Science.gov

Sample records for alignment analysis showed

  1. Enviroment, from southwest, showing Castle Garden Bridge and alignment of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Enviroment, from southwest, showing Castle Garden Bridge and alignment of Township Road 343 over Bennetts Branch of Sinnemahoning Creek - Castle Garden Bridge, Township Route 343 over Bennetts Branch of Sinnemahoning Creek, Driftwood, Cameron County, PA

  2. 9. VIEW, LOOKING SOUTHEAST, SHOWING MITRE RAILS WITH RAIL ALIGNMENT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. VIEW, LOOKING SOUTHEAST, SHOWING MITRE RAILS WITH RAIL ALIGNMENT GUIDES ON MOVABLE SPAN - New York, New Haven & Hartford Railroad, Mystic River Bridge, Spanning Mystic River between Groton & Stonington, Groton, New London County, CT

  3. 19. VIEW OF GRAND CANAL, SHOWING NEW ALIGNMENT, LOOKING NORTH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    19. VIEW OF GRAND CANAL, SHOWING NEW ALIGNMENT, LOOKING NORTH TOWARD CROSSCUT HYDRO PLANT ROOF WITH FOUR CUPOLAS VISIBLE. Photographer: Mark Durben, May 1990 - Grand Canal, North side of Salt River, Tempe, Maricopa County, AZ

  4. 21. VIEW OF GRAND CANAL, SHOWING OLD ALIGNMENT, LOOKING WEST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    21. VIEW OF GRAND CANAL, SHOWING OLD ALIGNMENT, LOOKING WEST LOCATION UNKNOWN. THE WIDE DRY BED OF THE SALT RIVER SPANS THE BACKGROUND. Photographer: Mark Durben, April 1989 - Grand Canal, North side of Salt River, Tempe, Maricopa County, AZ

  5. 5. INTERIOR VIEW OF SOUTH ROOM SHOWING ALIGNMENT GUIDANCE EQUIPMENT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. INTERIOR VIEW OF SOUTH ROOM SHOWING ALIGNMENT GUIDANCE EQUIPMENT MOUNT; VIEW TO EAST. - Cape Canaveral Air Station, Launch Complex 17, Facility 28403, East end of Lighthouse Road, Cape Canaveral, Brevard County, FL

  6. View to southwest along bridge alignment, showing reverse curve; photographer ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View to southwest along bridge alignment, showing reverse curve; photographer unknown; 1933 photo from collection of Office-of Structures Maintenance, California Department of Transportation, Sacramento - Carroll Overhead Bridge, Altamont Pass Road, Livermore, Alameda County, CA

  7. Orbit IMU alignment: Error analysis

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

    A comprehensive accuracy analysis of orbit inertial measurement unit (IMU) alignments using the shuttle star trackers was completed and the results are presented. Monte Carlo techniques were used in a computer simulation of the IMU alignment hardware and software systems to: (1) determine the expected Space Transportation System 1 Flight (STS-1) manual mode IMU alignment accuracy; (2) investigate the accuracy of alignments in later shuttle flights when the automatic mode of star acquisition may be used; and (3) verify that an analytical model previously used for estimating the alignment error is a valid model. The analysis results do not differ significantly from expectations. The standard deviation in the IMU alignment error for STS-1 alignments was determined to the 68 arc seconds per axis. This corresponds to a 99.7% probability that the magnitude of the total alignment error is less than 258 arc seconds.

  8. 8. Detail, below platform, showing usuallysubmerged chains aligned in metal ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Detail, below platform, showing usually-submerged chains aligned in metal guides at low tide; view to east. - Charlestown Navy Yard, Marine Railway, Between Piers 2 & 3, on Charlestown Waterfront at west end of Navy Yard, Boston, Suffolk County, MA

  9. View to southwest along bridge alignment, showing reverse curve from ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View to southwest along bridge alignment, showing reverse curve from near deck level; Southern Pacific Railroad track passing beneath bridge; Western Pacific Railroad track out of sight behind bridge; photographer unknown; 1933 photo from collection of Office of Structures Maintenance, California Department of Transportation, Sacramento - Carroll Overhead Bridge, Altamont Pass Road, Livermore, Alameda County, CA

  10. 22. VIEW OF GRAND CANAL, SHOWING OLD ALIGNMENT, LOOKING WEST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    22. VIEW OF GRAND CANAL, SHOWING OLD ALIGNMENT, LOOKING WEST FROM BELOW THE SETTLING BASIN (see HAER Photograph No. AZ-30-17, Crosscut Hydro Plant). Photographer: Mark Durben, April 1989 - Grand Canal, North side of Salt River, Tempe, Maricopa County, AZ

  11. 23. VIEW OF GRAND CANAL, SHOWING NEW ALIGNMENT CANAL ON ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    23. VIEW OF GRAND CANAL, SHOWING NEW ALIGNMENT CANAL ON RIGHT. THIS PHOTO WAS TAKEN FROM APPROXIMATELY THE SAME SPOT AS THE PREVIOUS PHOTOGRAPH (AZ-17-22). Photographer: Kevin Kreisel-Coons, May 1990 - Grand Canal, North side of Salt River, Tempe, Maricopa County, AZ

  12. 18. VIEW OF GRAND CANAL, SHOWING OLD ALIGNMENT BEFORE 1989 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. VIEW OF GRAND CANAL, SHOWING OLD ALIGNMENT BEFORE 1989 REALIGNMENT, LOOKING NORTH TOWARD RAILROAD CROSSING AND CROSSCUT STEAM PLANT LARGE WHITE BUILDING. THE CROSSCUT HYDRO PLANT IS HIDDEN BY TREES TO RIGHT OF STEAM PLANT. Photographer: Mark Durben, April 1989 - Grand Canal, North side of Salt River, Tempe, Maricopa County, AZ

  13. 20. VIEW OF GRAND CANAL, SHOWING OLD ALIGNMENT, LOOKING EAST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    20. VIEW OF GRAND CANAL, SHOWING OLD ALIGNMENT, LOOKING EAST FROM SOUTH BANK NEAR SETTLING BASIN (see HAER Photograph No. AZ-30-17, Crosscut Hydro Plant). THE LARGE FOREGROUND PIPE CARRIED WATER ACROSS THE CANAL FROM THE SETTLING BASIN TO THE CROSSCUT STEAM PLANT. Photographer: Mark Durben, April 1989 - Grand Canal, North side of Salt River, Tempe, Maricopa County, AZ

  14. 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

  15. Shod wear and foot alignment in clinical gait analysis.

    PubMed

    Louey, Melissa Gar Yee; Sangeux, Morgan

    2016-09-01

    Sagittal plane alignment of the foot presents challenges when the subject wears shoes during gait analysis. Typically, visual alignment is performed by positioning two markers, the heel and toe markers, aligned with the foot within the shoe. Alternatively, software alignment is possible when the sole of the shoe lies parallel to the ground, and the change in the shoe's sole thickness is measured and entered as a parameter. The aim of this technical note was to evaluate the accuracy of visual and software foot alignment during shod gait analysis. We calculated the static standing ankle angles of 8 participants (mean age: 8.7 years, SD: 2.9 years) wearing bilateral solid ankle foot orthoses (BSAFOs) with and without shoes using the visual and software alignment methods. All participants were able to stand with flat feet in both static trials and the ankle angles obtained in BSAFOs without shoes was considered the reference. We showed that the current implementation of software alignment introduces a bias towards more ankle dorsiflexion, mean=3°, SD=3.4°, p=0.006, and proposed an adjusted software alignment method. We found no statistical differences using visual alignment and adjusted software alignment between the shoe and shoeless conditions, p=0.19 for both. Visual alignment or adjusted software alignment are advised to represent foot alignment accurately.

  16. Shod wear and foot alignment in clinical gait analysis.

    PubMed

    Louey, Melissa Gar Yee; Sangeux, Morgan

    2016-09-01

    Sagittal plane alignment of the foot presents challenges when the subject wears shoes during gait analysis. Typically, visual alignment is performed by positioning two markers, the heel and toe markers, aligned with the foot within the shoe. Alternatively, software alignment is possible when the sole of the shoe lies parallel to the ground, and the change in the shoe's sole thickness is measured and entered as a parameter. The aim of this technical note was to evaluate the accuracy of visual and software foot alignment during shod gait analysis. We calculated the static standing ankle angles of 8 participants (mean age: 8.7 years, SD: 2.9 years) wearing bilateral solid ankle foot orthoses (BSAFOs) with and without shoes using the visual and software alignment methods. All participants were able to stand with flat feet in both static trials and the ankle angles obtained in BSAFOs without shoes was considered the reference. We showed that the current implementation of software alignment introduces a bias towards more ankle dorsiflexion, mean=3°, SD=3.4°, p=0.006, and proposed an adjusted software alignment method. We found no statistical differences using visual alignment and adjusted software alignment between the shoe and shoeless conditions, p=0.19 for both. Visual alignment or adjusted software alignment are advised to represent foot alignment accurately. PMID:27420611

  17. Lunar Alignments - Identification and Analysis

    NASA Astrophysics Data System (ADS)

    González-García, A. César

    Lunar alignments are difficult to establish given the apparent lack of written accounts clearly pointing toward lunar alignments for individual temples. While some individual cases are reviewed and highlighted, the weight of the proof must fall on statistical sampling. Some definitions for the lunar alignments are provided in order to clarify the targets, and thus, some new tools are provided to try to test the lunar hypothesis in several cases, especially in megalithic astronomy.

  18. [Tabular excel editor for analysis of aligned nucleotide sequences].

    PubMed

    Demkin, V V

    2010-01-01

    Excel platform was used for transition of results of multiple aligned nucleotide sequences obtained using the BLAST network service to the form appropriate for visual analysis and editing. Two macros operators for MS Excel 2007 were constructed. The array of aligned sequences transformed into Excel table and processed using macros operators is more appropriate for analysis than initial html data.

  19. A comparative analysis of multiple sequence alignments for biological data.

    PubMed

    Manzoor, Umar; Shahid, Sarosh; Zafar, Bassam

    2015-01-01

    Multiple sequence alignment plays a key role in the computational analysis of biological data. Different programs are developed to analyze the sequence similarity. This paper highlights the algorithmic techniques of the most popular multiple sequence alignment programs. These programs are then evaluated on the basis of execution time and scalability. The overall performance of these programs is assessed to highlight their strengths and weaknesses with reference to their algorithmic techniques. In terms of overall alignment quality, T-Coffee and Mafft attain the highest average scores, whereas K-align has the minimum computation time. PMID:26405947

  20. Subwavelength alignment mark signal analysis of advanced memory products

    NASA Astrophysics Data System (ADS)

    Yin, Xiaoming; Wong, Alfred K. K.; Wheeler, Donald C.; Williams, Gary; Lehner, Eric A.; Zach, Franz X.; Kim, Byeong Y.; Fukuzaki, Yuzo; Lu, Zhijian G.; Credendino, Santo; Wiltshire, Timothy J.

    2000-06-01

    The impact of alignment mark structure, mark geometry, and stepper alignment optical system on mark signal contrast was investigated using computer simulation. Several sub-wavelength poly silicon recessed film stack alignment targets of advanced memory products were studied. Stimulated alignment mark signals for both dark-field and bright-field systems using the rigorous electromagnetic simulation program TEMPEST showed excellent agreement with experimental data. For a dark-field alignment system, the critical parameters affecting signal contrast were found to be mark size and mark recess depth below silicon surface. On the other hand, film stack thickness and mark recess depth below/above silicon surface are the important parameters for a bright-field alignment system. From observed simulation results optimal process parameters are determined. Based on the simulation results some signal enhancement techniques will be discussed.

  1. PipeAlign: A new toolkit for protein family analysis.

    PubMed

    Plewniak, Frédéric; Bianchetti, Laurent; Brelivet, Yann; Carles, Annaick; Chalmel, Frédéric; Lecompte, Odile; Mochel, Thiebaut; Moulinier, Luc; Muller, Arnaud; Muller, Jean; Prigent, Veronique; Ripp, Raymond; Thierry, Jean-Claude; Thompson, Julie D; Wicker, Nicolas; Poch, Olivier

    2003-07-01

    PipeAlign is a protein family analysis tool integrating a five step process ranging from the search for sequence homologues in protein and 3D structure databases to the definition of the hierarchical relationships within and between subfamilies. The complete, automatic pipeline takes a single sequence or a set of sequences as input and constructs a high-quality, validated MACS (multiple alignment of complete sequences) in which sequences are clustered into potential functional subgroups. For the more experienced user, the PipeAlign server also provides numerous options to run only a part of the analysis, with the possibility to modify the default parameters of each software module. For example, the user can choose to enter an existing multiple sequence alignment for refinement, validation and subsequent clustering of the sequences. The aim is to provide an interactive workbench for the validation, integration and presentation of a protein family, not only at the sequence level, but also at the structural and functional levels. PipeAlign is available at http://igbmc.u-strasbg.fr/PipeAlign/.

  2. Survey and alignment data analysis for the ALS storage ring

    SciTech Connect

    Keller, R.

    1993-05-01

    The survey and alignment effort for the Advanced Light Source (ALS) accelerator complex has been described elsewhere. Data analysis for this task comprises the creation of ideal data, comparison of measured coordinates with ideal ones, and computation of alignment values, taking into account the effects caused by finite observation accuracy. A novel approach has been taken, using personal computer spreadsheets rather than more conventional programming methods. This approach was induced by the necessities to create and frequently refine the analysis procedures while measurements were already underway, and further by hardware constraints that limited the use of an available surveying code. A major benefit consists in the ability to identify and deal with discrepancies that occasionally arise when different techniques are used to observe the same object, in a timely and efficient manner. As a result of the performed survey and alignment work, the ALS lattice magnets have been positioned with accuracies well exceeding the original specifications.

  3. Alignment error analysis of the snapshot imaging polarimeter.

    PubMed

    Liu, Zhen; Yang, Wei-Feng; Ye, Qing-Hao; Hong, Jin; Gong, Guan-Yuan; Zheng, Xiao-Bing

    2016-03-10

    A snapshot imaging polarimeter (SIP) system is able to reconstruct two-dimensional spatial polarization information through a single interferogram. In this system, the alignment errors of the half-wave plate (HWP) and the analyzer have a predominant impact on the accuracies of reconstructed complete Stokes parameters. A theoretical model for analyzing the alignment errors in the SIP system is presented in this paper. Based on this model, the accuracy of the reconstructed Stokes parameters has been evaluated by using different incident states of polarization. An optimum thickness of the Savart plate for alleviating the perturbation introduced by the alignment error of the HWP is found by using the condition number of the system measurement matrix as an objective function in a minimization procedure. The result shows that when the thickness of a Savart plate is 23 mm, corresponding to the condition number 2.06, the precision of the SIP system can reach to 0.21% at 1° alignment tolerance of the HWP. PMID:26974785

  4. MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis

    SciTech Connect

    Lamarche, Brian L.; Crowell, Kevin L.; Jaitly, Navdeep; Petyuk, Vladislav A.; Shah, Anuj R.; Polpitiya, Ashoka D.; Sandoval, John D.; Kiebel, Gary R.; Monroe, Matthew E.; Callister, Stephen J.; Metz, Thomas O.; Anderson, Gordon A.; Smith, Richard D.

    2013-02-12

    MultiAlign is a free software tool that aligns multiple liquid chromatography-mass spectrometry datasets to one another by clustering mass and LC elution features across datasets. Applicable to both label-free proteomics and metabolomics comparative analyses, the software can be operated in several modes. Clustered features can be matched to a reference database to identify analytes, used to generate abundance profiles, linked to tandem mass spectra based on parent precursor masses, and culled for targeted liquid chromatography-tandem mass spectrometric analysis. MultiAlign is also capable of tandem mass spectral clustering to describe proteome structure and find similarity in subsequent sample runs.

  5. Comparative Analysis of the Measurement of Total Instructional Alignment

    ERIC Educational Resources Information Center

    Kick, Laura C.

    2013-01-01

    In 2007, Lisa Carter created the Total Instructional Alignment system--a process that aligns standards, curriculum, assessment, and instruction. Employed in several hundred school systems, the TIA process is a successful professional development program. The researcher developed an instrument to measure the success of the TIA process with the…

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

    PubMed

    Dinu, Liviu P; Ionescu, Radu Tudor; Tomescu, Alexandru I

    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 [Formula: see text]-mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown) organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.

  7. Manufacturing and alignment tolerance analysis through Montecarlo approach for PLATO

    NASA Astrophysics Data System (ADS)

    Magrin, Demetrio; Ragazzoni, Roberto; Bergomi, Maria; Biondi, Federico; Chinellato, Simonetta; Dima, Marco; Farinato, Jacopo; Greggio, Davide; Gullieuszik, Marco; Marafatto, Luca; Viotto, Valentina; Munari, Matteo; Pagano, Isabella; Sicilia, Daniela; Basso, Stefano; Borsa, Francesco; Ghigo, Mauro; Spiga, Daniele; Bandy, Timothy; Brändli, Mathias; Benz, Willy; Bruno, Giordano; De Roche, Thierry; Piazza, Daniele; Rieder, Martin; Brandeker, Alexis; Klebor, Maximilian; Mogulsky, Valery; Schweitzer, Mario; Wieser, Matthias; Erikson, Anders; Rauer, Heike

    2016-07-01

    The project PLAnetary Transits and Oscillations of stars (PLATO) is one of the selected medium class (M class) missions in the framework of the ESA Cosmic Vision 2015-2025 program. The main scientific goal of PLATO is the discovery and study of extrasolar planetary systems by means of planetary transits detection. According to the current baseline, the scientific payload consists of 34 all refractive telescopes having small aperture (120mm) and wide field of view (diameter greater than 37 degrees) observing over 0.5-1 micron wavelength band. The telescopes are mounted on a common optical bench and are divided in four families of eight telescopes with an overlapping line-of-sight in order to maximize the science return. Remaining two telescopes will be dedicated to support on-board star-tracking system and will be specialized on two different photometric bands for science purposes. The performance requirement, adopted as merit function during the analysis, is specified as 90% enclosed energy contained in a square having size 2 pixels over the whole field of view with a depth of focus of +/-20 micron. Given the complexity of the system, we have followed a Montecarlo analysis approach for manufacturing and alignment tolerances. We will describe here the tolerance method and the preliminary results, speculating on the assumed risks and expected performances.

  8. Comparative Topological Analysis of Neuronal Arbors via Sequence Representation and Alignment

    NASA Astrophysics Data System (ADS)

    Gillette, Todd Aaron

    Neuronal morphology is a key mediator of neuronal function, defining the profile of connectivity and shaping signal integration and propagation. Reconstructing neurite processes is technically challenging and thus data has historically been relatively sparse. Data collection and curation along with more efficient and reliable data production methods provide opportunities for the application of informatics to find new relationships and more effectively explore the field. This dissertation presents a method for aiding the development of data production as well as a novel representation and set of analyses for extracting morphological patterns. The DIADEM Challenge was organized for the purposes of determining the state of the art in automated neuronal reconstruction and what existing challenges remained. As one of the co-organizers of the Challenge, I developed the DIADEM metric, a tool designed to measure the effectiveness of automated reconstruction algorithms by comparing resulting reconstructions to expert-produced gold standards and identifying errors of various types. It has been used in the DIADEM Challenge and in the testing of several algorithms since. Further, this dissertation describes a topological sequence representation of neuronal trees amenable to various forms of sequence analysis, notably motif analysis, global pairwise alignment, clustering, and multiple sequence alignment. Motif analysis of neuronal arbors shows a large difference in bifurcation type proportions between axons and dendrites, but that relatively simple growth mechanisms account for most higher order motifs. Pairwise global alignment of topological sequences, modified from traditional sequence alignment to preserve tree relationships, enabled cluster analysis which displayed strong correspondence with known cell classes by cell type, species, and brain region. Multiple alignment of sequences in selected clusters enabled the extraction of conserved features, revealing mouse

  9. Analysis of alignment effect on carbon nanotube layer in nanocomposites

    NASA Astrophysics Data System (ADS)

    Joshi, Preeti; Upadhyay, S. H.

    2015-02-01

    In this work, effect of various alignments of double walled carbon nanotubes (DWCNTs) in composite is evaluated for axial, lateral and through plane properties. Layers of DWCNTs are incorporated in the matrix. Four models with different layer combinations are analysed using 3D representative volume element. The highest value of axial modulus is observed for composite in which DWCNTs are aligned in direction of loading. Enhancement in lateral stiffness is observed for the models in which layers are aligned in plane perpendicular direction. Through plane stiffness is improved in vertically aligned DWCNT composite. It is observed that both axial and lateral moduli of composite behave non-linearly with respect to DWCNT volume fraction. This is because of the effect of agglomeration, due to the higher content of DWCNT in the composite. The proposed simulation is based on the experimentally adopted alignment of carbon nanotubes. DWCNT based composites with specific properties along various directions can be designed by controlling the volume fractions and alignment of the DWCNT sheets.

  10. 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.…

  11. RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis.

    PubMed

    Navarro, Elisabeth; Fabrègue, Olivier; Scorretti, Riccardo; Reboulet, Jérémy; Simonet, Pascal; Dawson, Lorna; Demanèche, Sandrine

    2015-12-01

    Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.

  12. RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis.

    PubMed

    Navarro, Elisabeth; Fabrègue, Olivier; Scorretti, Riccardo; Reboulet, Jérémy; Simonet, Pascal; Dawson, Lorna; Demanèche, Sandrine

    2015-12-01

    Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips. PMID:26651514

  13. Alignment-independent technique for 3D QSAR analysis.

    PubMed

    Wilkes, Jon G; Stoyanova-Slavova, Iva B; Buzatu, Dan A

    2016-04-01

    Molecular biochemistry is controlled by 3D phenomena but structure-activity models based on 3D descriptors are infrequently used for large data sets because of the computational overhead for determining molecular conformations. A diverse dataset of 146 androgen receptor binders was used to investigate how different methods for defining molecular conformations affect the performance of 3D-quantitative spectral data activity relationship models. Molecular conformations tested: (1) global minimum of molecules' potential energy surface; (2) alignment-to-templates using equal electronic and steric force field contributions; (3) alignment using contributions "Best-for-Each" template; (4) non-energy optimized, non-aligned (2D > 3D). Aggregate predictions from models were compared. Highest average coefficients of determination ranged from R Test (2) = 0.56 to 0.61. The best model using 2D > 3D (imported directly from ChemSpider) produced R Test (2) = 0.61. It was superior to energy-minimized and conformation-aligned models and was achieved in only 3-7 % of the time required using the other conformation strategies. Predictions averaged from models built on different conformations achieved a consensus R Test (2) = 0.65. The best 2D > 3D model was analyzed for underlying structure-activity relationships. For the compound strongest binding to the androgen receptor, 10 substructural features contributing to binding were flagged. Utility of 2D > 3D was compared for two other activity endpoints, each modeling a medium sized data set. Results suggested that large scale, accurate predictions using 2D > 3D SDAR descriptors may be produced for interactions involving endocrine system nuclear receptors and other data sets in which strongest activities are produced by fairly inflexible substrates.

  14. PROCESSING AND ANALYSIS OF THE MEASURED ALIGNMENT ERRORS FOR RHIC.

    SciTech Connect

    PILAT,F.; HEMMER,M.; PTITSIN,V.; TEPIKIAN,S.; TRBOJEVIC,D.

    1999-03-29

    All elements of the Relativistic Heavy Ion Collider (RHIC) have been installed in ideal survey locations, which are defined as the optimum locations of the fiducials with respect to the positions generated by the design. The alignment process included the presurvey of all elements which could affect the beams. During this procedure a special attention was paid to the precise determination of the quadrupole centers as well as the roll angles of the quadrupoles and dipoles. After installation the machine has been surveyed and the resulting as-built measured position of the fiducials have been stored and structured in the survey database. We describe how the alignment errors, inferred by comparison of ideal and as-built data, have been processed and analyzed by including them in the RHIC modeling software. The RHIC model, which also includes individual measured errors for all magnets in the machine and is automatically generated from databases, allows the study of the impact of the measured alignment errors on the machine.

  15. Linac Alignment Algorithm: Analysis on 1-to-1 Steering

    SciTech Connect

    Sun, Yipeng; Adolphsen, Chris; /SLAC

    2011-08-19

    In a linear accelerator, it is important to achieve a good alignment between all of its components (such as quadrupoles, RF cavities, beam position monitors et al.), in order to better preserve the beam quality during acceleration. After the survey of the main linac components, there are several beam-based alignment (BBA) techniques to be applied, to further optimize the beam trajectory and calculate the corresponding steering magnets strength. Among these techniques the most simple and straightforward one is the one-to-one (1-to-1) steering technique, which steers the beam from quad center to center, and removes the betatron oscillation from quad focusing. For a future linear collider such as the International Linear Collider (ILC), the initial beam emittance is very small in the vertical plane (flat beam with {gamma}{epsilon}{sub y} = 20-40nm), which means the alignment requirement is very tight. In this note, we evaluate the emittance growth with one-to-one correction algorithm employed, both analytically and numerically. Then the ILC main linac accelerator is taken as an example to compare the vertical emittance growth after 1-to-1 steering, both from analytical formulae and multi-particle tracking simulation. It is demonstrated that the estimated emittance growth from the derived formulae agrees well with the results from numerical simulation, with and without acceleration, respectively.

  16. Detail, Face C (rear), showing Interference Analysis System Linear Test ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Detail, Face C (rear), showing Interference Analysis System Linear Test Array mounted at Level 4A - Beale Air Force Base, Perimeter Acquisition Vehicle Entry Phased-Array Warning System, Techinical Equipment Building, End of Spencer Paul Road, north of Warren Shingle Road (14th Street), Marysville, Yuba County, CA

  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. Snacking on Television: A Content Analysis of Adolescents’ Favorite Shows

    PubMed Central

    Larson, Nicole I.; Gollust, Sarah E.; Neumark-Sztainer, Dianne

    2016-01-01

    Introduction Snacking is a complex behavior that may be influenced by entertainment media. Research suggests that snacking and unhealthy foods are commonly shown in programming that targets young audiences, but shows selected for study have been limited. We conducted a content analysis on shows that were named as favorites by adolescents to characterize portrayals of snacking on popular television. Methods A diverse sample of 2,130 adolescents (mean age, 14.3 y) listed 3 favorite television shows in a 2010 school-based survey. Three episodes each of the 25 most popular shows were coded for food-related content, including healthfulness, portion size, screen time use, setting, and social context. We also analyzed the characteristics of characters involved in eating incidents, the show type, and the show rating. We used χ2 tests, binomial tests, and multilevel regression models to compare incidence of snacks versus meals, the characteristics of those involved, and snacking across show characteristics. Results Almost half of food incidents on television shows were snacks. Snacks were significantly more likely than meals to be “mostly unhealthy” (69.3% vs 22.6%, P < .001) and were more likely to include screen time use (25.0% of snacking incidents vs 4.0% of meals, P < .001). Young characters and those coded as being of low socioeconomic status or overweight were overrepresented in snacking incidents. Sitcoms and shows rated for a youth audience were significantly more likely to portray snacking than were shows for adult audiences. Conclusion Media awareness and literacy programs should include foods and snacking behaviors among the issues they address. More healthful portrayals of food and dietary intake in entertainment shows’ content would create a healthier media environment for youth. PMID:27197079

  19. Adaptive removal of show-through artifacts by histogram analysis

    NASA Astrophysics Data System (ADS)

    Hong, Jin-Kyung; Kang, Ki-Min; Kim, Sang-Ho

    2010-01-01

    When scanning a document that is printed on both sides, the image on the reverse can show through with high luminance. We propose an adaptive method of removing show-through artifacts based on histogram analysis. Instead of attempting to measure the physical parameters of the paper and the scanning system, or making multiple scans, we analyze the color distribution to remove unwanted artifacts, using an image of the front of the document alone. First, we accumulate histogram information to find the lightness distribution of pixels in the scanned image. Using this data, we set thresholds on both luminance and chrominance to determine candidate regions of show-through. Finally, we classify these regions into foreground and background of the image on the front of the paper, and show-through from the back. The background and show-through regions become candidates for erasure, and they are adaptively updated as the process proceeds. This approach preserves the chrominance of the image on the front of the papers without introducing artifacts. It does not make the whole image brighter, which is what happens when a fixed threshold is used to remove show-through.

  20. Collective cell traction force analysis on aligned smooth muscle cell sheet between three-dimensional microwalls

    PubMed Central

    Zhang, Ying; Ng, Soon Seng; Wang, Yilei; Feng, Huixing; Chen, Wei Ning; Chan-Park, Mary B.; Li, Chuan; Chan, Vincent

    2014-01-01

    During the past two decades, novel biomaterial scaffold for cell attachment and culture has been developed for applications in tissue engineering, biosensing and regeneration medicine. Tissue engineering of blood vessels remains a challenge owing to the complex three-layer histology involved. In order to engineer functional blood vessels, it is essential to recapitulate the characteristics of vascular smooth muscle cells (SMCs) inside the tunica media, which is known to be critical for vasoconstriction and vasodilation of the circulatory system. Until now, there has been a lack of understanding on the mechanotransduction of the SMC layer during the transformation from viable synthetic to quiescent contractile phenotypes. In this study, microfabricated arrays of discontinuous microwalls coated with fluorescence microbeads were developed to probe the mechanotransduction of the SMC layer. First, the system was exploited for stimulating the formation of a highly aligned orientation of SMCs in native tunica medium. Second, atomic force microscopy in combination with regression analysis was applied to measure the elastic modulus of a polyacrylamide gel layer coated on the discontinuous microwall arrays. Third, the conventional traction force assay for single cell measurement was extended for applications in three-dimensional cell aggregates. Then, the biophysical effects of discontinuous microwalls on the mechanotransduction of the SMC layer undergoing cell alignment were probed. Generally, the cooperative multiple cell–cell and cell–microwall interactions were accessed quantitatively by the newly developed assay with the aid of finite-element modelling. The results show that the traction forces of highly aligned cells lying in the middle region between two opposing microwalls were significantly lower than those lying adjacent to the microwalls. Moreover, the spatial distributions of Von Mises stress during the cell alignment process were dependent on the collective

  1. HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis

    PubMed Central

    Santana-Quintero, Luis; Dingerdissen, Hayley; Thierry-Mieg, Jean; Mazumder, Raja; Simonyan, Vahan

    2014-01-01

    Due to the size of Next-Generation Sequencing data, the computational challenge of sequence alignment has been vast. Inexact alignments can take up to 90% of total CPU time in bioinformatics pipelines. High-performance Integrated Virtual Environment (HIVE), a cloud-based environment optimized for storage and analysis of extra-large data, presents an algorithmic solution: the HIVE-hexagon DNA sequence aligner. HIVE-hexagon implements novel approaches to exploit both characteristics of sequence space and CPU, RAM and Input/Output (I/O) architecture to quickly compute accurate alignments. Key components of HIVE-hexagon include non-redundification and sorting of sequences; floating diagonals of linearized dynamic programming matrices; and consideration of cross-similarity to minimize computations. Availability https://hive.biochemistry.gwu.edu/hive/ PMID:24918764

  2. 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

  3. Hourly analysis of cerebrospinal fluid glucose shows large diurnal fluctuations.

    PubMed

    Verbeek, Marcel M; Leen, Wilhelmina G; Willemsen, Michèl A; Slats, Diane; Claassen, Jurgen A

    2016-05-01

    Cerebrospinal fluid analysis is important in the diagnostics of many neurological disorders. Since the influence of food intake on the cerebrospinal fluid glucose concentration and the cerebrospinal fluid/plasma glucose ratio is largely unknown, we studied fluctuations in these parameters in healthy adult volunteers during a period of 36 h. Our observations show large physiological fluctuations of cerebrospinal fluid glucose and the cerebrospinal fluid/plasma glucose ratio, and their relation to food intake. These findings provide novel insights into the physiology of cerebral processes dependent on glucose levels such as energy formation (e.g. glycolysis), enzymatic reactions (e.g. glycosylation), and non-enzymatic reactions (e.g. advanced endproduct glycation).

  4. Quantitative analysis of gold nanorod alignment after electric field-assisted deposition.

    PubMed

    Ahmed, Waqqar; Kooij, E Stefan; van Silfhout, Arend; Poelsema, Bene

    2009-11-01

    We have studied the alignment of colloidal gold nanorods, deposited from solution onto well-defined substrates in the presence of an AC electric field generated by micrometer spaced electrodes. The field strengths employed in our experiments are sufficiently large to overcome Brownian motion and induce accumulation and alignment of the nanorods in the region near the electrodes with their long axis parallel to the field. However, despite the large fields, we find that the degree of alignment is considerably smaller than what was previously reported for field-induced nanorod alignment in suspension. We show that hydrodynamic interactions and capillary effects during drying, as well as friction of nanorods on the substrate surface, to not play a major role. The limited alignment of nanorods is ascribed to the different experimental configuration and the correspondingly larger density of nanorods. The mutual interactions of nanorods give rise to a disturbance of the local electric field and therewith their orientation. For sufficiently large field strengths, these interactions lead to the formation of nanorod chains that ultimately bridge the electrode gap. Furthermore, for small electrode spacing, the nanorods accumulate on the electrode surface, and the screening of their mutual interactions results into considerably improved alignment. PMID:19719154

  5. Alignment of an acoustic manipulation device with cepstral analysis of electronic impedance data.

    PubMed

    Hughes, D A; Qiu, Y; Démoré, C; Weijer, C J; Cochran, S

    2015-02-01

    Acoustic particle manipulation is an emerging technology that uses ultrasonic standing waves to position objects with pressure gradients and acoustic radiation forces. To produce strong standing waves, the transducer and the reflector must be aligned properly such that they are parallel to each other. This can be a difficult process due to the need to visualise the ultrasound waves and as higher frequencies are introduced, this alignment requires higher accuracy. In this paper, we present a method for aligning acoustic resonators with cepstral analysis. This is a simple signal processing technique that requires only the electrical impedance measurement data of the resonator, which is usually recorded during the fabrication process of the device. We first introduce the mathematical basis of cepstral analysis and then demonstrate and validate it using a computer simulation of an acoustic resonator. Finally, the technique is demonstrated experimentally to create many parallel linear traps for 10 μm fluorescent beads inside an acoustic resonator.

  6. Spin-Orbit Alignment of Exoplanet Systems: Ensemble Analysis Using Asteroseismology

    NASA Astrophysics Data System (ADS)

    Campante, T. L.; Lund, M. N.; Kuszlewicz, J. S.; Davies, G. R.; Chaplin, W. J.; Albrecht, S.; Winn, J. N.; Bedding, T. R.; Benomar, O.; Bossini, D.; Handberg, R.; Santos, A. R. G.; Van Eylen, V.; Basu, S.; Christensen-Dalsgaard, J.; Elsworth, Y. P.; Hekker, S.; Hirano, T.; Huber, D.; Karoff, C.; Kjeldsen, H.; Lundkvist, M. S.; North, T. S. H.; Silva Aguirre, V.; Stello, D.; White, T. R.

    2016-03-01

    The angle ψ between a planet’s orbital axis and the spin axis of its parent star is an important diagnostic of planet formation, migration, and tidal evolution. We seek empirical constraints on ψ by measuring the stellar inclination is via asteroseismology for an ensemble of 25 solar-type hosts observed with NASA’s Kepler satellite. Our results for is are consistent with alignment at the 2σ level for all stars in the sample, meaning that the system surrounding the red-giant star Kepler-56 remains as the only unambiguous misaligned multiple-planet system detected to date. The availability of a measurement of the projected spin-orbit angle λ for two of the systems allows us to estimate ψ. We find that the orbit of the hot Jupiter HAT-P-7b is likely to be retrograde (\\psi =116\\buildrel{\\circ}\\over{.} {4}-14.7+30.2), whereas that of Kepler-25c seems to be well aligned with the stellar spin axis (\\psi =12\\buildrel{\\circ}\\over{.} {6}-11.0+6.7). While the latter result is in apparent contradiction with a statement made previously in the literature that the multi-transiting system Kepler-25 is misaligned, we show that the results are consistent, given the large associated uncertainties. Finally, we perform a hierarchical Bayesian analysis based on the asteroseismic sample in order to recover the underlying distribution of ψ. The ensemble analysis suggests that the directions of the stellar spin and planetary orbital axes are correlated, as conveyed by a tendency of the host stars to display large values of inclination.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  8. Spial: analysis of subtype-specific features in multiple sequence alignments of proteins

    PubMed Central

    Wuster, Arthur; Venkatakrishnan, A. J.; Schertler, Gebhard F. X.; Babu, M. Madan

    2010-01-01

    Motivation: Spial (Specificity in alignments) is a tool for the comparative analysis of two alignments of evolutionarily related sequences that differ in their function, such as two receptor subtypes. It highlights functionally important residues that are either specific to one of the two alignments or conserved across both alignments. It permits visualization of this information in three complementary ways: by colour-coding alignment positions, by sequence logos and optionally by colour-coding the residues of a protein structure provided by the user. This can aid in the detection of residues that are involved in the subtype-specific interaction with a ligand, other proteins or nucleic acids. Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences. Availability: http://www.mrc-lmb.cam.ac.uk/genomes/spial/; supplementary information is available at http://www.mrc-lmb.cam.ac.uk/genomes/spial/help.html Contact: ajv@mrc-lmb.cam.ac.uk PMID:20880955

  9. Descriptive Quantitative Analysis of Rearfoot Alignment Radiographic Parameters.

    PubMed

    Meyr, Andrew J; Wagoner, Matthew R

    2015-01-01

    Although the radiographic parameters of the transverse talocalcaneal angle (tTCA), calcaneocuboid angle (CCA), talar head uncovering (THU), calcaneal inclination angle (CIA), talar declination angle (TDA), lateral talar-first metatarsal angle (lTFA), and lateral talocalcaneal angle (lTCA) form the basis of the preoperative evaluation and procedure selection for pes planovalgus deformity, the so-called normal values of these measurements are not well-established. The objectives of the present study were to retrospectively evaluate the descriptive statistics of these radiographic parameters (tTCA, CCA, THU, CIA, TDA, lTFA, and lTCA) in a large population, and, second, to determine an objective basis for defining "normal" versus "abnormal" measurements. As a secondary outcome, the relationship of these variables to the body mass index was assessed. Anteroposterior and lateral foot radiographs from 250 consecutive patients without a history of previous foot and ankle surgery and/or trauma were evaluated. The results revealed a mean measurement of 24.12°, 13.20°, 74.32%, 16.41°, 26.64°, 8.37°, and 43.41° for the tTCA, CCA, THU, CIA, TDA, lTFA, and lTCA, respectively. These were generally in line with the reported historical normal values. Descriptive statistical analysis demonstrated that the tTCA, THU, and TDA met the standards to be considered normally distributed but that the CCA, CIA, lTFA, and lTCA demonstrated data characteristics of both parametric and nonparametric distributions. Furthermore, only the CIA (R = -0.2428) and lTCA (R = -0.2449) demonstrated substantial correlation with the body mass index. No differentiations in deformity progression were observed when the radiographic parameters were plotted against each other to lead to a quantitative basis for defining "normal" versus "abnormal" measurements. PMID:26002682

  10. Authenticity and TV Shows: A Multidimensional Analysis Perspective

    ERIC Educational Resources Information Center

    Al-Surmi, Mansoor

    2012-01-01

    Television shows, especially soap operas and sitcoms, are usually considered by English as a second language practitioners as a source of authentic spoken conversational materials presumably because they reflect the linguistic features of natural conversation. However, practitioners are faced with the dilemma of how to assess whether such…

  11. Kernel-aligned multi-view canonical correlation analysis for image recognition

    NASA Astrophysics Data System (ADS)

    Su, Shuzhi; Ge, Hongwei; Yuan, Yun-Hao

    2016-09-01

    Existing kernel-based correlation analysis methods mainly adopt a single kernel in each view. However, only a single kernel is usually insufficient to characterize nonlinear distribution information of a view. To solve the problem, we transform each original feature vector into a 2-dimensional feature matrix by means of kernel alignment, and then propose a novel kernel-aligned multi-view canonical correlation analysis (KAMCCA) method on the basis of the feature matrices. Our proposed method can simultaneously employ multiple kernels to better capture the nonlinear distribution information of each view, so that correlation features learned by KAMCCA can have well discriminating power in real-world image recognition. Extensive experiments are designed on five real-world image datasets, including NIR face images, thermal face images, visible face images, handwritten digit images, and object images. Promising experimental results on the datasets have manifested the effectiveness of our proposed method.

