we have studied its base pairing potentials involving WatsonCrick and sugar edges, which undergo major charge redistribution upon N7 protonation. We have carried out quantum chemical geometry optimization at the M05-2X/6-311G+(2d,2p) level, followed by interaction energy calculation at the MP2/aug-cc-pVDZ level, along with the analysis of the context of occurrence for selected base pairs involving the sugar edge or the WatsonCrick edge of guanine within a non-redundant set of 167 RNA crystal structures. Our results suggest that, four base pairs - G:C W:W trans, G:rC W:S cis, G:G W:H cis and G:G S:H trans may involve N7 protonated guanine. These base pairs deviate significantly from their respective experimental geometries upon QM optimization, but they retain their experimental geometries if guanine N7 protonation is considered during optimization. Our study also reveals the role of guanine N7 protonation (i) in stabilizing important RNA structural motifs, (ii) in providing a framework for designing pH driven molecular motors and (iii) in providing an alternative strategy to mimic the effect of post-transcriptional changes. PMID:26382322

  8. Protein structure alignment beyond spatial proximity

    PubMed Central

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

    2013-01-01

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

  9. Comparison of Three Cre-LoxP Based Paired-End Library Construction Methods

    SciTech Connect

    Peng, Ze; Nath, Nandita; Tritt, Andrew; Liang, Shoudan; Han, James; Pennacchio, Len; Chen, Feng

    2013-03-26

    Paired-end library sequencing has been proven useful in scaffold construction during de novo whole genome shotgun assembly. The ability of generating mate pairs with > 8 Kb insert sizes is especially important for genomes containing long repeats. To make mate paired libraries for next generation sequencing, DNA fragments need to be circularized to bring the ends together. There are several methods that can be used for DNA circulation, namely ligation, hybridization and Cre-LoxP recombination. With higher circularization efficiency with large insert DNA fragments, Cre-LoxP recombination method generally has been used for constructing >8 kb insert size paired-end libraries. Second fragmentation step is also crucial for maintaining high library complexity and uniform genome coverage. Here we will describe the following three fragmentation methods: restriction enzyme digestion, random shearing and nick translation. We will present the comparison results for these three methods. Our data showed that all three methods are able to generate paired-end libraries with greater than 20 kb insert. Advantages and disadvantages of these three methods will be discussed as well.

  10. Mitochondrial DNA 4977-base pair common deletion in blood leukocytes and melanoma risk.

    PubMed

    Shen, Jie; Wan, Jie; Huff, Chad; Fang, Shenying; Lee, Jeffrey E; Zhao, Hua

    2016-05-01

    The 4977-base pair common deletion DmtDNA4977 is the most frequently observed mitochondrial DNA mutation in human tissues. Because mitochondrial DNA mutations are mainly caused by reactive oxygen species (ROS), and given that oxidative stress plays an important role in melanoma carcinogenesis, the investigation of DmtDNA4977 may be particularly relevant to the development of melanoma. In this study, we compared DmtDNA4977 levels in blood leukocytes from 206 melanoma patients and 219 healthy controls. Overall, melanoma cases had significantly higher levels of DmtDNA4977 than healthy controls (median: 0.60 vs 0.20, P = 0.008). The difference was evident among individuals who were older than 47 yrs, women, and had pigmentation risk factors (e.g., blond or red hair, blue eye, fair skin, light, or none tanning ability after prolonged sun exposure, and freckling in the sun as a child). The difference was also evident among those who had at least one lifetime sunburn with blistering and had no reported use of a sunlamp. Interestingly, among controls, DmtDNA4977 levels differed by phenotypic index and reported use of a sunlamp. In the risk assessment, increased levels of DmtDNA4977 were associated with a 1.23-fold increased risk of melanoma (odds ratio (OR): 1.23, 95% confidence interval (90% CI): 1.01, 1.50). A significant dose-response relationship was observed in quartile analysis (P = 0.001). In summary, our study suggests that high levels of DmtDNA4977 in blood leukocytes are associated with increased risk of melanoma and that association is affected by both pigmentation and personal history of sun exposure. PMID:26988264

  11. Fast Reconnection Rates Based on Group Velocity Cones: Whistler Regime and Pair Plasmas

    NASA Astrophysics Data System (ADS)

    Singh, N.