  12. CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences.

    PubMed

    Afonnikov, Dmitry A; Kolchanov, Nikolay A

    2004-07-01

    Recent results suggest that during evolution certain substitutions at protein sites may occur in a coordinated manner due to interactions between amino acid residues. Information on these coordinated substitutions may be useful for analysis of protein structure and function. CRASP is an Internet-available software tool for the detection and analysis of coordinated substitutions in multiple alignments of protein sequences. The approach is based on estimation of the correlation coefficient between the values of a physicochemical parameter at a pair of positions of sequence alignment. The program enables the user to detect and analyze pairwise relationships between amino acid substitutions at protein sequence positions, estimate the contribution of the coordinated substitutions to the evolutionary invariance or variability in integral protein physicochemical characteristics such as the net charge of protein residues and hydrophobic core volume. The CRASP program is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/.

  13. Analysis of cellular adhesion on superhydrophobic and superhydrophilic vertically aligned carbon nanotube scaffolds.

    PubMed

    Machado, M M; Lobo, A O; Marciano, F R; Corat, E J; Corat, M A F

    2015-03-01

    We analyzed GFP cells after 24h cultivated on superhydrophilic vertically aligned carbon nanotube scaffolds. We produced two different densities of VACNT scaffolds on Ti using Ni or Fe catalysts. A simple and fast oxygen plasma treatment promoted the superhydrophilicity of them. We used five different substrates, such as: as-grown VACNT produced using Ni as catalyst (Ni), as-grown VACNT produced using Fe as catalyst (Fe), VACNT-O produced using Ni as catalyst (NiO), VACNT-O produced using Fe as catalyst (FeO) and Ti (control). The 4',6-diamidino-2-phenylindole reagent nuclei stained the adherent cells cultivated on five different analyzed scaffolds. We used fluorescence microscopy for image collect, ImageJ® to count adhered cell and GraphPad Prism 5® for statistical analysis. We demonstrated in crescent order: Fe, Ni, NiO, FeO and Ti scaffolds that had an improved cellular adhesion. Oxygen treatment associated to high VACNT density (group FeO) presented significantly superior cell adhesion up to 24h. However, they do not show significant differences compared with Ti substrates (control). We demonstrated that all the analyzed substrates were nontoxic. Also, we proposed that the density and hydrophilicity influenced the cell adhesion behavior. PMID:25579935

  14. Multi-resolution Shape Analysis via Non-Euclidean Wavelets: Applications to Mesh Segmentation and Surface Alignment Problems.

    PubMed

    Kim, Won Hwa; Chung, Moo K; Singh, Vikas

    2013-01-01

    The analysis of 3-D shape meshes is a fundamental problem in computer vision, graphics, and medical imaging. Frequently, the needs of the application require that our analysis take a multi-resolution view of the shape's local and global topology, and that the solution is consistent across multiple scales. Unfortunately, the preferred mathematical construct which offers this behavior in classical image/signal processing, Wavelets, is no longer applicable in this general setting (data with non-uniform topology). In particular, the traditional definition does not allow writing out an expansion for graphs that do not correspond to the uniformly sampled lattice (e.g., images). In this paper, we adapt recent results in harmonic analysis, to derive Non-Euclidean Wavelets based algorithms for a range of shape analysis problems in vision and medical imaging. We show how descriptors derived from the dual domain representation offer native multi-resolution behavior for characterizing local/global topology around vertices. With only minor modifications, the framework yields a method for extracting interest/key points from shapes, a surprisingly simple algorithm for 3-D shape segmentation (competitive with state of the art), and a method for surface alignment (without landmarks). We give an extensive set of comparison results on a large shape segmentation benchmark and derive a uniqueness theorem for the surface alignment problem.

  15. Software tool for the analysis and visualization of whole genome alignments

    2011-08-01

    GenomeVISTA is a tool which performs and displays pairwise and multiple whole genome DNA alignments. The tools provides a graphical user interface by which users can navigate alignments and multiple levels of resolution and get imformation about individual aligned regions. Users can load their own sequences into GenomeVISTA or view pre-computed alignments for genomes in the VISTA database.

  16. Using participative inquiry in usability analysis to align a development team's mental model with its users' needs

    NASA Technical Reports Server (NTRS)

    Kneifel, A. A.; Guerrero, C.

    2003-01-01

    In this web site usability case study, two methods of participative inquiry are used to align a development team's objectives with their users' needs and to promote the team awareness of the benefit of qualitative usability analysis.

  17. Survey and alignment analysis for the ALS storage ring using computer spreadsheets

    SciTech Connect

    Keller, R.

    1993-07-01

    The general survey and alignment concept for the ALS is based on a network of fixed, three-dimensional monuments installed in the building floor, to which all accelerator component positions are referred. The survey of these monuments is performed separately for horizontal and vertical coordinates, following the scheme imposed by the code PC-GEONET that is used for monument data analysis. For most of the accelerator objects the tasks of data acquisition, bundling, and transformations from observation-station into object coordinate-systems are being handled by the commercial software package ECDS rather than by PC-GEONET. This choice had to be made because no instrument stands are presently available at LBL that can be placed exactly over monuments and are high enough to permit observing the fiducials of installed magnets from above. Theodolites only are used with ECDS as observation instruments, and absolute scaling has to be provided by observing some object of precisely known length. To create ideal data and compute alignment values for all accelerator components, spreadsheets were developed by the author using the application EXCEL for Macintosh computers. Choice of a spreadsheet method rather than conventional programming techniques proved very convenient when in the course of this work the sheets had to be created and progressively modified under severe time pressure to include new effects and help redefine the observation procedures. With spreadsheets, varying input data formats coming from the survey crew could be easily accommodated, and adding numerous consistency checks as well as generating additional ideal data for special alignment tasks was possible with comparatively little effort. Dedicated spreadsheets were created for each of the 12 curved sectors of the storage ring. In this paper, the main features of the spreadsheets are presented, and the alignment results for lattice and corrector magnets are listed and discussed.

  18. Dynamic finite element analysis of the crack-inclusion interaction in aligned CNF composites under impact loading conditions

    NASA Astrophysics Data System (ADS)

    Ting, Huat Tung

    The interaction between a crack and an inclusion of microfiber in an aligned carbon nanofiber (CNF) toughened composite under impact loading conditions was studied by using dynamic finite element analysis (FEA). The nanocomposite material used in this study was T300/Epon 862 enhanced with aligned carbon nanofibers (CNFs). The dynamic stress intensity factors (DSIFs) were evaluated to describe the dynamic fracture behavior of the fracture model. In this study, a numerical homogenization model using FEA was first employed to determine the effective material properties of the equivalent matrix material of Epon 862 and aligned CNFs. The effects of T300 microfiber inclusion eccentricity and CNF alignment angle on the DSIFs were examined in this study. The displacement extrapolation method for monoclinic materials was utilized to calculate the DSIFs. The numerical results demonstrated a mechanism known as "crack-tip shielding" and demonstrated that the CNF alignment angle has an impact on the DSIFs.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  20. Observability analysis of inertial navigation systems during in-flight alignment

    NASA Technical Reports Server (NTRS)

    Bar-Itzhack, I. Y.; Goshen-Meskin, D.

    1988-01-01

    In this work the observability of an Inertial Navigation System (INS) during In-Flight Alignment (IFA) is investigated. A systematic approach to the observability analysis of a piece-wise constant system is presented and its use is justified mathematically. As a tool for the investigation a Stepped Observability Matrix (SOM) is constructed and a corresponding Stepped Space is defined. The INS error model is transformed into the Stepped Space during a specially chosen IFA trajectory and a full observability is carried out. The results of the mathematical analysis are checked against the results of covariance simulation and a full agreement is found between the two. Finally, the practical implications of this analysis are outlined.

  1. ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.

    PubMed

    Schwarz, Roland F; Tamuri, Asif U; Kultys, Marek; King, James; Godwin, James; Florescu, Ana M; Schultz, Jörg; Goldman, Nick

    2016-05-01

    Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles). PMID:26819408

  2. ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.

    PubMed

    Schwarz, Roland F; Tamuri, Asif U; Kultys, Marek; King, James; Godwin, James; Florescu, Ana M; Schultz, Jörg; Goldman, Nick

    2016-05-01

    Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles).

  3. ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments

    PubMed Central

    Schwarz, Roland F.; Tamuri, Asif U.; Kultys, Marek; King, James; Godwin, James; Florescu, Ana M.; Schultz, Jörg; Goldman, Nick

    2016-01-01

    Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles). PMID:26819408

  4. Comparison and analysis of linear alignments from Landsat imagery of diverse geologic terrane

    SciTech Connect

    Frederking, R.L.; Allenbach, R.T.; Jackson, R.B.; Keefer, W.D.; Motamedi, A.R.; Von Der Heyde, W.S.; Wingo, R.D.

    1985-01-01

    Geometric alignments referred to as linears, linear features or lineaments are routinely observed on Landsat imagery. Alignments that cannot be accounted for by cultural, known geologic or other recognized sources are classed as speculative and of dubious geologic significance. These features may in fact be imaginary. Speculative alignments are however, important to exploration because of their frequent association with known hydrocarbon accumulations and/or areas of mineralization. Data pertaining to speculative linear alignments in diverse geologic terrane have been obtained. Alignment frequency rose diagrams are prepared for each area and statistical profiles are developed. Replication of linear alignments suggest that these features are real elements of the imagery and not imaginary lines. Observed orientation modal frequencies are consistent with alignment trends of known structural features in the different areas. Variation in spatial density of alignments appears to be related to lithologic factors.

  5. Image alignment

    SciTech Connect

    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.

  6. 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…

  7. NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles

    PubMed Central

    Leggett, Richard M.; Heavens, Darren; Caccamo, Mario; Clark, Matthew D.; Davey, Robert P.

    2016-01-01

    Motivation: The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to provide comprehensive alignment-based quality control and error profile analysis—something that is extremely important given the speed with which the platform is evolving. Results: NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF report including error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it is easily extensible to include others. Availability and implementation: NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https://github.com/TGAC/NanoOK. A VirtualBox VM containing all dependencies and the DH10B read set used in this article is available from http://opendata.tgac.ac.uk/nanook/. A Docker image is also available from Docker Hub—see program documentation https://documentation.tgac.ac.uk/display/NANOOK. Contact: richard.leggett@tgac.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26382197

  8. ANALYSIS OF SPIN-ORBIT ALIGNMENT IN THE WASP-32, WASP-38, AND HAT-P-27/WASP-40 SYSTEMS

    SciTech Connect

    Brown, D. J. A.; Collier Cameron, A.; Enoch, B.; Miller, G. R. M.; Diaz, R. F.; Doyle, A. P.; Smalley, B.; Anderson, D. R.; Hellier, C.; Maxted, P. F. L.; Gillon, M.; Lendl, M.; Triaud, A. H. M. J.; Queloz, D.; Pollacco, D.; Boisse, I.; Hebrard, G.

    2012-12-01

    We present measurements of the spin-orbit alignment angle, {lambda}, for the hot Jupiter systems WASP-32, WASP-38, and HAT-P-27/WASP-40, based on data obtained using the HARPS spectrograph. We analyze the Rossiter-McLaughlin effect for all three systems and also carry out Doppler tomography for WASP-32 and WASP-38. We find that WASP-32 (T {sub eff} = 6140{sup +90} {sub -100} K) is aligned, with an alignment angle of {lambda} = 10.{sup 0}5{sup +6.4} {sub -6.5} obtained through tomography, and that WASP-38 (T {sub eff} = 6180{sup +40} {sub -60} K) is also aligned, with tomographic analysis yielding {lambda} = 7.{sup 0}5{sup +4.7} {sub -6.1}. The latter result provides an order-of-magnitude improvement in the uncertainty in {lambda} compared to the previous analysis of Simpson et al. We are only able to loosely constrain the angle for HAT-P-27/WASP-40 (T{sub eff} = 5190{sup +160} {sub -170} K) to {lambda} = 24.{sup 0}2{sup +76.0}{sub -44.5}, owing to the poor signal-to-noise ratio of our data. We consider this result a non-detection under a slightly updated version of the alignment test of Brown et al. We place our results in the context of the full sample of spin-orbit alignment measurements, finding that they provide further support for previously established trends.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  11. Photoluminescence analysis of self induced planer alignment in azo dye dispersed nematic liquid crystal complex

    SciTech Connect

    Kumar, Rishi Sood, Srishti Raina, K. K.

    2014-04-24

    We have developed azo dye doped nematic liquid crystal complex for advanced photonic liquid crystal display technology aspects. Disperse orange azo dye self introduced planer alignment in the nematic liquid crystal without any surface anchoring treatment. Planer alignment was characterized by optical polarizing microscopy. The electro-optical switching response of dye disperse planer aligned nematic cell was investigated as a function of applied voltage with the help of photoluminescence spectrophotometer for the tuning of photoluminescence contrast.

  12. A systematic review and meta-analysis of patient-specific instrumentation for improving alignment of the components in total knee replacement.

    PubMed

    Thienpont, E; Schwab, P E; Fennema, P

    2014-08-01

    We conducted a meta-analysis, including randomised controlled trials (RCTs) and cohort studies, to examine the effect of patient-specific instruments (PSI) on radiological outcomes after total knee replacement (TKR) including: mechanical axis alignment and malalignment of the femoral and tibial components in the coronal, sagittal and axial planes, at a threshold of > 3º from neutral. Relative risks (RR) for malalignment were determined for all studies and for RCTs and cohort studies separately. Of 325 studies initially identified, 16 met the eligibility criteria, including eight RCTs and eight cohort studies. There was no significant difference in the likelihood of mechanical axis malalignment with PSI versus conventional TKR across all studies (RR = 0.84, p = 0.304), in the RCTs (RR = 1.14, p = 0.445) or in the cohort studies (RR = 0.70, p = 0.289). The results for the alignment of the tibial component were significantly worse using PSI TKR than conventional TKR in the coronal and sagittal planes (RR = 1.75, p = 0.028; and RR = 1.34, p = 0.019, respectively, on pooled analysis). PSI TKR showed a significant advantage over conventional TKR for alignment of the femoral component in the coronal plane (RR = 0.65, p = 0.028 on pooled analysis), but not in the sagittal plane (RR = 1.12, p = 0.437). Axial alignment of the tibial (p = 0.460) and femoral components (p = 0.127) was not significantly different. We conclude that PSI does not improve the accuracy of alignment of the components in TKR compared with conventional instrumentation.

  13. SCDU Testbed Automated In-Situ Alignment, Data Acquisition and Analysis

    NASA Technical Reports Server (NTRS)

    Werne, Thomas A.; Wehmeier, Udo J.; Wu, Janet P.; An, Xin; Goullioud, Renaud; Nemati, Bijan; Shao, Michael; Shen, Tsae-Pyng J.; Wang, Xu; Weilert, Mark A.; Zhai, Chengxing

    2010-01-01

    In the course of fulfilling its mandate, the Spectral Calibration Development Unit (SCDU) testbed for SIM-Lite produces copious amounts of raw data. To effectively spend time attempting to understand the science driving the data, the team devised computerized automations to limit the time spent bringing the testbed to a healthy state and commanding it, and instead focus on analyzing the processed results. We developed a multi-layered scripting language that emphasized the scientific experiments we conducted, which drastically shortened our experiment scripts, improved their readability, and all-but-eliminated testbed operator errors. In addition to scientific experiment functions, we also developed a set of automated alignments that bring the testbed up to a well-aligned state with little more than the push of a button. These scripts were written in the scripting language, and in Matlab via an interface library, allowing all members of the team to augment the existing scripting language with complex analysis scripts. To keep track of these results, we created an easily-parseable state log in which we logged both the state of the testbed and relevant metadata. Finally, we designed a distributed processing system that allowed us to farm lengthy analyses to a collection of client computers which reported their results in a central log. Since these logs were parseable, we wrote query scripts that gave us an effortless way to compare results collected under different conditions. This paper serves as a case-study, detailing the motivating requirements for the decisions we made and explaining the implementation process.

  14. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

    PubMed

    Kumar, Sudhir; Tamura, Koichiro; Nei, Masatoshi

    2004-06-01

    With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

  15. Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species.

    PubMed

    Guilliams, Martin; Dutertre, Charles-Antoine; Scott, Charlotte L; McGovern, Naomi; Sichien, Dorine; Chakarov, Svetoslav; Van Gassen, Sofie; Chen, Jinmiao; Poidinger, Michael; De Prijck, Sofie; Tavernier, Simon J; Low, Ivy; Irac, Sergio Erdal; Mattar, Citra Nurfarah; Sumatoh, Hermi Rizal; Low, Gillian Hui Ling; Chung, Tam John Kit; Chan, Dedrick Kok Hong; Tan, Ker Kan; Hon, Tony Lim Kiat; Fossum, Even; Bogen, Bjarne; Choolani, Mahesh; Chan, Jerry Kok Yen; Larbi, Anis; Luche, Hervé; Henri, Sandrine; Saeys, Yvan; Newell, Evan William; Lambrecht, Bart N; Malissen, Bernard; Ginhoux, Florent

    2016-09-20

    Dendritic cells (DCs) are professional antigen-presenting cells that hold great therapeutic potential. Multiple DC subsets have been described, and it remains challenging to align them across tissues and species to analyze their function in the absence of macrophage contamination. Here, we provide and validate a universal toolbox for the automated identification of DCs through unsupervised analysis of conventional flow cytometry and mass cytometry data obtained from multiple mouse, macaque, and human tissues. The use of a minimal set of lineage-imprinted markers was sufficient to subdivide DCs into conventional type 1 (cDC1s), conventional type 2 (cDC2s), and plasmacytoid DCs (pDCs) across tissues and species. This way, a large number of additional markers can still be used to further characterize the heterogeneity of DCs across tissues and during inflammation. This framework represents the way forward to a universal, high-throughput, and standardized analysis of DC populations from mutant mice and human patients. PMID:27637149

  16. 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…

  17. Alignment Content Analysis of TIMSS and PISA Mathematics and Science Assessments Using the Surveys of Enacted Curriculum Methodology

    ERIC Educational Resources Information Center

    Council of Chief State School Officers, 2009

    2009-01-01

    In Fall 2008, the Council of Chief State School Officers (CCSSO) conducted an alignment content analysis of the 2007 TIMSS Mathematics and Science education assessments for students at grades 4 and 8 and the 2006 PISA Mathematics and Science Literacy assessments for students at age 15 (i.e., TIMSS--Trends in Mathematics and Science Study,…

  18. Angular and local spectroscopic analysis to probe the vertical alignment of N-doped well-separated carbon nanotubes.

    PubMed

    Minea, T M; Bouchet-Fabre, B; Lazar, S; Point, S; Zandbergen, H W

    2006-08-17

    Vertically aligned well-separated N-doped multiwalled carbon nanotubes (CNTs) were grown on a silicon substrate by plasma enhanced chemical vapor deposition (PECVD). Angular near-edge X-ray absorption fine structure (NEXAFS) was used to investigate the vertical alignment of as-grown CNTs. In addition, both individual tubes and tube bundles were characterized by high-resolution electron energy loss spectroscopy (HREELS). Simultaneous analysis of both spectroscopic techniques provides information on chemical environment, orbital orientation between carbon and heteroatoms, and local curvature effects. We demonstrate the utility of NEXAFS as an in situ probe of CNTs. PMID:16898707

  19. PROMALS web server for accurate multiple protein sequence alignments.

    PubMed

    Pei, Jimin; Kim, Bong-Hyun; Tang, Ming; Grishin, Nick V

    2007-07-01

    Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS shows higher alignment accuracy than other advanced methods, such as MUMMALS, ProbCons, MAFFT and SPEM. The PROMALS web server takes FASTA format protein sequences as input. The output includes a colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS web server is available at: http://prodata.swmed.edu/promals/ PMID:17452345

  20. RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments.

    PubMed

    Schnattinger, Thomas; Schöning, Uwe; Marchfelder, Anita; Kestler, Hans A

    2013-12-01

    Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions, which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto, which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set.

  1. 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

  2. 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.

  3. Bridging the continuum: Analysis of the alignment of undergraduate and postgraduate accreditation standards.

    PubMed

    Andrew, Susan E; Oswald, Anna; Stobart, Kent

    2014-09-01

    Several influential national/international bodies including The Bologna Accord, The Carnegie Foundation and The Future of Medical Education in Canada (FMEC) have called for increased coordination across the medical education continuum. FMEC recognizes accreditation as a "powerful lever" and encourages the alignment of undergraduate and postgraduate standards. The Carnegie Foundation includes a similar call for the creation of a more coherent accreditation system. As a first step, using the Canadian context, we present a methodological approach that assesses the example of how well LCME/CACMS undergraduate accreditation standards align with the Royal College of Physician and Surgeons of Canada (RCPSC) postgraduate training standards. We analyzed how closely the 132 LCME/CACMS Medical School accreditation standards aligned with the 155 post-graduate standards from the RCPSC accreditation General Standards (A and B). This comparative evaluation demonstrates that the standards do not align closely. Gaps, redundancies and key differences are highlighted. These results are the first step in understanding how accreditation needs to be adapted and re-aligned across the education continuum to provide consistent and coordinated training and these methods could easily be applied to other contexts and jurisdictions.

  4. Prevalence and risk factor analysis of lower extremity abnormal alignment characteristics among rice farmers

    PubMed Central

    Karukunchit, Usa; Puntumetakul, Rungthip; Swangnetr, Manida; Boucaut, Rose

    2015-01-01

    Background Rice farming activities involve prolonged manual work and human–machine interaction. Prolonged farming risk-exposure may result in lower limb malalignment. This malalignment may increase the risk of lower extremity injury and physical disabilities. However, the prevalence and factors associated with lower extremity malalignment have not yet been reported. This study aimed to investigate the prevalence and risk factors of lower extremity malalignment among rice farmers. Methods A cross-sectional survey was conducted with 249 rice farmers. Lower extremity alignment assessment included: pelvic tilt angle, limb length equality, femoral torsion, quadriceps (Q) angle, tibiofemoral angle, genu recurvatum, rearfoot angle, and medial longitudinal arch angle. Descriptive statistics were used to analyze participant characteristics and prevalence of lower extremity malalignment. Logistic regression analysis was used to identify risk factors. Results The highest prevalence of lower extremity malalignment was foot pronation (36.14%), followed by the abnormal Q angle (34.94%), tibiofemoral angle (31.73%), pelvic tilt angle (30.52%), femoral antetorsion (28.11%), limb length inequality (22.49%), tibial torsion (21.29%), and genu recurvatum (11.24%). In females, the risk factors were abnormal Q angle, tibiofemoral angle, and genu recurvatum. Being overweight was a risk factor for abnormal pelvic tilt angle, Q angle, and tibiofemoral angle. Age was a risk factor for limb length inequality. Years of farming were a major risk factor for abnormal Q angle, tibiofemoral angle, and foot malalignment. Conclusion Prevalence of lower extremity malalignment was reported in this study. Female sex, being overweight, and years of farming were major risk factors for lower extremity malalignment. Lower extremity screening should assist in the identification of foot and knee malalignment in rice farmers. This may then lead to early prevention of musculoskeletal disorders arising from

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

    PubMed

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

    2012-09-01

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

  6. Measurement error analysis of the 3D four-wheel aligner

    NASA Astrophysics Data System (ADS)

    Zhao, Qiancheng; Yang, Tianlong; Huang, Dongzhao; Ding, Xun

    2013-10-01

    Positioning parameters of four-wheel have significant effects on maneuverabilities, securities and energy saving abilities of automobiles. Aiming at this issue, the error factors of 3D four-wheel aligner, which exist in extracting image feature points, calibrating internal and exeternal parameters of cameras, calculating positional parameters and measuring target pose, are analyzed respectively based on the elaborations of structure and measurement principle of 3D four-wheel aligner, as well as toe-in and camber of four-wheel, kingpin inclination and caster, and other major positional parameters. After that, some technical solutions are proposed for reducing the above error factors, and on this basis, a new type of aligner is developed and marketed, it's highly estimated among customers because the technical indicators meet requirements well.

  7. Alignability of Optical Interconnects

    NASA Astrophysics Data System (ADS)

    Beech, Russell Scott

    With the continuing drive towards higher speed, density, and functionality in electronics, electrical interconnects become inadequate. Due to optics' high speed and bandwidth, freedom from capacitive loading effects, and freedom from crosstalk, optical interconnects can meet more stringent interconnect requirements. But, an optical interconnect requires additional components, such as an optical source and detector, lenses, holographic elements, etc. Fabrication and assembly of an optical interconnect requires precise alignment of these components. The successful development and deployment of optical interconnects depend on how easily the interconnect components can be aligned and/or how tolerant the interconnect is to misalignments. In this thesis, a method of quantitatively specifying the relative difficulty of properly aligning an optical interconnect is described. Ways of using this theory of alignment to obtain design and packaging guidelines for optical interconnects are examined. The measure of the ease with which an optical interconnect can be aligned, called the alignability, uses the efficiency of power transfer as a measure of alignment quality. The alignability is related to interconnect package design through the overall cost measure, which depends upon various physical parameters of the interconnect, such as the cost of the components and the time required for fabrication and alignment. Through a mutual dependence on detector size, the relationship between an interconnect's alignability and its bandwidth, signal-to-noise ratio, and bit-error -rate is examined. The results indicate that a range of device sizes exists for which given performance threshold values are satisfied. Next, the alignability of integrated planar-optic backplanes is analyzed in detail. The resulting data show that the alignability can be optimized by varying the substrate thickness or the angle of reflection. By including the effects of crosstalk, in a multi-channel backplane, the

  8. Conoscopic analysis of electric field driven planar aligned nematic liquid crystal.

    PubMed

    Ranjini, Radhakrishnan; Matham, Murukeshan Vadakke; Nguyen, Nam-Trung

    2014-05-01

    This paper illustrates the conoscopic observation of a molecular reconstruction occurring across a nematic liquid crystal (NLC) medium in the presence of an external electric field. Conoscopy is an optical interferometric method, employed to determine the orientation of an optic axis in uniaxial crystals. Here a planar aligned NLC medium is used, and the topological changes with respect to various applied voltages are monitored simultaneously. Homogenous planar alignment is obtained by providing suitable surface treatments to the ITO coated cell walls. The variation in the conoscopic interferometric patterns clearly demonstrates the transition from planar to homeotropic state through various intermediate states. PMID:24921859

  9. An Analysis of Gateway Technical College Instructors' Opinions on Secondary and Postsecondary Program Alignment

    ERIC Educational Resources Information Center

    Albrecht, Bryan D.

    2011-01-01

    The purpose of this study was to determine what opinions Gateway Technical College instructors had toward secondary and postsecondary program alignment. Student transition is critical to supporting the mission and vision of Gateway Technical College. The impetus for this study was twofold. First, the quality improvement process established at…

  10. Microwave systems analysis, solar power satellite. [alignment of the antenna array

    NASA Technical Reports Server (NTRS)

    1979-01-01

    Various alternative active approaches to achieving aand maintaining flatness for the microwave power transmission system (MPTS) were studied. A baseline active alignment scheme was developed which includes subarray attachment mechanisms, height and tilting adjustments, service corridors, a rotating laser beam reference system, monopulse pointing techniques, and the design of a beam-centering photoconductive sensor.

  11. Intrinsic alignments of galaxies in the MassiveBlack-II simulation: analysis of two-point statistics

    NASA Astrophysics Data System (ADS)

    Tenneti, Ananth; Singh, Sukhdeep; Mandelbaum, Rachel; Matteo, Tiziana Di; Feng, Yu; Khandai, Nishikanta

    2015-04-01

    The intrinsic alignment of galaxies with the large-scale density field is an important astrophysical contaminant in upcoming weak lensing surveys. We present detailed measurements of the galaxy intrinsic alignments and associated ellipticity-direction (ED) and projected shape (wg+) correlation functions for galaxies in the cosmological hydrodynamic MassiveBlack-II simulation. We carefully assess the effects on galaxy shapes, misalignment of the stellar component with the dark matter shape and two-point statistics of iterative weighted (by mass and luminosity) definitions of the (reduced and unreduced) inertia tensor. We find that iterative procedures must be adopted for a reliable measurement of the reduced tensor but that luminosity versus mass weighting has only negligible effects. Both ED and wg+ correlations increase in amplitude with subhalo mass (in the range of 1010-6.0 × 1014 h-1 M⊙), with a weak redshift dependence (from z = 1 to 0.06) at fixed mass. At z ˜ 0.3, we predict a wg+ that is in reasonable agreement with Sloan Digital Sky Survey luminous red galaxy measurements and that decreases in amplitude by a factor of ˜5-18 for galaxies in the Large Synoptic Survey Telescope survey. We also compared the intrinsic alignments of centrals and satellites, with clear detection of satellite radial alignments within their host haloes. Finally, we show that wg+ (using subhaloes as tracers of density) and wδ+ (using dark matter density) predictions from the simulations agree with that of non-linear alignment (NLA) models at scales where the two-halo term dominates in the correlations (and tabulate associated NLA fitting parameters). The one-halo term induces a scale-dependent bias at small scales which is not modelled in the NLA model.

  12. Intrinsic alignments of galaxies in the MassiveBlack-II simulation: Analysis of two-point statistics

    DOE PAGES

    Tenneti, Ananth; Singh, Sukhdeep; Mandelbaum, Rachel; Matteo, Tiziana Di; Feng, Yu; Khandai, Nishikanta

    2015-03-11

    The intrinsic alignment of galaxies with the large-scale density field in an important astrophysical contaminant in upcoming weak lensing surveys. We present detailed measurements of the galaxy intrinsic alignments and associated ellipticity-direction (ED) and projected shape (wg₊) correlation functions for galaxies in the cosmological hydrodynamic MassiveBlack-II (MB-II) simulation. We carefully assess the effects on galaxy shapes, misalignment of the stellar component with the dark matter shape and two-point statistics of iterative weighted (by mass and luminosity) definitions of the (reduced and unreduced) inertia tensor. We find that iterative procedures must be adopted for a reliable measurement of the reduced tensormore » but that luminosity versus mass weighting has only negligible effects. Both ED and wg₊ correlations increase in amplitude with subhalo mass (in the range of 10¹⁰ – 6.0 X 10¹⁴h⁻¹ M⊙), with a weak redshift dependence (from z = 1 to z = 0.06) at fixed mass. At z ~ 0.3, we predict a wg₊ that is in reasonable agreement with SDSS LRG measurements and that decreases in amplitude by a factor of ~ 5–18 for galaxies in the LSST survey. We also compared the intrinsic alignment of centrals and satellites, with clear detection of satellite radial alignments within the host halos. Finally, we show that wg₊ (using subhalos as tracers of density and wδ (using dark matter density) predictions from the simulations agree with that of non-linear alignment models (NLA) at scales where the 2-halo term dominates in the correlations (and tabulate associated NLA fitting parameters). The 1-halo term induces a scale dependent bias at small scales which is not modeled in the NLA model.« less

  13. Intrinsic alignments of galaxies in the MassiveBlack-II simulation: Analysis of two-point statistics

    SciTech Connect

    Tenneti, Ananth; Singh, Sukhdeep; Mandelbaum, Rachel; Matteo, Tiziana Di; Feng, Yu; Khandai, Nishikanta

    2015-03-11

    The intrinsic alignment of galaxies with the large-scale density field in an important astrophysical contaminant in upcoming weak lensing surveys. We present detailed measurements of the galaxy intrinsic alignments and associated ellipticity-direction (ED) and projected shape (wg₊) correlation functions for galaxies in the cosmological hydrodynamic MassiveBlack-II (MB-II) simulation. We carefully assess the effects on galaxy shapes, misalignment of the stellar component with the dark matter shape and two-point statistics of iterative weighted (by mass and luminosity) definitions of the (reduced and unreduced) inertia tensor. We find that iterative procedures must be adopted for a reliable measurement of the reduced tensor but that luminosity versus mass weighting has only negligible effects. Both ED and wg₊ correlations increase in amplitude with subhalo mass (in the range of 10¹⁰ – 6.0 X 10¹⁴h⁻¹ M), with a weak redshift dependence (from z = 1 to z = 0.06) at fixed mass. At z ~ 0.3, we predict a wg₊ that is in reasonable agreement with SDSS LRG measurements and that decreases in amplitude by a factor of ~ 5–18 for galaxies in the LSST survey. We also compared the intrinsic alignment of centrals and satellites, with clear detection of satellite radial alignments within the host halos. Finally, we show that wg₊ (using subhalos as tracers of density and wδ (using dark matter density) predictions from the simulations agree with that of non-linear alignment models (NLA) at scales where the 2-halo term dominates in the correlations (and tabulate associated NLA fitting parameters). The 1-halo term induces a scale dependent bias at small scales which is not modeled in the NLA model.

  14. A phylogenetic analysis of the brassicales clade based on an alignment-free sequence comparison method.

    PubMed

    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.

  15. 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.

  16. GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis

    PubMed Central

    Heltshe, Sonya L.; Hayden, Hillary S.; Radey, Matthew C.; Weiss, Eli J.; Damman, Christopher J.; Zisman, Timothy L.; Suskind, David L.; Miller, Samuel I.

    2016-01-01

    Background Comparative analysis of gut microbiomes in clinical studies of human diseases typically rely on identification and quantification of species or genes. In addition to exploring specific functional characteristics of the microbiome and potential significance of species diversity or expansion, microbiome similarity is also calculated to study change in response to therapies directed at altering the microbiome. Established ecological measures of similarity can be constructed from species abundances, however methods for calculating these commonly used ecological measures of similarity directly from whole genome shotgun (WGS) metagenomic sequence are lacking. Results We present an alignment-free method for calculating similarity of WGS metagenomic sequences that is analogous to the Bray–Curtis index for species, implemented by the General Utility for Testing Sequence Similarity (GUTSS) software application. This method was applied to intestinal microbiomes of healthy young children to measure developmental changes toward an adult microbiome during the first 3 years of life. We also calculate similarity of donor and recipient microbiomes to measure establishment, or engraftment, of donor microbiota in fecal microbiota transplantation (FMT) studies focused on mild to moderate Crohn's disease. We show how a relative index of similarity to donor can be calculated as a measure of change in a patient's microbiome toward that of the donor in response to FMT. Conclusion Because clinical efficacy of the transplant procedure cannot be fully evaluated without analysis methods to quantify actual FMT engraftment, we developed a method for detecting change in the gut microbiome that is independent of species identification and database bias, sensitive to changes in relative abundance of the microbial constituents, and can be formulated as an index for correlating engraftment success with clinical measures of disease. More generally, this method may be applied to clinical

  17. Shuttle onboard IMU alignment methods

    NASA Technical Reports Server (NTRS)

    Henderson, D. M.

    1976-01-01

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

  18. The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Oryza Map Alignment Project (OMAP) provides the first comprehensive experimental system for understanding the evolution, physiology and biochemistry of a full genus in plants or animals. We have constructed twelve deep-coverage BAC libraries that are representative of both diploid and tetraploid...

  19. A magnetically actuated cellular strain assessment tool for quantitative analysis of strain induced cellular reorientation and actin alignment

    NASA Astrophysics Data System (ADS)

    Khademolhosseini, F.; Liu, C.-C.; Lim, C. J.; Chiao, M.

    2016-08-01

    Commercially available cell strain tools, such as pneumatically actuated elastomer substrates, require special culture plates, pumps, and incubator setups. In this work, we present a magnetically actuated cellular strain assessment tool (MACSAT) that can be implemented using off-the-shelf components and conventional incubators. We determine the strain field on the MACSAT elastomer substrate using numerical models and experimental measurements and show that a specific region of the elastomer substrate undergoes a quasi-uniaxial 2D stretch, and that cells confined to this region of the MACSAT elastomer substrate undergo tensile, compressive, or zero axial strain depending on their angle of orientation. Using the MACSAT to apply cyclic strain on endothelial cells, we demonstrate that actin filaments within the cells reorient away from the stretching direction, towards the directions of minimum axial strain. We show that the final actin orientation angles in strained cells are spread over a region of compressive axial strain, confirming previous findings on the existence of a varied pre-tension in the actin filaments of the cytoskeleton. We also demonstrate that strained cells exhibit distinctly different values of actin alignment coherency compared to unstrained cells and therefore propose that this parameter, i.e., the coherency of actin alignment, can be used as a new readout to determine the occurrence/extent of actin alignment in cell strain experiments. The tools and methods demonstrated in this study are simple and accessible and can be easily replicated by other researchers to study the strain response of other adherent cells.

  20. Multivariate curve resolution based chromatographic peak alignment combined with parallel factor analysis to exploit second-order advantage in complex chromatographic measurements.

    PubMed

    Parastar, Hadi; Akvan, Nadia

    2014-03-13

    In the present contribution, a new combination of multivariate curve resolution-correlation optimized warping (MCR-COW) with trilinear parallel factor analysis (PARAFAC) is developed to exploit second-order advantage in complex chromatographic measurements. In MCR-COW, the complexity of the chromatographic data is reduced by arranging the data in a column-wise augmented matrix, analyzing using MCR bilinear model and aligning the resolved elution profiles using COW in a component-wise manner. The aligned chromatographic data is then decomposed using trilinear model of PARAFAC in order to exploit pure chromatographic and spectroscopic information. The performance of this strategy is evaluated using simulated and real high-performance liquid chromatography-diode array detection (HPLC-DAD) datasets. The obtained results showed that the MCR-COW can efficiently correct elution time shifts of target compounds that are completely overlapped by coeluted interferences in complex chromatographic data. In addition, the PARAFAC analysis of aligned chromatographic data has the advantage of unique decomposition of overlapped chromatographic peaks to identify and quantify the target compounds in the presence of interferences. Finally, to confirm the reliability of the proposed strategy, the performance of the MCR-COW-PARAFAC is compared with the frequently used methods of PARAFAC, COW-PARAFAC, multivariate curve resolution-alternating least squares (MCR-ALS), and MCR-COW-MCR. In general, in most of the cases the MCR-COW-PARAFAC showed an improvement in terms of lack of fit (LOF), relative error (RE) and spectral correlation coefficients in comparison to the PARAFAC, COW-PARAFAC, MCR-ALS and MCR-COW-MCR results.

  1. Finite element analysis of in-situ alignment of nanoparticles in polymeric nanofibers using magnetic field assisted electrospinning

    NASA Astrophysics Data System (ADS)

    Jayaseelan, D.; Biji, P.

    2015-09-01

    In this study, a three-dimensional magnetic field assisted electrospinning (MFAES) system has been modeled to understand the correlation between the applied magnetic field and electric field distributions during nanoparticle alignment. The results reveal that the electric field distribution has been altered by positioning the magnets at the needle end. The analysis explored the possibility to create a stable liquid jet under a magnetic field, which allows the formation of organized nanostructures in nanofibers. The polarity of the magnet has been used to manipulate the electric field distribution in the electrospinning system. Based on the configuration of magnetic flux lines, the distribution of the electric field has been found to be altered. An axial magnetic field has been provided by the repulsive mode configuration, which could be the reason for alignment of nanoparticles during electrospinning. Simulation proved that the bending instability of the charged liquid jet can be efficiently controlled by placing the magnets on both sides of the fiber formation path in the electrospinning system. The impact of an axial magnetic field on nanofiber formation and nanoparticle alignment during the MFAES process was further experimentally validated.

  2. Sparse alignment for robust tensor learning.

    PubMed

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

    2014-10-01

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

  3. Protein structure alignment beyond spatial proximity.

    PubMed

    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.

  4. Alignment fixture

    DOEpatents

    Bell, Grover C.; Gibson, O. Theodore

    1980-01-01

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

  5. Curriculum Alignment.

    ERIC Educational Resources Information Center

    Crowell, Ronald; Tissot, Paula

    Curriculum alignment (CA) refers to the congruence of all the elements of a school's curriculum: curriculum goals; instructional program--what is taught and the materials used; and tests used to judge outcomes. CA can be a very powerful can be a very powerful factor in improving schools. Although further research is needed on CA, there is…

  6. FESEM Analysis showing evidence of aerosol Mixing over Indo-Gangetic Plains

    NASA Astrophysics Data System (ADS)

    Singh, R. P.; Huth, J.; Wagner, T.; Sharma, M.; Chauhan, A.; Singh, S.; Pandey, S. N.

    2012-12-01

    Kanpur AERONET deployed in January 2001 has provided a long-term dataset which has been used to understand the aerosol properties and aerosol long term trend in the Indo-Gangetic Plains (IGP). Recent studies have revealed higher black carbon (BC) mass concentrations in the IGP, home to 900 million people. We present analysis of black carbon mass concentrations obtained from several locations in the IGP - namely Varanasi, Lucknow, Kanpur, Greater Noida and Delhi. Measurements show significant diurnal variation with higher BC concentrations in the morning hours and low concentrations during afternoon and evening time. Seasonally, BC concentrations are generally found to be higher during winter months compared to spring and summer monsoon season showing high seasonal variability. The higher winter-time BC is associated with a stable and shallow boundary layer which favors accumulation of pollutants over the IGP, resulting in dense haze conditions. Filter-based analysis, obtained from samples used in Aethalometer and high vacuum sampler, were analyzed to study aerosol surface characteristics and size of particles. Additionally, FESEM (Field Emission Scanning Electron Microscope) analysis show many dust minerals (Na, Al, Si, K, Fe), biogenic substances, fly ash of varying sizes 15 nanometer to 5 micron. The SEM imagery also show heterogeneous aerosol particles, sometimes these mineral grains are seen separately and sometime coating of fly ash and mineral particles are clearly seen. Similarly, Kanpur AERONET data is analyzed during winter and pre-monsoon season, contrasting aerosol properties (SSA, Refractive index and Size distribution) are found that are associated with large aerosol mixing, also supported from the FESEM analysis.

  7. Improving ASM stepper alignment accuracy by alignment signal intensity simulation

    NASA Astrophysics Data System (ADS)

    Li, Gerald; Pushpala, Sagar M.; Bradford, Bradley; Peng, Zezhong; Gottipati, Mohan

    1993-08-01

    As photolithography technology advances into submicron regime, the requirement for alignment accuracy also becomes much tighter. The alignment accuracy is a function of the strength of the alignment signal. Therefore, a detailed alignment signal intensity simulation for 0.8 micrometers EPROM poly-1 layer on ASM stepper was done based on the process of record in the fab to reduce misalignment and improve die yield. Oxide thickness variation did not have significant impact on the alignment signal intensity. However, poly-1 thickness was the most important parameter to affect optical alignments. The real alignment intensity data versus resist thickness on production wafers was collected and it showed good agreement with the simulated results. Similar results were obtained for ONO dielectric layer at a different fab.

  8. A High-resolution Model of Field-aligned Currents Through Empirical Orthogonal Functions Analysis (MFACE)

    NASA Technical Reports Server (NTRS)

    He, Maosheng; Vogt, Joachim; Luehr, Hermann; Sorbalo, Eugen; Blagau, Adrian; Le, Guan; Lu, Gang

    2012-01-01

    Ten years of CHAMP magnetic field measurements are integrated into MFACE, a model of field-aligned currents (FACs) using empirical orthogonal functions (EOFs). EOF1 gives the basic Region-1/Region-2 pattern varying mainly with the interplanetary magnetic field Bz component. EOF2 captures separately the cusp current signature and By-related variability. Compared to existing models, MFACE yields significantly better spatial resolution, reproduces typically observed FAC thickness and intensity, improves on the magnetic local time (MLT) distribution, and gives the seasonal dependence of FAC latitudes and the NBZ current signature. MFACE further reveals systematic dependences on By, including 1) Region-1/Region-2 topology modifications around noon; 2) imbalance between upward and downward maximum current density; 3) MLT location of the Harang discontinuity. Furthermore, our procedure allows quantifying response times of FACs to solar wind driving at the bow shock nose: we obtain 20 minutes and 35-40 minutes lags for the FAC density and latitude, respectively.

  9. A magnetically actuated cellular strain assessment tool for quantitative analysis of strain induced cellular reorientation and actin alignment.

    PubMed

    Khademolhosseini, F; Liu, C-C; Lim, C J; Chiao, M

    2016-08-01

    Commercially available cell strain tools, such as pneumatically actuated elastomer substrates, require special culture plates, pumps, and incubator setups. In this work, we present a magnetically actuated cellular strain assessment tool (MACSAT) that can be implemented using off-the-shelf components and conventional incubators. We determine the strain field on the MACSAT elastomer substrate using numerical models and experimental measurements and show that a specific region of the elastomer substrate undergoes a quasi-uniaxial 2D stretch, and that cells confined to this region of the MACSAT elastomer substrate undergo tensile, compressive, or zero axial strain depending on their angle of orientation. Using the MACSAT to apply cyclic strain on endothelial cells, we demonstrate that actin filaments within the cells reorient away from the stretching direction, towards the directions of minimum axial strain. We show that the final actin orientation angles in strained cells are spread over a region of compressive axial strain, confirming previous findings on the existence of a varied pre-tension in the actin filaments of the cytoskeleton. We also demonstrate that strained cells exhibit distinctly different values of actin alignment coherency compared to unstrained cells and therefore propose that this parameter, i.e., the coherency of actin alignment, can be used as a new readout to determine the occurrence/extent of actin alignment in cell strain experiments. The tools and methods demonstrated in this study are simple and accessible and can be easily replicated by other researchers to study the strain response of other adherent cells. PMID:27587150

  10. Analysis of spinal alignment and pelvic parameters on upright radiographs: implications for acetabular development

    PubMed Central

    Pytiak, Andrew; Bomar, James D.; Peterson, Jonathan B.; Schmitz, Matthew R.; Pennock, Andrew T.; Wenger, Dennis R.; Upasani, Vidyadhar V.

    2016-01-01

    The purpose of this study was to correlate measures of sagittal spinopelvic alignment [lumbar lordosis (LL), sacral slope (SS), pelvic tilt (PT) and pelvic incidence (PI)] and measures of acetabular coverage [lateral center edge angle (LCEA) and Tonnis angle] in asymptomatic adolescents on standing biplanar radiographs. We hypothesized that subjects with increased pelvic incidence and LL would have increased anterior PT and increased measures of acetabular coverage. Upright anteroposterior and lateral spinopelvic radiographs were obtained using EOS imaging technique. LCEA and Tonnis angle were calculated on the anteroposterior images and the lateral images were analyzed for LL, PI, PT and SS. LL was found to have a strong correlation with SS (rs = 0.786, P  <  0.001), moderate correlation with PI (rs  =  0.529, P  <  0.001), and a poor inverse correlation with PT (rs  = −0.167, P  =  0.018). However, LCEA was not found to be significantly correlated with PT (rs  =  0.084, P  =  0.238) and Tonnis angle was not found to be correlated with any of the sagittal spinopelvic measures. Healthy, asymptomatic adolescents with increased pelvic incidence and lumbar lordosis did not have increased anterior PT or increased measures of acetabular coverage. The correlations identified in previous cadaveric studies or clinical studies evaluating changes between supine and standing radiographs are not supported in this healthy adolescent population. Our findings may suggest that an individual’s acetabulum develops as a dynamic adaptation to one's particular sagittal spinopelvic alignment to optimize femoral head coverage. Level III. Diagnostic – Investigating a diagnostic test. PMID:27583160

  11. 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

  12. Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic.

    PubMed

    Storfer, Andrew; Alfaro, Michael E; Ridenhour, Benjamin J; Jancovich, James K; Mech, Stephen G; Parris, Matthew J; Collins, James P

    2007-11-01

    Distinguishing whether pathogens are novel or endemic is critical for controlling emerging infectious diseases, an increasing threat to wildlife and human health. To test the endemic vs. novel pathogen hypothesis, we present a unique analysis of intraspecific host-pathogen phylogenetic concordance of tiger salamanders and an emerging Ranavirus throughout Western North America. There is significant non-concordance of host and virus gene trees, suggesting pathogen novelty. However, non-concordance has likely resulted from virus introductions by human movement of infected salamanders. When human-associated viral introductions are excluded, host and virus gene trees are identical, strongly supporting coevolution and endemism. A laboratory experiment showed an introduced virus strain is significantly more virulent than endemic strains, likely due to artificial selection for high virulence. Thus, our analysis of intraspecific phylogenetic concordance revealed that human introduction of viruses is the mechanism underlying tree non-concordance and possibly disease emergence via artificial selection.

  13. ALIGNING JIG

    DOEpatents

    Culver, J.S.; Tunnell, W.C.

    1958-08-01

    A jig or device is described for setting or aligning an opening in one member relative to another member or structure, with a predetermined offset, or it may be used for measuring the amount of offset with which the parts have previously been sct. This jig comprises two blocks rabbeted to each other, with means for securing thc upper block to the lower block. The upper block has fingers for contacting one of the members to be a1igmed, the lower block is designed to ride in grooves within the reference member, and calibration marks are provided to determine the amount of offset. This jig is specially designed to align the collimating slits of a mass spectrometer.

  14. Alternating current impedance spectroscopic analysis of biofunctionalized vertically-aligned silica nanospring surface for biosensor applications

    NASA Astrophysics Data System (ADS)

    Timalsina, Yukta P.

    In this dissertation, a process of vertically-aligned (silica) nanosprings (VANS) based biosensor development is presented. Alternating current (AC) impedance spectroscopy has been used to analyze sensor response as a function of saline phosphate (SP) buffer and biological solutions. The sensor is a parallel plate capacitor consisting of two glass substrates coated with indium tin oxide (ITO), where the VANS [or randomly-aligned nanosprings (RANS)] grown on one substrate serve as the dielectric spacer layer. The response of a VANS device as a function of ionic concentration in SP buffer was examined and an equivalent circuit model was developed. The results demonstrated that VANS sensors exhibited greater sensitivity to the changes in SP concentration relative to the ITO sensors, which serve as controls. The biofunctionalized VANS surface via physisorption and the cross-linker method demonstrates the repeatability, specificity, and selectivity of the binding. The physisorption of biotinylated immunoglobulin G (B-IgG) onto the VANS surface simplifies the whole sensing procedure for the detection of glucose oxidase, since the avidin-conjugated glucose oxidase (Av-GOx) can directly be immobilized on the B-IgG. The cross linker method involves the covalent attachment of antibodies onto the functionalized VANS surface via imine bond. The experiments revealed that the VANS sensor response is solely the result of the interaction of target molecule i.e. mouse IgG with the probe layer, i.e. goat antimouse IgG (GalphaM IgG). It was determined that VANS-based sensors exhibit a greater magnitude of change between successive bio-layers relative to the controls above 100 Hz, which indicates that the addition of biomolecules inhibits the diffusion of ions and changes the effective dielectric response of the VANS via biomolecular polarization. The study of ionic transport in nanosprings suggested that conductance follows a scaling law. It was demonstrated that a VANS-based device

  15. Aligning Experimental and Theoretical Anisotropic B-Factors: Water Models, Normal-Mode Analysis Methods, and Metrics

    PubMed Central

    2014-01-01

    The strength of X-ray crystallography in providing the information for protein dynamics has been under appreciated. The anisotropic B-factors (ADPs) from high-resolution structures are invaluable in studying the relationship among structure, dynamics, and function. Here, starting from an in-depth evaluation of the metrics used for comparing the overlap between two ellipsoids, we applied normal-mode analysis (NMA) to predict the theoretical ADPs and then align them with experimental results. Adding an extra layer of explicitly treated water on protein surface significantly improved the energy minimization results and better reproduced the anisotropy of experimental ADPs. In comparing experimental and theoretical ADPs, we focused on the overlap in shape, the alignment of dominant directions, and the similarity in magnitude. The choices of water molecules, NMA methods, and the metrics for evaluating the overlap of ADPs determined final results. This study provides useful information for exploring the physical basis and the application potential of experimental ADPs. PMID:24673391

  16. Network Analysis Shows Novel Molecular Mechanisms of Action for Copper-Based Chemotherapy

    PubMed Central

    Espinal-Enríquez, Jesús; Hernández-Lemus, Enrique; Mejía, Carmen; Ruiz-Azuara, Lena

    2016-01-01

    The understanding of the mechanisms associated with the action of chemotherapeutic agents is fundamental to assess and account for possible side-effects of such treatments. Casiopeínas have demonstrated a cytotoxic effect by activation of pro-apoptotic processes in malignant cells. Such processes have been proved to activate the apoptotic intrinsic route, as well as cell cycle arrest. Despite this knowledge, the whole mechanism of action of Casiopeínas is yet to be completely understood. In this work we implement a systems biology approach based on two pathway analysis tools (Over-Representation Analysis and Causal Network Analysis) to observe changes in some hallmarks of cancer, induced by this copper-based chemotherapeutic agent in HeLa cell lines. We find that the metabolism of metal ions is exacerbated, as well as cell division processes being globally diminished. We also show that cellular migration and proliferation events are decreased. Moreover, the molecular mechanisms of liver protection are increased in the cell cultures under the actions of Casiopeínas, unlike the case in many other cytotoxic drugs. We argue that this chemotherapeutic agent may be promising, given its protective hepatic function, concomitant with its cytotoxic participation in the onset of apoptotic processes in malignant cells. PMID:26793116

  17. 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.

  18. Global network alignment using multiscale spectral signatures

    PubMed Central

    Patro, Rob; Kingsford, Carl

    2012-01-01

    Motivation: Protein interaction networks provide an important system-level view of biological processes. One of the fundamental problems in biological network analysis is the global alignment of a pair of networks, which puts the proteins of one network into correspondence with the proteins of another network in a manner that conserves their interactions while respecting other evidence of their homology. By providing a mapping between the networks of different species, alignments can be used to inform hypotheses about the functions of unannotated proteins, the existence of unobserved interactions, the evolutionary divergence between the two species and the evolution of complexes and pathways. Results: We introduce GHOST, a global pairwise network aligner that uses a novel spectral signature to measure topological similarity between subnetworks. It combines a seed-and-extend global alignment phase with a local search procedure and exceeds state-of-the-art performance on several network alignment tasks. We show that the spectral signature used by GHOST is highly discriminative, whereas the alignments it produces are also robust to experimental noise. When compared with other recent approaches, we find that GHOST is able to recover larger and more biologically significant, shared subnetworks between species. Availability: An efficient and parallelized implementation of GHOST, released under the Apache 2.0 license, is available at http://cbcb.umd.edu/kingsford_group/ghost Contact: rob@cs.umd.edu PMID:23047556

  19. Analysis of multiple internal reflections in a parallel aligned liquid crystal on silicon SLM.

    PubMed

    Martínez, José Luis; Moreno, Ignacio; del Mar Sánchez-López, María; Vargas, Asticio; García-Martínez, Pascuala

    2014-10-20

    Multiple internal reflection effects on the optical modulation of a commercial reflective parallel-aligned liquid-crystal on silicon (PAL-LCoS) spatial light modulator (SLM) are analyzed. The display is illuminated with different wavelengths and different angles of incidence. Non-negligible Fabry-Perot (FP) effect is observed due to the sandwiched LC layer structure. A simplified physical model that quantitatively accounts for the observed phenomena is proposed. It is shown how the expected pure phase modulation response is substantially modified in the following aspects: 1) a coupled amplitude modulation, 2) a non-linear behavior of the phase modulation, 3) some amount of unmodulated light, and 4) a reduction of the effective phase modulation as the angle of incidence increases. Finally, it is shown that multiple reflections can be useful since the effect of a displayed diffraction grating is doubled on a beam that is reflected twice through the LC layer, thus rendering gratings with doubled phase modulation depth. PMID:25401619

  20. Alternative Computational Analysis Shows No Evidence for Nucleosome Enrichment at Repetitive Sequences in Mammalian Spermatozoa.

    PubMed

    Royo, Hélène; Stadler, Michael Beda; Peters, Antoine Hendrik Felix Marie

    2016-04-01

    Samans et al. (2014) reported the enrichment of nucleosomes in human and bovine spermatozoa at centromere repeats and retrotransposon sequences such as LINE-1 and SINE. We demonstrate here that nucleosomal enrichments at repetitive sequences as reported result from bioinformatic analyses that make redundant use of sequencing reads that map to multiple locations in the genome. To illustrate that this computational approach is flawed, we observed comparable artificial enrichments at repetitive sequences when aligning control genomic DNA or simulated reads of uniform genome coverage. These results imply that the main conclusions of the article by Samans et al. (2014) are confounded by an inappropriate computational methodology used to analyze the primary data. PMID:27046835

  1. Transcriptional and functional analysis shows sodium houttuyfonate-mediated inhibition of autolysis in Staphylococcus aureus.

    PubMed

    Liu, Guoxing; Xiang, Hua; Tang, Xudong; Zhang, Kaiyu; Wu, Xiuping; Wang, Xuelin; Guo, Na; Feng, Haihua; Wang, Guangming; Liu, Lihui; Shi, Qiyun; Shen, Fengge; Xing, Mingxun; Yuan, Peng; Liu, Mingyuan; Yu, Lu

    2011-01-01

    Sodium houttuyfonate (SH), an addition compound of sodium bisulfite and houttuynin, showed in vitro antibacterial activity against 21 Staphylococcus aureus (S. aureus) strains grown in planktonic cultures. Microarray results showed decreased levels of autolysin atl, sle1, cidA and lytN transcripts in the SH-treated strain as compared to the control strain, consistent with the induction of the autolytic repressors lrgAB and sarA and with the downregulation of the positive regulators agrA and RNAIII. Triton X-100-induced autolysis was significantly decreased by SH in S. aureus ATCC 25923, and quantitative bacteriolytic assays and zymographic analysis demonstrated SH-mediated reduction of extracellular murein hydrolase activity in these cells. Anti-biofilm assay showed that SH is poorly active against S. aureus grown in biofilm cultures, whereas SH diminished the amounts of extracellular DNA (eDNA) of S. aureus in a dose-dependent manner, which suggested that SH may impede biofilm formation by reducing the expression of cidA to inhibit autolysis and eDNA release in the early phase. Some of the microarray results were confirmed by real-time RT-PCR. PMID:22019573

  2. Pareto optimal pairwise sequence alignment.

    PubMed

    DeRonne, Kevin W; Karypis, George

    2013-01-01

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

  3. Alignment of the Fibrin Network Within an Autologous Plasma Clot.

    PubMed

    Gessmann, Jan; Seybold, Dominik; Peter, Elvira; Schildhauer, Thomas Armin; Köller, Manfred

    2016-01-01

    Autologous plasma clots with longitudinally aligned fibrin fibers could serve as a scaffold for longitudinal axonal regrowth in cases of traumatic peripheral nerve injuries. Three different techniques for assembling longitudinally oriented fibrin fibers during the fibrin polymerization process were investigated as follows: fiber alignment was induced by the application of either a magnetic field or-as a novel approach-electric field or by the induction of orientated flow. Fiber alignment was characterized by scanning electron microscopy analysis followed by image processing using fast Fourier transformation (FFT). Besides FFT output images, area xmin to xmax, as well as full width at half maximum (FWHM) of the FFT graph plot peaks, was calculated to determine the relative degree of fiber alignment. In addition, fluorescently labeled human fibrinogen and mesenchymal stem cells (MSCs) were used to visualize fibrin and cell orientation in aligned and nonaligned plasma clots. Varying degrees of fiber alignment were achieved by the three different methods, with the electric field application producing the highest degree of fiber alignment. The embedded MSCs showed a longitudinal orientation in the electric field-aligned plasma clots. The key feature of this study is the ability to produce autologous plasma clots with aligned fibrin fibers using physical techniques. This orientated internal structure of an autologous biomaterial is promising for distinct therapeutic applications, such as a guiding structure for cell migration and growth dynamics.

  4. Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis.

    PubMed

    Dunlap, Christopher A

    2015-10-01

    ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this strain was assembled and yielded a length of 3.71 Mbp with a DNA G+C content of 46.3 mol%. Comparative genomic analysis with its nearest relatives showed only minor differences between this strain and the genome of the Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T), with a calculated DNA–DNA hybridization (DDH) value of 91.2 % and an average nucleotide identity (ANI) of 98.9 %. This DDH value is well above the recommended 70 % threshold for species delineation, as well as the ANI threshold of 95 %. In addition, the results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar with phenotype coherence. A core genome multi-locus sequencing analysis was conducted for the strains and the results show that ‘Bacillus vanillea’ XY18 clusters closely to the type strain of Bacillus siamensis. Therefore, it is proposed that the species ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) should be reclassified as a later heterotypic synonym of Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T). An emended description of Bacillus siamensis is provided. PMID:26296875

  5. Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis.

    PubMed

    Dunlap, Christopher A

    2015-10-01

    ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this strain was assembled and yielded a length of 3.71 Mbp with a DNA G+C content of 46.3 mol%. Comparative genomic analysis with its nearest relatives showed only minor differences between this strain and the genome of the Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T), with a calculated DNA–DNA hybridization (DDH) value of 91.2 % and an average nucleotide identity (ANI) of 98.9 %. This DDH value is well above the recommended 70 % threshold for species delineation, as well as the ANI threshold of 95 %. In addition, the results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar with phenotype coherence. A core genome multi-locus sequencing analysis was conducted for the strains and the results show that ‘Bacillus vanillea’ XY18 clusters closely to the type strain of Bacillus siamensis. Therefore, it is proposed that the species ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) should be reclassified as a later heterotypic synonym of Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T). An emended description of Bacillus siamensis is provided.

  6. PILOT optical alignment

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  7. Extramedullary versus intramedullary tibial alignment technique in total knee arthroplasty: A meta-analysis of randomized controlled trials

    PubMed Central

    Zeng, Huan Bei; Ying, Xiao Zhou; Chen, Guang Jun; Yang, Xia Qing; Lin, Duo Duo; Li, Zhi Jie; Liu, Hai Xiao

    2015-01-01

    The aim of this study was to establish whether the use of an extramedullary or intramedullary tibial cutting guide leads to superior mechanical leg axis and implant positioning. A meta-analysis of six randomized controlled trials including 350 knees was performed. For the mechanical axis, frontal tibial component angle and tibial slope, there were no significant differences in the mean values or the number of outliers (±3°) between the extramedullary and intramedullary groups. A reduced tourniquet time was associated with the intramedullary guide. No significant difference in the complication rate was noted between the two groups. Neither extramedullary nor intramedullary tibial alignment was more accurate in facilitating the tibial cut. Use of an intramedullary guide results in a shorter tourniquet time and exhibits a similar complication rate as the extramedullary guide. PMID:26598086

  8. HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues.

    PubMed

    Lamers, Susanna L; Gray, Rebecca R; Salemi, Marco; Huysentruyt, Leanne C; McGrath, Michael S

    2011-01-01

    Brain infection by the human immunodeficiency virus type 1 (HIV-1) has been investigated in many reports with a variety of conclusions concerning the time of entry and degree of viral compartmentalization. To address these diverse findings, we sequenced HIV-1 gp120 clones from a wide range of brain, peripheral and meningeal tissues from five patients who died from several HIV-1 associated disease pathologies. High-resolution phylogenetic analysis confirmed previous studies that showed a significant degree of compartmentalization in brain and peripheral tissue subpopulations. Some intermixing between the HIV-1 subpopulations was evident, especially in patients that died from pathologies other than HIV-associated dementia. Interestingly, the major tissue harboring virus from both the brain and peripheral tissues was the meninges. These results show that (1) HIV-1 is clearly capable of migrating out of the brain, (2) the meninges are the most likely primary transport tissues, and (3) infected brain macrophages comprise an important HIV reservoir during highly active antiretroviral therapy.

  9. Nova laser alignment control system

    SciTech Connect

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

    1984-03-29

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

  10. Onorbit IMU alignment error budget

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

    The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

  11. Computer simulated screening of dentin bonding primer monomers through analysis of their chemical functions and their spatial 3D alignment.

    PubMed

    Vaidyanathan, J; Vaidyanathan, T K; Ravichandran, S

    2009-02-01

    Binding interactions between dentin bonding primer monomers and dentinal collagen were studied by an analysis of their chemical functions and their spatial 3D alignment. A trial set of 12 monomers used as primers in dentin adhesives was characterized to assess them for binding to a complementary target. HipHop utility in the Catalyst software from Accelrys was used for the study. Ten hypotheses were generated by HipHop procedures involving (a) conformational generation using a poling technique to promote conformational variation, (b) extraction of functions to remodel ligands as function-based structures, and (c) identification of common patterns of functional alignment displayed by low energy conformations. The hypotheses, designated as pharmacaphores, were also scored and ranked. Analysis of pharmacaphore models through mapping of ligands revealed important differences between ligands. Top-ranked poses from direct docking simulations using type 1 collagen target were mapped in a rigid manner to the highest ranked pharmacophore model. The visual match observed in mapping and associated fit values suggest a strong correspondence between direct and indirect docking simulations. The results elegantly demonstrate that an indirect approach used to identify pharmacaphore models from adhesive ligands without a target may be a simple and viable approach to assess their intermolecular interactions with an intended target. Inexpensive indirect/direct virtual screening of hydrophilic monomer candidates may be a practical way to assess their initial promise for dentin primer use well before additional experimental evaluation of their priming/bonding efficacy. This is also of value in the search/design of new compounds for priming dentin. PMID:18546179

  12. Computer simulated screening of dentin bonding primer monomers through analysis of their chemical functions and their spatial 3D alignment.

    PubMed

    Vaidyanathan, J; Vaidyanathan, T K; Ravichandran, S

    2009-02-01

    Binding interactions between dentin bonding primer monomers and dentinal collagen were studied by an analysis of their chemical functions and their spatial 3D alignment. A trial set of 12 monomers used as primers in dentin adhesives was characterized to assess them for binding to a complementary target. HipHop utility in the Catalyst software from Accelrys was used for the study. Ten hypotheses were generated by HipHop procedures involving (a) conformational generation using a poling technique to promote conformational variation, (b) extraction of functions to remodel ligands as function-based structures, and (c) identification of common patterns of functional alignment displayed by low energy conformations. The hypotheses, designated as pharmacaphores, were also scored and ranked. Analysis of pharmacaphore models through mapping of ligands revealed important differences between ligands. Top-ranked poses from direct docking simulations using type 1 collagen target were mapped in a rigid manner to the highest ranked pharmacophore model. The visual match observed in mapping and associated fit values suggest a strong correspondence between direct and indirect docking simulations. The results elegantly demonstrate that an indirect approach used to identify pharmacaphore models from adhesive ligands without a target may be a simple and viable approach to assess their intermolecular interactions with an intended target. Inexpensive indirect/direct virtual screening of hydrophilic monomer candidates may be a practical way to assess their initial promise for dentin primer use well before additional experimental evaluation of their priming/bonding efficacy. This is also of value in the search/design of new compounds for priming dentin.

  13. Mapping self-assembled dots and line arrays by image analysis for quantification of defect density and alignment

    NASA Astrophysics Data System (ADS)

    Simão, C.; Tuchapsky, D.; Khunsin, W.; Amann, A.; Morris, M. A.; Sotomayor Torres, C. M.

    2015-03-01

    Bottom-up alternative lithographic masks from directed self-assembly systems have been extending the limits of critical dimensions in a cost-effective manner although great challenges in controlling defectivity remain open. Particularly, defectivity and dimensional metrology are two main challenges in lithography due to the increasing miniaturisation of circuits. To gain insights about the percentage of alignment, defectivity and order quantification, directed self-assembly block copolymer fingerprints were investigated via an image analysis methodology. Here we present the analysis of hexagonal phase of polystyrene-b-polydimethylsiloxane (PS-b-PDMS) forming linear patterns in topological substrates. From our methodology, we have performed dimensional metrology estimating pitch size and error, and the linewidth of the lines was estimated. In parallel, the methodology allowed us identification and quantification of typical defects observable in self-assembly, such as turning points, disclination or branching points, break or lone points and end points. The methodology presented here yields high volume statistical data useful for advancing dimensional metrology and defect analysis of self- and directed assembly systems.

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

    PubMed Central

    Zhou, Jie; Zhong, Pianyu; Zhang, Tinghui

    2016-01-01

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

  15. Molecular genetic analysis of oligodendroglial tumors shows preferential allelic deletions on 19q and 1p.

    PubMed Central

    Reifenberger, J.; Reifenberger, G.; Liu, L.; James, C. D.; Wechsler, W.; Collins, V. P.

    1994-01-01

    The molecular genetic alterations of oligodendroglial tumors and mixed gliomas of the central nervous system were studied in a series of 37 cases (8 oligodendrogliomas, 13 anaplastic oligodendrogliomas, 8 oligoastrocytomas, and 8 anaplastic oligoastrocytomas). A total of 180 polymorphic loci and 5 nonpolymorphic gene loci, distributed over all chromosomes, were examined by restriction fragment length polymorphism analysis. Loss of heterozygosity was most frequently observed for loci on 19q with a commonly deleted region at 19q13.2-q13.4 distal to the CYP2a gene and proximal to the D19S22 locus. The incidence of allelic loss on 19q was particularly high (81%) in oligodendroglial tumors and equal to 31% in mixed gliomas. More than 75% of the tumors with allelic deletions on 19q also showed loss of heterozygosity for loci on 1p with one tumor showing only loss of alleles distal to the NGFB gene (1p13-pter). Seven (19%) tumors had lost alleles from 17p with the deleted region including the TP53 tumor suppressor gene in all cases. Sequencing of the TP53 transcripts from exons 2 to 10, however, did not reveal mutations of the remaining allele in any of these tumors. Anaplastic oligodendrogliomas and anaplastic oligoastrocytomas demonstrated an increased incidence of additional allelic losses involving most frequently chromosomes 9p and 10. Gene amplification was detected in two anaplastic tumors, affecting the epidermal growth factor receptor gene in both cases, with additional amplification of the renin gene at 1q32 in one of these cases. In total our results indicate both differences and similarities between the molecular genetic alterations in tumors with oligodendroglial and astrocytic differentiation. The loss of genetic information from 19q and 1p as well as the rarity of TP53 mutations in oligodendroglial tumors suggests that the early events in their oncogenesis are distinct from those associated with astrocytic tumors. However, similarities are indicated by the

  16. A Discourse Analytic Approach to Video Analysis of Teaching: Aligning Desired Identities with Practice

    ERIC Educational Resources Information Center

    Schieble, Melissa; Vetter, Amy; Meacham, Mark

    2015-01-01

    The authors present findings from a qualitative study of an experience that supports teacher candidates to use discourse analysis and positioning theory to analyze videos of their practice during student teaching. The research relies on the theoretical concept that learning to teach is an identity process. In particular, teachers construct and…

  17. Analysis of Opportunity to Learn for Students with Disabilities: Effects of Standards-Aligned Instruction

    ERIC Educational Resources Information Center

    Blank, Rolf K.; Smithson, John L.

    2014-01-01

    The paper presents a model for addressing the critical question of opportunity to learn for students with disabilities. The model was tested through a two-year study with schools and teachers in three states. Opportunity to learn analysis is critical in this educational era of push toward access and inclusion. The study results indicate that…

  18. Thermal and Alignment Analysis of the Instrument-Level ATLAS Thermal Vacuum Test

    NASA Technical Reports Server (NTRS)

    Bradshaw, Heather

    2012-01-01

    This paper describes the thermal analysis and test design performed in preparation for the ATLAS thermal vacuum test. NASA's Advanced Topographic Laser Altimeter System (ATLAS) will be flown as the sole instrument aboard the Ice, Cloud, and land Elevation Satellite-2 (ICESat-2). It will be used to take measurements of topography and ice thickness for Arctic and Antarctic regions, providing crucial data used to predict future changes in worldwide sea levels. Due to the precise measurements ATLAS is taking, the laser altimeter has very tight pointing requirements. Therefore, the instrument is very sensitive to temperature-induced thermal distortions. For this reason, it is necessary to perform a Structural, Thermal, Optical Performance (STOP) analysis not only for flight, but also to ensure performance requirements can be operationally met during instrument-level thermal vacuum testing. This paper describes the thermal model created for the chamber setup, which was used to generate inputs for the environmental STOP analysis. This paper also presents the results of the STOP analysis, which indicate that the test predictions adequately replicate the thermal distortions predicted for flight. This is a new application of an existing process, as STOP analyses are generally performed to predict flight behavior only. Another novel aspect of this test is that it presents the opportunity to verify pointing results of a STOP model, which is not generally done. It is possible in this case, however, because the actual pointing will be measured using flight hardware during thermal vacuum testing and can be compared to STOP predictions.

  19. Global alignment: Finding rearrangements during alignment

    SciTech Connect

    Brudno, Michael; Malde, Sanket; Poliakov, Alexander; Do, Chuong B.; Couronne, Olivier; Dubchak, Inna; Batzoglou, Serafim

    2003-01-06

    Motivation: To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. The two main classes of pairwise alignments are global alignment, where one string is transformed into the other, and local alignment, where all locations of similarity between the two strings are returned. Global alignments are less prone to demonstrating false homology as each letter of one sequence is constrained to being aligned to only one letter of the other. Local alignments, on the other hand, can cope with rearrangements between non-syntenic, orthologous sequences by identifying similar regions in sequences; this, however, comes at the expense of a higher false positive rate due to the inability of local aligners to take into account overall conservation maps.

  20. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

    PubMed

    Loh, Yong-Hwee Eddie; Shen, Li

    2016-01-01

    The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases. PMID:27115642

  1. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

    PubMed

    Loh, Yong-Hwee Eddie; Shen, Li

    2016-01-01

    The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.

  2. Automatic alignment of double optical paths in excimer laser amplifier

    NASA Astrophysics Data System (ADS)

    Wang, Dahui; Zhao, Xueqing; Hua, Hengqi; Zhang, Yongsheng; Hu, Yun; Yi, Aiping; Zhao, Jun

    2013-05-01

    A kind of beam automatic alignment method used for double paths amplification in the electron pumped excimer laser system is demonstrated. In this way, the beams from the amplifiers can be transferred along the designated direction and accordingly irradiate on the target with high stabilization and accuracy. However, owing to nonexistence of natural alignment references in excimer laser amplifiers, two cross-hairs structure is used to align the beams. Here, one crosshair put into the input beam is regarded as the near-field reference while the other put into output beam is regarded as the far-field reference. The two cross-hairs are transmitted onto Charge Coupled Devices (CCD) by image-relaying structures separately. The errors between intersection points of two cross-talk images and centroid coordinates of actual beam are recorded automatically and sent to closed loop feedback control mechanism. Negative feedback keeps running until preset accuracy is reached. On the basis of above-mentioned design, the alignment optical path is built and the software is compiled, whereafter the experiment of double paths automatic alignment in electron pumped excimer laser amplifier is carried through. Meanwhile, the related influencing factors and the alignment precision are analyzed. Experimental results indicate that the alignment system can achieve the aiming direction of automatic aligning beams in short time. The analysis shows that the accuracy of alignment system is 0.63μrad and the beam maximum restoration error is 13.75μm. Furthermore, the bigger distance between the two cross-hairs, the higher precision of the system is. Therefore, the automatic alignment system has been used in angular multiplexing excimer Main Oscillation Power Amplification (MOPA) system and can satisfy the requirement of beam alignment precision on the whole.

  3. Optical Alignment and Diffraction Analysis for AIRES: An Airborne Infrared Echelle Spectrometer

    NASA Technical Reports Server (NTRS)

    Haas, Michael R.; Fonda, Mark (Technical Monitor)

    2002-01-01

    The optical design is presented for a long-slit grating spectrometer known as AIRES (Airborne InfraRed Echelle Spectrometer). The instrument employs two gratings in series: a small order sorter and a large steeply blazed echelle. The optical path includes four pupil and four field stops, including two narrow slits. A detailed diffraction analysis is performed using GLAD by Applied Optics Research to evaluate critical trade-offs between optical throughput, spectral resolution, and system weight and volume. The effects of slit width, slit length, oversizing the second slit relative to the first, on- vs off-axis throughput, and clipping at the pupil stops and other optical elements are discussed.

  4. Field aligned current observations in the polar cusp ionosphere

    NASA Technical Reports Server (NTRS)

    Ledley, B. G.; Farthing, W. H.

    1973-01-01

    Vector magnetic field measurements made during a sounding rocket flight in the polar cusp ionosphere show field fluctuations in the lower F-region which are interpreted as being caused by the payload's passage through a structured field aligned current system. The field aligned currents have a characteristic horizontal scale size of one kilometer. Analysis of one large field fluctuation gives a current density of 0.0001 amp/m sq.

  5. X ray microscope assembly and alignment support and advanced x ray microscope design and analysis

    NASA Technical Reports Server (NTRS)

    Shealy, David L.

    1991-01-01

    Considerable efforts have been devoted recently to the design, analysis, fabrication, and testing of spherical Schwarzschild microscopes for soft x ray application in microscopy and projection lithography. The spherical Schwarzschild microscope consists of two concentric spherical mirrors configured such that the third order spherical aberration and coma are zero. Since multilayers are used on the mirror substrates for x ray applications, it is desirable to have only two reflecting surfaces in a microscope. In order to reduce microscope aberrations and increase the field of view, generalized mirror surface profiles have been considered in this investigation. Based on incoherent and sine wave modulation transfer function (MTF) calculations, the object plane resolution of a microscope has been analyzed as a function of the object height and numerical aperture (NA) of the primary for several spherical Schwarzschild, conic, and aspherical head reflecting two mirror microscope configurations.

  6. More than Meets the Ear: A Factor Analysis of Student Impressions of Television Talk Show Hosts.

    ERIC Educational Resources Information Center

    Walker, James R.

    To identify the descriptors most frequently associated with four popular television talk show hosts and to isolate the fundamental dimensions of the images of those talk show hosts, a study surveyed 209 students from Memphis State University and the University of Arkansas (Little Rock) about their impressions of Johnny Carson, David Letterman,…

  7. Nonlinear analysis of motor activity shows differences between schizophrenia and depression: a study using Fourier analysis and sample entropy.

    PubMed

    Hauge, Erik R; Berle, Jan Øystein; Oedegaard, Ketil J; Holsten, Fred; Fasmer, Ole Bernt

    2011-01-28

    The purpose of this study has been to describe motor activity data obtained by using wrist-worn actigraphs in patients with schizophrenia and major depression by the use of linear and non-linear methods of analysis. Different time frames were investigated, i.e., activity counts measured every minute for up to five hours and activity counts made hourly for up to two weeks. The results show that motor activity was lower in the schizophrenic patients and in patients with major depression, compared to controls. Using one minute intervals the depressed patients had a higher standard deviation (SD) compared to both the schizophrenic patients and the controls. The ratio between the root mean square successive differences (RMSSD) and SD was higher in the schizophrenic patients compared to controls. The Fourier analysis of the activity counts measured every minute showed that the relation between variance in the low and the high frequency range was lower in the schizophrenic patients compared to the controls. The sample entropy was higher in the schizophrenic patients compared to controls in the time series from the activity counts made every minute. The main conclusions of the study are that schizophrenic and depressive patients have distinctly different profiles of motor activity and that the results differ according to period length analysed.

  8. Show me the money: cost-benefit analysis in the work environment.

    PubMed

    Levenstein, Charles; Dunn, Mary Lee

    2005-01-01

    During the last several decades, Cost-Benefit Analysis (CBA) has become a widely used technique in public policy-making. This review examines CBA from perspectives of both advocates and critics; it looks at its theory and practice, its purported advantages and shortcomings in application. It also proposes several ways in which the process can be made more accountable.

  9. Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘Bacillus vanillea’ XY18T (=CGMCC 8629 T =NCCB 100507 T) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this type strain was assembled and yielded a length of 3.72 Mbp and a GC content of 46.3%. Comparative genomic analysis with its ...

  10. Aligning ontologies and integrating textual evidence for pathway analysis of microarray data

    SciTech Connect

    Gopalan, Banu; Posse, Christian; Sanfilippo, Antonio P.; Stenzel-Poore, Mary; Stevens, S.L.; Castano, Jose; Beagley, Nathaniel; Riensche, Roderick M.; Baddeley, Bob; Simon, R.P.; Pustejovsky, James

    2006-10-08

    Expression arrays are introducing a paradigmatic change in biology by shifting experimental approaches from single gene studies to genome-level analysis, monitoring the ex-pression levels of several thousands of genes in parallel. The massive amounts of data obtained from the microarray data needs to be integrated and interpreted to infer biological meaning within the context of information-rich pathways. In this paper, we present a methodology that integrates textual information with annotations from cross-referenced ontolo-gies to map genes to pathways in a semi-automated way. We illustrate this approach and compare it favorably to other tools by analyzing the gene expression changes underlying the biological phenomena related to stroke. Stroke is the third leading cause of death and a major disabler in the United States. Through years of study, researchers have amassed a significant knowledge base about stroke, and this knowledge, coupled with new technologies, is providing a wealth of new scientific opportunities. The potential for neu-roprotective stroke therapy is enormous. However, the roles of neurogenesis, angiogenesis, and other proliferative re-sponses in the recovery process following ischemia and the molecular mechanisms that lead to these processes still need to be uncovered. Improved annotation of genomic and pro-teomic data, including annotation of pathways in which genes and proteins are involved, is required to facilitate their interpretation and clinical application. While our approach is not aimed at replacing existing curated pathway databases, it reveals multiple hidden relationships that are not evident with the way these databases analyze functional groupings of genes from the Gene Ontology.

  11. 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.