    2009-05-01

    Based on the group velocity vector of the whistler mode, we predict the range of whistler-regime reconnection rate depending on the half width (w) of the current sheet (CS. During the reconnection process electromagnetic perturbations (EMPs) are generated in the localized diffusion region (DR, which acts like an antenna and radiates whistler waves for certain range of CS widths. The reconnection structure (exhaust) is approximately the radiation pattern of the DR antenna and it is determined by the group velocity directions. Since the whistler waves originate from the electromagnetic perturbations (EMPs) localized in the DR, we calculate R over a range of the discrete values of the perpendicular wave number (k'') contained in the Fourier spectrum of the EMPs. We have used such calculations to determine the reconnection rates averaged over the wave number spectrum of a Gaussian shaped EMP as a function of the CS width. We find that has a fairly constant value at ˜ 0.23 for CS widths in the range 0.4 < w/di ˜ 1 and for w < 0.3di it decreases with decreasing w and it attains a value ˜ 0.06 in an extremely thin CS with w ˜ 0.05di, where di is the ion skin depth. We compare the values of and R with those found from simulations and experiments, and find them in good agreement. We also report the properties of the whistler waves radiated from the DR into the exhaust region. We also demonstrate that our theoretical method developed for whistler regime reconnection could be easily adopted to predict fast reconnection rates in pair plasmas, which support inertial Alfven waves.

  12. Relationship between pairing symmetries and interaction parameters in iron-based superconductors from functional renormalization group calculations

    NASA Astrophysics Data System (ADS)

    Yuan, Jing; Hu, Jiangping

    2016-03-01

    Pairing symmetries of iron-based superconductors are investigated systematically in a five-orbital model within the different regions of interaction parameters by functional renormalization group (FRG). Even for a fixed Fermi surface with both hole and electron pockets, it is found that depending on interaction parameters, a variety of pairing symmetries, including two types of d-wave and two types of s-wave pairing symmetries, can emerge. Only the dx^2-y^2 - and the s±-waves are robustly supported by the nearest-neighbor (NN) intra-orbital J 1 and the next-nearest-neighbor (NNN) intra-orbital J 2 antiferromagnetic (AFM) exchange couplings, respectively. This study suggests that the accurate initial input of the interaction parameters is essential to make FRG a useful method to determine the leading channel of superconducting instability.

  13. Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution

    PubMed Central

    Wagner, Dominic; Rinnenthal, Jörg; Narberhaus, Franz; Schwalbe, Harald

    2015-01-01

    The cyanobacterial hsp17 ribonucleicacid thermometer (RNAT) is one of the smallest naturally occurring RNAT. It forms a single hairpin with an internal 1×3-bulge separating the start codon in stem I from the ribosome binding site (RBS) in stem II. We investigated the temperature-dependent regulation of hsp17 by mapping individual base-pair stabilities from solvent exchange nuclear magnetic resonance (NMR) spectroscopy. The wild-type RNAT was found to be stabilized by two critical CG base pairs (C14-G27 and C13-G28). Replacing the internal 1×3 bulge by a stable CG base pair in hsp17rep significantly increased the global stability and unfolding cooperativity as evidenced by circular dichroism spectroscopy. From the NMR analysis, remote stabilization and non-nearest neighbour effects exist at the base-pair level, in particular for nucleotide G28 (five nucleotides apart from the side of mutation). Individual base-pair stabilities are coupled to the stability of the entire thermometer within both the natural and the stabilized RNATs by enthalpy–entropy compensation presumably mediated by the hydration shell. At the melting point the Gibbs energies of the individual nucleobases are equalized suggesting a consecutive zipper-type unfolding mechanism of the RBS leading to a dimmer-like function of hsp17 and switch-like regulation behaviour of hsp17rep. The data show how minor changes in the nucleotide sequence not only offset the melting temperature but also alter the mode of temperature sensing. The cyanobacterial thermosensor demonstrates the remarkable adjustment of natural RNATs to execute precise temperature control. PMID:25940621

  14. Cooper pairing in the insulating valence band in iron-based superconductors

    NASA Astrophysics Data System (ADS)

    Hu, Lun-Hui; Chen, Wei-Qiang; Zhang, Fu-Chun

    2015-04-01

    Conventional Cooper pairing arises from attractive interaction of electrons in the metallic bands. A recent experiment on Co-doped LiFeAs shows superconductivity in the insulating valence band, which is evolved from a metallic hole band upon doping. Here we examine this phenomenon by studying superconductivity in a three-orbital Hamiltonian relevant to the doped LiFeAs. We show explicitly that Cooper pairing of the insulating hole band requires a finite pairing interaction strength. For strong coupling, the superconductivity in the hole band is robust against the sink of the hole band below the Fermi level. Our theory predicts a substantial upward shift of the chemical potential in the superconducting transition for Co-doped LiFeAs.