  12. 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

  13. 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

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

    PubMed

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

    2009-01-01

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

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

    PubMed Central

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

    2009-01-01

    The traditional approach to bioinformatics analyses relies on independent task-specific services and applications, using different input and output formats, often idiosyncratic, and frequently not designed to inter-operate. In general, such analyses were performed by experts who manually verified the results obtained at each step in the process. Today, the amount of bioinformatics information continuously being produced means that handling the various applications used to study this information presents a major data management and analysis challenge to researchers. It is now impossible to manually analyse all this information and new approaches are needed that are capable of processing the large-scale heterogeneous data in order to extract the pertinent information. We review the recent use of integrated expert systems aimed at providing more efficient knowledge extraction for bioinformatics research. A general methodology for building knowledge-based expert systems is described, focusing on the unstructured information management architecture, UIMA, which provides facilities for both data and process management. A case study involving a multiple alignment expert system prototype called AlexSys is also presented. PMID:18971242

  16. Orientational alignment in solids from bidimensional isotropic-anisotropic nuclear magnetic resonance spectroscopy: applications to the analysis of aramide fibers.

    PubMed

    Sachleben, J R; Frydman, L

    1997-02-01

    The use of two-dimensional isotropic-anisotropic correlation spectroscopy for the analysis of orientational alignment in solids is presented. The theoretical background and advantages of this natural-abundance 13C NMR method of measurement are discussed, and demonstrated with a series of powder and single-crystal variable-angle correlation spectroscopy (VACSY) experiments on model systems. The technique is subsequently employed to analyze the orientational distributions of three polymer fibers: Kevlar 29, Kevlar 49 and Kevlar 149. Using complementary two-dimensional NMR data recorded on synthetic samples of poly(p-phenyleneterephthalamide), the precursor of Kevlar, it was found that these commercial fibers possess molecules distributed over a very narrow orientational range with respect to the macroscopic director. The widths measured for these director distribution arrangements were (12 +/- 1.5) degrees for Kevlar 29, (15 +/- 1.5) degrees for Kevlar 49, and (8 +/- 1.5) degrees for Kevlar 149. These figures compare well with previous results obtained for non-commercial fiber samples derived from the same polymer.

  17. The Coordination of Verbal and Nonverbal Interaction towards Three Parties: The Analysis of a Talk Show.

    ERIC Educational Resources Information Center

    von Raffler-Engel, Walburga

    A study of randomly selected "Donahue" shows revealed how host Phil Donahue interacts with several parties at one time and how he subordinates various interactions to suit the hierarchy of importance he attributes to each party, with the television viewer being the most important. Donahue organizes his body movement mainly for television viewers.…

  18. Molecular Analysis of Mixed Endometrial Carcinomas Shows Clonality in Most Cases.

    PubMed

    Köbel, Martin; Meng, Bo; Hoang, Lien N; Almadani, Noorah; Li, Xiaodong; Soslow, Robert A; Gilks, C Blake; Lee, Cheng-Han

    2016-02-01

    Mixed endometrial carcinoma refers to a tumor that comprises 2 or more distinct histotypes. We studied 18 mixed-type endometrial carcinomas-11 mixed serous and low-grade endometrioid carcinomas (SC/EC), 5 mixed clear cell and low-grade ECs (CCC/EC), and 2 mixed CCC and SCs (CCC/SC), using targeted next-generation sequencing and immunohistochemistry to compare the molecular profiles of the different histotypes present in each case. In 16 of 18 cases there was molecular evidence that both components shared a clonal origin. Eight cases (6 EC/SC, 1 EC/CCC, and 1 SC/CCC) showed an SC molecular profile that was the same in both components. Five cases (3 CCC/EC and 2 SC/EC) showed a shared endometrioid molecular profile and identical mismatch-repair protein deficiency in both components. A single SC/EC case harbored the same POLE exonuclease domain mutation in both components. One SC/CCC and 1 EC/CCC case showed both shared and unique molecular features in the 2 histotype components, suggesting early molecular divergence from a common clonal origin. In 2 cases, there were no shared molecular features, and these appear to be biologically unrelated synchronous tumors. Overall, these results show that the different histologic components in mixed endometrial carcinomas typically share the same molecular aberrations. Mixed endometrial carcinomas most commonly occur through morphologic mimicry, whereby tumors with serous-type molecular profile show morphologic features of EC or CCC, or through underlying deficiency in DNA nucleotide repair, with resulting rapid accrual of mutations and intratumoral phenotypic heterogeneity. Less commonly, mixed endometrial carcinomas are the result of early molecular divergence from a common progenitor clone or are synchronous biologically unrelated tumors (collision tumors).

  19. Lexical alignment in triadic communication.

    PubMed

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

    2015-01-01

    Lexical alignment refers to the adoption of one's interlocutor's lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants' lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment.

  20. Lexical alignment in triadic communication

    PubMed Central

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

    2015-01-01

    Lexical alignment refers to the adoption of one’s interlocutor’s lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants’ lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment. PMID:25762955

  1. Social Network Analysis Shows Direct Evidence for Social Transmission of Tool Use in Wild Chimpanzees

    PubMed Central

    Hobaiter, Catherine; Poisot, Timothée; Zuberbühler, Klaus; Hoppitt, William; Gruber, Thibaud

    2014-01-01

    Social network analysis methods have made it possible to test whether novel behaviors in animals spread through individual or social learning. To date, however, social network analysis of wild populations has been limited to static models that cannot precisely reflect the dynamics of learning, for instance, the impact of multiple observations across time. Here, we present a novel dynamic version of network analysis that is capable of capturing temporal aspects of acquisition—that is, how successive observations by an individual influence its acquisition of the novel behavior. We apply this model to studying the spread of two novel tool-use variants, “moss-sponging” and “leaf-sponge re-use,” in the Sonso chimpanzee community of Budongo Forest, Uganda. Chimpanzees are widely considered the most “cultural” of all animal species, with 39 behaviors suspected as socially acquired, most of them in the domain of tool-use. The cultural hypothesis is supported by experimental data from captive chimpanzees and a range of observational data. However, for wild groups, there is still no direct experimental evidence for social learning, nor has there been any direct observation of social diffusion of behavioral innovations. Here, we tested both a static and a dynamic network model and found strong evidence that diffusion patterns of moss-sponging, but not leaf-sponge re-use, were significantly better explained by social than individual learning. The most conservative estimate of social transmission accounted for 85% of observed events, with an estimated 15-fold increase in learning rate for each time a novice observed an informed individual moss-sponging. We conclude that group-specific behavioral variants in wild chimpanzees can be socially learned, adding to the evidence that this prerequisite for culture originated in a common ancestor of great apes and humans, long before the advent of modern humans. PMID:25268798

  2. Numerical analysis of lamination effect in a vortex micro T-mixer with non-aligned inputs

    NASA Astrophysics Data System (ADS)

    Rabani, Ramin; Talebi, Shahram; Rabani, Mehrdad

    2016-03-01

    In the present study, the lamination effect in a micro T-mixer with non-aligned inputs on the mixing index has been investigated numerically in four different cases. The multi-block lattice Boltzmann method has been implemented for the flow field simulation and the second order upwind finite difference scheme has been used to simulate mass transfer. Reynolds numbers includes in the range of 10 ≤ Re ≤ 70. The simulation results show that the lamination effect in the mixer inputs, despite of its simple design, causes the interface of two fluids to increase and also to make the vortex effect stronger in the confluence of two fluid streams that increases the mixing index considerably. Of four lamination cases included for the mixing input, the maximum mixing index is for the vertical and asymmetrical lamination at the Reynolds number of 70 that is equal 0.689 and the minimum mixing index is for the horizontal and asymmetrical lamination at the Reynolds number of 10 that is equal 0.198.

  3. Analysis of lymphocytes in, and host environment of, mice showing conditioned immunosuppression to cyclophosphamide

    SciTech Connect

    Gorczynski, R.M.

    1987-03-01

    Mice were subjected to repeated exposures to cyclophosphamide: saccharin (conditioned) or cyclophosphamide:saccharin followed by saccharin only (conditioned:extinguished). Animals in the former group but not the latter subsequently showed diminished IgG antibody-forming cells (AFC) after challenge with sheep red blood cells followed by reexposure to immunologically inert cues (saccharin). When these animals were used as irradiated recipients of syngeneic spleen lymphocytes, reconstituted irradiated conditioned mice showed augmented IgG AFC on transfer of naive spleen cells and reexposure to saccharin. The expected diminished IgG AFC response was seen when cells from conditioned mice were transferred. However, the latter cells gave augmented IgG AFC when transferred to naive irradiated mice. Both of the effects seen with cells from conditioned animals (increased IgG AFC in control recipients; decreased IgG AFC in conditioned mice reexposed to saccharin) were regulated by adoptively transferred T cells in the spleen cell population.

  4. Higher dimensional analysis shows reduced dynamism of time-varying network connectivity in schizophrenia patients.

    PubMed

    Miller, Robyn L; Yaesoubi, Maziar; Calhoun, Vince D

    2014-01-01

    Assessments of functional connectivity between brain networks is a fixture of resting state fMRI research. Until very recently most of this work proceeded from an assumption of stationarity in resting state network connectivity. In the last few years however, interest in moving beyond this simplifying assumption has grown considerably. Applying group temporal independent component analysis (tICA) to a set of time-varying functional network connectivity (FNC) matrices derived from a large multi-site fMRI dataset (N=314; 163 healthy, 151 schizophrenia patients), we obtain a set of five basic correlation patterns (component spatial maps (SMs)) from which observed FNCs can be expressed as mutually independent linear combinations, i.e., the coefficient on each SM in the linear combination is maximally independent of the others. We study dynamic properties of network connectivity as they are reflected in this five-dimensional space, and report stark differences in connectivity dynamics between schizophrenia patients and healthy controls. We also find that the most important global differences in FNC dynamism between patient and control groups are replicated when the same dynamical analysis is performed on sets of correlation patterns obtained from either PCA or spatial ICA, giving us additional confidence in the results.

  5. Quantitative analysis of intra-Golgi transport shows intercisternal exchange for all cargo

    PubMed Central

    Dmitrieff, Serge; Rao, Madan; Sens, Pierre

    2013-01-01

    The mechanisms controlling the transport of proteins through the Golgi stack of mammalian and plant cells is the subject of intense debate, with two models, cisternal progression and intercisternal exchange, emerging as major contenders. A variety of transport experiments have claimed support for each of these models. We reevaluate these experiments using a single quantitative coarse-grained framework of intra-Golgi transport that accounts for both transport models and their many variants. Our analysis makes a definitive case for the existence of intercisternal exchange both for small membrane proteins and large protein complexes––this implies that membrane structures larger than the typical protein-coated vesicles must be involved in transport. Notwithstanding, we find that current observations on protein transport cannot rule out cisternal progression as contributing significantly to the transport process. To discriminate between the different models of intra-Golgi transport, we suggest experiments and an analysis based on our extended theoretical framework that compare the dynamics of transiting and resident proteins. PMID:24019488

  6. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  7. Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency

    PubMed Central

    2012-01-01

    Background Plants react to iron deficiency stress adopting different kind of adaptive responses. Tomato, a Strategy I plant, improves iron uptake through acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Large-scale transcriptional analyses of roots under iron deficiency are only available for a very limited number of plant species with particular emphasis for Arabidopsis thaliana. Regarding tomato, an interesting model species for Strategy I plants and an economically important crop, physiological responses to Fe-deficiency have been thoroughly described and molecular analyses have provided evidence for genes involved in iron uptake mechanisms and their regulation. However, no detailed transcriptome analysis has been described so far. Results A genome-wide transcriptional analysis, performed with a chip that allows to monitor the expression of more than 25,000 tomato transcripts, identified 97 differentially expressed transcripts by comparing roots of Fe-deficient and Fe-sufficient tomato plants. These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle. Other genes play a role in flavonoid biosynthesis and hormonal metabolism. Conclusions The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency. PMID:22433273

  8. Classification of gasoline data obtained by gas chromatography using a piecewise alignment algorithm combined with feature selection and principal component analysis

    SciTech Connect

    Pierce, Karisa M.; Hope, Janiece L.; Johnson, Kevin J.; Wright, Bob W.; Synovec, Robert E.

    2005-11-25

    A fast and objective chemometric classification method is developed and applied to the analysis of gas chromatography (GC) data from five commercial gasoline samples. The gasoline samples serve as model mixtures, whereas the focus is on the development and demonstration of the classification method. The method is based on objective retention time alignment (referred to as piecewise alignment) coupled with analysis of variance (ANOVA) feature selection prior to classification by principal component analysis (PCA) using optimal parameters. The degree-of-class-separation is used as a metric to objectively optimize the alignment and feature selection parameters using a suitable training set thereby reducing user subjectivity, as well as to indicate the success of the PCA clustering and classification. The degree-of-class-separation is calculated using Euclidean distances between the PCA scores of a subset of the replicate runs from two of the five fuel types, i.e., the training set. The unaligned training set that was directly submitted to PCA had a low degree-of-class-separation (0.4), and the PCA scores plot for the raw training set combined with the raw test set failed to correctly cluster the five sample types. After submitting the training set to piecewise alignment, the degree-of-class-separation increased (1.2), but when the same alignment parameters were applied to the training set combined with the test set, the scores plot clustering still did not yield five distinct groups. Applying feature selection to the unaligned training set increased the degree-of-class-separation (4.8), but chemical variations were still obscured by retention time variation and when the same feature selection conditions were used for the training set combined with the test set, only one of the five fuels was clustered correctly. However, piecewise alignment coupled with feature selection yielded a reasonably optimal degree-of-class-separation for the training set (9.2), and when the

  9. AlignNemo: A Local Network Alignment Method to Integrate Homology and Topology

    PubMed Central

    Guzzi, Pietro H.; Cannataro, Mario; Guerra, Concettina

    2012-01-01

    Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo. PMID:22719866

  10. Analysis of Cylinder-pressure-indicator Diagrams Showing Effects of Mixture Strength and Spark Timing

    NASA Technical Reports Server (NTRS)

    Gerrish, Harold C; Voss, Fred

    1940-01-01

    An investigation was made to determine the effect of mixture strength and of normal as well as optimum spark timing on the combustion, on the cylinder temperature, and on the performance characteristics of an engine. A single-cylinder test unit utilizing an air-cooled cylinder and a carburetor and operating with gasoline having an octane rating of 92 was used. The investigation covered a range of fuel-air ratios from 0.053 to 0.118. Indicator diagrams and engine-performance data were taken for each change in engine conditions. Examination of the indicator shows that for fuel-air ratios less than and greater than 0.082 the rate and the amount of effective fuel burned decreased. For a fuel-air ratio of 0.118 the combustion efficiency was only 58 percent. Advancing the spark timing increased the rate of pressure rise. This effect was more pronounced with leaner mixtures.

  11. Hereditary Sensory Neuropathy Type I: Haplotype Analysis Shows Founders in Southern England and Europe

    PubMed Central

    Nicholson, G. A.; Dawkins, J. L.; Blair, I. P.; Auer-Grumbach, M.; Brahmbhatt, S. B.; Hulme, D. J.

    2001-01-01

    Hereditary sensory neuropathy type I (HSN1) is the most common dominantly inherited degenerative disorder of sensory neurons. The gene mutation was mapped to chromosome 9 in a large Australian family, descended from an ancestor from southern England who was a convict. Dawkins et al. recently reported gene mutations in the SPTLC1 gene, in this and other families. The first description of hereditary sensory neuropathy, by Hicks, was in a family from London and Exeter. To determine if the families in the present study that have SPTLC1 mutations are related to English families with HSN1 and, possibly, to the family studied by Hicks, we performed haplotype analysis of four Australian families of English extraction, four English families, and one Austrian family. Three Australian families of English extraction and three English families (two of whom have been described elsewhere) had the 399T→G SPTLC1 mutation, the same chromosome 9 haplotype, and the same phenotype. The Australian and English families may therefore have a common founder who, on the basis of historical information, has been determined to have lived in southern England prior to 1800. The sensorimotor neuropathy phenotype caused by the 399T→G SPTLC1 mutation is the same as that reported by Campbell and Hoffman and, possibly, the same as that originally described by Hicks. PMID:11479835

  12. Hereditary sensory neuropathy type I: haplotype analysis shows founders in southern England and Europe.

    PubMed

    Nicholson, G A; Dawkins, J L; Blair, I P; Auer-Grumbach, M; Brahmbhatt, S B; Hulme, D J

    2001-09-01

    Hereditary sensory neuropathy type I (HSN1) is the most common dominantly inherited degenerative disorder of sensory neurons. The gene mutation was mapped to chromosome 9 in a large Australian family, descended from an ancestor from southern England who was a convict. Dawkins et al. recently reported gene mutations in the SPTLC1 gene, in this and other families. The first description of hereditary sensory neuropathy, by Hicks, was in a family from London and Exeter. To determine if the families in the present study that have SPTLC1 mutations are related to English families with HSN1 and, possibly, to the family studied by Hicks, we performed haplotype analysis of four Australian families of English extraction, four English families, and one Austrian family. Three Australian families of English extraction and three English families (two of whom have been described elsewhere) had the 399T-->G SPTLC1 mutation, the same chromosome 9 haplotype, and the same phenotype. The Australian and English families may therefore have a common founder who, on the basis of historical information, has been determined to have lived in southern England prior to 1800. The sensorimotor neuropathy phenotype caused by the 399T-->G SPTLC1 mutation is the same as that reported by Campbell and Hoffman and, possibly, the same as that originally described by Hicks. PMID:11479835

  13. Testing the tidal alignment model of galaxy intrinsic alignment

    SciTech Connect

    Blazek, Jonathan; Seljak, Uroš; McQuinn, Matthew E-mail: mmcquinn@berkeley.edu

    2011-05-01

    Weak gravitational lensing has become a powerful probe of large-scale structure and cosmological parameters. Precision weak lensing measurements require an understanding of the intrinsic alignment of galaxy ellipticities, which can in turn inform models of galaxy formation. It is hypothesized that elliptical galaxies align with the background tidal field and that this alignment mechanism dominates the correlation between ellipticities on cosmological scales (in the absence of lensing). We use recent large-scale structure measurements from the Sloan Digital Sky Survey to test this picture with several statistics: (1) the correlation between ellipticity and galaxy overdensity, w{sub g+}; (2) the intrinsic alignment auto-correlation functions; (3) the correlation functions of curl-free, E, and divergence-free, B, modes, the latter of which is zero in the linear tidal alignment theory; (4) the alignment correlation function, w{sub g}(r{sub p},θ), a recently developed statistic that generalizes the galaxy correlation function to account for the angle between the galaxy separation vector and the principle axis of ellipticity. We show that recent measurements are largely consistent with the tidal alignment model and discuss dependence on galaxy luminosity. In addition, we show that at linear order the tidal alignment model predicts that the angular dependence of w{sub g}(r{sub p},θ) is simply w{sub g+}(r{sub p})cos (2θ) and that this dependence is consistent with recent measurements. We also study how stochastic nonlinear contributions to galaxy ellipticity impact these statistics. We find that a significant fraction of the observed LRG ellipticity can be explained by alignment with the tidal field on scales ∼> 10 \\hMpc. These considerations are relevant to galaxy formation and evolution.

  14. Transcriptome analysis of Bifidobacterium longum strains that show a differential response to hydrogen peroxide stress.

    PubMed

    Oberg, Taylor S; Ward, Robert E; Steele, James L; Broadbent, Jeff R

    2015-10-20

    Consumer and commercial interest in foods containing probiotic bifidobacteria is increasing. However, because bifidobacteria are anaerobic, oxidative stress can diminish cell viability during production and storage of bioactive foods. We previously found Bifidobacterium longum strain NCC2705 had significantly greater intrinsic and inducible resistance to hydrogen peroxide (H2O2) than strain D2957. Here, we explored the basis for these differences by examining the transcriptional responses of both strains to sub-lethal H2O2 exposure for 5- or 60-min. Strain NCC2705 had 288 genes that were differentially expressed after the 5-min treatment and 114 differentially expressed genes after the 60-min treatment. In contrast, strain D2957 had only 21 and 90 differentially expressed genes after the 5- and 60-min treatments, respectively. Both strains showed up-regulation of genes coding enzymes implicated in oxidative stress resistance, such as thioredoxin, thioredoxin reductase, peroxiredoxin, ferredoxin, glutaredoxin, and anaerobic ribonucleotide reductase, but induction levels were typically highest in NCC2705. Compared to D2957, NCC2705 also had more up-regulated genes involved in transcriptional regulation and more down-regulated genes involved in sugar transport and metabolism. These results provide a greater understanding of the molecular basis for oxidative stress resistance in B. longum and the factors that contribute to strain-to-strain variability in survival in bioactive food products. PMID:26299205

  15. Computational analysis shows why transcranial alternating current stimulation induces retinal phosphenes

    NASA Astrophysics Data System (ADS)

    Laakso, Ilkka; Hirata, Akimasa

    2013-08-01

    Objective. Transcranial alternating current stimulation (tACS), which is a novel technique for the manipulation of cortical oscillations, can generate subjective visual sensations (phosphenes). In this work, we computationally investigate the current that reaches the eyes from tACS electrodes in order to show that phosphenes induced by tACS are retinal in origin. Approach. The finite-element method is used for modelling the path of the current in an anatomically realistic model of the head for various electrode montages. The computational results are used for analysing previous experimental data to investigate the sensitivity of the eye to electrical stimulation. Main results. Depending on the locations of both the stimulating and reference electrodes, a small portion of the stimulation current chooses a path that goes through the eyes. Due to the sensitivity of the retina to electrical stimulation, even distant electrodes can produce a sufficiently strong current at the eyes for inducing retinal phosphenes. Significance. The interference from retinal phosphenes needs to be considered in the design of tACS experiments. The occurrence of phosphenes can be reduced by optimizing the locations of the electrodes, or potentially increasing the number of reference electrodes to two or more. Computational modelling is an effective tool for guiding the electrode positioning.

  16. Genome-Wide Expression Analysis of Soybean MADS Genes Showing Potential Function in the Seed Development

    PubMed Central

    Hu, Rui-Bo; Zhang, Xiao-Mei; Chen, Jian-Xin; Fu, Yong-Fu

    2013-01-01

    The MADS family is an ancient and best-studied transcription factor and plays fundamental roles in almost every developmental process in plants. In the plant evolutionary history, the whole genome duplication (WGD) events are important not only to the plant species evolution, but to expansion of members of the gene families. Soybean as a model legume crop has experience three rounds of WGD events. Members of some MIKCC subfamilies, such as SOC, AGL6, SQUA, SVP, AGL17 and DEF/GLO, were expanded after soybean three rounds of WGD events. And some MIKCC subfamilies, MIKC* and type I MADS families had experienced faster birth-and-death evolution and their traces before the Glycine WGD event were not found. Transposed duplication played important roles in tandem arrangements among the members of different subfamilies. According to the expression profiles of type I and MIKC paralog pair genes, the fates of MIKC paralog gene pairs were subfunctionalization, and the fates of type I MADS paralog gene pairs were nonfunctionalization. 137 out of 163 MADS genes were close to 186 loci within 2 Mb genomic regions associated with seed-relative QTLs, among which 115 genes expressed during the seed development. Although MIKCC genes kept the important and conserved functions of the flower development, most MIKCC genes showed potentially essential roles in the seed development as well as the type I MADS. PMID:23638026

  17. Inflation by alignment

    SciTech Connect

    Burgess, C.P.; Roest, Diederik

    2015-06-08

    Pseudo-Goldstone bosons (pGBs) can provide technically natural inflatons, as has been comparatively well-explored in the simplest axion examples. Although inflationary success requires trans-Planckian decay constants, f≳M{sub p}, several mechanisms have been proposed to obtain this, relying on (mis-)alignments between potential and kinetic energies in multiple-field models. We extend these mechanisms to a broader class of inflationary models, including in particular the exponential potentials that arise for pGB potentials based on noncompact groups (and so which might apply to moduli in an extra-dimensional setting). The resulting potentials provide natural large-field inflationary models and can predict a larger primordial tensor signal than is true for simpler single-field versions of these models. In so doing we provide a unified treatment of several alignment mechanisms, showing how each emerges as a limit of the more general setup.

  18. Magnetic alignment and the Poisson alignment reference system

    NASA Astrophysics Data System (ADS)

    Griffith, L. V.; Schenz, R. F.; Sommargren, G. E.

    1990-08-01

    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This article begins with a review of the motivation for developing an alignment system that will assure better than 100-μm accuracy in the alignment of the magnetic axis throughout an FEL. The 100-μm accuracy is an error circle about an ideal axis for 300 m or more. The article describes techniques for identifying the magnetic axes of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development of a straight-line reference based on the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. The Poisson alignment reference system should be accurate to 25 μm over 300 m, which is believed to be a factor-of-4 improvement over earlier techniques. An error budget shows that only 25% of the total budgeted tolerance is used for the alignment reference system, so the remaining tolerances should fall within the allowable range for FEL alignment.

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

    PubMed Central

    2015-01-01

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

  20. Vertically Aligned Nitrogen-Doped Carbon Nanotube Carpet Electrodes: Highly Sensitive Interfaces for the Analysis of Serum from Patients with Inflammatory Bowel Disease.

    PubMed

    Wang, Qian; Subramanian, Palaniappan; Schechter, Alex; Teblum, Eti; Yemini, Reut; Nessim, Gilbert Daniel; Vasilescu, Alina; Li, Musen; Boukherroub, Rabah; Szunerits, Sabine

    2016-04-20

    The number of patients suffering from inflammatory bowel disease (IBD) is increasing worldwide. The development of noninvasive tests that are rapid, sensitive, specific, and simple would allow preventing patient discomfort, delay in diagnosis, and the follow-up of the status of the disease. Herein, we show the interest of vertically aligned nitrogen-doped carbon nanotube (VA-NCNT) electrodes for the required sensitive electrochemical detection of lysozyme in serum, a protein that is up-regulated in IBD. To achieve selective lysozyme detection, biotinylated lysozyme aptamers were covalently immobilized onto the VA-NCNTs. Detection of lysozyme in serum was achieved by measuring the decrease in the peak current of the Fe(CN)6(3-/4-) redox couple by differential pulse voltammetry upon addition of the analyte. We achieved a detection limit as low as 100 fM with a linear range up to 7 pM, in line with the required demands for the determination of lysozyme level in patients suffering from IBD. We attained the sensitive detection of biomarkers in clinical samples of healthy patients and individuals suffering from IBD and compared the results to a classical turbidimetric assay. The results clearly indicate that the newly developed sensor allows for a reliable and efficient analysis of lysozyme in serum.

  1. Vertically Aligned Nitrogen-Doped Carbon Nanotube Carpet Electrodes: Highly Sensitive Interfaces for the Analysis of Serum from Patients with Inflammatory Bowel Disease.

    PubMed

    Wang, Qian; Subramanian, Palaniappan; Schechter, Alex; Teblum, Eti; Yemini, Reut; Nessim, Gilbert Daniel; Vasilescu, Alina; Li, Musen; Boukherroub, Rabah; Szunerits, Sabine

    2016-04-20

    The number of patients suffering from inflammatory bowel disease (IBD) is increasing worldwide. The development of noninvasive tests that are rapid, sensitive, specific, and simple would allow preventing patient discomfort, delay in diagnosis, and the follow-up of the status of the disease. Herein, we show the interest of vertically aligned nitrogen-doped carbon nanotube (VA-NCNT) electrodes for the required sensitive electrochemical detection of lysozyme in serum, a protein that is up-regulated in IBD. To achieve selective lysozyme detection, biotinylated lysozyme aptamers were covalently immobilized onto the VA-NCNTs. Detection of lysozyme in serum was achieved by measuring the decrease in the peak current of the Fe(CN)6(3-/4-) redox couple by differential pulse voltammetry upon addition of the analyte. We achieved a detection limit as low as 100 fM with a linear range up to 7 pM, in line with the required demands for the determination of lysozyme level in patients suffering from IBD. We attained the sensitive detection of biomarkers in clinical samples of healthy patients and individuals suffering from IBD and compared the results to a classical turbidimetric assay. The results clearly indicate that the newly developed sensor allows for a reliable and efficient analysis of lysozyme in serum. PMID:27015265

  2. Structure alignment of membrane proteins: Accuracy of available tools and a consensus strategy.

    PubMed

    Stamm, Marcus; Forrest, Lucy R

    2015-09-01

    Protein structure alignment methods are used for the detection of evolutionary and functionally related positions in proteins. A wide array of different methods are available, but the choice of the best method is often not apparent to the user. Several studies have assessed the alignment accuracy and consistency of structure alignment methods, but none of these explicitly considered membrane proteins, which are important targets for drug development and have distinct structural features. Here, we compared 13 widely used pairwise structural alignment methods on a test set of homologous membrane protein structures (called HOMEP3). Each pair of structures was aligned and the corresponding sequence alignment was used to construct homology models. The model accuracy compared to the known structures was assessed using scoring functions not incorporated in the tested structural alignment methods. The analysis shows that fragment-based approaches such as FR-TM-align are the most useful for aligning structures of membrane proteins. Moreover, fragment-based approaches are more suitable for comparison of protein structures that have undergone large conformational changes. Nevertheless, no method was clearly superior to all other methods. Additionally, all methods lack a measure to rate the reliability of a position within a structure alignment. To solve both of these problems, we propose a consensus-type approach, combining alignments from four different methods, namely FR-TM-align, DaliLite, MATT, and FATCAT. Agreement between the methods is used to assign confidence values to each position of the alignment. Overall, we conclude that there remains scope for the improvement of structural alignment methods for membrane proteins.

  3. Dynamic Alignment at SLS

    SciTech Connect

    Ruland, Robert E.

    2003-04-23

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

  4. A Mixed-Method Analysis of the Alignment of Title I Achieving Schools' Professional Development to NCLB Professional Development Provisions

    ERIC Educational Resources Information Center

    Quinn, Kerry

    2013-01-01

    The improvement of schools has been a central discussion among educators, legislators, and stakeholders, with professional development being acknowledged as a fundamental topic for the success of the education system. Studying the alignment of professional development programs provided at Title I Achieving schools to NCLB research based…

  5. Lessons Learned in Systemic District Reform: A Cross-District Analysis from the Comprehensive Aligned Instructional System (CAIS) Benchmarking Study

    ERIC Educational Resources Information Center

    Waters, Louise Bay; Vargo, Merrill

    2008-01-01

    Urban district reform has been hampered by the challenge of understanding and supporting the tremendous complexity of district change. Improving this understanding through actionable, practice-based research is the purpose of this study. The authors began the study with the hypothesis that achieving districts both align their instructional systems…

  6. Aligned genomic data compression via improved modeling.

    PubMed

    Ochoa, Idoia; Hernaez, Mikel; Weissman, Tsachy

    2014-12-01

    With the release of the latest Next-Generation Sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing the whole genome of a human is expected to drop to a mere $1000. This milestone in sequencing history marks the era of affordable sequencing of individuals and opens the doors to personalized medicine. In accord, unprecedented volumes of genomic data will require storage for processing. There will be dire need not only of compressing aligned data, but also of generating compressed files that can be fed directly to downstream applications to facilitate the analysis of and inference on the data. Several approaches to this challenge have been proposed in the literature; however, focus thus far has been on the low coverage regime and most of the suggested compressors are not based on effective modeling of the data. We demonstrate the benefit of data modeling for compressing aligned reads. Specifically, we show that, by working with data models designed for the aligned data, we can improve considerably over the best compression ratio achieved by previously proposed algorithms. Our results indicate that the pareto-optimal barrier for compression rate and speed claimed by Bonfield and Mahoney (2013) [Bonfield JK and Mahoneys MV, Compression of FASTQ and SAM format sequencing data, PLOS ONE, 8(3):e59190, 2013.] does not apply for high coverage aligned data. Furthermore, our improved compression ratio is achieved by splitting the data in a manner conducive to operations in the compressed domain by downstream applications.

  7. Aligned genomic data compression via improved modeling.

    PubMed

    Ochoa, Idoia; Hernaez, Mikel; Weissman, Tsachy

    2014-12-01

    With the release of the latest Next-Generation Sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing the whole genome of a human is expected to drop to a mere $1000. This milestone in sequencing history marks the era of affordable sequencing of individuals and opens the doors to personalized medicine. In accord, unprecedented volumes of genomic data will require storage for processing. There will be dire need not only of compressing aligned data, but also of generating compressed files that can be fed directly to downstream applications to facilitate the analysis of and inference on the data. Several approaches to this challenge have been proposed in the literature; however, focus thus far has been on the low coverage regime and most of the suggested compressors are not based on effective modeling of the data. We demonstrate the benefit of data modeling for compressing aligned reads. Specifically, we show that, by working with data models designed for the aligned data, we can improve considerably over the best compression ratio achieved by previously proposed algorithms. Our results indicate that the pareto-optimal barrier for compression rate and speed claimed by Bonfield and Mahoney (2013) [Bonfield JK and Mahoneys MV, Compression of FASTQ and SAM format sequencing data, PLOS ONE, 8(3):e59190, 2013.] does not apply for high coverage aligned data. Furthermore, our improved compression ratio is achieved by splitting the data in a manner conducive to operations in the compressed domain by downstream applications. PMID:25395305

  8. Strain-Induced Alignment in Collagen Gels

    PubMed Central

    Vader, David; Kabla, Alexandre; Weitz, David; Mahadevan, Lakshminarayana

    2009-01-01

    Collagen is the most abundant extracellular-network-forming protein in animal biology and is important in both natural and artificial tissues, where it serves as a material of great mechanical versatility. This versatility arises from its almost unique ability to remodel under applied loads into anisotropic and inhomogeneous structures. To explore the origins of this property, we develop a set of analysis tools and a novel experimental setup that probes the mechanical response of fibrous networks in a geometry that mimics a typical deformation profile imposed by cells in vivo. We observe strong fiber alignment and densification as a function of applied strain for both uncrosslinked and crosslinked collagenous networks. This alignment is found to be irreversibly imprinted in uncrosslinked collagen networks, suggesting a simple mechanism for tissue organization at the microscale. However, crosslinked networks display similar fiber alignment and the same geometrical properties as uncrosslinked gels, but with full reversibility. Plasticity is therefore not required to align fibers. On the contrary, our data show that this effect is part of the fundamental non-linear properties of fibrous biological networks. PMID:19529768

  9. Magnetic axis alignment and the Poisson alignment reference system

    NASA Astrophysics Data System (ADS)

    Griffith, Lee V.; Schenz, Richard F.; Sommargren, Gary E.

    1989-01-01

    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This paper begins with a review of the motivation for developing an alignment system that will assure better than 100 micrometer accuracy in the alignment of the magnetic axis throughout an FEL. The paper describes techniques for identifying the magnetic axis of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development and use of the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. An error budget shows that the Poisson alignment reference system will make it possible to meet the alignment tolerances for an FEL.

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

    NASA Astrophysics Data System (ADS)

    Gajek, A.; Strzępek, P.

    2016-09-01

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

  11. Modulation of anisotropy in electrospun tissue-engineering scaffolds: Analysis of fiber alignment by the fast Fourier transform

    PubMed Central

    Ayres, Chantal; Bowlin, Gary L.; Henderson, Scott C.; Taylor, Leander; Shultz, Jackie; Alexander, John; Telemeco, Todd A.; Simpson, David G.

    2010-01-01

    We describe the use of the fast Fourier transform (FFT) in the measurement of anisotropy in electrospun scaffolds of gelatin as a function of the starting conditions. In electrospinning, fiber alignment and overall scaffold anisotropy can be manipulated by controlling the motion of the collecting mandrel with respect to the source electrospinning solution. By using FFT to assign relative alignment values to an electrospun matrix it is possible to systematically evaluate how different processing variables impact the structure and material properties of a scaffold. Gelatin was suspended at varying concentrations (80, 100, 130, 150 mg/ml) and electrospun from 2,2,2 trifluoroethanol onto rotating mandrels (200–7000 RPM). At each starting concentration, fiber diameter remained constant over a wide range of mandrel RPM. Scaffold anisotropy developed as a function of fiber diameter and mandrel RPM. The induction of varying degrees of anisotropy imparted distinctive material properties to the electrospun scaffolds. The FFT is a rapid method for evaluating fiber alignment in tissue-engineering materials. PMID:16859744

  12. Simultaneous Alignment and Folding of Protein Sequences

    PubMed Central

    Waldispühl, Jérôme; O'Donnell, Charles W.; Will, Sebastian; Devadas, Srinivas; Backofen, Rolf

    2014-01-01

    Abstract Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments, partiFold-Align significantly outperforms state-of-the-art pairwise and multiple sequence alignment tools in the most difficult low-sequence homology case. It also improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families (partiFold-Align is available at http://partifold.csail.mit.edu/). PMID:24766258

  13. "The Show"

    ERIC Educational Resources Information Center

    Gehring, John

    2004-01-01

    For the past 16 years, the blue-collar city of Huntington, West Virginia, has rolled out the red carpet to welcome young wrestlers and their families as old friends. They have come to town chasing the same dream for a spot in what many of them call "The Show". For three days, under the lights of an arena packed with 5,000 fans, the state's best…

  14. MAVID multiple alignment server.

    PubMed

    Bray, Nicolas; Pachter, Lior

    2003-07-01

    MAVID is a multiple alignment program suitable for many large genomic regions. The MAVID web server allows biomedical researchers to quickly obtain multiple alignments for genomic sequences and to subsequently analyse the alignments for conserved regions. MAVID has been successfully used for the alignment of closely related species such as primates and also for the alignment of more distant organisms such as human and fugu. The server is fast, capable of aligning hundreds of kilobases in less than a minute. The multiple alignment is used to build a phylogenetic tree for the sequences, which is subsequently used as a basis for identifying conserved regions in the alignment. The server can be accessed at http://baboon.math.berkeley.edu/mavid/.

  15. 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.

  16. 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.

  17. Classification of High Speed Gas Chromatography-Mass Spectrometry Data by Principal Component Analysis Coupled with Piecewise Alignment and Feature Selection

    SciTech Connect

    Watson, Nathaniel E.; VanWingerden, Matthew M.; Pierce, Karisa M.; Wright, Bob W.; Synovec, Robert E.

    2006-09-01

    A useful procedure is introduced for the analysis of data obtained via gas chromatography with mass spectrometry (GC-MS) utilizing a complete mass spectrum at each retention time interval in which a mass spectrum was collected. Principal component analysis (PCA) with preprocessing by both piecewise retention time alignment and analysis of variance (ANOVA) feature selection is applied to all mass channels collected. The procedure involves concatenating all concurrently measured individual m/z chromatograms from m/z 20 to 120 for each GC-MS separation into a row vector. All of the sample row vectors are incorporated into a matrix where each row is a sample vector. This matrix is piecewise aligned and reduced by ANOVA feature selection. Application of the preprocessing steps (retention time alignment and feature selection) to all mass channels collected during the chromatographic separation allows considerably more selective chemical information to be incorporated in the PCA classification, and is the primary novelty of the report. This procedure is objective and requires no knowledge of the specific analytes of interest, as in selective ion monitoring (SIM), and does not restrict the mass spectral data used, as in both SIM and total ion current (TIC) methods. Significantly, the procedure allows for the classification of data with low resolution in the chromatographic dimension because of the added selectivity from the complete mass spectral dimension. This allows for the successful classification of data over significantly decreased chromatographic separation times, since high-speed separations can be employed. The procedure is demonstrated through the analysis of a set of four differing gasoline samples that serve as model complex samples. For comparison, the gasoline samples are analyzed by GC-MS over both ten-minute and ten-second separation times. The ten-minute GC-MS TIC data served as the benchmark analysis to compare to the ten-second data. When only alignment

  18. Multi-threading the generation of Burrows-Wheeler Alignment.

    PubMed

    Jo, H

    2016-01-01

    Along with recent progress in next-generation sequencing technology, it has become easier to process larger amounts of genome sequencing data at a lower cost. The most time-consuming step of next-generation sequencing data analysis involves the mapping of read data into a reference genome. Although the Burrows-Wheeler Alignment (BWA) tool is one of the most widely used open-source software tools for aligning read sequences, it still has a limitation in that it does not fully support a multi-thread mechanism during the alignment generation step. In this article, we propose a BWA-MT tool based on BWA that supports multi-thread mechanisms for processing alignment generation. To evaluate BWA-MT, we used an evaluation system equipped with 24 cores and 128 GB of memory. As workloads, we used the hg19 human genome reference sequence and sequences of various read sizes from the 1 to 40 M spots. In our evaluation, BWA-MT showed a maximum of 3.66-times better performance, and generated the same Sequence Alignment/Map result file as that of BWA. Although the ability to speed up the procedure might be dependent on computing resources, we confirmed that BWA-MT is a highly effective and fast alignment tool. PMID:27323088

  19. Cellular self-organization by autocatalytic alignment feedback

    PubMed Central

    Junkin, Michael; Leung, Siu Ling; Whitman, Samantha; Gregorio, Carol C.; Wong, Pak Kin

    2011-01-01

    Myoblasts aggregate, differentiate and fuse to form skeletal muscle during both embryogenesis and tissue regeneration. For proper muscle function, long-range self-organization of myoblasts is required to create organized muscle architecture globally aligned to neighboring tissue. However, how the cells process geometric information over distances considerably longer than individual cells to self-organize into well-ordered, aligned and multinucleated myofibers remains a central question in developmental biology and regenerative medicine. Using plasma lithography micropatterning to create spatial cues for cell guidance, we show a physical mechanism by which orientation information can propagate for a long distance from a geometric boundary to guide development of muscle tissue. This long-range alignment occurs only in differentiating myoblasts, but not in non-fusing myoblasts perturbed by microfluidic disturbances or other non-fusing cell types. Computational cellular automata analysis of the spatiotemporal evolution of the self-organization process reveals that myogenic fusion in conjunction with rotational inertia functions in a self-reinforcing manner to enhance long-range propagation of alignment information. With this autocatalytic alignment feedback, well-ordered alignment of muscle could reinforce existing orientations and help promote proper arrangement with neighboring tissue and overall organization. Such physical self-enhancement might represent a fundamental mechanism for long-range pattern formation during tissue morphogenesis. PMID:22193956

  20. Girder Alignment Plan

    SciTech Connect

    Wolf, Zackary; Ruland, Robert; LeCocq, Catherine; Lundahl, Eric; Levashov, Yurii; Reese, Ed; Rago, Carl; Poling, Ben; Schafer, Donald; Nuhn, Heinz-Dieter; Wienands, Uli; /SLAC

    2010-11-18

    The girders for the LCLS undulator system contain components which must be aligned with high accuracy relative to each other. The alignment is one of the last steps before the girders go into the tunnel, so the alignment must be done efficiently, on a tight schedule. This note documents the alignment plan which includes efficiency and high accuracy. The motivation for girder alignment involves the following considerations. Using beam based alignment, the girder position will be adjusted until the beam goes through the center of the quadrupole and beam finder wire. For the machine to work properly, the undulator axis must be on this line and the center of the undulator beam pipe must be on this line. The physics reasons for the undulator axis and undulator beam pipe axis to be centered on the beam are different, but the alignment tolerance for both are similar. In addition, the beam position monitor must be centered on the beam to preserve its calibration. Thus, the undulator, undulator beam pipe, quadrupole, beam finder wire, and beam position monitor axes must all be aligned to a common line. All relative alignments are equally important, not just, for example, between quadrupole and undulator. We begin by making the common axis the nominal beam axis in the girder coordinate system. All components will be initially aligned to this axis. A more accurate alignment will then position the components relative to each other, without incorporating the girder itself.

  1. Interstellar Dust Grain Alignment

    NASA Astrophysics Data System (ADS)

    Andersson, B.-G.; Lazarian, A.; Vaillancourt, John E.

    2015-08-01

    Interstellar polarization at optical-to-infrared wavelengths is known to arise from asymmetric dust grains aligned with the magnetic field. This effect provides a potentially powerful probe of magnetic field structure and strength if the details of the grain alignment can be reliably understood. Theory and observations have recently converged on a quantitative, predictive description of interstellar grain alignment based on radiative processes. The development of a general, analytical model for this radiative alignment torque (RAT) theory has allowed specific, testable predictions for realistic interstellar conditions. We outline the theoretical and observational arguments in favor of RAT alignment, as well as reasons the "classical" paramagnetic alignment mechanism is unlikely to work, except possibly for the very smallest grains. With further detailed characterization of the RAT mechanism, grain alignment and polarimetry promise to not only better constrain the interstellar magnetic field but also provide new information on the dust characteristics.

  2. An automated system for the analysis of G protein-coupled receptor transmembrane binding pockets: alignment, receptor-based pharmacophores, and their application.

    PubMed

    Kratochwil, Nicole A; Malherbe, Pari; Lindemann, Lothar; Ebeling, Martin; Hoener, Marius C; Mühlemann, Andreas; Porter, Richard H P; Stahl, Martin; Gerber, Paul R

    2005-01-01

    G protein-coupled receptors (GPCRs) share a common architecture consisting of seven transmembrane (TM) domains. Various lines of evidence suggest that this fold provides a generic binding pocket within the TM region for hosting agonists, antagonists, and allosteric modulators. Here, a comprehensive and automated method allowing fast analysis and comparison of these putative binding pockets across the entire GPCR family is presented. The method relies on a robust alignment algorithm based on conservation indices, focusing on pharmacophore-like relationships between amino acids. Analysis of conservation patterns across the GPCR family and alignment to the rhodopsin X-ray structure allows the extraction of the amino acids lining the TM binding pocket in a so-called ligand binding pocket vector (LPV). In a second step, LPVs are translated to simple 3D receptor pharmacophore models, where each amino acid is represented by a single spherical pharmacophore feature and all atomic detail is omitted. Applications of the method include the assessment of selectivity issues, support of mutagenesis studies, and the derivation of rules for focused screening to identify chemical starting points in early drug discovery projects. Because of the coarseness of this 3D receptor pharmacophore model, however, meaningful scoring and ranking procedures of large sets of molecules are not justified. The LPV analysis of the trace amine-associated receptor family and its experimental validation is discussed as an example. The value of the 3D receptor model is demonstrated for a class C GPCR family, the metabotropic glutamate receptors.

  3. Advances in process overlay: alignment solutions for future technology nodes

    NASA Astrophysics Data System (ADS)

    Megens, Henry; van Haren, Richard; Musa, Sami; Doytcheva, Maya; Lalbahadoersing, Sanjay; van Kemenade, Marc; Lee, Hyun-Woo; Hinnen, Paul; van Bilsen, Frank

    2007-03-01

    Semiconductor industry has an increasing demand for improvement of the total lithographic overlay performance. To improve the level of on-product overlay control the number of alignment measurements increases. Since more mask levels will be integrated, more alignment marks need to be printed when using direct-alignment (also called layer-to-layer alignment). Accordingly, the alignment mark size needs to become smaller, to fit all marks into the scribelane. For an in-direct alignment scheme, e.g. a scheme that aligns to another layer than the layer to which overlay is being measured, the number of needed alignment marks can be reduced. Simultaneously there is a requirement to reduce the size of alignment mark sub-segmentations without compromising the alignment and overlay performance. Smaller features within alignment marks can prevent processing issues like erosion, dishing and contamination. However, when the sub-segmentation size within an alignment mark becomes comparable to the critical dimension, and thus smaller than the alignment-illuminating wavelength, polarization effects might start to occur. Polarization effects are a challenge for optical alignment systems to maintain mark detectability. Nevertheless, this paper shows how to actually utilize those effects in order to obtain enhanced alignment and overlay performance to support future technology nodes. Finally, another challenge to be met for new semiconductor product technologies is the ability to align through semi-opaque materials, like for instance new hard-mask materials. Enhancement of alignment signal strength can be reached by adapting to new alignment marks that generate a higher alignment signal. This paper provides a description of an integral alignment solution that meets with these emerging customer application requirements. Complying with these requirements will significantly enhance the flexibility in production strategies while maintaining or improving the alignment and overlay

  4. Galaxy alignment on large and small scales

    NASA Astrophysics Data System (ADS)

    Kang, X.; Lin, W. P.; Dong, X.; Wang, Y. O.; Dutton, A.; Macciò, A.

    2016-10-01

    Galaxies are not randomly distributed across the universe but showing different kinds of alignment on different scales. On small scales satellite galaxies have a tendency to distribute along the major axis of the central galaxy, with dependence on galaxy properties that both red satellites and centrals have stronger alignment than their blue counterparts. On large scales, it is found that the major axes of Luminous Red Galaxies (LRGs) have correlation up to 30Mpc/h. Using hydro-dynamical simulation with star formation, we investigate the origin of galaxy alignment on different scales. It is found that most red satellite galaxies stay in the inner region of dark matter halo inside which the shape of central galaxy is well aligned with the dark matter distribution. Red centrals have stronger alignment than blue ones as they live in massive haloes and the central galaxy-halo alignment increases with halo mass. On large scales, the alignment of LRGs is also from the galaxy-halo shape correlation, but with some extent of mis-alignment. The massive haloes have stronger alignment than haloes in filament which connect massive haloes. This is contrary to the naive expectation that cosmic filament is the cause of halo alignment.

  5. Supplemental vibrational force during orthodontic alignment: a randomized trial.

    PubMed

    Woodhouse, N R; DiBiase, A T; Johnson, N; Slipper, C; Grant, J; Alsaleh, M; Donaldson, A N A; Cobourne, M T

    2015-05-01

    This prospective 3-arm parallel-group randomized clinical trial investigated the effect of supplemental vibrational force on rate of orthodontic tooth alignment with fixed appliances. Eighty-one subjects (40 males, 41 females; mean age, 14.1 y) undergoing first premolar extraction-based fixed appliance treatment were randomly allocated to treatment supplemented with daily use (20 min) of a removable intraoral vibrational device (AcceleDent; OrthoAccel Technologies Inc.; n = 29), an identical nonfunctional (sham) device (n = 25), or fixed appliances only (n = 27). Mandibular study casts were taken at baseline (treatment start: placement of 0.014-in. nickel-titanium arch wire), initial alignment (0.018-in. nickel-titanium arch wire), and final alignment (0.019 x 0.025-in. stainless steel arch wire). Overall mean irregularity index in the mandibular arch at baseline was 8.5 ± 3.8 mm (95% CI, 7.6 to 9.3) with no significant difference between groups (P = 0.73). For the total sample, mean irregularity index at initial alignment was 2.7 ± 2.8 mm (95% CI, 2.2 to 3.4) with no significant difference between groups (P = 0.40). Mean time from baseline to initial alignment was 59 ± 25 d (95% CI, 54.5 to 65.6); from initial to final alignment, 150 ± 62.5 d (95% CI, 136 to 165); and baseline to final alignment, 209 ± 65 d (95% CI, 195 to 224). Kaplan-Meier analysis demonstrated that patterns of alignment were not significantly different among the 3 groups (P = 0.66). Multivariate linear regression for initial and overall alignment rates using initial irregularity index as the covariate showed no significant differences among groups. The most important influence on both initial and overall rates of alignment was initial irregularity (P = 0.1 × 10(-4)). This prospective randomized clinical trial found no evidence that supplemental vibrational force can significantly increase the rate of initial tooth movement or reduce the amount of time required to achieve final alignment

  6. Alignment performance monitoring for ASML systems

    NASA Astrophysics Data System (ADS)

    Chung, Woong-Jae; Temchenko, Vlad; Hauck, Tarja; Schmidt, Sebastian

    2006-03-01

    In today's semiconductor industry downscaling of the IC design puts a stringent requirement on pattern overlay control. Tighter overlay requirements lead to exceedingly higher rework rates, meaning additional costs to manufacturing. Better alignment control became a target of engineering efforts to decrease rework rate for high-end technologies. Overlay performance is influenced by known parameters such as "Shift, Scaling, Rotation, etc", and unknown parameters defined as "Process Induced Variation", which are difficult to control by means of a process automation system. In reality, this process-induced variation leads to a strong wafer to wafer, or lot to lot variation, which are not easy to detect in the mass-production environment which uses sampling overlay measurements for only several wafers in a lot. An engineering task of finding and correcting a root cause for Process Induced Variations of overlay performance will be greatly simplified if the unknown parameters could be tracked for each wafer. This paper introduces an alignment performance monitoring method based on analysis of automatically generated "AWE" files for ASML scanner systems. Because "AWE" files include alignment results for each aligned wafer, it is possible to use them for monitoring, controlling and correcting the causes of "process induced" overlay performance without requiring extra measurement time. Since "AWE" files include alignment information for different alignment marks, it is also possible to select and optimize the best alignment recipe for each alignment strategy. Several case studies provided in our paper will demonstrate how AWE file analysis can be used to assist engineer in interpreting pattern alignment data. Since implementing our alignment data monitoring method, we were able to achieve significant improvement of alignment and overlay performance without additional overlay measurement time. We also noticed that the rework rate coming from alignment went down and

  7. Relationship of lower extremity alignment during the wall squat and single-leg jump: assessment of single-leg landing using three-dimensional motion analysis

    PubMed Central

    Watanabe, Manabu; Matsumoto, Takaaki; Ono, Susumu; Koseki, Hirohisa; Watarai, Koji

    2016-01-01

    [Purpose] The purpose of this study was to evaluate the relationship between malalignment and lower-extremity injury and to determine the optimal dynamic alignment of the lower extremity with wall squats. [Subjects and Methods] Healthy individuals from one therapy school were enrolled and assigned to a wall squat normal or abnormal group based on their forms during wall squats. The abnormal group was found to be more prone to lower-extremity injury on three-dimensional motion analysis. Eight students from each group were randomly chosen for the study. The effects of single-leg landing movements were assessed using three-dimensional motion analysis. [Results] In the sagittal plane, significant flexion of the hip and knee joints occurred 0.02 and 0.04 seconds after initial foot contact with the ground in the normal and abnormal groups, respectively. In the frontal plane, significant adduction of the hip joint occurred at 0.07 seconds in the abnormal group. [Conclusion] The abnormal group tended to display later flexion of the hip and knee joints and narrower hip, knee, and ankle range of motion than the normal group, suggesting that dynamic alignment of the lower extremity in the abnormal group likely made them susceptible to injury. PMID:27390393

  8. Relationship of lower extremity alignment during the wall squat and single-leg jump: assessment of single-leg landing using three-dimensional motion analysis.

    PubMed

    Watanabe, Manabu; Matsumoto, Takaaki; Ono, Susumu; Koseki, Hirohisa; Watarai, Koji

    2016-06-01

    [Purpose] The purpose of this study was to evaluate the relationship between malalignment and lower-extremity injury and to determine the optimal dynamic alignment of the lower extremity with wall squats. [Subjects and Methods] Healthy individuals from one therapy school were enrolled and assigned to a wall squat normal or abnormal group based on their forms during wall squats. The abnormal group was found to be more prone to lower-extremity injury on three-dimensional motion analysis. Eight students from each group were randomly chosen for the study. The effects of single-leg landing movements were assessed using three-dimensional motion analysis. [Results] In the sagittal plane, significant flexion of the hip and knee joints occurred 0.02 and 0.04 seconds after initial foot contact with the ground in the normal and abnormal groups, respectively. In the frontal plane, significant adduction of the hip joint occurred at 0.07 seconds in the abnormal group. [Conclusion] The abnormal group tended to display later flexion of the hip and knee joints and narrower hip, knee, and ankle range of motion than the normal group, suggesting that dynamic alignment of the lower extremity in the abnormal group likely made them susceptible to injury. PMID:27390393

  9. RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data.

    PubMed

    Michel, Audrey M; Mullan, James P A; Velayudhan, Vimalkumar; O'Connor, Patrick B F; Donohue, Claire A; Baranov, Pavel V

    2016-01-01

    Ribosome profiling (ribo-seq) is a technique that uses high-throughput sequencing to reveal the exact locations and densities of translating ribosomes at the entire transcriptome level. The technique has become very popular since its inception in 2009. Yet experimentalists who generate ribo-seq data often have to rely on bioinformaticians to process and analyze their data. We present RiboGalaxy ( http://ribogalaxy.ucc.ie ), a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz ( http://gwips.ucc.ie ). RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyze the relative impact of mRNA sequence features on local read density. RiboGalaxy is accompanied by extensive documentation and tips for helping users. In addition we provide a forum ( http://gwips.ucc.ie/Forum ) where we encourage users to post their questions and feedback to improve the overall RiboGalaxy service.

  10. Finite Element Analysis of Mobile-bearing Unicompartmental Knee Arthroplasty: The Influence of Tibial Component Coronal Alignment

    PubMed Central

    Zhu, Guang-Duo; Guo, Wan-Shou; Zhang, Qi-Dong; Liu, Zhao-Hui; Cheng, Li-Ming

    2015-01-01

    Background: Controversies about the rational positioning of the tibial component in unicompartmental knee arthroplasty (UKA) still exist. Previous finite element (FE) studies were rare, and the results varied. This FE study aimed to analyze the influence of the tibial component coronal alignment on knee biomechanics in mobile-bearing UKA and find a ration range of inclination angles. Methods: A three-dimensional FE model of the intact knee was constructed from image data of one normal subject. A 1000 N compressive load was applied to the intact knee model for validating. Then a set of eleven UKA FE models was developed with the coronal inclination angles of the tibial tray ranging from 10° valgus to 10° varus. Tibial bone stresses and strains, contact pressures and load distribution in all UKA models were calculated and analyzed under the unified loading and boundary conditions. Results: Load distribution, contact pressures, and contact areas in intact knee model were validated. In UKA models, von Mises stress and compressive strain at proximal medial cortical bone increased significantly as the tibial tray was in valgus inclination >4°, which may increase the risk of residual pain. Compressive strains at tibial keel slot were above the high threshold with varus inclination >4°, which may result in greater risk of component migration. Tibial bone resection corner acted as a strain-raiser regardless of the inclination angles. Compressive strains at the resected surface slightly changed with the varying inclinations and were not supposed to induce bone resorption and component loosening. Contact pressures and load percentage in lateral compartment increased with the more varus inclination, which may lead to osteoarthritis progression. Conclusions: Static knee biomechanics after UKA can be greatly affected by tibial component coronal alignment. A range from 4° valgus to 4° varus inclination of tibial component can be recommended in mobile-bearing UKA. PMID

  11. Aligned natural-synthetic polyblend nanofibers for peripheral nerve regeneration.

    PubMed

    Wang, Chun-Yang; Zhang, Kui-Hua; Fan, Cun-Yi; Mo, Xiu-Mei; Ruan, Hong-Jiang; Li, Feng-Feng

    2011-02-01

    Peripheral nerve regeneration remains a significant clinical challenge to researchers. Progress in the design of tissue engineering scaffolds provides an alternative approach for neural regeneration. In this study aligned silk fibroin (SF) blended poly(L-lactic acid-co-ε-caprolactone) (P(LLA-CL)) nanofibrous scaffolds were fabricated by electrospinning methods and then reeled into aligned nerve guidance conduits (NGC) to promote nerve regeneration. The aligned SF/P(LLA-CL) NGC was used as a bridge implanted across a 10mm defect in the sciatic nerve of rats and the outcome in terms of of regenerated nerve at 4 and 8 weeks was evaluated by a combination of electrophysiological assessment and histological and immunohistological analysis, as well as electron microscopy. The electrophysiological examination showed that functional recovery of the regenerated nerve in the SF/P(LLA-CL) NGC group was superior to that in the P(LLA-CL) NGC group. The morphological analysis also indicated that the regenerated nerve in the SF/P(LLA-CL) NGC was more mature. All the results demonstrated that the aligned SF/P(LLA-CL) NGC promoted peripheral nerve regeneration significantly better in comparison with the aligned P(LLA-CL) NGC, thus suggesting a potential application in nerve regeneration.

  12. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment-distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  13. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  14. Full-length sequence analysis of hepatitis E virus isolates: showing potential determinants of virus genotype and identity.

    PubMed

    Yang, Dong; Jiang, Mei; Jin, Min; Qiu, Zhigang; Cui, Weihong; Shen, Zhiqiang; Li, Bo; Gong, Lianfeng; Chen, Zhaoli; Wang, Xinwei; Li, Jun-Wen

    2013-12-01

    The complete genome sequence of a genotype 4 strain of hepatitis E virus (CH-YT-HEV02) from a patient (in Yantai, China) has been determined. Phylogenetic analysis showed that CH-YT-HEV02 belongs to genotype 4, subtype 4a. However, the phylogenetic analysis indicated that it was most closely related to JKO-CHiSai98C (AB197673) strain, sharing only 91.6% sequence identity with it. Judging from the phylogenetic tree based on the full-length nucleotide sequences of all 70 genotype 4 HEV isolates retrieved from GenBank up to May, 2013, the CH-YT-HEV02 isolates could serve as a Yantai-indigenous strain. A broader comparison with other genotype isolates revealed that there are a few conserved amino acids in the HVR region of different HEV genotypes, and two amino acid motifs in ORF2 and ORF3 might serve as signatures of genotype diversity of HEV.

  15. A comprehensive evaluation of alignment algorithms in the context of RNA-seq.

    PubMed

    Lindner, Robert; Friedel, Caroline C

    2012-01-01

    Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete.

  16. Deconvoluting nonaxial recoil in Coulomb explosion measurements of molecular axis alignment

    NASA Astrophysics Data System (ADS)

    Christensen, Lauge; Christiansen, Lars; Shepperson, Benjamin; Stapelfeldt, Henrik

    2016-08-01

    We report a quantitative study of the effect of nonaxial recoil during Coulomb explosion of laser-aligned molecules and introduce a method to remove the blurring caused by nonaxial recoil in the fragment-ion angular distributions. Simulations show that nonaxial recoil affects correlations between the emission directions of fragment ions differently from the effect caused by imperfect molecular alignment. The method, based on analysis of the correlation between the emission directions of the fragment ions from Coulomb explosion, is used to deconvolute the effect of nonaxial recoil from experimental fragment angular distributions. The deconvolution method is then applied to a number of experimental data sets to correct the degree of alignment for nonaxial recoil, to select optimal Coulomb explosion channels for probing molecular alignment, and to estimate the highest degree of alignment that can be observed from selected Coulomb explosion channels.

  17. Alignment of interstellar grains by mechanical torques: suprathermally rotating Gaussian random spheres

    NASA Astrophysics Data System (ADS)

    Das, Indrajit; Weingartner, Joseph C.

    2016-04-01

    Collisions of gas particles with a drifting grain give rise to a mechanical torque on the grain. Recent work by Lazarian & Hoang showed that mechanical torques might play a significant role in aligning helical grains along the interstellar magnetic field direction, even in the case of subsonic drift. We compute the mechanical torques on 13 different irregular grains and examine their resulting rotational dynamics, assuming steady rotation about the principal axis of greatest moment of inertia. We find that the alignment efficiency in the subsonic drift regime depends sensitively on the grain shape, with more efficient alignment for shapes with a substantial mechanical torque even in the case of no drift. The alignment is typically more efficient for supersonic drift. A more rigorous analysis of the dynamics is required to definitively appraise the role of mechanical torques in grain alignment.

  18. 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

  19. 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

  20. Alignment of the CMS silicon strip tracker during stand-alone commissioning

    SciTech Connect

    Adam, W.; et al.

    2009-07-01

    The results of the CMS tracker alignment analysis are presented using the data from cosmic tracks, optical survey information, and the laser alignment system at the Tracker Integration Facility at CERN. During several months of operation in the spring and summer of 2007, about five million cosmic track events were collected with a partially active CMS Tracker. This allowed us to perform first alignment of the active silicon modules with the cosmic tracks using three different statistical approaches; validate the survey and laser alignment system performance; and test the stability of Tracker structures under various stresses and temperatures ranging from +15C to -15C. Comparison with simulation shows that the achieved alignment precision in the barrel part of the tracker leads to residual distributions similar to those obtained with a random misalignment of 50 (80) microns in the outer (inner) part of the barrel.

  1. Horizontal carbon nanotube alignment.

    PubMed

    Cole, Matthew T; Cientanni, Vito; Milne, William I

    2016-09-21

    The production of horizontally aligned carbon nanotubes offers a rapid means of realizing a myriad of self-assembled near-atom-scale technologies - from novel photonic crystals to nanoscale transistors. The ability to reproducibly align anisotropic nanostructures has huge technological value. Here we review the present state-of-the-art in horizontal carbon nanotube alignment. For both in and ex situ approaches, we quantitatively assess the reported linear packing densities alongside the degree of alignment possible for each of these core methodologies. PMID:27546174

  2. Horizontal carbon nanotube alignment.

    PubMed

    Cole, Matthew T; Cientanni, Vito; Milne, William I

    2016-09-21

    The production of horizontally aligned carbon nanotubes offers a rapid means of realizing a myriad of self-assembled near-atom-scale technologies - from novel photonic crystals to nanoscale transistors. The ability to reproducibly align anisotropic nanostructures has huge technological value. Here we review the present state-of-the-art in horizontal carbon nanotube alignment. For both in and ex situ approaches, we quantitatively assess the reported linear packing densities alongside the degree of alignment possible for each of these core methodologies.

  3. Orthodontics and Aligners

    MedlinePlus

    ... Repairing Chipped Teeth Teeth Whitening Tooth-Colored Fillings Orthodontics and Aligners Straighten teeth for a healthier smile. Orthodontics When consumers think about orthodontics, braces are the ...

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

    PubMed

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

    2015-01-01

    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.

  5. 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

  6. Single agent carboplatin for pediatric low-grade glioma: A retrospective analysis shows equivalent efficacy to multiagent chemotherapy.

    PubMed

    Dodgshun, Andrew J; Maixner, Wirginia J; Heath, John A; Sullivan, Michael J; Hansford, Jordan R

    2016-01-15

    Pediatric low-grade gliomas (LGG) that are unresectable often require adjuvant chemotherapy such as carboplatin/vincristine. Small Phase II studies have suggested equivalent efficacy of single agent 4-weekly carboplatin. A single-institution retrospective review captured all patients aged 0 to 18 years diagnosed with LGG between 1996 and 2013 and treated with carboplatin monotherapy. The response and survival according to tumor site was compared to published results for multiagent chemotherapy. Of 268 children diagnosed with LGG diagnosed in this period, 117 received chemotherapy and 104 children received single agent carboplatin as first line chemotherapy. All patients received carboplatin at 560 mg/m(2), four-weekly for a median of 12 courses. The mean age at diagnosis was 5.8 years (range 3m-16y) and 32% had neurofibromatosis type 1. With a mean followup of 54 months, 86% of patients achieved stabilisation or better (SD/PR/CR). 3-year progression free survival (PFS) 66% (95% CI 57-76%), and 5-year PFS was 51% (95% CI 41-63%). 5-year overall survival was 97%. Multivariate analysis showed poorer PFS for those with chiasmatic/hypothalamic tumors. In this retrospective analysis single agent carboplatin shows comparable efficacy to historical multiagent chemotherapy for the treatment of patients with unresectable LGG. Equivalent outcomes are achieved with less chemotherapy, reduced side effects and fewer hospital visits. Further research is required to establish the place of this simplified regimen in the up-front treatment of unresectable LGG.

  7. Pioneer 10 and 11 orbit determination analysis shows no discrepancy with Newton-Einstein laws of gravity

    NASA Astrophysics Data System (ADS)

    Modenini, D.; Tortora, P.

    2014-07-01

    The present work describes our investigation of the navigation anomaly of the Pioneer 10 and 11 probes which became known as the Pioneer Anomaly. It appeared as a linear drift in the Doppler data received by the spacecraft, which has been ascribed to an approximately constant Sunward acceleration of about 8.5×10-13 km/s2. Since then, the existence of the anomaly has been confirmed independently by several groups and a large effort was devoted to find its origin. Recently, different analyses were published where the authors claimed the acceleration due to anisotropic thermal emission to be the most likely cause of the unexplained acceleration. Here we report the methodology and the results of an independent study carried out in the last years, aimed at supporting the thermal origin of the anomaly. This work consists of two main parts: thermal modeling of the spacecraft throughout its trajectory, and orbit determination analysis. Based on existing documentation and published telemetry data, we built a thermal finite element model of the spacecraft, whose complexity has been constrained to a degree allowing for sensitivity analysis, leading to the computation of its formal uncertainty. The trajectory analysis and orbit determination were carried out using NASA/JPL's Orbit Determination Program, and our results show that orbital solutions are achieved that do not require the addition of any "unknown" acceleration other than that of thermal origin.

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

    PubMed Central

    Kolodny, Rachel; Koehl, Patrice; Levitt, Michael

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Cox, Marie E.; Dunand, David C.

    2013-07-01

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

  10. Hole-Aligning Tool

    NASA Technical Reports Server (NTRS)

    Collins, Frank A.; Saude, Frank; Sep, Martin J.

    1996-01-01

    Tool designed for use in aligning holes in plates or other structural members to be joined by bolt through holes. Holes aligned without exerting forces perpendicular to planes of holes. Tool features screw-driven-wedge design similar to (but simpler than) that of some automotive exhaust-pipe-expanding tools.

  11. Linkage analysis in a Dutch population isolate shows no major gene for left-handedness or atypical language lateralization.

    PubMed

    Somers, Metten; Ophoff, Roel A; Aukes, Maartje F; Cantor, Rita M; Boks, Marco P; Dauwan, Meenakshi; de Visser, Kees L; Kahn, René S; Sommer, Iris E

    2015-06-10

    Cerebral dominance of language function and hand preference are suggested to be heritable traits with possible shared genetic background. However, joined genetic studies of these traits have never been conducted. We performed a genetic linkage study in 37 multigenerational human pedigrees of both sexes (consisting of 355 subjects) enriched with left-handedness in which we also measured language lateralization. Hand preference was measured with the Edinburgh Handedness Inventory, and language lateralization was measured with functional transcranial Doppler during language production. The estimated heritability of left-handedness and language lateralization in these pedigrees is 0.24 and 0.31, respectively. A parametric major gene model was tested for left-handedness. Nonparametric analyses were performed for left-handedness, atypical lateralization, and degree of language lateralization. We did not observe genome-wide evidence for linkage in the parametric or nonparametric analyses for any of the phenotypes tested. However, multiple regions showed suggestive evidence of linkage. The parametric model showed suggestive linkage for left-handedness in the 22q13 region [heterogeneity logarithm of odds (HLOD) = 2.18]. Nonparametric multipoint analysis of left-handedness showed suggestive linkage in the same region [logarithm of odds (LOD) = 2.80]. Atypical language lateralization showed suggestive linkage in the 7q34 region (LODMax = 2.35). For strength of language lateralization, we observed suggestive linkage in the 6p22 (LODMax = 2.54), 7q32 (LODMax = 1.93), and 9q33 (LODMax = 2.10) regions. We did not observe any overlap of suggestive genetic signal between handedness and the extent of language lateralization. The absence of significant linkage argues against the presence of a major gene coding for both traits; rather, our results are suggestive of these traits being two independent polygenic complex traits.

  12. Algorithms for Automatic Alignment of Arrays

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Oliker, Leonid; Schreiber, Robert; Sheffler, Thomas J.

    1996-01-01

    Aggregate data objects (such as arrays) are distributed across the processor memories when compiling a data-parallel language for a distributed-memory machine. The mapping determines the amount of communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: an alignment that maps all the objects to an abstract template, followed by a distribution that maps the template to the processors. This paper describes algorithms for solving the various facets of the alignment problem: axis and stride alignment, static and mobile offset alignment, and replication labeling. We show that optimal axis and stride alignment is NP-complete for general program graphs, and give a heuristic method that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. We also show how local graph contractions can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. We show how to model the static offset alignment problem using linear programming, and we show that loop-dependent mobile offset alignment is sometimes necessary for optimum performance. We describe an algorithm with for determining mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself or can be used to improve performance. We describe an algorithm based on network flow that replicates objects so as to minimize the total amount of broadcast communication in replication.

  13. MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules.

    PubMed

    Sinha, Saurabh; He, Xin

    2007-11-01

    The discovery and analysis of cis-regulatory modules (CRMs) in metazoan genomes is crucial for understanding the transcriptional control of development and many other biological processes. Cross-species sequence comparison holds much promise for improving computational prediction of CRMs, for elucidating their binding site composition, and for understanding how they evolve. Current methods for analyzing orthologous CRMs from multiple species rely upon sequence alignments produced by off-the-shelf alignment algorithms, which do not exploit the presence of binding sites in the sequences. We present here a unified probabilistic framework, called MORPH, that integrates the alignment task with binding site predictions, allowing more robust CRM analysis in two species. The framework sums over all possible alignments of two sequences, thus accounting for alignment ambiguities in a natural way. We perform extensive tests on orthologous CRMs from two moderately diverged species Drosophila melanogaster and D. mojavensis, to demonstrate the advantages of the new approach. We show that it can overcome certain computational artifacts of traditional alignment tools and provide a different, likely more accurate, picture of cis-regulatory evolution than that obtained from existing methods. The burgeoning field of cis-regulatory evolution, which is amply supported by the availability of many related genomes, is currently thwarted by the lack of accurate alignments of regulatory regions. Our work will fill in this void and enable more reliable analysis of CRM evolution.

  14. MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules.

    PubMed

    Sinha, Saurabh; He, Xin

    2007-11-01

    The discovery and analysis of cis-regulatory modules (CRMs) in metazoan genomes is crucial for understanding the transcriptional control of development and many other biological processes. Cross-species sequence comparison holds much promise for improving computational prediction of CRMs, for elucidating their binding site composition, and for understanding how they evolve. Current methods for analyzing orthologous CRMs from multiple species rely upon sequence alignments produced by off-the-shelf alignment algorithms, which do not exploit the presence of binding sites in the sequences. We present here a unified probabilistic framework, called MORPH, that integrates the alignment task with binding site predictions, allowing more robust CRM analysis in two species. The framework sums over all possible alignments of two sequences, thus accounting for alignment ambiguities in a natural way. We perform extensive tests on orthologous CRMs from two moderately diverged species Drosophila melanogaster and D. mojavensis, to demonstrate the advantages of the new approach. We show that it can overcome certain computational artifacts of traditional alignment tools and provide a different, likely more accurate, picture of cis-regulatory evolution than that obtained from existing methods. The burgeoning field of cis-regulatory evolution, which is amply supported by the availability of many related genomes, is currently thwarted by the lack of accurate alignments of regulatory regions. Our work will fill in this void and enable more reliable analysis of CRM evolution. PMID:17997594

  15. Do invasive species show higher phenotypic plasticity than native species and, if so, is it adaptive? A meta-analysis.

    PubMed

    Davidson, Amy Michelle; Jennions, Michael; Nicotra, Adrienne B

    2011-04-01

    Do invasive plant species have greater phenotypic plasticity than non-invasive species? And, if so, how does this affect their fitness relative to native, non-invasive species? What role might this play in plant invasions? To answer these long-standing questions, we conducted a meta-analysis using data from 75 invasive/non-invasive species pairs. Our analysis shows that invasive species demonstrate significantly higher phenotypic plasticity than non-invasive species. To examine the adaptive benefit of this plasticity, we plotted fitness proxies against measures of plasticity in several growth, morphological and physiological traits to test whether greater plasticity is associated with an improvement in estimated fitness. Invasive species were nearly always more plastic in their response to greater resource availability than non-invasives but this plasticity was only sometimes associated with a fitness benefit. Intriguingly, non-invasive species maintained greater fitness homoeostasis when comparing growth between low and average resource availability. Our finding that invasive species are more plastic in a variety of traits but that non-invasive species respond just as well, if not better, when resources are limiting, has interesting implications for predicting responses to global change.

  16. Analysis of a large dataset of mycorrhiza inoculation field trials on potato shows highly significant increases in yield.

    PubMed

    Hijri, Mohamed

    2016-04-01

    An increasing human population requires more food production in nutrient-efficient systems in order to simultaneously meet global food needs while reducing the environmental footprint of agriculture. Arbuscular mycorrhizal fungi (AMF) have the potential to enhance crop yield, but their efficiency has yet to be demonstrated in large-scale crop production systems. This study reports an analysis of a dataset consisting of 231 field trials in which the same AMF inoculant (Rhizophagus irregularis DAOM 197198) was applied to potato over a 4-year period in North America and Europe under authentic field conditions. The inoculation was performed using a liquid suspension of AMF spores that was sprayed onto potato seed pieces, yielding a calculated 71 spores per seed piece. Statistical analysis showed a highly significant increase in marketable potato yield (ANOVA, P < 0.0001) for inoculated fields (42.2 tons/ha) compared with non-inoculated controls (38.3 tons/ha), irrespective of trial year. The average yield increase was 3.9 tons/ha, representing 9.5 % of total crop yield. Inoculation was profitable with a 0.67-tons/ha increase in yield, a threshold reached in almost 79 % of all trials. This finding clearly demonstrates the benefits of mycorrhizal-based inoculation on crop yield, using potato as a case study. Further improvements of these beneficial inoculants will help compensate for crop production deficits, both now and in the future.

  17. Genome-Wide Gene Expression Analysis Shows AKAP13-Mediated PKD1 Signaling Regulates the Transcriptional Response to Cardiac Hypertrophy

    PubMed Central

    Johnson, Keven R.; Nicodemus-Johnson, Jessie; Spindler, Mathew J.

    2015-01-01

    In the heart, scaffolding proteins such as A-Kinase Anchoring Proteins (AKAPs) play a crucial role in normal cellular function by serving as a signaling hub for multiple protein kinases including protein kinase D1 (PKD1). Under cardiac hypertrophic conditions AKAP13 anchored PKD1 activates the transcription factor MEF2 leading to subsequent fetal gene activation and hypertrophic response. We used an expression microarray to identify the global transcriptional response in the hearts of wild-type mice expressing the native form of AKAP13 compared to a gene-trap mouse model expressing a truncated form of AKAP13 that is unable to bind PKD1 (AKAP13-ΔPKD1). Microarray analysis showed that AKAP13-ΔPKD1 mice broadly failed to exhibit the transcriptional profile normally associated with compensatory cardiac hypertrophy following trans-aortic constriction (TAC). The identified differentially expressed genes in WT and AKAP13-ΔPKD1 hearts are vital for the compensatory hypertrophic response to pressure-overload and include myofilament, apoptotic, and cell growth/differentiation genes in addition to genes not previously identified as affected by AKAP13-anchored PKD1. Our results show that AKAP13-PKD1 signaling is critical for transcriptional regulation of key contractile, cell death, and metabolic pathways during the development of compensatory hypertrophy in vivo. PMID:26192751

  18. Geochemical analysis of potash mine seep oils, collapsed breccia pipe oil shows and selected crude oils, Eddy County, New Mexico

    USGS Publications Warehouse

    Palacas, J.G.; Snyder, R.P.; Baysinger, J.P.; Threlkeld, C.N.

    1982-01-01

    Oil shows, in the form of oil stains and bleeding oil, in core samples from two breccia pipes, Hills A and C, Eddy County, New Mexico, and seepage oils in a potash mine near Hill C breccia pipe are geochemically similar. The geochemical similarities strongly suggest that they belong to the same family of oils and were derived from similar sources. The oils are relatively high in sulfur (0.89 to 1.23 percent), rich in hydrocarbons (average 82 percent), relatively high in saturated hydrocarbon/aromatic hydrocarbon ratios (average 2.9), and based on analysis of seep oils alone, have a low API gravity (average 19.4?). The oils are for the most part severely biodegraded as attested by the loss of n-paraffin molecules. Geochemical comparison of seven crude oils collected in the vicinity of the breccia pipes indicates that the Yates oils are the likely source of the above family of oils. Six barrels of crude oil that were dumped into a potash exploration borehole near Hill C breccia pipe, to release stuck casing, are considered an unlikely source of the breccia pipe and mine seep oils. Volumetric and hydrodynamic constraints make it highly improbable that such a small volume of 'dumped' oil could migrate over distances ranging from about 600 feet to 2.5 miles to the sites of the oil shows.

  19. Immunohistochemical Analysis of Brainstem Lesions in the Autopsy Cases with Severe Motor and Intellectual Disabilities Showing Sudden Unexplained Death

    PubMed Central

    Hayashi, Masaharu; Sakuma, Hiroshi

    2016-01-01

    It is known that patients with severe motor and intellectual disabilities (SMID) showed sudden unexplained death (SUD), in which autopsy failed to identify causes of death. Although the involvement of brainstem dysfunction is speculated, the detailed neuropathological analysis still remains to be performed. In order to clarify pathogenesis, we investigated the brainstem functions in autopsy cases of SMID showing SUD. We immunohistochemically examined expressions of tyrosine hydroxylase, tryptophan hydroxylase, substance P, methionine-enkephalin, and c-fos in the serial sections of the midbrain, pons, and medulla oblongata in eight SUD cases and seven controls, having neither unexplained death nor pathological changes in the brain. Expressions of tyrosine hydroxylase and tryptophan hydroxylase were reduced in two of eight cases, and those of substance P and/or methionine-enkephalin were augmented in the pons and medulla oblongata in seven of eight cases, including the aforementioned two cases, when compared with those in controls. The hypoglossal nucleus and/or the dorsal vagal nucleus demonstrated increased neuronal immunoreactivity for c-fos in seven of eight cases, although there was no neuronal loss or gliosis in both the nuclei. Controls rarely showed immunoreactivity for c-fos in the medulla oblongata. These data suggest the possible involvement of brainstem dysfunction in SUD in patients with SMID, and consecutive neurophysiological evaluation of brainstem functions, such as all-night polysomnography and blink reflex, may be useful for the prevention of SUD, because some parameters in the neurophysiological examination are known to be related to the brainstem catecholamine neurons and the spinal tract nucleus of trigeminal nerve. PMID:27445960

  20. Immunohistochemical Analysis of Brainstem Lesions in the Autopsy Cases with Severe Motor and Intellectual Disabilities Showing Sudden Unexplained Death.