  15. Statistics for critical clinical decision making based on readings of pairs of implanted sensors.

    PubMed

    Schmidtke, D W; Pishko, M V; Quinn, C P; Heller, A

    1996-09-01

    Low error rates are essential if lives of patients are to depend on readings of implanted sensors, such as glucose sensors in insulin-dependent diabetic patients. To verify the operation and to calibrate on demand an implanted sensor, it is necessary that calibration through a single, independent measurement involving withdrawal of only one sample of blood and its independent analysis be feasible. Such a one-point calibration must be accurate. Borrowing from nuclear reactor safety assurance, where a likelihood ratio test is applied to readings of pairs of pressure sensors for shutdown/no shutdown decisions, we apply a similar test to sensor pairs implanted in rats. We show, for five sets of glucose sensor pairs, calibrated in vivo by withdrawal of a single sample of blood, that application of the likelihood ratio test increases the fraction of the clinically correct readings from 92.4% for their averaged readings to 98.8%. PMID:8794921

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

    SciTech Connect

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

    2013-09-15

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

  17. Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments

    PubMed Central

    Yamanishi, Yoshihiro; Tabei, Yasuo; Kotera, Masaaki

    2015-01-01

    Motivation: Recent advances in mass spectrometry and related metabolomics technologies have enabled the rapid and comprehensive analysis of numerous metabolites. However, biosynthetic and biodegradation pathways are only known for a small portion of metabolites, with most metabolic pathways remaining uncharacterized. Results: In this study, we developed a novel method for supervised de novo metabolic pathway reconstruction with an improved graph alignment-based approach in the reaction-filling framework. We proposed a novel chemical graph alignment algorithm, which we called PACHA (Pairwise Chemical Aligner), to detect the regioisomer-sensitive connectivities between the aligned substructures of two compounds. Unlike other existing graph alignment methods, PACHA can efficiently detect only one common subgraph between two compounds. Our results show that the proposed method outperforms previous descriptor-based methods or existing graph alignment-based methods in the enzymatic reaction-likeness prediction for isomer-enriched reactions. It is also useful for reaction annotation that assigns potential reaction characteristics such as EC (Enzyme Commission) numbers and PIERO (Enzymatic Reaction Ontology for Partial Information) terms to substrate–product pairs. Finally, we conducted a comprehensive enzymatic reaction-likeness prediction for all possible uncharacterized compound pairs, suggesting potential metabolic pathways for newly predicted substrate–product pairs. Contact: maskot@bio.titech.ac.jp PMID:26072478

  18. A terrain-based paired-site sampling design to assess biodiversity losses from eastern hemlock decline

    USGS Publications Warehouse

    Young, J.A.; Smith, D.R.; Snyder, C.D.; Lemarie, D.P.

    2002-01-01

    Biodiversity surveys are often hampered by the inability to control extraneous sources of variability introduced into comparisons of populations across a heterogenous landscape. If not specifically accounted for a priori, this noise can weaken comparisons between sites, and can make it difficult to draw inferences about specific ecological processes. We developed a terrain-based, paired-site sampling design to analyze differences in aquatic biodiversity between streams draining eastern hemlock (Tsuga canadensis) forests, and those draining mixed hardwood forests in Delaware Water Gap National Recreation Area (USA). The goal of this design was to minimize variance due to terrain influences on stream communities, while representing the range of hemlock dominated stream environments present in the park. We used geographic information systems (GIS) and cluster analysis to define and partition hemlock dominated streams into terrain types based on topographic variables and stream order. We computed similarity of forest stands within terrain types and used this information to pair hemlock-dominated streams with hardwood counterparts prior to sampling. We evaluated the effectiveness of the design through power analysis and found that power to detect differences in aquatic invertebrate taxa richness was highest when sites were paired and terrain type was included as a factor in the analysis. Precision of the estimated difference in mean richness was nearly doubled using the terrain-based, paired site design in comparison to other evaluated designs. Use of this method allowed us to sample stream communities representative of park-wide forest conditions while effectively controlling for landscape variability.

  19. Pairwise Sequence Alignment Library

    2015-05-20

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

  20. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    2015-05-20

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