    PubMed

    Hayashi, Masaharu; Sakuma, Hiroshi

    2016-01-01

    It is known that patients with severe motor and intellectual disabilities (SMID) showed sudden unexplained death (SUD), in which autopsy failed to identify causes of death. Although the involvement of brainstem dysfunction is speculated, the detailed neuropathological analysis still remains to be performed. In order to clarify pathogenesis, we investigated the brainstem functions in autopsy cases of SMID showing SUD. We immunohistochemically examined expressions of tyrosine hydroxylase, tryptophan hydroxylase, substance P, methionine-enkephalin, and c-fos in the serial sections of the midbrain, pons, and medulla oblongata in eight SUD cases and seven controls, having neither unexplained death nor pathological changes in the brain. Expressions of tyrosine hydroxylase and tryptophan hydroxylase were reduced in two of eight cases, and those of substance P and/or methionine-enkephalin were augmented in the pons and medulla oblongata in seven of eight cases, including the aforementioned two cases, when compared with those in controls. The hypoglossal nucleus and/or the dorsal vagal nucleus demonstrated increased neuronal immunoreactivity for c-fos in seven of eight cases, although there was no neuronal loss or gliosis in both the nuclei. Controls rarely showed immunoreactivity for c-fos in the medulla oblongata. These data suggest the possible involvement of brainstem dysfunction in SUD in patients with SMID, and consecutive neurophysiological evaluation of brainstem functions, such as all-night polysomnography and blink reflex, may be useful for the prevention of SUD, because some parameters in the neurophysiological examination are known to be related to the brainstem catecholamine neurons and the spinal tract nucleus of trigeminal nerve. PMID:27445960

  1. An algorithm for linear metabolic pathway alignment.

    PubMed

    Chen, Ming; Hofestaedt, Ralf

    2005-01-01

    Metabolic pathway alignment represents one of the most powerful tools for comparative analysis of metabolism. It involves recognition of metabolites common to a set of functionally-related metabolic pathways, interpretation of biological evolution processes and determination of alternative metabolic pathways. Moreover, it is of assistance in function prediction and metabolism modeling. Although research on genomic sequence alignment is extensive, the problem of aligning metabolic pathways has received less attention. We are motivated to develop an algorithm of metabolic pathway alignment to reveal the similarities between metabolic pathways. A new definition of the metabolic pathway is introduced. The algorithm has been implemented into the PathAligner system; its web-based interface is available at http://bibiserv.techfak.uni-bielefeld.de/pathaligner/.

  2. MOST light-curve analysis of the γ Doradus pulsator HR 8799, showing resonances and amplitude variations

    NASA Astrophysics Data System (ADS)

    Sódor, Á.; Chené, A.-N.; De Cat, P.; Bognár, Zs.; Wright, D. J.; Marois, C.; Walker, G. A. H.; Matthews, J. M.; Kallinger, T.; Rowe, J. F.; Kuschnig, R.; Guenther, D. B.; Moffat, A. F. J.; Rucinski, S. M.; Sasselov, D.; Weiss, W. W.

    2014-08-01

    Context. The central star of the HR 8799 system is a γ Doradus-type pulsator. The system harbours four planetary-mass companions detected by direct imaging, and is a good solar system analogue. The masses of the companions are not accurately known because the estimation depends greatly on the age of the system, which is also not known with sufficient accuracy. Asteroseismic studies of the star might help to better constrain the age of HR 8799. We organized an extensive photometric and multi-site spectroscopic observing campaign to study the pulsations of the central star. Aims: The aim of the present study is to investigate the pulsation properties of HR 8799 in detail via the ultra-precise 47 d nearly continuous photometry obtained with the Microvariability and Oscillations in STars (MOST) space telescope, and to find as many independent pulsation modes as possible, which is the prerequisite for an asteroseismic age determination. Methods: We carried out Fourier analysis of the wide-band photometric time series. Results: We find that resonance and sudden amplitude changes characterize the pulsation of HR 8799. The dominant frequency is always at f1 = 1.978 d-1.Many multiples of one-ninth of the dominant frequency appear in the Fourier spectrum of the MOST data: n/9 f1, where n = {1,2,3,4,5,6,7,8,9,10,13,14,17,18}. Our analysis also reveals that many of these peaks show strong amplitude decrease and phase variations even on the 47 d time scale. The dependencies between the pulsation frequencies of HR 8799 make the planned subsequent asteroseismic analysis rather difficult. We point out some resemblance between the light curve of HR 8799 and the modulated pulsation light curves of Blazhko RR Lyrae stars. Based on data from the MOST satellite, a Canadian Space Agency mission, jointly operated by Dynacon Inc., the University of Toronto Institute for Aerospace Studies and the University of British Columbia, with the assistance of the University of Vienna.

  3. Phylogenetic Inference From Conserved sites Alignments

    SciTech Connect

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

    1999-08-15

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

  4. Genotypic analysis of β-tubulin in Onchocerca volvulus from communities and individuals showing poor parasitological response to ivermectin treatment.

    PubMed

    Osei-Atweneboana, Mike Y; Boakye, Daniel A; Awadzi, Kwablah; Gyapong, John O; Prichard, Roger K

    2012-12-01

    Ivermectin (IVM) has been in operational use for the control of onchocerciasis for two decades and remains the only drug of choice. To investigate the parasitological responses and genetic profile of Onchocerca volvulus, we carried out a 21 month epidemiological study to determine the response of the parasite to IVM in 10 Ghanaian endemic communities. Onchocerca nodules were surgically removed from patients in three IVM response categories (good, intermediate and poor) and one IVM naïve community. DNA from adult worms was analyzed to determine any association between genotype and IVM response phenotypic. Embryogramme analysis showed significantly higher reproductive activity in worms from poor response communities, which had up to 41% of females with live stretched microfilaria (mf) in utero, despite IVM treatment, compared with good response communities, which had no intra-uterine stretched mf. β-tubulin isotype 1 gene has been shown to be linked to IVM selection in O. volvulus and also known to be associated with IVM resistance in veterinary nematodes. We have genotyped the full length genomic DNA sequence of the β-tubulin gene from 127 adult worms obtained from the four community categories. We found SNPs at 24 sites over the entire 3696 bp. Eight of the SNPs occurred at significantly higher (p < 0.05) frequencies in the poor response communities compared with the good response communities and the IVM naïve community. Phenotypic and genotypic analyses show that IVM resistance has been selected and the genotype (1183GG/1188CC/1308TT/1545GG) was strongly associated with the resistance phenotype. Since the region in the β-tubulin gene where these four SNPs occur is within 362 bp, it is feasible to develop a genetic marker for the early detection of IVM resistance. PMID:24533268

  5. Precision alignment device

    DOEpatents

    Jones, Nelson E.

    1990-01-01

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam.

  6. Precision alignment device

    DOEpatents

    Jones, N.E.

    1988-03-10

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

  7. Galaxy Alignments: An Overview

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    The alignments between galaxies, their underlying matter structures, and the cosmic web constitute vital ingredients for a comprehensive understanding of gravity, the nature of matter, and structure formation in the Universe. We provide an overview on the state of the art in the study of these alignment processes and their observational signatures, aimed at a non-specialist audience. The development of the field over the past one hundred years is briefly reviewed. We also discuss the impact of galaxy alignments on measurements of weak gravitational lensing, and discuss avenues for making theoretical and observational progress over the coming decade.

  8. Radiative Grain Alignment

    NASA Astrophysics Data System (ADS)

    Andersson, B. G.

    2015-12-01

    Polarization due to aligned dust grains was discovered in the interstellar medium more than 60 years ago. A quantitative, observationally well tested theory of the phenomenon has finally emerged in the last decade, promising not only an improved understanding of interstellar magnetic fields, but new tools for studying the dust environments and grain characteristics. This Radiative Alignment Torque (RAT) theory also has many potential applications in solar system physics, including for comet dust characteristics. I will review the main aspects of the theory and the observational tests performed to date, as well as some of the new possibilities for using polarization as a tool to study dust and its environment, with RAT alignment.

  9. Hybrid vehicle motor alignment

    DOEpatents

    Levin, Michael Benjamin

    2001-07-03

    A rotor of an electric motor for a motor vehicle is aligned to an axis of rotation for a crankshaft of an internal combustion engine having an internal combustion engine and an electric motor. A locator is provided on the crankshaft, a piloting tool is located radially by the first locator to the crankshaft. A stator of the electric motor is aligned to a second locator provided on the piloting tool. The stator is secured to the engine block. The rotor is aligned to the crankshaft and secured thereto.

  10. Silicon oxides as alignment surfaces for vertically-aligned nematics in photonic devices

    NASA Astrophysics Data System (ADS)

    Oton, E.; López-Andrés, S.; Bennis, N.; Otón, J. M.; Geday, M. A.

    2014-06-01

    A comparative study on alignment performance and microstructure of inorganic layers used for liquid crystal cell conditioning has been carried out. The study has focused on two specific materials, SiOx and SiO2, deposited under different conditions. The purpose was to establish a relationship between layer microstructure and liquid crystal alignment. The surface morphology has been studied by FESEM and AFM. An analysis on liquid crystal alignment, pretilt angle, response time, contrast ratio and the conditions to develop backflow effect (significant rise time increase due to pure homeotropic alignment) on vertically-aligned nematic cells has been carried out. A technique to overcome the presence of backflow has been identified. The full comparative study of SiOx and SiO2 layer properties and their influence over liquid crystal alignment and electrooptic response is presented.

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

    PubMed Central

    2015-01-01

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

  12. 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

  13. 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.

  14. Aligning parallel arrays to reduce communication

    NASA Technical Reports Server (NTRS)

    Sheffler, Thomas J.; Schreiber, Robert; Gilbert, John R.; Chatterjee, Siddhartha

    1994-01-01

    Axis and stride alignment is an important optimization in compiling data-parallel programs for distributed-memory machines. We previously developed an optimal algorithm for aligning array expressions. Here, we examine alignment for more general program graphs. We show that optimal alignment is NP-complete in this setting, so we study heuristic methods. This paper makes two contributions. First, we show how local graph transformations can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. Second, we give a heuristic that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. Our algorithms have been implemented; we present experimental results showing their effect on the performance of some example programs running on the CM-5.

  15. 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.

  16. 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

  17. Human Reliability Analysis for In-Tank Precipitation Alignment and Startup of Emergency Purge Ventilation Equipment. Revision 3

    SciTech Connect

    Shapiro, B.J.; Britt, T.E.

    1994-10-01

    This report documents the methodology used for calculating the human error probability for establishing air based ventilation using emergency purge ventilation equipment on In-Tank Precipitation (ITP) processing tanks 48 and 49 after failure of the nitrogen purge system following a seismic event. The analyses were performed according to THERP (Technique for Human Error Rate Prediction) as described in NUREG/CR-1278-F, ``Handbook of Human Reliability Analysis with Emphasis on Nuclear Power Plant Applications.`` The calculated human error probabilities are provided as input to the Fault Tree Analysis for the ITP Nitrogen Purge System.

  18. Human reliability analysis for In-Tank Precipitation alignment and startup of emergency purge ventilation equipment. Revision 2

    SciTech Connect

    Olsen, L.M.; Shapiro, B.J.; Britt, T.E.

    1994-01-01

    This report documents the methodology used for calculating the human error probability for establishing air based ventilation using emergency purge ventilation equipment on In-Tank Precipitation (ITP) processing tanks 48 and 49 after a failure of the nitrogen purge system following a seismic event. The analyses were performed according to THERP (Technique for Human Error Rate Prediction) as described in NUREG/CR-1278-F, ``Handbook of Human Reliability Analysis with Emphasis on Nuclear Power Plant Application.`` The calculated human error probabilities are provided as input to the Fault Tree Analysis for the ITP Nitrogen Purge System.

  19. Human reliability analysis for In-Tank Precipitation alignment and startup of emergency purge ventilation equipment. Revision 1

    SciTech Connect

    Olsen, L.M.

    1993-08-01

    This report documents the methodology used for calculating the human error probability for establishing air based ventilation using emergency purge ventilation equipment on In-Tank Precipitation (ITP) processing tanks 48 and 49 after a failure of the nitrogen purge system following a seismic event. The analyses were performed according to THERP (Technique for Human Error Rate Prediction). The calculated human error probabilities are provided as input to the Fault Tree Analysis for the ITP Nitrogen Purge System. The analysis assumes a seismic event initiator leading to establishing air based ventilation on the ITP processing tanks 48 and 49. At the time of this analysis only the tanks and the emergency purge ventilation equipment are seismically qualified. Consequently, onsite and offsite power is assumed to be unavailable and all operator control actions are to be performed locally on the tank top. Assumptions regarding procedures, staffing, equipment locations, equipment tagging, equipment availability, and training were made and are documented in this report. The human error probability for establishing air based ventilation using the emergency purge ventilation equipment on In-Tank Precipitation processing tanks 48 and 49 after a failure of the nitrogen purge system following a seismic event is 4.2E-6 (median value on the lognormal scale). It is important to note that this result is predicated on the implementation of all of the assumptions listed in the ``Assumptions`` section of this report. This analysis was not based on the current conditions in ITP. The analysis is to be used as a tool to aid ITP operations personnel in achieving the training, procedural, and operational goals outlined in this document.

  20. PDV Probe Alignment Technique

    SciTech Connect

    Whitworth, T L; May, C M; Strand, O T

    2007-10-26

    This alignment technique was developed while performing heterodyne velocimetry measurements at LLNL. There are a few minor items needed, such as a white card with aperture in center, visible alignment laser, IR back reflection meter, and a microscope to view the bridge surface. The work was performed on KCP flyers that were 6 and 8 mils wide. The probes used were Oz Optics manufactured with focal distances of 42mm and 26mm. Both probes provide a spot size of approximately 80?m at 1550nm. The 42mm probes were specified to provide an internal back reflection of -35 to -40dB, and the probe back reflections were measured to be -37dB and -33dB. The 26mm probes were specified as -30dB and both measured -30.5dB. The probe is initially aligned normal to the flyer/bridge surface. This provides a very high return signal, up to -2dB, due to the bridge reflectivity. A white card with a hole in the center as an aperture can be used to check the reflected beam position relative to the probe and launch beam, and the alignment laser spot centered on the bridge, see Figure 1 and Figure 2. The IR back reflection meter is used to measure the dB return from the probe and surface, and a white card or similar object is inserted between the probe and surface to block surface reflection. It may take several iterations between the visible alignment laser and the IR back reflection meter to complete this alignment procedure. Once aligned normal to the surface, the probe should be tilted to position the visible alignment beam as shown in Figure 3, and the flyer should be translated in the X and Y axis to reposition the alignment beam onto the flyer as shown in Figure 4. This tilting of the probe minimizes the amount of light from the bridge reflection into the fiber within the probe while maintaining the alignment as near normal to the flyer surface as possible. When the back reflection is measured after the tilt adjustment, the level should be about -3dB to -6dB higher than the probes

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

    PubMed Central

    Hashemifar, Somaye; Xu, Jinbo

    2014-01-01

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

  2. Optics Alignment Panel

    NASA Technical Reports Server (NTRS)

    Schroeder, Daniel J.

    1992-01-01

    The Optics Alignment Panel (OAP) was commissioned by the HST Science Working Group to determine the optimum alignment of the OTA optics. The goal was to find the position of the secondary mirror (SM) for which there is no coma or astigmatism in the camera images due to misaligned optics, either tilt or decenter. The despace position was reviewed of the SM and the optimum focus was sought. The results of these efforts are as follows: (1) the best estimate of the aligned position of the SM in the notation of HDOS is (DZ,DY,TZ,TY) = (+248 microns, +8 microns, +53 arcsec, -79 arcsec), and (2) the best focus, defined to be that despace which maximizes the fractional energy at 486 nm in a 0.1 arcsec radius of a stellar image, is 12.2 mm beyond paraxial focus. The data leading to these conclusions, and the estimated uncertainties in the final results, are presented.

  3. Barrel alignment fixture

    NASA Astrophysics Data System (ADS)

    Sheeley, J. D.

    1981-04-01

    Fabrication of slapper type detonator cables requires bonding of a thin barrel over a bridge. Location of the barrel hole with respect to the bridge is critical: the barrel hole must be centered over the bridge uniform spacing on each side. An alignment fixture which permits rapid adjustment of the barrel position with respect to the bridge is described. The barrel is manipulated by pincer-type fingers which are mounted on a small x-y table equipped with micrometer adjustments. Barrel positioning, performed under a binocular microscopy, is rapid and accurate. After alignment, the microscope is moved out of position and an infrared (IR) heat source is aimed at the barrel. A 5-second pulse of infrared heat flows the adhesive under the barrel and bonds it to the cable. Sapphire and Fotoform glass barrels were bonded successfully with the alignment fixture.

  4. Magnetically aligned supramolecular hydrogels.

    PubMed

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

    2014-12-01

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

  5. MUSE optical alignment procedure

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

    2012-09-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

  6. Segment alignment control system

    NASA Technical Reports Server (NTRS)

    Aubrun, JEAN-N.; Lorell, Ken R.

    1988-01-01

    The segmented primary mirror for the LDR will require a special segment alignment control system to precisely control the orientation of each of the segments so that the resulting composite reflector behaves like a monolith. The W.M. Keck Ten Meter Telescope will utilize a primary mirror made up of 36 actively controlled segments. Thus the primary mirror and its segment alignment control system are directly analogous to the LDR. The problems of controlling the segments in the face of disturbances and control/structures interaction, as analyzed for the TMT, are virtually identical to those for the LDR. The two systems are briefly compared.

  7. Molecular focusing and alignment with plasmon fields.

    PubMed

    Artamonov, Maxim; Seideman, Tamar

    2010-12-01

    We show the possibility of simultaneously aligning molecules and focusing their center-of-mass motion near a metal nanoparticle in the field intensity gradient created by the surface plasmon enhancement of incident light. The rotational motion is described quantum mechanically while the translation is treated classically. The effects of the nanoparticle shape on the alignment and focusing are explored. Our results carry interesting implications to the field of molecular nanoplasmonics and suggest several potential applications in nanochemistry.

  8. Direct characterization of the energy level alignments and molecular components in an organic hetero-junction by integrated photoemission spectroscopy and reflection electron energy loss spectroscopy analysis.

    PubMed

    Yun, Dong-Jin; Shin, Weon-Ho; Bulliard, Xavier; Park, Jong Hwan; Kim, Seyun; Chung, Jae Gwan; Kim, Yongsu; Heo, Sung; Kim, Seong Heon

    2016-08-26

    A novel, direct method for the characterization of the energy level alignments at bulk-heterojunction (BHJ)/electrode interfaces on the basis of electronic spectroscopy measurements is proposed. The home-made in situ photoemission system is used to perform x-ray/ultraviolet photoemission spectroscopy (XPS/UPS), reflection electron energy loss spectroscopy (REELS) and inverse photoemission spectroscopy of organic-semiconductors (OSCs) deposited onto a Au substrate. Through this analysis system, we are able to obtain the electronic structures of a boron subphthalocyanine chloride:fullerene (SubPC:C60) BHJ and those of the separate OSC/electrode structures (SubPC/Au and C60/Au). Morphology and chemical composition analyses confirm that the original SubPC and C60 electronic structures remain unchanged in the electrodes prepared. Using this technique, we ascertain that the position and area of the nearest peak to the Fermi energy (EF = 0 eV) in the UPS (REELS) spectra of SubPC:C60 BHJ provide information on the highest occupied molecular orbital level (optical band gap) and combination ratio of the materials, respectively. Thus, extracting the adjusted spectrum from the corresponding SubPC:C60 BHJ UPS (REELS) spectrum reveals its electronic structure, equivalent to that of the C60 materials. This novel analytical approach allows complete energy-level determination for each combination ratio by separating its electronic structure information from the BHJ spectrum. PMID:27420635

  9. Direct characterization of the energy level alignments and molecular components in an organic hetero-junction by integrated photoemission spectroscopy and reflection electron energy loss spectroscopy analysis

    NASA Astrophysics Data System (ADS)

    Yun, Dong-Jin; Shin, Weon-Ho; Bulliard, Xavier; Park, Jong Hwan; Kim, Seyun; Chung, Jae Gwan; Kim, Yongsu; Heo, Sung; Kim, Seong Heon

    2016-08-01

    A novel, direct method for the characterization of the energy level alignments at bulk-heterojunction (BHJ)/electrode interfaces on the basis of electronic spectroscopy measurements is proposed. The home-made in situ photoemission system is used to perform x-ray/ultraviolet photoemission spectroscopy (XPS/UPS), reflection electron energy loss spectroscopy (REELS) and inverse photoemission spectroscopy of organic-semiconductors (OSCs) deposited onto a Au substrate. Through this analysis system, we are able to obtain the electronic structures of a boron subphthalocyanine chloride:fullerene (SubPC:C60) BHJ and those of the separate OSC/electrode structures (SubPC/Au and C60/Au). Morphology and chemical composition analyses confirm that the original SubPC and C60 electronic structures remain unchanged in the electrodes prepared. Using this technique, we ascertain that the position and area of the nearest peak to the Fermi energy (EF = 0 eV) in the UPS (REELS) spectra of SubPC:C60 BHJ provide information on the highest occupied molecular orbital level (optical band gap) and combination ratio of the materials, respectively. Thus, extracting the adjusted spectrum from the corresponding SubPC:C60 BHJ UPS (REELS) spectrum reveals its electronic structure, equivalent to that of the C60 materials. This novel analytical approach allows complete energy-level determination for each combination ratio by separating its electronic structure information from the BHJ spectrum.

  10. Virulent strain of Lichtheimia corymbifera shows increased phagocytosis by macrophages as revealed by automated microscopy image analysis.

    PubMed

    Kraibooj, Kaswara; Park, Hea-Reung; Dahse, Hans-Martin; Skerka, Christine; Voigt, Kerstin; Figge, Marc Thilo

    2014-12-01

    Lichtheimia corymbifera is a ubiquitous soilborne zygomycete fungus, which is an opportunistic human pathogen in immunocompromised patients. The fungus can cause life-threatening diseases by attacking the lung during early stages of invasion and by disseminating during later phases causing systemic infection. Since infections have drastically increased during the last decades, it is a major goal to investigate the mechanisms underlying pathogenicity of L. corymbifera. One of the first barriers, which the fungus needs to cope with in the lung tissue, is phagocytosis by alveolar macrophages. Here, we report on phagocytosis assays for murine alveolar macrophages co-incubated with resting, swollen and opsonised spores of a virulent and an attenuated L. corymbifera strain. A major finding of this study is the significantly increased phagocytosis ratio of the virulent strain if compared to the attenuated strain. We quantify the phagocytosis by performing automated analysis of fluorescence microscopy images and by computing ratios for (i) fungal phagocytosis, (ii) fungal adhesion to phagocytes and (iii) fungal aggregation and spore cluster distribution in space. Automation of the image analysis yields objective results that overcome the disadvantages of manual analyses being time consuming, error-prone and subjective. Therefore, it can be expected that automated image analysis of confrontation assays will play a crucial role in future investigations of host-pathogen interactions.

  11. MULTAN: a program to align multiple DNA sequences.

    PubMed Central

    Bains, W

    1986-01-01

    I describe a computer program which can align a large number of nucleic acid sequences with one another. The program uses an heuristic, iterative algorithm which has been tested extensively, and is found to produce useful alignments of a variety of sequence families. The algorithm is fast enough to be practical for the analysis of large number of sequences, and is implemented in a program which contains a variety of other functions to facilitate the analysis of the aligned result. PMID:3003672

  12. Curriculum Alignment: Establishing Coherence

    ERIC Educational Resources Information Center

    Gagné, Philippe; Dumont, Laurence; Brunet, Sabine; Boucher, Geneviève

    2013-01-01

    In this paper, we present a step-by-step guide to implement a curricular alignment project, directed at professional development and student support, and developed in a higher education French as a second language department. We outline best practices and preliminary results from our experience and provide ways to adapt our experience to other…

  13. Optically Aligned Drill Press

    NASA Technical Reports Server (NTRS)

    Adderholdt, Bruce M.

    1994-01-01

    Precise drill press equipped with rotary-indexing microscope. Microscope and drill exchange places when turret rotated. Microscope axis first aligned over future hole, then rotated out of way so drill axis assumes its precise position. New procedure takes less time to locate drilling positions and produces more accurate results. Apparatus adapted to such other machine tools as milling and measuring machines.

  14. Aligning brains and minds

    PubMed Central

    Tong, Frank

    2012-01-01

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

  15. Aligned-or Not?

    ERIC Educational Resources Information Center

    Roseman, Jo Ellen; Koppal, Mary

    2015-01-01

    When state leaders and national partners in the development of the Next Generation Science Standards met to consider implementation strategies, states and school districts wanted to know which materials were aligned to the new standards. The answer from the developers was short but not sweet: You won't find much now, and it's going to…

  16. Ridge effect and alignment phenomenon

    SciTech Connect

    Lokhtin, I. P. Managadze, A. K. Snigirev, A. M.

    2013-05-15

    It is assumed that the ridge effect observed by the CMS Collaboration in proton-proton collisions at the LHC and the phenomenon observed by the Pamir Collaboration in emulsion experiments with cosmic rays and characterized by the alignment of spots on a film is a manifestation of the same as-yet-unknown mechanism of the emergence of a coplanar structure of events. A large coplanar effect at the LHC in the region of forward rapidities is predicted on the basis of this hypothesis and an analysis of experimental data.

  17. Grain alignment by radiative torques in special conditions and implications

    NASA Astrophysics Data System (ADS)

    Hoang, Thiem; Lazarian, A.

    2014-02-01

    Grain alignment by radiative torques (RATs) has been extensively studied for various environment conditions, including interstellar medium, dense molecular clouds and accretion discs, thanks to significant progress in observational, theoretical and numerical studies. In this paper, we explore the alignment by RATs and provide quantitative predictions of dust polarization for a set of astrophysical environments that can be tested observationally. We first consider the alignment of grains in the local interstellar medium and compare predictions for linear polarization by aligned grains with recent observational data for nearby stars. We then revisit the problem of grain alignment in accretions discs by taking into account the dependence of RAT alignment efficiency on the anisotropic direction of radiation fields relative to magnetic fields. Moreover, we study the grain alignment in interplanetary medium, including diffuse Zodiacal cloud and cometary comae, and calculate the degree of circular polarization (CP) of scattered light arising from single scattering by aligned grains. We also discuss a new type of grain alignment, namely the alignment with respect to the ambient electric field instead of the alignment with the magnetic field. We show that this type of alignment can allow us to reproduce the systematic features of CP observed across a cometary coma. Our findings suggest that polarized Zodiacal dust emission may be an important polarized foreground component, which should be treated carefully in cosmic microwave background experiments.

  18. A novel approach for preparation of aligned electrospun polyacrylonitrile nanofibers

    NASA Astrophysics Data System (ADS)

    Heidari, Iman; Mosavi Mashhadi, Mahmoud; Faraji, Ghader

    2013-12-01

    In this Letter, a new type of collector named ‘rotating grid collector’ was introduced and its capability in aligning the nanofibers was examined. The results showed that electrospinning using rotating grid collector could produce well aligned fibers with fiber alignment percent of 76%. It was found that in a constant solution flow rate increasing collector rotation speed and eccentric distance improved the fiber alignments. Having prepared the fiber textiles, we found that increasing the rotation speed improved the tensile strength of the fiber textile. This new collector is promising for future application in aligning nanofibers.

  19. Systems analysis of the NCI-60 cancer cell lines by alignment of protein pathway activation modules with "-OMIC" data fields and therapeutic response signatures.

    PubMed

    Federici, Giulia; Gao, Xi; Slawek, Janusz; Arodz, Tomasz; Shitaye, Amanuel; Wulfkuhle, Julia D; De Maria, Ruggero; Liotta, Lance A; Petricoin, Emanuel F

    2013-06-01

    The NCI-60 cell line set is likely the most molecularly profiled set of human tumor cell lines in the world. However, a critical missing component of previous analyses has been the inability to place the massive amounts of "-omic" data in the context of functional protein signaling networks, which often contain many of the drug targets for new targeted therapeutics. We used reverse-phase protein array (RPPA) analysis to measure the activation/phosphorylation state of 135 proteins, with a total analysis of nearly 200 key protein isoforms involved in cell proliferation, survival, migration, adhesion, etc., in all 60 cell lines. We aggregated the signaling data into biochemical modules of interconnected kinase substrates for 6 key cancer signaling pathways: AKT, mTOR, EGF receptor (EGFR), insulin-like growth factor-1 receptor (IGF-1R), integrin, and apoptosis signaling. The net activation state of these protein network modules was correlated to available individual protein, phosphoprotein, mutational, metabolomic, miRNA, transcriptional, and drug sensitivity data. Pathway activation mapping identified reproducible and distinct signaling cohorts that transcended organ-type distinctions. Direct correlations with the protein network modules involved largely protein phosphorylation data but we also identified direct correlations of signaling networks with metabolites, miRNA, and DNA data. The integration of protein activation measurements into biochemically interconnected modules provided a novel means to align the functional protein architecture with multiple "-omic" data sets and therapeutic response correlations. This approach may provide a deeper understanding of how cellular biochemistry defines therapeutic response. Such "-omic" portraits could inform rational anticancer agent screenings and drive personalized therapeutic approaches. PMID:23635402

  20. Magnetic alignment of the Tara tandem mirror

    SciTech Connect

    Post, R.S.; Coleman, J.W.; Irby, J.H.; Olmstead, M.M.; Torti, R.P.

    1985-06-01

    Techniques developed for the alignment of high-energy accelerators have been applied to the alignment of the Tara tandem mirror magnetic confinement device. Tools used were: a transit/laser surveyor's system for establishing an invariant reference; optical scattering from ferromagnetic crystallites for establishing magnetic centers in the quadrupole anchor/transition modules; an electron-optical circle-generating wand for alignment of the solenoidal plug and central cell modules; and four differently configured electron emissive probes, including a 40-beam flux mapping e gun, for testing the alignment of the coils under vacuum. Procedures are outlined, and results are given which show that the magnetic axes of the individual coils in the Tara set have been made colinear with each other and with the reference to within +- 1.0 mm over the length of the machine between the anchor midplanes.

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

    PubMed

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

    2016-08-01

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

  2. Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity

    PubMed Central

    2012-01-01

    Background Thellungiella salsuginea is an important model plant due to its natural tolerance to abiotic stresses including salt, cold, and water deficits. Microarray and metabolite profiling have shown that Thellungiella undergoes stress-responsive changes in transcript and organic solute abundance when grown under controlled environmental conditions. However, few reports assess the capacity of plants to display stress-responsive traits in natural habitats where concurrent stresses are the norm. Results To determine whether stress-responsive changes observed in cabinet-grown plants are recapitulated in the field, we analyzed leaf transcript and metabolic profiles of Thellungiella growing in its native Yukon habitat during two years of contrasting meteorological conditions. We found 673 genes showing differential expression between field and unstressed, chamber-grown plants. There were comparatively few overlaps between genes expressed under field and cabinet treatment-specific conditions. Only 20 of 99 drought-responsive genes were expressed both in the field during a year of low precipitation and in plants subjected to drought treatments in cabinets. There was also a general pattern of lower abundance among metabolites found in field plants relative to control or stress-treated plants in growth cabinets. Nutrient availability may explain some of the observed differences. For example, proline accumulated to high levels in cold and salt-stressed cabinet-grown plants but proline content was, by comparison, negligible in plants at a saline Yukon field site. We show that proline accumulated in a stress-responsive manner in Thellungiella plants salinized in growth cabinets and in salt-stressed seedlings when nitrogen was provided at 1.0 mM. In seedlings grown on 0.1 mM nitrogen medium, the proline content was low while carbohydrates increased. The relatively higher content of sugar-like compounds in field plants and seedlings on low nitrogen media suggests that

  3. Radar Image and Rain-gauge Alignment using the Multi-resolution Viscous Alignment (MVA) Algorithm

    NASA Astrophysics Data System (ADS)

    Chatdarong, V.

    2007-12-01

    Rainfall is a complex environmental variable that is difficult to describe either deterministically or statistically. To understand rainfall behaviors, many types of instruments are employed to detect and collect rainfall information. Among them, radar seems to provide the most comprehensive rainfall measurement at fine spatial and temporal resolution and over a relatively wide area. Nevertheless, it does not detects surface rainfall directly like what rain-gauge does. The accuracy radar rainfall, therefore, depends greatly on the Z-R relationship which convert radar reflectivity (Z) to surface rainrate (R). This calibration is usually done by fitting the rain-gauge data with the corresponding radar reflectivity using the regression analysis. To best fit the data, the radar reflectivity at neighbor pixels are usually used to best match the rain-gauge data. However, when applying the Z-R relationship to the radar image, there is no position adjustment despite the calibration technique. Hence, it is desirable to adjust the position of the radar reflectivity images prior to applying the Z-R relationship to improve the accuracy of the rainfall estimation. In this research, the Multi-resolution Viscous Alignment (MVA) algorithm is applied to best align radar reflectivity images to rain-gauge data in order to improve rainfall estimation from the Z-R relationship. The MVA algorithm solves the motion estimation problems using a Bayesian formulation to minimize misfits between two data sets. In general, the problem are ill-posed; therefore, some regularizations and constraints based on smoothness and non-divergence assumptions are employed. This algorithm is superior to the conventional techniques and correlation based techniques. It is fast, robust, easy to implement, and does not require data training. In addition, it can handle higher-order, missing data, and small-scale deformations. The algorithm provides spatially dense, consistency, and smooth transition vector. The

  4. SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data.

    PubMed

    Abuín, José M; Pichel, Juan C; Pena, Tomás F; Amigo, Jorge

    2016-01-01

    Next-generation sequencing (NGS) technologies have led to a huge amount of genomic data that need to be analyzed and interpreted. This fact has a huge impact on the DNA sequence alignment process, which nowadays requires the mapping of billions of small DNA sequences onto a reference genome. In this way, sequence alignment remains the most time-consuming stage in the sequence analysis workflow. To deal with this issue, state of the art aligners take advantage of parallelization strategies. However, the existent solutions show limited scalability and have a complex implementation. In this work we introduce SparkBWA, a new tool that exploits the capabilities of a big data technology as Spark to boost the performance of one of the most widely adopted aligner, the Burrows-Wheeler Aligner (BWA). The design of SparkBWA uses two independent software layers in such a way that no modifications to the original BWA source code are required, which assures its compatibility with any BWA version (future or legacy). SparkBWA is evaluated in different scenarios showing noticeable results in terms of performance and scalability. A comparison to other parallel BWA-based aligners validates the benefits of our approach. Finally, an intuitive and flexible API is provided to NGS professionals in order to facilitate the acceptance and adoption of the new tool. The source code of the software described in this paper is publicly available at https://github.com/citiususc/SparkBWA, with a GPL3 license. PMID:27182962

  5. SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data

    PubMed Central

    2016-01-01

    Next-generation sequencing (NGS) technologies have led to a huge amount of genomic data that need to be analyzed and interpreted. This fact has a huge impact on the DNA sequence alignment process, which nowadays requires the mapping of billions of small DNA sequences onto a reference genome. In this way, sequence alignment remains the most time-consuming stage in the sequence analysis workflow. To deal with this issue, state of the art aligners take advantage of parallelization strategies. However, the existent solutions show limited scalability and have a complex implementation. In this work we introduce SparkBWA, a new tool that exploits the capabilities of a big data technology as Spark to boost the performance of one of the most widely adopted aligner, the Burrows-Wheeler Aligner (BWA). The design of SparkBWA uses two independent software layers in such a way that no modifications to the original BWA source code are required, which assures its compatibility with any BWA version (future or legacy). SparkBWA is evaluated in different scenarios showing noticeable results in terms of performance and scalability. A comparison to other parallel BWA-based aligners validates the benefits of our approach. Finally, an intuitive and flexible API is provided to NGS professionals in order to facilitate the acceptance and adoption of the new tool. The source code of the software described in this paper is publicly available at https://github.com/citiususc/SparkBWA, with a GPL3 license. PMID:27182962

  6. Anatomical network analysis shows decoupling of modular lability and complexity in the evolution of the primate skull.

    PubMed

    Esteve-Altava, Borja; Boughner, Julia C; Diogo, Rui; Villmoare, Brian A; Rasskin-Gutman, Diego

    2015-01-01

    Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon's general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates.

  7. Phylogenetic analysis shows that Neolithic slate plaques from the southwestern Iberian Peninsula are not genealogical recording systems.

    PubMed

    García Rivero, Daniel; O'Brien, Michael J

    2014-01-01

    Prehistoric material culture proposed to be symbolic in nature has been the object of considerable archaeological work from diverse theoretical perspectives, yet rarely are methodological tools used to test the interpretations. The lack of testing is often justified by invoking the opinion that the slippery nature of past human symbolism cannot easily be tackled by the scientific method. One such case, from the southwestern Iberian Peninsula, involves engraved stone plaques from megalithic funerary monuments dating ca. 3,500-2,750 B.C. (calibrated age). One widely accepted proposal is that the plaques are ancient mnemonic devices that record genealogies. The analysis reported here demonstrates that this is not the case, even when the most supportive data and techniques are used. Rather, we suspect there was a common ideological background to the use of plaques that overlay the southwestern Iberian Peninsula, with little or no geographic patterning. This would entail a cultural system in which plaque design was based on a fundamental core idea, with a number of mutable and variable elements surrounding it.

  8. Analysis of somatic hypermutation in X-linked hyper-IgM syndrome shows specific deficiencies in mutational targeting.

    PubMed

    Longo, Nancy S; Lugar, Patricia L; Yavuz, Sule; Zhang, Wen; Krijger, Peter H L; Russ, Daniel E; Jima, Dereje D; Dave, Sandeep S; Grammer, Amrie C; Lipsky, Peter E

    2009-04-16

    Subjects with X-linked hyper-IgM syndrome (X-HIgM) have a markedly reduced frequency of CD27(+) memory B cells, and their Ig genes have a low level of somatic hypermutation (SHM). To analyze the nature of SHM in X-HIgM, we sequenced 209 nonproductive and 926 productive Ig heavy chain genes. In nonproductive rearrangements that were not subjected to selection, as well as productive rearrangements, most of the mutations were within targeted RGYW, WRCY, WA, or TW motifs (R = purine, Y = pyrimidine, and W = A or T). However, there was significantly decreased targeting of the hypermutable G in RGYW motifs. Moreover, the ratio of transitions to transversions was markedly increased compared with normal. Microarray analysis documented that specific genes involved in SHM, including activation-induced cytidine deaminase (AICDA) and uracil-DNA glycosylase (UNG2), were up-regulated in normal germinal center (GC) B cells, but not induced by CD40 ligation. Similar results were obtained from light chain rearrangements. These results indicate that in the absence of CD40-CD154 interactions, there is a marked reduction in SHM and, specifically, mutations of AICDA-targeted G residues in RGYW motifs along with a decrease in transversions normally related to UNG2 activity.

  9. Analysis of somatic hypermutation in X-linked hyper-IgM syndrome shows specific deficiencies in mutational targeting

    PubMed Central

    Longo, Nancy S.; Lugar, Patricia L.; Yavuz, Sule; Zhang, Wen; Krijger, Peter H. L.; Russ, Daniel E.; Jima, Dereje D.; Dave, Sandeep S.; Grammer, Amrie C.

    2009-01-01

    Subjects with X-linked hyper-IgM syndrome (X-HIgM) have a markedly reduced frequency of CD27+ memory B cells, and their Ig genes have a low level of somatic hypermutation (SHM). To analyze the nature of SHM in X-HIgM, we sequenced 209 nonproductive and 926 productive Ig heavy chain genes. In nonproductive rearrangements that were not subjected to selection, as well as productive rearrangements, most of the mutations were within targeted RGYW, WRCY, WA, or TW motifs (R = purine, Y = pyrimidine, and W = A or T). However, there was significantly decreased targeting of the hypermutable G in RGYW motifs. Moreover, the ratio of transitions to transversions was markedly increased compared with normal. Microarray analysis documented that specific genes involved in SHM, including activation-induced cytidine deaminase (AICDA) and uracil-DNA glycosylase (UNG2), were up-regulated in normal germinal center (GC) B cells, but not induced by CD40 ligation. Similar results were obtained from light chain rearrangements. These results indicate that in the absence of CD40-CD154 interactions, there is a marked reduction in SHM and, specifically, mutations of AICDA-targeted G residues in RGYW motifs along with a decrease in transversions normally related to UNG2 activity. PMID:19023113

  10. Phylogenetic analysis shows that Neolithic slate plaques from the southwestern Iberian Peninsula are not genealogical recording systems.

    PubMed

    García Rivero, Daniel; O'Brien, Michael J

    2014-01-01

    Prehistoric material culture proposed to be symbolic in nature has been the object of considerable archaeological work from diverse theoretical perspectives, yet rarely are methodological tools used to test the interpretations. The lack of testing is often justified by invoking the opinion that the slippery nature of past human symbolism cannot easily be tackled by the scientific method. One such case, from the southwestern Iberian Peninsula, involves engraved stone plaques from megalithic funerary monuments dating ca. 3,500-2,750 B.C. (calibrated age). One widely accepted proposal is that the plaques are ancient mnemonic devices that record genealogies. The analysis reported here demonstrates that this is not the case, even when the most supportive data and techniques are used. Rather, we suspect there was a common ideological background to the use of plaques that overlay the southwestern Iberian Peninsula, with little or no geographic patterning. This would entail a cultural system in which plaque design was based on a fundamental core idea, with a number of mutable and variable elements surrounding it. PMID:24558384

  11. Phylogenetic Analysis Shows That Neolithic Slate Plaques from the Southwestern Iberian Peninsula Are Not Genealogical Recording Systems

    PubMed Central

    García Rivero, Daniel; O'Brien, Michael J.

    2014-01-01

    Prehistoric material culture proposed to be symbolic in nature has been the object of considerable archaeological work from diverse theoretical perspectives, yet rarely are methodological tools used to test the interpretations. The lack of testing is often justified by invoking the opinion that the slippery nature of past human symbolism cannot easily be tackled by the scientific method. One such case, from the southwestern Iberian Peninsula, involves engraved stone plaques from megalithic funerary monuments dating ca. 3,500–2,750 B.C. (calibrated age). One widely accepted proposal is that the plaques are ancient mnemonic devices that record genealogies. The analysis reported here demonstrates that this is not the case, even when the most supportive data and techniques are used. Rather, we suspect there was a common ideological background to the use of plaques that overlay the southwestern Iberian Peninsula, with little or no geographic patterning. This would entail a cultural system in which plaque design was based on a fundamental core idea, with a number of mutable and variable elements surrounding it. PMID:24558384

  12. Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels.

    PubMed

    Bhardwaj, Nitin; Yan, Koon-Kiu; Gerstein, Mark B

    2010-04-13

    Gene regulatory networks have been shown to share some common aspects with commonplace social governance structures. Thus, we can get some intuition into their organization by arranging them into well-known hierarchical layouts. These hierarchies, in turn, can be placed between the extremes of autocracies, with well-defined levels and clear chains of command, and democracies, without such defined levels and with more co-regulatory partnerships between regulators. In general, the presence of partnerships decreases the variation in information flow amongst nodes within a level, more evenly distributing stress. Here we study various regulatory networks (transcriptional, modification, and phosphorylation) for five diverse species, Escherichia coli to human. We specify three levels of regulators--top, middle, and bottom--which collectively govern the non-regulator targets lying in the lowest fourth level. We define quantities for nodes, levels, and entire networks that measure their degree of collaboration and autocratic vs. democratic character. We show individual regulators have a range of partnership tendencies: Some regulate their targets in combination with other regulators in local instantiations of democratic structure, whereas others regulate mostly in isolation, in more autocratic fashion. Overall, we show that in all networks studied the middle level has the highest collaborative propensity and coregulatory partnerships occur most frequently amongst midlevel regulators, an observation that has parallels in corporate settings where middle managers must interact most to ensure organizational effectiveness. There is, however, one notable difference between networks in different species: The amount of collaborative regulation and democratic character increases markedly with overall genomic complexity. PMID:20351254

  13. Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

    PubMed Central

    May, Megan K.; Kevorkian, Richard T.; Steen, Andrew D.

    2013-01-01

    There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined “yield” to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly. PMID:24096423

  14. Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels.

    PubMed

    Bhardwaj, Nitin; Yan, Koon-Kiu; Gerstein, Mark B

    2010-04-13

    Gene regulatory networks have been shown to share some common aspects with commonplace social governance structures. Thus, we can get some intuition into their organization by arranging them into well-known hierarchical layouts. These hierarchies, in turn, can be placed between the extremes of autocracies, with well-defined levels and clear chains of command, and democracies, without such defined levels and with more co-regulatory partnerships between regulators. In general, the presence of partnerships decreases the variation in information flow amongst nodes within a level, more evenly distributing stress. Here we study various regulatory networks (transcriptional, modification, and phosphorylation) for five diverse species, Escherichia coli to human. We specify three levels of regulators--top, middle, and bottom--which collectively govern the non-regulator targets lying in the lowest fourth level. We define quantities for nodes, levels, and entire networks that measure their degree of collaboration and autocratic vs. democratic character. We show individual regulators have a range of partnership tendencies: Some regulate their targets in combination with other regulators in local instantiations of democratic structure, whereas others regulate mostly in isolation, in more autocratic fashion. Overall, we show that in all networks studied the middle level has the highest collaborative propensity and coregulatory partnerships occur most frequently amongst midlevel regulators, an observation that has parallels in corporate settings where middle managers must interact most to ensure organizational effectiveness. There is, however, one notable difference between networks in different species: The amount of collaborative regulation and democratic character increases markedly with overall genomic complexity.

  15. Meta-analysis of quantification methods shows that archaea and bacteria have similar abundances in the subseafloor.

    PubMed

    Lloyd, Karen G; May, Megan K; Kevorkian, Richard T; Steen, Andrew D

    2013-12-01

    There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined "yield" to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly.

  16. Scanning electron microscopy analysis of the growth of dental plaque on the surfaces of removable orthodontic aligners after the use of different cleaning methods

    PubMed Central

    Levrini, Luca; Novara, Francesca; Margherini, Silvia; Tenconi, Camilla; Raspanti, Mario

    2015-01-01

    Background Advances in orthodontics are leading to the use of minimally invasive technologies, such as transparent removable aligners, and are able to meet high demands in terms of performance and esthetics. However, the most correct method of cleaning these appliances, in order to minimize the effects of microbial colonization, remains to be determined. Purpose The aim of the present study was to identify the most effective method of cleaning removable orthodontic aligners, analyzing the growth of dental plaque as observed under scanning electron microscopy. Methods Twelve subjects were selected for the study. All were free from caries and periodontal disease and were candidates for orthodontic therapy with invisible orthodontic aligners. The trial had a duration of 6 weeks, divided into three 2-week stages, during which three sets of aligners were used. In each stage, the subjects were asked to use a different method of cleaning their aligners: 1) running water (control condition); 2) effervescent tablets containing sodium carbonate and sulfate crystals followed by brushing with a toothbrush; and 3) brushing alone (with a toothbrush and toothpaste). At the end of each 2-week stage, the surfaces of the aligners were analyzed under scanning electron microscopy. Results The best results were obtained with brushing combined with the use of sodium carbonate and sulfate crystals; brushing alone gave slightly inferior results. Conclusion On the basis of previous literature results relating to devices in resin, studies evaluating the reliability of domestic ultrasonic baths for domestic use should be encouraged. At present, pending the availability of experimental evidence, it can be suggested that dental hygienists should strongly advise patients wearing orthodontic aligners to clean them using a combination of brushing and commercially available tablets for cleaning oral appliances. PMID:26719726

  17. Morphometric analysis of molars in a Middle Pleistocene population shows a mosaic of ‘modern’ and Neanderthal features

    PubMed Central

    Martinón-Torres, María; Spěváčková, Petra; Gracia-Téllez, Ana; Martínez, Ignacio; Bruner, Emiliano; Arsuaga, Juan Luis; Bermúdez de Castro, José María

    2013-01-01

    Previous studies of upper first molar (M1) crown shape have shown significant differences between Homo sapiens and Homo neanderthalensis that were already present in the European Middle Pleistocene populations, including the large dental sample from Atapuerca-Sima de los Huesos (SH). Analysis of other M1 features such as the total crown base area, cusp proportions, cusp angles and occlusal polygon have confirmed the differences between both lineages, becoming a useful tool for the taxonomic assignment of isolated teeth from Late Pleistocene sites. However, until now the pattern of expression of these variables has not been known for the SH sample. This fossil sample, the largest collection from the European Middle Pleistocene, is generally interpreted as being from the direct ancestors of Neanderthals, and thus is a reference sample for assessing the origin of the Neanderthal morphologies. Surprisingly, our study reveals that SH M1s present a unique mosaic of H. neanderthalensis and H. sapiens features. Regarding the cusp angles and the relative occlusal polygon area, SH matches the H. neanderthalensis pattern. However, regarding the total crown base area and relative cusps size, SH M1s are similar to H. sapiens, with a small crown area, a strong hypocone reduction and a protocone enlargement, although the protocone expansion in SH is significantly larger than in any other group studied. The SH dental sample calls into question the uniqueness of some so-called modern traits. Our study also sounds a note of caution on the use of M1 occlusal morphology for the alpha taxonomy of isolated M1s. PMID:23914934

  18. Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs

    PubMed Central

    Edwards, Ceiridwen J; Bollongino, Ruth; Scheu, Amelie; Chamberlain, Andrew; Tresset, Anne; Vigne, Jean-Denis; Baird, Jillian F; Larson, Greger; Ho, Simon Y.W; Heupink, Tim H; Shapiro, Beth; Freeman, Abigail R; Thomas, Mark G; Arbogast, Rose-Marie; Arndt, Betty; Bartosiewicz, László; Benecke, Norbert; Budja, Mihael; Chaix, Louis; Choyke, Alice M; Coqueugniot, Eric; Döhle, Hans-Jürgen; Göldner, Holger; Hartz, Sönke; Helmer, Daniel; Herzig, Barabara; Hongo, Hitomi; Mashkour, Marjan; Özdogan, Mehmet; Pucher, Erich; Roth, Georg; Schade-Lindig, Sabine; Schmölcke, Ulrich; Schulting, Rick J; Stephan, Elisabeth; Uerpmann, Hans-Peter; Vörös, István; Voytek, Barbara; Bradley, Daniel G; Burger, Joachim

    2007-01-01

    The extinct aurochs (Bos primigenius primigenius) was a large type of cattle that ranged over almost the whole Eurasian continent. The aurochs is the wild progenitor of modern cattle, but it is unclear whether European aurochs contributed to this process. To provide new insights into the demographic history of aurochs and domestic cattle, we have generated high-confidence mitochondrial DNA sequences from 59 archaeological skeletal finds, which were attributed to wild European cattle populations based on their chronological date and/or morphology. All pre-Neolithic aurochs belonged to the previously designated P haplogroup, indicating that this represents the Late Glacial Central European signature. We also report one new and highly divergent haplotype in a Neolithic aurochs sample from Germany, which points to greater variability during the Pleistocene. Furthermore, the Neolithic and Bronze Age samples that were classified with confidence as European aurochs using morphological criteria all carry P haplotype mitochondrial DNA, suggesting continuity of Late Glacial and Early Holocene aurochs populations in Europe. Bayesian analysis indicates that recent population growth gives a significantly better fit to our data than a constant-sized population, an observation consistent with a postglacial expansion scenario, possibly from a single European refugial population. Previous work has shown that most ancient and modern European domestic cattle carry haplotypes previously designated T. This, in combination with our new finding of a T haplotype in a very Early Neolithic site in Syria, lends persuasive support to a scenario whereby gracile Near Eastern domestic populations, carrying predominantly T haplotypes, replaced P haplotype-carrying robust autochthonous aurochs populations in Europe, from the Early Neolithic onward. During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare. PMID

  19. Genetic analysis shows that morphology alone cannot distinguish asian carp eggs from those of other cyprinid species

    USGS Publications Warehouse

    Larson, James H.; McCalla, Sunnie; Chapman, Duane C.; Rees, Christopher B.; Knights, Brent C.; Vallazza, Jon; George, Amy E.; Richardson, William B.; Amberg, Jon

    2016-01-01

    Fish eggs and embryos (hereafter collectively referred to as “eggs”) were collected in the upper Mississippi River main stem (~300 km upstream of previously reported spawning by invasive Asian carp) during summer 2013. Based on previously published morphological characteristics, the eggs were identified as belonging to Asian carp. A subsample of the eggs was subsequently analyzed by using molecular methods to determine species identity. Genetic identification using the cytochrome-c oxidase 1 gene was attempted for a total of 41 eggs. Due to the preservation technique used (formalin) and the resulting DNA degradation, sequences were recovered from only 17 individual eggs. In all 17 cases, cyprinids other than Asian carp (usually Notropis sp.) were identified as the most likely species. In previously published reports, a key characteristic that distinguished Asian carp eggs from those of other cyprinids was size: Asian carp eggs exhibited diameters ranging from 4.0 to 6.0 mm and were thought to be much larger than the otherwise similar eggs of native species. Eggs from endemic cyprinids were believed to rarely reach 3.0 mm and had not been observed to exceed 3.3 mm. However, many of the eggs that were genetically identified as originating from native cyprinids were as large as 4.0 mm in diameter (at early developmental stages) and were therefore large enough to over- lap with the lower end of the size range observed for Asian carp eggs. Researchers studying the egg stages of Asian carp and other cyprinids should plan on preserving subsets of eggs for genetic analysis to confirm morphological identifications.

  20. Selection Indices and Multivariate Analysis Show Similar Results in the Evaluation of Growth and Carcass Traits in Beef Cattle

    PubMed Central

    Brito Lopes, Fernando; da Silva, Marcelo Corrêa; Magnabosco, Cláudio Ulhôa; Goncalves Narciso, Marcelo; Sainz, Roberto Daniel

    2016-01-01

    This research evaluated a multivariate approach as an alternative tool for the purpose of selection regarding expected progeny differences (EPDs). Data were fitted using a multi-trait model and consisted of growth traits (birth weight and weights at 120, 210, 365 and 450 days of age) and carcass traits (longissimus muscle area (LMA), back-fat thickness (BF), and rump fat thickness (RF)), registered over 21 years in extensive breeding systems of Polled Nellore cattle in Brazil. Multivariate analyses were performed using standardized (zero mean and unit variance) EPDs. The k mean method revealed that the best fit of data occurred using three clusters (k = 3) (P < 0.001). Estimates of genetic correlation among growth and carcass traits and the estimates of heritability were moderate to high, suggesting that a correlated response approach is suitable for practical decision making. Estimates of correlation between selection indices and the multivariate index (LD1) were moderate to high, ranging from 0.48 to 0.97. This reveals that both types of indices give similar results and that the multivariate approach is reliable for the purpose of selection. The alternative tool seems very handy when economic weights are not available or in cases where more rapid identification of the best animals is desired. Interestingly, multivariate analysis allowed forecasting information based on the relationships among breeding values (EPDs). Also, it enabled fine discrimination, rapid data summarization after genetic evaluation, and permitted accounting for maternal ability and the genetic direct potential of the animals. In addition, we recommend the use of longissimus muscle area and subcutaneous fat thickness as selection criteria, to allow estimation of breeding values before the first mating season in order to accelerate the response to individual selection. PMID:26789008

  1. MUSE alignment onto VLT

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dupuy, Christophe; Jarno, Aurélien; Lizon, Jean-Louis; Migniau, Jean-Emmanuel; Nicklas, Harald; Piqueras, Laure

    2014-07-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation Very Large Telescope (VLT) integral field spectrograph developed for the European Southern Observatory (ESO). It combines a 1' x 1' field of view sampled at 0.2 arcsec for its Wide Field Mode (WFM) and a 7.5"x7.5" field of view for its Narrow Field Mode (NFM). Both modes will operate with the improved spatial resolution provided by GALACSI (Ground Atmospheric Layer Adaptive Optics for Spectroscopic Imaging), that will use the VLT deformable secondary mirror and 4 Laser Guide Stars (LGS) foreseen in 2015. MUSE operates in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently commissioning MUSE in the Very Large Telescope for the Preliminary Acceptance in Chile, scheduled for September, 2014. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2012 and 2013, all MUSE subsystems were integrated, aligned and tested to the P.I. institute at Lyon. After successful PAE in September 2013, MUSE instrument was shipped to the Very Large Telescope in Chile where that was aligned and tested in ESO integration hall at Paranal. After, MUSE was directly transported, fully aligned and without any optomechanical dismounting, onto VLT telescope where the first light was overcame the 7th of February, 2014. This paper describes the alignment procedure of the whole MUSE instrument with respect to the Very Large Telescope (VLT). It describes how 6 tons could be move with accuracy better than 0.025mm and less than 0.25 arcmin in order to reach alignment requirements. The success

  2. Transcriptomic analysis of inbreeding depression in cold-sensitive Drosophila melanogaster shows upregulation of the immune response.

    PubMed

    Vermeulen, C J; Sørensen, P; Kirilova Gagalova, K; Loeschcke, V

    2013-09-01

    In sexually reproducing species, increased homozygosity often causes a decline in fitness, called inbreeding depression. Recently, researchers started describing the functional genomic changes that occur during inbreeding, both in benign conditions and under environmental stress. To further this aim, we have performed a genome-wide gene expression study of inbreeding depression, manifesting as cold sensitivity and conditional lethality. Our focus was to describe general patterns of gene expression during inbreeding depression and to identify specific processes affected in our line. There was a clear difference in gene expression between the stressful restrictive environment and the benign permissive environment in both the affected inbred line and the inbred control line. We noted a strong inbreeding-by-environment interaction, whereby virtually all transcriptional differences between lines were found in the restrictive environment. Functional annotation showed enrichment of transcripts coding for serine proteases and their inhibitors (serpins and BPTI/Kunitz family), which indicates activation of the innate immune response. These genes have previously been shown to respond transcriptionally to cold stress, suggesting the conditional lethal effect is associated with an exaggerated cold stress response. The set of differentially expressed genes significantly overlapped with those found in three other studies of inbreeding depression, demonstrating that it is possible to detect a common signature across different genetic backgrounds.

  3. Strand-specific analysis shows protein binding at replication forks and PCNA unloading from lagging strands when forks stall.

    PubMed

    Yu, Chuanhe; Gan, Haiyun; Han, Junhong; Zhou, Zhi-Xiong; Jia, Shaodong; Chabes, Andrei; Farrugia, Gianrico; Ordog, Tamas; Zhang, Zhiguo

    2014-11-20

    In eukaryotic cells, DNA replication proceeds with continuous synthesis of leading-strand DNA and discontinuous synthesis of lagging-strand DNA. Here we describe a method, eSPAN (enrichment and sequencing of protein-associated nascent DNA), which reveals the genome-wide association of proteins with leading and lagging strands of DNA replication forks. Using this approach in budding yeast, we confirm the strand specificities of DNA polymerases delta and epsilon and show that the PCNA clamp is enriched at lagging strands compared with leading-strand replication. Surprisingly, at stalled forks, PCNA is unloaded specifically from lagging strands. PCNA unloading depends on the Elg1-containing alternative RFC complex, ubiquitination of PCNA, and the checkpoint kinases Mec1 and Rad53. Cells deficient in PCNA unloading exhibit increased chromosome breaks. Our studies provide a tool for studying replication-related processes and reveal a mechanism whereby checkpoint kinases regulate strand-specific unloading of PCNA from stalled replication forks to maintain genome stability.

  4. High-resolution structural analysis shows how Tah1 tethers Hsp90 to the R2TP complex.

    PubMed

    Back, Régis; Dominguez, Cyril; Rothé, Benjamin; Bobo, Claude; Beaufils, Chrystel; Moréra, Solange; Meyer, Philippe; Charpentier, Bruno; Branlant, Christiane; Allain, Frédéric H-T; Manival, Xavier

    2013-10-01

    The ubiquitous Hsp90 chaperone participates in snoRNP and RNA polymerase assembly through interaction with the R2TP complex. This complex includes the proteins Tah1, Pih1, Rvb1, and Rvb2. Tah1 bridges Hsp90 to R2TP. Its minimal TPR domain includes two TPR motifs and a capping helix. We established the high-resolution solution structures of Tah1 free and in complex with the Hsp90 C-terminal peptide. The TPR fold is similar in the free and bound forms and we show experimentally that in addition to its solvating/stabilizing role, the capping helix is essential for the recognition of the Hsp90 (704)EMEEVD(709) motif. In addition to Lys79 and Arg83 from the carboxylate clamp, this helix bears Tyr82 forming a π/S-CH3 interaction with Hsp90 M(705) from the peptide 310 helix. The Tah1 C-terminal region is unfolded, and we demonstrate that it is essential for the recruitment of the Pih1 C-terminal domain and folds upon binding. PMID:24012479

  5. A pedigree analysis with minimised ascertainment bias shows anticipation in Met30-transthyretin related familial amyloid polyneuropathy.

    PubMed Central

    Yamamoto, K; Ikeda, S; Hanyu, N; Takeda, S; Yanagisawa, N

    1998-01-01

    In type I familial amyloid polyneuropathy (FAP) caused by a variant Met30-transthyretin (TTR), genetic anticipation has been reported. To determine whether anticipation of the disease is a true biological phenomenon or the result of ascertainment bias, we compared age at onset of the affected child with that of the affected parent in 68 parent-child pairs (including data on assumed age at onset and on asymptomatic obligate heterozygotes and parents at obligate 50% risk) in 15 families. Excluding the parent-child pairs involving the proband and "bilineal pairs", onset occurred earlier in the child than in the transmitting parent in 60 out of 68 "unilineal pairs". After correction for ascertainment bias resulting from incomplete penetrance and reduced biological fitness in early onset patients, the number of anticipation pairs (60 pairs) was still significantly larger than that of non-anticipation pairs (29.7 pairs) (p < 0.05). When the children were sons, the difference in age at onset was significantly greater in the mother-son pairs than in the father-son pairs (p = 0.023). Although not all ascertainment biases could be eliminated, these data show strong evidence that anticipation in the transmission of Met30-TTR FAP is a true biological phenomenon. PMID:9475090

  6. X-ray survival characteristics and genetic analysis for nine saccharomyces deletion mutants that show altered radiation sensitivity

    SciTech Connect

    Game, John C.; Williamson, Marsha S.; Baccari, Clelia

    2004-01-07

    The availability of a genome-wide set of Saccharomyces deletion mutants provides a chance to identify all the yeast genes involved in DNA repair. Using X-rays, we are screening these mutants to identify additional genes that show increased sensitivity to the lethal effects of ionizing radiation. For each mutant identified as sensitive, we are confirming that the sensitivity phenotype co-segregates with the deletion allele and are obtaining multipoint survival-versus-dose assays in at least two haploid and one homozygous diploid strains. We present data for deletion mutants involving the genes DOT1, MDM20, NAT3, SPT7, SPT20, GCN5, HFI1, DCC1 and VID21/EAF1, and discuss their potential roles in repair. Eight of these genes have a clear radiation-sensitive phenotype when deleted, but the ninth, GCN5, has at most a borderline phenotype. None of the deletions confer substantial sensitivity to ultra-violet radiation, although one or two may confer marginal sensitivity. The DOT1 gene is of interest because its only known function is to methylate one lysine residue in the core of the histone H3 protein. We find that histone H3 mutants (supplied by K. Struhl) in which this residue is replaced by other amino-acids are also X-ray sensitive, seeming to confirm that methylation of the lysine-79 residue is required for effective repair of radiation damage.

  7. An actuarial analysis shows that offering lung cancer screening as an insurance benefit would save lives at relatively low cost.

    PubMed

    Pyenson, Bruce S; Sander, Marcia S; Jiang, Yiding; Kahn, Howard; Mulshine, James L

    2012-04-01

    Lung cancer screening is not established as a public health practice, yet the results of a recent large randomized controlled trial showed that screening with low-dose spiral computed tomography reduces lung cancer mortality. Using actuarial models, this study estimated the costs and benefits of annual lung cancer screening offered as a commercial insurance benefit in the high-risk US population ages 50-64. Assuming current commercial reimbursement rates for treatment, we found that screening would cost about $1 per insured member per month in 2012 dollars. The cost per life-year saved would be below $19,000, an amount that compares favorably with screening for cervical, breast, and colorectal cancers. Our results suggest that commercial insurers should consider lung cancer screening of high-risk individuals to be high-value coverage and provide it as a benefit to people who are at least fifty years old and have a smoking history of thirty pack-years or more. We also believe that payers and patients should demand screening from high-quality, low-cost providers, thus helping set an example of efficient system innovation.

  8. Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake1234

    PubMed Central

    Tanaka, Toshiko; Ngwa, Julius S; van Rooij, Frank JA; Zillikens, M Carola; Wojczynski, Mary K; Frazier-Wood, Alexis C; Houston, Denise K; Kanoni, Stavroula; Lemaitre, Rozenn N; Luan, Jian'an; Mikkilä, Vera; Renstrom, Frida; Sonestedt, Emily; Zhao, Jing Hua; Chu, Audrey Y; Qi, Lu; Chasman, Daniel I; de Oliveira Otto, Marcia C; Dhurandhar, Emily J; Feitosa, Mary F; Johansson, Ingegerd; Khaw, Kay-Tee; Lohman, Kurt K; Manichaikul, Ani; McKeown, Nicola M; Mozaffarian, Dariush; Singleton, Andrew; Stirrups, Kathleen; Viikari, Jorma; Ye, Zheng; Bandinelli, Stefania; Barroso, Inês; Deloukas, Panos; Forouhi, Nita G; Hofman, Albert; Liu, Yongmei; Lyytikäinen, Leo-Pekka; North, Kari E; Dimitriou, Maria; Hallmans, Goran; Kähönen, Mika; Langenberg, Claudia; Ordovas, Jose M; Uitterlinden, André G; Hu, Frank B; Kalafati, Ioanna-Panagiota; Raitakari, Olli; Franco, Oscar H; Johnson, Andrew; Emilsson, Valur; Schrack, Jennifer A; Semba, Richard D; Siscovick, David S; Arnett, Donna K; Borecki, Ingrid B; Franks, Paul W; Kritchevsky, Stephen B; Lehtimäki, Terho; Loos, Ruth JF; Orho-Melander, Marju; Rotter, Jerome I; Wareham, Nicholas J; Witteman, Jacqueline CM; Ferrucci, Luigi; Dedoussis, George; Cupples, L Adrienne; Nettleton, Jennifer A

    2013-01-01

    Background: Macronutrient intake varies substantially between individuals, and there is evidence that this variation is partly accounted for by genetic variants. Objective: The objective of the study was to identify common genetic variants that are associated with macronutrient intake. Design: We performed 2-stage genome-wide association (GWA) meta-analysis of macronutrient intake in populations of European descent. Macronutrients were assessed by using food-frequency questionnaires and analyzed as percentages of total energy consumption from total fat, protein, and carbohydrate. From the discovery GWA (n = 38,360), 35 independent loci associated with macronutrient intake at P < 5 × 10−6 were identified and taken forward to replication in 3 additional cohorts (n = 33,533) from the DietGen Consortium. For one locus, fat mass obesity-associated protein (FTO), cohorts with Illumina MetaboChip genotype data (n = 7724) provided additional replication data. Results: A variant in the chromosome 19 locus (rs838145) was associated with higher carbohydrate (β ± SE: 0.25 ± 0.04%; P = 1.68 × 10−8) and lower fat (β ± SE: −0.21 ± 0.04%; P = 1.57 × 10−9) consumption. A candidate gene in this region, fibroblast growth factor 21 (FGF21), encodes a fibroblast growth factor involved in glucose and lipid metabolism. The variants in this locus were associated with circulating FGF21 protein concentrations (P < 0.05) but not mRNA concentrations in blood or brain. The body mass index (BMI)–increasing allele of the FTO variant (rs1421085) was associated with higher protein intake (β ± SE: 0.10 ± 0.02%; P = 9.96 × 10−10), independent of BMI (after adjustment for BMI, β ± SE: 0.08 ± 0.02%; P = 3.15 × 10−7). Conclusion: Our results indicate that variants in genes involved in nutrient metabolism and obesity are associated with macronutrient consumption in humans. Trials related to this study were registered at clinicaltrials.gov as NCT00005131 (Atherosclerosis

  9. FICTION-TSA analysis of the B-cell compartment in myeloma shows no significant expansion of myeloma precursor cells.

    PubMed

    Davies, F E; Rawstron, A C; Pratt, G; O'Connor, S; Su'ut, L; Blythe, D; Fenton, J; Claydon, D; Child, J A; Jack, A S; Morgan, G J

    1999-07-01

    Studies utilizing flow cytometry and PCR have shown that the B-cell compartment in myeloma contains cells which are clonally related to the myelomatous plasma cells. Current data, however, remains inconclusive regarding the extent of this involvement. By combining fluorescent immunophenotyping, tyramine signal amplification and fluorescence in-situ hybridization (FICTION-TSA), we have used the presence of numerical chromosomal abnormalities within plasma cells as a clonal marker to examine the CD20+ B-cell compartment for the presence of aneuploidy. A series of 54 cases of myeloma were screened for the presence of numerical abnormalities of chromosomes 3 and 11. FICTION-TSA was performed on 13 cases with either trisomy 3 or 11 and on a control group of six cases known to be disomic for the two chromosomes. B-cell numbers were reduced in the myeloma cases compared to the normal controls (median 1.8% v 3.0%, P = 0.05). In the cases with a chromosomal marker, three signals were seen in a median of 1.88% of CD20+ B cells compared to 2.58% within the control group. Comparison of the two groups using a Wilcoxon-Mann-Whitney U test showed no statistical significant difference. Using this data set, it was possible to exclude a 3.03% expansion of clonally related B cells (95% confidence level). We conclude that the B-cell compartment in myeloma does not represent the major site of clonal expansion, and if clonally related cells are present then the numbers are few. PMID:10444161

  10. Transcriptome Analysis of Enterococcus faecalis during Mammalian Infection Shows Cells Undergo Adaptation and Exist in a Stringent Response State

    PubMed Central

    Frank, Kristi L.; Colomer-Winter, Cristina; Grindle, Suzanne M.; Lemos, José A.; Schlievert, Patrick M.; Dunny, Gary M.

    2014-01-01

    As both a commensal and a major cause of healthcare-associated infections in humans, Enterococcus faecalis is a remarkably adaptable organism. We investigated how E. faecalis adapts in a mammalian host as a pathogen by characterizing changes in the transcriptome during infection in a rabbit model of subdermal abscess formation using transcriptional microarrays. The microarray experiments detected 222 and 291 differentially regulated genes in E. faecalis OG1RF at two and eight hours after subdermal chamber inoculation, respectively. The profile of significantly regulated genes at two hours post-inoculation included genes involved in stress response, metabolism, nutrient acquisition, and cell surface components, suggesting genome-wide adaptation to growth in an altered environment. At eight hours post-inoculation, 88% of the differentially expressed genes were down-regulated and matched a transcriptional profile consistent with a (p)ppGpp-mediated stringent response. Subsequent subdermal abscess infections with E. faecalis mutants lacking the (p)ppGpp synthetase/hydrolase RSH, the small synthetase RelQ, or both enzymes, suggest that intracellular (p)ppGpp levels, but not stringent response activation, influence persistence in the model. The ability of cells to synthesize (p)ppGpp was also found to be important for growth in human serum and whole blood. The data presented in this report provide the first genome-wide insights on E. faecalis in vivo gene expression and regulation measured by transcriptional profiling during infection in a mammalian host and show that (p)ppGpp levels affect viability of E. faecalis in multiple conditions relevant to mammalian infection. The subdermal abscess model can serve as a novel experimental system for studying the E. faecalis stringent response in the context of the mammalian immune system. PMID:25545155

  11. Radiative torque alignment: essential physical processes

    NASA Astrophysics Data System (ADS)

    Hoang, Thiem; Lazarian, A.

    2008-07-01

    We study the physical processes that affect the alignment of grains subject to radiative torques (RATs). To describe the action of RATs, we use the analytical model (AMO) of RATs introduced in our previous paper. We focus our discussion on the alignment by anisotropic radiation flux with respect to the magnetic field, which defines the axis of grain Larmor precession. Such an alignment does not invoke paramagnetic dissipation (i.e. the Davis-Greenstein mechanism), but, nevertheless, grains tend to be aligned with long axes perpendicular to the magnetic field. When we account for thermal fluctuations within grains, we show that for grains that are characterized by a triaxial ellipsoid of inertia, the zero-J attractor point obtained in our earlier study develops into a low-J attractor point. The value of angular momentum at the low-J attractor point is of the order of the thermal angular momentum corresponding to the grain temperature. We show that, for situations when the direction of radiative flux is nearly perpendicular to a magnetic field, the alignment of grains with long axes parallel to the magnetic field (i.e. `wrong alignment') reported in our previous paper, disappears in the presence of thermal fluctuations. Thus, all grains are aligned with their long axes perpendicular to the magnetic field. We study the effects of stochastic gaseous bombardment and show that gaseous bombardment can drive grains from low-J to high-J attractor points in cases when high-J attractor points are present. As the alignment of grain axes with respect to angular momentum is higher for higher values of J, counter-intuitively, gaseous bombardment can increase the degree of grain alignment with respect to the magnetic field. We also study the effects of torques induced by H2 formation and show that they can change the value of angular momentum at high-J attractor points, but marginally affect the value of angular momentum at low-J attractor points. We compare the AMO results with

  12. Uncertainty in homology inferences: Assessing and improving genomic sequence alignment

    PubMed Central

    Lunter, Gerton; Rocco, Andrea; Mimouni, Naila; Heger, Andreas; Caldeira, Alexandre; Hein, Jotun

    2008-01-01

    Sequence alignment underpins all of comparative genomics, yet it remains an incompletely solved problem. In particular, the statistical uncertainty within inferred alignments is often disregarded, while parametric or phylogenetic inferences are considered meaningless without confidence estimates. Here, we report on a theoretical and simulation study of pairwise alignments of genomic DNA at human–mouse divergence. We find that >15% of aligned bases are incorrect in existing whole-genome alignments, and we identify three types of alignment error, each leading to systematic biases in all algorithms considered. Careful modeling of the evolutionary process improves alignment quality; however, these improvements are modest compared with the remaining alignment errors, even with exact knowledge of the evolutionary model, emphasizing the need for statistical approaches to account for uncertainty. We develop a new algorithm, Marginalized Posterior Decoding (MPD), which explicitly accounts for uncertainties, is less biased and more accurate than other algorithms we consider, and reduces the proportion of misaligned bases by a third compared with the best existing algorithm. To our knowledge, this is the first nonheuristic algorithm for DNA sequence alignment to show robust improvements over the classic Needleman–Wunsch algorithm. Despite this, considerable uncertainty remains even in the improved alignments. We conclude that a probabilistic treatment is essential, both to improve alignment quality and to quantify the remaining uncertainty. This is becoming increasingly relevant with the growing appreciation of the importance of noncoding DNA, whose study relies heavily on alignments. Alignment errors are inevitable, and should be considered when drawing conclusions from alignments. Software and alignments to assist researchers in doing this are provided at http://genserv.anat.ox.ac.uk/grape/. PMID:18073381

  13. Does Cognitive Behavior Therapy for psychosis (CBTp) show a sustainable effect on delusions? A meta-analysis

    PubMed Central

    Mehl, Stephanie; Werner, Dirk; Lincoln, Tania M.

    2015-01-01

    Cognitive Behavior Therapy for psychosis (CBTp) is an effective treatment resulting in small to medium effect sizes with regard to changes in positive symptoms and psychopathology. As a consequence, CBTp is recommended by national guidelines for all patients with schizophrenia. However, although CBTp was originally developed as a means to improve delusions, meta-analyses have generally integrated effects for positive symptoms rather than for delusions. Thus, it is still an open question whether CBTp is more effective with regard to change in delusions compared to treatment as usual (TAU) and to other interventions, and whether this effect remains stable over a follow-up period. Moreover, it would be interesting to explore whether newer studies that focus on specific factors involved in the formation and maintenance of delusions (causal-interventionist approach) are more effective than the first generation of CBTp studies. A systematic search of the trial literature identified 19 RCTs that compared CBTp with TAU and/or other interventions and reported delusions as an outcome measure. Meta-analytic integration resulted in a significant small to medium effect size for CBTp in comparison to TAU at end-of-therapy (k = 13; d¯= 0.27) and after an average follow-up period of 47 weeks (k = 12; d¯= 0.25). When compared with other interventions, there was no significant effect of CBTp at end-of-therapy (k = 8; d¯= 0.16) and after a follow-up period (k = 5; d¯=-0.04). Comparison between newer studies taking a causal-interventionist approach (k = 4) and first-generation studies showed a difference of 0.33 in mean effect sizes in favor of newer studies at end-of-therapy. The findings suggest that CBTp is superior to TAU, but is not superior to other interventions, in bringing about a change in delusions, and that this superiority is maintained over the follow-up period. Moreover, interventions that focus on causal factors of delusions seem to be a promising approach to

  14. Beginning Learners' Development of Interactional Competence: Alignment Activity

    ERIC Educational Resources Information Center

    Tecedor, Marta

    2016-01-01

    This study examined the development of interactional competence (Hall, 1993; He & Young, 1998) by beginning learners of Spanish as indexed by their use of alignment moves. Discourse analysis techniques and quantitative data analysis were used to explore how 52 learners expressed alignment and changes in participation patterns in two sets of…

  15. Nuclear reactor alignment plate configuration

    DOEpatents

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

    2014-01-28

    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  16. An implicit spatial memory alignment effect.

    PubMed

    Cerles, Mélanie; Gomez, Alice; Rousset, Stéphane

    2015-09-01

    The memory alignment effect is the advantage of reasoning from a perspective which is aligned with the frame of reference used to encode an environment in memory. It usually occurs when participants have to consciously take a perspective to perform a spatial memory task. The present experiment assesses whether the memory alignment effect can occur without requiring to consciously take a given perspective, when the misaligned perspective is only perceptively provided. In others words, does the memory alignment effect still arise when it is only implicitly prompted? Thirty participants learned a sequence of four objects' positions in a room from a north-as-up survey perspective. During the testing phase, they had to point to the direction of a target object from another object ('the reference') with a fixed north-up orientation. The background behind the reference object displayed either a uniform color (control condition) or a misaligned ground-level perspective. The latter displayed a reference object's position information which was either congruent with the studied environment (congruent misaligned condition) or incongruent (incongruent misaligned condition). Mean pointing errors were higher in the congruent misaligned condition than in the control condition, whereas the incongruent misaligned condition did not differ from the control one. The present study shows that the memory alignment effect can arise without requiring a conscious misaligned perspective taking. Moreover, the perceived misaligned perspective must share the same spatial content as the memorized spatial representation in order to induce an alignment effect. PMID:26233526

  17. Radiative Torque Alignment: Essential Physical Processes

    NASA Astrophysics Data System (ADS)

    Hoang, Thiem; Lazarian, A.

    2007-05-01

    Aligned grains provide a unique way to trace magnetic field topology in many astrophysical environments. In Lazarian & Hoang (2006), we derived analytical expressions for radiative torque (RAT) components, and studied the dynamics of grains assuming that the maximal inertia axis is always parallel to angular momentum. In this paper, to get insight into the dynamics of grains when thermal fluctuations are accounted for, we use AMO, and perform analytically averaging for RAT components. In addition, we study the RAT alignment for irregular grains (shape 1 and 3). We also evaluate the influence of suprathermal torques arising from H2 formation, as well as randomizing collisions with atomic gas on the alignment of grains driven by radiative torques (RATs). Our study is both based on the analytical model (AMO) and numerical calculations of RATs for irregular grains. To describe the H2 formation torques and random collisions we use the Langevin equation approach. We show that when thermal fluctuations are included, for both AMO and irregular grains, RATs tend to align grains at attractor points with low angular momentum (low-J attractor point). We found that random collisions by atomic gas act to substantially disalign the grain alignment in the case the phase trajectory map has only the low-J attractor point. In particular, if there exist attractor points at high angular momentum in the phase trajectory map, gas bombardment can move grains from the low- J attractor point to the high-J attractor point. Thus the degree of alignment increases.

  18. Observational Evidence for Radiative Interstellar Grain Alignment

    NASA Astrophysics Data System (ADS)

    Andersson, B.; Potter, S. B.; Andersson, B.; Potter, S.

    2011-11-01

    The alignment mechanisms of interstellar dust grains is a long standing astrophysical problem. Interstellar polarization was first discovered in 1949 and soon thereafter attributed to dichroic extinction caused by asymmetric dust grains aligned with the magnetic field. For a long time the alignment mechanism was thought to involve paramagnetic relaxation in rapidly spinning dust grains. Modern theory indicates that the classical alignment mechanisms are likely not efficient, but rather favor alignment through direct radiative torques. We have used multi-band polarimetry towards stars probing six nearby clouds to show that the wavelength of maximum polarization is linearly correlated with the visual extinction (Andersson & Potter 2007; AP07; where further details can be found). We find a universal relation with a common positive slope between the clouds and a DC offset correlated with the average of the total-to-selective extinction < RV > . These results provide strong observational support for radiatively driven grain alignment. Recent observations of an additional set of ≍60 sightlines in the Taurus cloud confirm and strengthen these results.

  19. Can technology improve alignment during knee arthroplasty.

    PubMed

    Thienpont, Emmanuel; Fennema, Peter; Price, Andrew

    2013-09-01

    Component malalignment remains a concern in total knee arthroplasty (TKA); therefore, a series of technologies have been developed to improve alignment. The authors conducted a systematic review to compare computer-assisted navigation with conventional instrumentation, and assess the current evidence for patient-matched instrumentation and robot-assisted implantation. An extensive search of the PubMed database for relevant meta-analyses, systematic reviews and original articles was performed, with each study scrutinised by two reviewers. Data on study characteristics and outcomes were extracted from each study and compared. In total 30 studies were included: 10 meta-analyses comparing computer-assisted navigation and conventional instrumentation, 13 studies examining patient-matched instrumentation, and seven investigating robot-assisted implantation. Computer-assisted navigation showed significant and reproducible improvements in mechanical alignment over conventional instrumentation. Patient-matched instrumentation appeared to achieve a high degree of mechanical alignment, although the majority of studies were of poor quality. The data for robot-assisted surgery was less indicative. Computer-assisted navigation improves alignment during TKA over conventional instrumentation. For patient-matched instrumentation and robot-assisted implantation, alignment benefits have not been reliably demonstrated. For all three technologies, clinical benefits cannot currently be assumed, and further studies are required. Although current technologies to improve alignment during TKA appear to result in intra-operative benefits, their clinical impact remains unclear, and surgeons should take this into account when considering their adoption.

  20. Alignment reference device

    DOEpatents

    Patton, Gail Y.; Torgerson, Darrel D.

    1987-01-01

    An alignment reference device provides a collimated laser beam that minimizes angular deviations therein. A laser beam source outputs the beam into a single mode optical fiber. The output end of the optical fiber acts as a source of radiant energy and is positioned at the focal point of a lens system where the focal point is positioned within the lens. The output beam reflects off a mirror back to the lens that produces a collimated beam.

  1. Pairwise alignment of protein interaction networks.

    PubMed

    Koyutürk, Mehmet; Kim, Yohan; Topkara, Umut; Subramaniam, Shankar; Szpankowski, Wojciech; Grama, Ananth

    2006-03-01

    With an ever-increasing amount of available data on protein-protein interaction (PPI) networks and research revealing that these networks evolve at a modular level, discovery of conserved patterns in these networks becomes an important problem. Although available data on protein-protein interactions is currently limited, recently developed algorithms have been shown to convey novel biological insights through employment of elegant mathematical models. The main challenge in aligning PPI networks is to define a graph theoretical measure of similarity between graph structures that captures underlying biological phenomena accurately. In this respect, modeling of conservation and divergence of interactions, as well as the interpretation of resulting alignments, are important design parameters. In this paper, we develop a framework for comprehensive alignment of PPI networks, which is inspired by duplication/divergence models that focus on understanding the evolution of protein interactions. We propose a mathematical model that extends the concepts of match, mismatch, and gap in sequence alignment to that of match, mismatch, and duplication in network alignment and evaluates similarity between graph structures through a scoring function that accounts for evolutionary events. By relying on evolutionary models, the proposed framework facilitates interpretation of resulting alignments in terms of not only conservation but also divergence of modularity in PPI networks. Furthermore, as in the case of sequence alignment, our model allows flexibility in adjusting parameters to quantify underlying evolutionary relationships. Based on the proposed model, we formulate PPI network alignment as an optimization problem and present fast algorithms to solve this problem. Detailed experimental results from an implementation of the proposed framework show that our algorithm is able to discover conserved interaction patterns very effectively, in terms of both accuracies and computational

  2. Genome alignment with graph data structures: a comparison

    PubMed Central

    2014-01-01

    Background Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. Results We compare the structures of commonly used graphs in terms of their abilities to represent alignment information. We describe how the graphs can be transformed into each other, and identify and classify graph substructures common to one or more graphs. Based on previous approaches, we compile a list of modifications that remove these substructures. Conclusion We show that crucial pieces of alignment information, associated with inversions and duplications, are not visible in the structure of all graphs. If we neglect vertex or edge labels, the graphs differ in their information content. Still, many ideas are shared among all graph-based approaches. Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools. PMID:24712884

  3. Alignment and alignment transition of bent core nematics

    NASA Astrophysics Data System (ADS)

    Elamain, Omaima; Hegde, Gurumurthy; Komitov, Lachezar

    2013-07-01

    We report on the alignment of nematics consisting of bimesogen bent core molecules of chlorine substituent of benzene derivative and their binary mixture with rod like nematics. It was found that the alignment layer made from polyimide material, which is usually used for promoting vertical (homeotropic) alignment of rod like nematics, promotes instead a planar alignment of the bent core nematic and its nematic mixtures. At higher concentration of the rod like nematic component in these mixtures, a temperature driven transition from vertical to planar alignment was found near the transition to isotropic phase.

  4. Polar cap arcs: Sun-aligned or cusp-aligned?

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Paxton, L. J.; Zhang, Qinghe; Xing, Zanyang

    2016-08-01

    Polar cap arcs are often called sun-aligned arcs. Satellite observations reveal that polar cap arcs join together at the cusp and are actually cusp aligned. Strong ionospheric plasma velocity shears, thus field aligned currents, were associated with polar arcs and they were likely caused by Kelvin-Helmholtz waves around the low-latitude magnetopause under a northward IMF Bz. The magnetic field lines around the magnetopause join together in the cusp region so are the field aligned currents and particle precipitation. This explains why polar arcs are cusp aligned.

  5. Prosody and alignment: a sequential perspective

    NASA Astrophysics Data System (ADS)

    Szczepek Reed, Beatrice

    2010-12-01

    In their analysis of a corpus of classroom interactions in an inner city high school, Roth and Tobin describe how teachers and students accomplish interactional alignment by prosodically matching each other's turns. Prosodic matching, and specific prosodic patterns are interpreted as signs of, and contributions to successful interactional outcomes and positive emotions. Lack of prosodic matching, and other specific prosodic patterns are interpreted as features of unsuccessful interactions, and negative emotions. This forum focuses on the article's analysis of the relation between interpersonal alignment, emotion and prosody. It argues that prosodic matching, and other prosodic linking practices, play a primarily sequential role, i.e. one that displays the way in which participants place and design their turns in relation to other participants' turns. Prosodic matching, rather than being a conversational action in itself, is argued to be an interactional practice (Schegloff 1997), which is not always employed for the accomplishment of `positive', or aligning actions.

  6. Partial analysis of hepatitis B virus DNA from hepatocellular carcinoma showing negative hepatitis B virus surface antigen: an analysis of two Japanese cases.

    PubMed

    Shiota, Goshi; Oyama, Kenji; Udagawa, Akihide; Nomi, Takahiro; Tanaka, Kiwamu; Tsutsumi, Atsushi; Noguchi, Noya; Okano, Jun-ichi; Kishimoto, Yosuke; Kanbe, Takamasa; Kishimoto, Hiroyuki; Kawasaki, Hironaka

    2009-01-01

    It has been reported that hepatitis B virus (HBV) DNA is detected in serum and/or liver in patients with hepatocellular carcinoma (HCC) without HBsAg. To adress this issue, we analyzed HBV genome in 2 HCC cases without HBsAg. The DNA from serum from patients with HCC was amplified with a nested PCR, and 'a' determinant of S region, core promoter region and precore region were sequenced. The first case, a 50 years-old male, was negative for HBsAg and HBeAg, and positive for anti-HBs, anti-HBe and anti-HBc. Viral load of HBV in serum was 4.0 log genome equivalent/ml by TMA assay, and was 1.1 X 105 copy/ml by real-time PCR system. A nucleotide analysis of the common 'a' determinant of S gene showed that the 5 first amino acids of 'a' determinant, CTIPA, were changed to CKTCTTPA. The second case, a 76 years-old male, was positive for anti-HBe, but negative for HBsAg, anti-HBs, HBeAg and anti-HBc. No missense or nonsense mutations were seen in 'a' determinant of S region. Viral load of serum HBV was < 3.7 log genome equivalent/ml by TMA assay, but was 2.4X103 copy/ml by real-time PCR system. The results of the present study suggest that the mechanisms of HBsAg loss are diverse among HCC patients without HBsAg, and that an analysis of HBV genome is a useful tool to dissolve molecular mechanisms losing HBs antigenicity. PMID:19950820

  7. Large Telescope Segmented Primary Mirror Alignment

    NASA Technical Reports Server (NTRS)

    Rud, Mayer

    2010-01-01

    A document discusses a broadband (white light) point source, located at the telescope Cassegrain focus, which generates a cone of light limited by the hole in the secondary mirror (SM). It propagates to the aspheric null-mirror, which is optimized to make all the reflected rays to be normal to the primary mirror (PM) upon reflection. PM retro-reflects the rays back through the system for wavefront analysis. The point source and the wavefront analysis subsystems are all located behind the PM. The PM phasing is absolute (white light) and does not involve the SM. A relatively small, aspheric null-mirror located near the PM center of curvature has been designed to deliver the high level of optical wavefront correction. The phasing of the segments is absolute due to the use of a broadband source. The segmented PM is optically aligned independently and separately from the SM alignment. The separation of the PM segments alignment from the PM to the SM, and other telescope optics alignments, may be a significant advantage, eliminating the errors coupling. The point source of this concept is fully cooperative, unlike a star or laser-generated guide-star, providing the necessary brightness for the optimal S/N ratio, the spectral content, and the stable on-axis position. This concept can be implemented in the lab for the PM initial alignment, or made to be a permanent feature of the space-based or groundbased telescope.

  8. 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

  9. 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

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

    We have optimized the magnetic alignment of phospholipid bilayered micelles (bicelles) for EPR spectroscopy, by varying lipid composition and temperature. Bicelles have been extensively used in NMR spectroscopy for several decades, in order to obtain aligned samples in a near-native membrane environment and take advantage of the intrinsic sensitivity of magnetic resonance to molecular orientation. Recently, bicelles have also seen increasing use in EPR, which offers superior sensitivity and orientational resolution. However, the low magnetic field strength (less than 1 T) of most conventional EPR spectrometers results in homogeneously oriented bicelles only at a temperature well above physiological. To optimize bicelle composition for magnetic alignment at reduced temperature, we prepared bicelles containing varying ratios of saturated (DMPC) and unsaturated (POPC) phospholipids, using EPR spectra of a spin-labeled fatty acid to assess alignment as a function of lipid composition and temperature. Spectral analysis showed that bicelles containing an equimolar mixture of DMPC and POPC homogeneously align at 298 K, 20 K lower than conventional DMPC-only bicelles. It is now possible to perform EPR studies of membrane protein structure and dynamics in well-aligned bicelles at physiological temperatures and below. PMID:25514061

  13. Optimization of Bicelle Lipid Composition and Temperature for EPR Spectroscopy of Aligned Membranes

    PubMed Central

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

    2014-01-01

    We have optimized the magnetic alignment of phospholipid bilayered micelles (bicelles) for EPR spectroscopy, by varying lipid composition and temperature. Bicelles have been extensively used in NMR spectroscopy for several decades, in order to obtain aligned samples in a near-native membrane environment and take advantage of the intrinsic sensitivity of magnetic resonance to molecular orientation. Recently, bicelles have also seen increasing use in EPR, which offers superior sensitivity and orientational resolution. However, the low magnetic field strength (less than 1 T) of most conventional EPR spectrometers results in homogeneously oriented bicelles only at a temperature well above physiological. To optimize bicelle composition for magnetic alignment at reduced temperature, we prepared bicelles containing varying ratios of saturated (DMPC) and unsaturated (POPC) phospholipids, using EPR spectra of a spin-labeled fatty acid to assess alignment as a function of lipid composition and temperature. Spectral analysis showed that bicelles containing an equimolar mixture of DMPC and POPC homogeneously align at 298 K, 20 K lower than conventional DMPC-only bicelles. It is now be possible to perform EPR studies of membrane protein structure and dynamics in well-aligned bicelles at physiological temperatures and below. PMID:25514061

  14. Dynamic mechanical analysis and high strain-rate energy absorption characteristics of vertically aligned carbon nanotube reinforced woven fiber-glass composites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The dynamic mechanical behavior and energy absorption characteristics of nano-enhanced functionally graded composites, consisting of 3 layers of vertically aligned carbon nanotube (VACNT) forests grown on woven fiber-glass (FG) layer and embedded within 10 layers of woven FG, with polyester (PE) and...

  15. Multifield optimization intensity-modulated proton therapy (MFO-IMPT) for prostate cancer: Robustness analysis through simulation of rotational and translational alignment errors

    SciTech Connect

    Pugh, Thomas J.; Amos, Richard A.; John Baptiste, Sandra; Choi, Seungtaek; Nhu Nguyen, Quyhn; Ronald Zhu, X.; Palmer, Matthew B.; Lee, Andrew K.

    2013-10-01

    To evaluate the dosimetric consequences of rotational and translational alignment errors in patients receiving intensity-modulated proton therapy with multifield optimization (MFO-IMPT) for prostate cancer. Ten control patients with localized prostate cancer underwent treatment planning for MFO-IMPT. Rotational and translation errors were simulated along each of 3 axes: anterior-posterior (A-P), superior-inferior (S-I), and left-right. Clinical target-volume (CTV) coverage remained high with all alignment errors simulated. Rotational errors did not result in significant rectum or bladder dose perturbations. Translational errors resulted in larger dose perturbations to the bladder and rectum. Perturbations in rectum and bladder doses were minimal for rotational errors and larger for translational errors. Rectum V45 and V70 increased most with A-P misalignment, whereas bladder V45 and V70 changed most with S-I misalignment. The bladder and rectum V45 and V70 remained acceptable even with extreme alignment errors. Even with S-I and A-P translational errors of up to 5 mm, the dosimetric profile of MFO-IMPT remained favorable. MFO-IMPT for localized prostate cancer results in robust coverage of the CTV without clinically meaningful dose perturbations to normal tissue despite extreme rotational and translational alignment errors.

  16. AVID: A global alignment program.

    PubMed

    Bray, Nick; Dubchak, Inna; Pachter, Lior

    2003-01-01

    In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper. PMID:12529311

  17. Engineering cell alignment in vitro.

    PubMed

    Li, Yuhui; Huang, Guoyou; Zhang, Xiaohui; Wang, Lin; Du, Yanan; Lu, Tian Jian; Xu, Feng

    2014-01-01

    Cell alignment plays a critical role in various cell behaviors including cytoskeleton reorganization, membrane protein relocation, nucleus gene expression, and ECM remodeling. Cell alignment is also known to exert significant effects on tissue regeneration (e.g., neuron) and modulate mechanical properties of tissues including skeleton, cardiac muscle and tendon. Therefore, it is essential to engineer cell alignment in vitro for biomechanics, cell biology, tissue engineering and regenerative medicine applications. With advances in nano- and micro-scale technologies, a variety of approaches have been developed to engineer cell alignment in vitro, including mechanical loading, topographical patterning, and surface chemical treatment. In this review, we first present alignments of various cell types and their functionality in different tissues in vivo including muscle and nerve tissues. Then, we provide an overview of recent approaches for engineering cell alignment in vitro. Finally, concluding remarks and perspectives are addressed for future improvement of engineering cell alignment.

  18. AVID: A global alignment program.

    PubMed

    Bray, Nick; Dubchak, Inna; Pachter, Lior

    2003-01-01

    In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper.

  19. TSGC and JSC Alignment

    NASA Technical Reports Server (NTRS)

    Sanchez, Humberto

    2013-01-01

    NASA and the SGCs are, by design, intended to work closely together and have synergistic Vision, Mission, and Goals. The TSGC affiliates and JSC have been working together, but not always in a concise, coordinated, nor strategic manner. Today we have a couple of simple ideas to present about how TSGC and JSC have started to work together in a more concise, coordinated, and strategic manner, and how JSC and non-TSG Jurisdiction members have started to collaborate: Idea I: TSGC and JSC Technical Alignment Idea II: Concept of Clusters.

  20. CELT optics Alignment Procedure

    NASA Astrophysics Data System (ADS)

    Mast, Terry S.; Nelson, Jerry E.; Chanan, Gary A.; Noethe, Lothar

    2003-01-01

    The California Extremely Large Telescope (CELT) is a project to build a 30-meter diameter telescope for research in astronomy at visible and infrared wavelengths. The current optical design calls for a primary, secondary, and tertiary mirror with Ritchey-Chretién foci at two Nasmyth platforms. The primary mirror is a mosaic of 1080 actively-stabilized hexagonal segments. This paper summarizes a CELT report that describes a step-by-step procedure for aligning the many degrees of freedom of the CELT optics.

  1. Multiple network alignment on quantum computers

    NASA Astrophysics Data System (ADS)

    Daskin, Anmer; Grama, Ananth; Kais, Sabre

    2014-12-01

    Comparative analyses of graph-structured datasets underly diverse problems. Examples of these problems include identification of conserved functional components (biochemical interactions) across species, structural similarity of large biomolecules, and recurring patterns of interactions in social networks. A large class of such analyses methods quantify the topological similarity of nodes across networks. The resulting correspondence of nodes across networks, also called node alignment, can be used to identify invariant subgraphs across the input graphs. Given graphs as input, alignment algorithms use topological information to assign a similarity score to each -tuple of nodes, with elements (nodes) drawn from each of the input graphs. Nodes are considered similar if their neighbors are also similar. An alternate, equivalent view of these network alignment algorithms is to consider the Kronecker product of the input graphs and to identify high-ranked nodes in the Kronecker product graph. Conventional methods such as PageRank and HITS (Hypertext-Induced Topic Selection) can be used for this purpose. These methods typically require computation of the principal eigenvector of a suitably modified Kronecker product matrix of the input graphs. We adopt this alternate view of the problem to address the problem of multiple network alignment. Using the phase estimation algorithm, we show that the multiple network alignment problem can be efficiently solved on quantum computers. We characterize the accuracy and performance of our method and show that it can deliver exponential speedups over conventional (non-quantum) methods.

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

    NASA Astrophysics Data System (ADS)

    Lizotte, Todd E.

    2011-10-01

    methodology showing how it is possible to reduce complex alignment directions into a simplified set of instructions for layman service engineers.

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

    PubMed Central

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

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  5. Refinement by shifting secondary structure elements improves sequence alignments.

    PubMed

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

    2015-03-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  6. Refinement by shifting secondary structure elements improves sequence alignments

    PubMed Central

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V.

    2015-01-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  7. Interactional Competence and the Development of Alignment Activity

    ERIC Educational Resources Information Center

    Dings, Abby

    2014-01-01

    Based on qualitative analysis of conversational interactions collected over the course of a Spanish language learner's academic year abroad, this article explores the development of interactional resources related to alignment activity in the learner's conversational participation. Alignment activity refers to the means interlocutors use…

  8. Alignment control study for the solar optical telescope

    NASA Technical Reports Server (NTRS)

    1976-01-01

    Analysis of the alignment and focus errors than can be tolerated, methods of sensing such errors, and mechanisms to make the necessary corrections were addressed. Alternate approaches and their relative merits were considered. The results of this study indicate that adequate alignment control can be achieved.

  9. FRESCO: flexible alignment with rectangle scoring schemes.

    PubMed

    Dalca, A V; Brudno, M

    2008-01-01

    While the popular DNA sequence alignment tools incorporate powerful heuristics to allow for fast and accurate alignment of DNA, most of them still optimize the classical Needleman Wunsch scoring scheme. The development of novel scoring schemes is often hampered by the difficulty of finding an optimizing algorithm for each non-trivial scheme. In this paper we define the broad class of rectangle scoring schemes, and describe an algorithm and tool that can align two sequences with an arbitrary rectangle scoring scheme in polynomial time. Rectangle scoring schemes encompass some of the popular alignment scoring metrics currently in use, as well as many other functions. We investigate a novel scoring function based on minimizing the expected number of random diagonals observed with the given scores and show that it rivals the LAGAN and Clustal-W aligners, without using any biological or evolutionary parameters. The FRESCO program, freely available at http://compbio.cs.toronto.edu/fresco, gives bioinformatics researchers the ability to quickly compare the performance of other complex scoring formulas without having to implement new algorithms to optimize them.

  10. Local Structural Alignment of RNA with Affine Gap Model

    NASA Astrophysics Data System (ADS)

    Wong, Thomas K. F.; Cheung, Brenda W. Y.; Lam, T. W.; Yiu, S. M.

    Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.

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

    PubMed

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

    2016-01-01

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

  12. Dust alignment in astrophysical environments

    NASA Astrophysics Data System (ADS)

    Lazarian, Alex; Thiem Hoang, Chi

    Dust is known to be aligned in interstellar medium and the arising polarization is extensively used to trace magnetic fields. What process aligns dust grains was one of the most long-standing problems of astrophysics in spite of the persistent efforts to solve it. For years the Davis-Greenstein paramagnetic alignment was the primary candidate for explaining grain alignment. However, the situation is different now and the most promising mechanism is associated with radiative torques (RATs) acting on irregular grains. I shall present the analytical theory of RAT alignment, discuss the observational tests that support this theory. I shall also discuss in what situations we expect to see the dominance of paramagnetic alignment.

  13. Nuclear reactor internals alignment configuration

    DOEpatents

    Gilmore, Charles B.; Singleton, Norman R.

    2009-11-10

    An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

  14. Terrestrial ionospheric signatures of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Friis-Christensen, E.

    1990-01-01

    The occurrence of traveling field-aligned current filaments and twin-vortex patterns is suggested to be related to sudden changes in solar wind dynamic pressure and/or the IMF. Greenland magnetometer observations of the cleft region magnetic perturbations associated with small-scale twin-vortex patterns show that these events occur on both sides of the magnetic local noon, contradicting Glassmeier at al.'s (1989) statistical analysis of 82 twin-vortex subauroral-latitude events obtained by the Scandinavian Magnetometer Array; the stations are closer to the ionospheric projection of the cleft earlier in magnetic local time, relative to the across-the-cleft-located Greenland stations.

  15. Microwave characterization of vertically aligned multiwalled carbon nanotube arrays

    NASA Astrophysics Data System (ADS)

    Katsounaros, Anestis; Rajab, Khalid Z.; Hao, Yang; Mann, Mark; Milne, William I.

    2011-05-01

    Vertically aligned multiwalled carbon nanotube (VACNT) films have been characterized by rectangular waveguide measurements. The complex scattering parameters (S-parameters) are measured by a vector network analyzer at X-band frequencies. The effective complex permittivity and permeability of the VACNT films have been extracted. The extracted parameters are verified by full wave simulations and very good agreement has been obtained. The results of the systematic error analysis are presented and the errors are within the acceptable range. The performance of VACNT films as an absorber is examined, and comparison with the conventional carbon loaded materials shows that a 90% size reduction is possible while maintaining the same absorption level.

  16. Ultralight anisotropic foams from layered aligned carbon nanotube sheets.

    PubMed

    Faraji, Shaghayegh; Stano, Kelly L; Yildiz, Ozkan; Li, Ang; Zhu, Yuntian; Bradford, Philip D

    2015-10-28

    In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm(-3), the foam structure is over 500 times less dense than bulk graphite. Microscopy revealed that PyC coated the junctions among CNTs, and also increased CNT surface roughness. These changes in the morphology explain the transition from inelastic behavior to foam-like recovery of the layered CNT sheet structure. Mechanical and thermal properties of the foams were tuned for different applications through variation of PyC deposition duration while dynamic mechanical analysis showed no change in mechanical properties over a large temperature range. Observation of a large and linear electrical resistance change during compression of the aligned CNT/carbon (ACNT/C) foams makes strain/pressure sensors a relevant application. The foams have high oil absorption capacities, up to 275 times their own weight, which suggests they may be useful in water treatment and oil spill cleanup. Finally, the ACNT/C foam's high porosity, surface area and stability allow for demonstration of the foams as catalyst support structures.

  17. Ultralight anisotropic foams from layered aligned carbon nanotube sheets.

    PubMed

    Faraji, Shaghayegh; Stano, Kelly L; Yildiz, Ozkan; Li, Ang; Zhu, Yuntian; Bradford, Philip D

    2015-10-28

    In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm(-3), the foam structure is over 500 times less dense than bulk graphite. Microscopy revealed that PyC coated the junctions among CNTs, and also increased CNT surface roughness. These changes in the morphology explain the transition from inelastic behavior to foam-like recovery of the layered CNT sheet structure. Mechanical and thermal properties of the foams were tuned for different applications through variation of PyC deposition duration while dynamic mechanical analysis showed no change in mechanical properties over a large temperature range. Observation of a large and linear electrical resistance change during compression of the aligned CNT/carbon (ACNT/C) foams makes strain/pressure sensors a relevant application. The foams have high oil absorption capacities, up to 275 times their own weight, which suggests they may be useful in water treatment and oil spill cleanup. Finally, the ACNT/C foam's high porosity, surface area and stability allow for demonstration of the foams as catalyst support structures. PMID:26419855

  18. [Alignment of malpositioned canines].

    PubMed

    Wagner, L

    1991-03-01

    This article presents a system for aligning impacted canines. The base of this system is the lingual arch, a rigid reaction unit of four teeth, molars and premolars. From this base unit an impacted canine can be extruded, moved distally, jumped over the occlusion and derotated by segment arches, coil springs and elastic ligatures. The efficiency of this appliance is due to the elimination of undesired reactive forces, the safe moving of teeth, the possibility of an exact force application and the simple manipulation; also the esthetic inconvenience is minimal. All this results in a better prognosis and an essentially shorter treatment time. This appliance can be used in the upper and the lower jaw. Schematic drawings and clinical examples demonstrate this method.

  19. Two Hybrid Algorithms for Multiple Sequence Alignment

    NASA Astrophysics Data System (ADS)

    Naznin, Farhana; Sarker, Ruhul; Essam, Daryl

    2010-01-01

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

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

    PubMed

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

    2012-12-01

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

  1. Alignments of galaxies and halos in hydrodynamical simulations

    NASA Astrophysics Data System (ADS)

    Pahwa, Isha; Libeskind, Noam I.

    2016-10-01

    We use a 200 h -1Mpc cosmological hydrodynamical simulation to examine the alignments of galaxies with respect to the host halo. We do separate study for the different components of the halo, such as stars, gas and dark matter. We show that angular momentum of gas is more aligned with the angular momentum of host halo compared with the stellar component.

  2. Measuring Parameters of Massive Black Hole Binaries with Partially-Aligned Spins

    NASA Technical Reports Server (NTRS)

    Lang, Ryan N.; Hughes, Scott A.; Cornish, Neil J.

    2010-01-01

    It is important to understand how well the gravitational-wave observatory LISA can measure parameters of massive black hole binaries. It has been shown that including spin precession in the waveform breaks degeneracies and produces smaller expected parameter errors than a simpler, precession-free analysis. However, recent work has shown that gas in binaries can partially align the spins with the orbital angular momentum, thus reducing the precession effect. We show how this degrades the earlier results, producing more pessimistic errors in gaseous mergers. However, we then add higher harmonics to the signal model; these also break degeneracies, but they are not affected by the presence of gas. The harmonics often restore the errors in partially-aligned binaries to the same as, or better than/ those that are obtained for fully precessing binaries with no harmonics. Finally, we investigate what LISA measurements of spin alignment can tell us about the nature of gas around a binary,

  3. ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output.

    PubMed

    Zaal, Dionne; Nota, Benjamin

    2016-01-01

    We present ADOMA, a command line tool that produces alternative outputs from ClustalW multiple alignments of nucleotide or protein sequences. ADOMA can simplify the output of alignments by showing only the different residues between sequences, which is often desirable when only small differences such as single nucleotide polymorphisms are present (e.g., between different alleles). Another feature of ADOMA is that it can enhance the ClustalW output by coloring the residues in the alignment. This tool is easily integrated into automated Linux pipelines for next-generation sequencing data analysis, and may be useful for researchers in a broad range of scientific disciplines including evolutionary biology and biomedical sciences. The source code is freely available at https://sourceforge. net/projects/adoma/. PMID:27491653

  4. How Graphene Islands Are Unidirectionally Aligned on the Ge(110) Surface.

    PubMed

    Dai, Jiayun; Wang, Danxia; Zhang, Miao; Niu, Tianchao; Li, Ang; Ye, Mao; Qiao, Shan; Ding, Guqiao; Xie, Xiaoming; Wang, Yongqiang; Chu, Paul K; Yuan, Qinghong; Di, Zengfeng; Wang, Xi; Ding, Feng; Yakobson, Boris I

    2016-05-11

    The unidirectional alignment of graphene islands is essential to the synthesis of wafer-scale single-crystal graphene on Ge(110) surface, but the underlying mechanism is not well-understood. Here we report that the necessary coalignment of the nucleating graphene islands on Ge(110) surface is caused by the presence of step-pattern; we show that on the preannealed Ge(110) textureless surface the graphene islands appear nonpreferentially orientated, while on the Ge(110) surfaces with natural step pattern, all graphene islands emerge coaligned. First-principles calculations and theoretical analysis reveal this different alignment behaviors originate from the strong chemical binding formed between the graphene island edges and the atomic steps on the Ge(110) surface, and the lattice matching at edge-step interface dictates the alignment of graphene islands with the armchair direction of graphene along the [-110] direction of the Ge(110) substrate.

  5. Quantitative trait locus analysis, pathway analysis, and consomic mapping show genetic variants of Tnni3k, Fpgt, or H28 control susceptibility to viral myocarditis.

    PubMed

    Wiltshire, Sean A; Leiva-Torres, Gabriel André; Vidal, Silvia M

    2011-06-01

    Coxsackievirus B3 (CVB3) infection is the most common cause of viral myocarditis. The pathogenesis of viral myocarditis is strongly controlled by host genetic factors. Although certain indispensable components of immunity have been identified, the genes and pathways underlying natural variation between individuals remain unclear. Previously, we isolated the viral myocarditis susceptibility 1 (Vms1) locus on chromosome 3, which influences pathogenesis. We hypothesized that confirmation and further study of Vms1 controlling CVB3-mediated pathology, combined with pathway analysis and consomic mapping approaches, would elucidate both pathological and protective mechanisms accounting for natural variation in response to CVB3 infection. Vms1 was originally mapped to chromosome 3 using a segregating cross between susceptible A/J and resistant B10.A mice. To validate Vms1, C57BL/6J-Chr 3(A)/NaJ (a chromosome substitution strain that carries a diploid A/J chromosome 3) were used to replicate susceptibility compared with resistant C57BL/6J (B6). A second segregating F2 cross was generated between these, confirming both the localization and effects of Vms1. Microarray analysis of the four strains (A/J, B10.A, C57BL/6J, and C57BL/6J-Chr 3(A)/NaJ) illuminated a core program of response to CVB3 in all strains that is comprised mainly of IFN-stimulated genes. Microarray analysis also revealed strain-specific differential expression programs and genes that may be prognostic or diagnostic of susceptibility to CVB3 infection. A combination of analyses revealed very strong evidence for the existence and location of Vms1. Differentially expressed pathways were identified by microarray, and candidate gene analysis revealed Fpgt, H28, and Tnni3k as likely candidates for Vms1.

  6. Approximate protein structural alignment in polynomial time.

    PubMed

    Kolodny, Rachel; Linial, Nathan

    2004-08-17

    Alignment of protein structures is a fundamental task in computational molecular biology. Good structural alignments can help detect distant evolutionary relationships that are hard or impossible to discern from protein sequences alone. Here, we study the structural alignment problem as a family of optimization problems and develop an approximate polynomial-time algorithm to solve them. For a commonly used scoring function, the algorithm runs in O(n(10)/epsilon(6)) time, for globular protein of length n, and it detects alignments that score within an additive error of epsilon from all optima. Thus, we prove that this task is computationally feasible, although the method that we introduce is too slow to be a useful everyday tool. We argue that such approximate solutions are, in fact, of greater interest than exact ones because of the noisy nature of experimentally determined protein coordinates. The measurement of similarity between a pair of protein structures used by our algorithm involves the Euclidean distance between the structures (appropriately rigidly transformed). We show that an alternative approach, which relies on internal distance matrices, must incorporate sophisticated geometric ingredients if it is to guarantee optimality and run in polynomial time. We use these observations to visualize the scoring function for several real instances of the problem. Our investigations yield insights on the computational complexity of protein alignment under various scoring functions. These insights can be used in the design of scoring functions for which the optimum can be approximated efficiently and perhaps in the development of efficient algorithms for the multiple structural alignment problem. PMID:15304646

  7. Kernel Manifold Alignment for Domain Adaptation.

    PubMed

    Tuia, Devis; Camps-Valls, Gustau

    2016-01-01

    The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors' knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational

  8. Kernel Manifold Alignment for Domain Adaptation

    PubMed Central

    Tuia, Devis; Camps-Valls, Gustau

    2016-01-01

    The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors’ knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational

  9. Interstellar Silicate Dust: Modeling and Grain Alignment

    NASA Astrophysics Data System (ADS)

    Das, Indrajit

    We examine some aspects of the alignment of silicate dust grains with respect to the interstellar magnetic field. First, we consider possible observational constraints on the magnetic properties of the grains. Second, we investigate the role of collisions with gas atoms and the production of H2 molecules on the grain surface in the alignment process when the grain is drifting in the gaseous medium. Paramagnetism associated with Fe content in the dust is thought to play a critical role in alignment. Min et al (2007) claimed that the Fe content of the silicate dust can be constrained by the shape of the 10 μm extinction feature. They found low Fe abundances, potentially posing problems for grain alignment theories. We revisit this analysis modeling the grains with irregularly shaped Gaussian Random Sphere (GRS). We give a comprehensive review of all the relevant constraints researchers apply and discuss their effects on the inferred mineralogy. Also, we extend this analysis to examine whether constraints can be placed on the presence of Fe-rich inclusions which could yield "super-paramagnetism". This possibility has long been speculated, but so far observational constraints are lacking. Every time a gas atom collides with a grain, the grain's angular momentum is slightly modified. Likewise when an H2 molecule forms on the surface and is ejected. Here also we model the grain with GRS shape and considered various scenarios about how the colliding gas particles depart the grain. We develop theoretical and computational tools to estimate the torques associated with these aforementioned events for a range of grain drift speeds---from low subsonic to high supersonic speeds. Code results were verified with spherical grain for which analytical results were available. Finally, the above torque results were used to study the grain rotational dynamics. Solving dynamical equations we examine how these torques influence the grain alignment process. Our analysis suggests that

  10. 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

  11. 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

  12. Liquid crystallinity driven highly aligned large graphene oxide composites

    SciTech Connect

    Lee, Kyung Eun; Oh, Jung Jae; Yun, Taeyeong; Kim, Sang Ouk

    2015-04-15

    Graphene is an emerging graphitic carbon materials, consisting of sp{sup 2} hybridized two dimensinal honeycomb structure. It has been widely studied to incorporate graphene with polymer to utilize unique property of graphene and reinforce electrical, mechanical and thermal property of polymer. In composite materials, orientation control of graphene significantly influences the property of composite. Until now, a few method has been developed for orientation control of graphene within polymer matrix. Here, we demonstrate facile fabrication of high aligned large graphene oxide (LGO) composites in polydimethylsiloxane (PDMS) matrix exploiting liquid crystallinity. Liquid crystalline aqueous dispersion of LGO is parallel oriented within flat confinement geometry. Freeze-drying of the aligned LGO dispersion and subsequent infiltration with PDMS produce highly aligned LGO/PDMS composites. Owing to the large shape anisotropy of LGO, liquid crystalline alignment occurred at low concentration of 2 mg/ml in aqueous dispersion, which leads to the 0.2 wt% LGO loaded composites. - Graphical abstract: Liquid crystalline LGO aqueous dispersions are spontaneous parallel aligned between geometric confinement for highly aligned LGO/polymer composite fabrication. - Highlights: • A simple fabrication method for highly aligned LGO/PDMS composites is proposed. • LGO aqueous dispersion shows nematic liquid crystalline phase at 0.8 mg/ml. • In nematic phase, LGO flakes are highly aligned by geometric confinement. • Infiltration of PDMS into freeze-dried LGO allows highly aligned LGO/PDMS composites.

  13. Instability of Ocular Alignment in Childhood Esotropia

    PubMed Central

    2008-01-01

    Objective Instability of ocular alignment may cause surgeons to delay surgical correction of childhood esotropia. We investigated the stability of ocular alignment over 18 weeks in children with infantile esotropia (IET), acquired non-accommodative esotropia (ANAET), or acquired partially-accommodative esotropia (APAET). Design Prospective observational study Participants Two hundred thirty-three children aged 2 months to <5 years with IET, ANAET, or APAET of less than 6 months duration Methods Ocular alignment was measured at baseline and at six-week intervals for 18 weeks. Main Outcome Measure Using definitions derived from a nested test-retest study and computer simulation modeling, ocular alignment was classified as ‘unstable’ if there was a change of ≥ 15 prism diopters (PD) between any two of the four measurements, as ‘stable’ if all four measurements were within ≤ 5 PD of one another, or as ‘uncertain’ if neither criteria was met. Results Of those who completed all three follow-up visits within time windows for analysis, 27 (46%) of 59 subjects with IET had ocular alignment classified as unstable (95% confidence interval (CI) = 33 to 59%), 20% as stable (95% CI = 11 to 33%), and 34% as uncertain (95% CI = 22 to 47%). Thirteen (22%) of 60 subjects with ANAET had ocular alignment classified as unstable (95% confidence interval (CI) = 12 to 34%), 37% as stable (95% CI = 25 to 50%), and 42% as uncertain (95% CI = 29 to 55%). Six (15%) of 41 subjects with APAET had ocular alignment classified as unstable (95% CI = 6 to 29%), 39% as stable (95% CI = 24 to 56%), and 46% as uncertain (95% CI = 31 to 63%). For IET, subjects who were older at presentation were less likely to have unstable angles than subjects who were younger at presentation (risk ratio for unstable vs. stable per additional month of age = 0.85, 99% CI = 0.74 to 0.99). Conclusions Ocular alignment instability is common in children with IET, ANAET and APAET. The impact of this finding

  14. Imaging Analysis of Collagen Fiber Networks in Cusps of Porcine Aortic Valves: Effect of their Local Distribution and Alignment on Valve Functionality

    PubMed Central

    Mega, Mor; Marom, Gil; Halevi, Rotem; Hamdan, Ashraf; Bluestein, Danny; Haj-Ali, Rami

    2015-01-01

    The cusps of native Aortic Valve (AV) are composed of collagen bundles embedded in soft tissue, creating a heterogenic tissue with asymmetric alignment in each cusp. This study compares native collagen fiber networks (CFNs) with a goal to better understand their influence on stress distribution and valve kinematics. Images of CFNs from five porcine tricuspid AVs are analyzed and fluid-structure interaction models are generated based on them. Although the valves had similar overall kinematics, the CFNs had distinctive influence on local mechanics. The regions with dilute CFN are more prone to damage since they are subjected to higher stress magnitudes. PMID:26406926

  15. Drive alignment pays maintenance dividends

    SciTech Connect

    Fedder, R.

    2008-12-15

    Proper alignment of the motor and gear drive on conveying and processing equipment will result in longer bearing and coupling life, along with lower maintenance costs. Selecting an alignment free drive package instead of a traditional foot mounted drive and motor is a major advancement toward these goals. 4 photos.

  16. Transformation and Alignment in Similarity

    ERIC Educational Resources Information Center

    Hodgetts, Carl J.; Hahn, Ulrike; Chater, Nick

    2009-01-01

    This paper contrasts two structural accounts of psychological similarity: structural alignment (SA) and Representational Distortion (RD). SA proposes that similarity is determined by how readily the structures of two objects can be brought into alignment; RD measures similarity by the complexity of the transformation that "distorts" one…

  17. Curriculum Alignment: Theory to Practice.

    ERIC Educational Resources Information Center

    Leitzel, Thomas C.; Vogler, Daniel E.

    Curriculum alignment is the conscious congruence of three educational elements: curriculum, instruction, and assessment. Alignment is rooted in the belief that instructional plans are established through outcomes-based content goals and the goal of assuring that delivery and assessment are congruent. Platform unity, based on the Principles of…

  18. Well-pump alignment system

    DOEpatents

    Drumheller, Douglas S.

    1998-01-01

    An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping.

  19. Botulinum alignment for congenital esotropia.

    PubMed Central

    Ing, M R

    1992-01-01

    This is the first report of a group of patients with congenital esotropia examined for motor and sensory evidence of binocularity a minimum of 3 years after alignment by botulinum. Evidence for binocularity was clearly present in approximately one half of the patients. Lag time to satisfactory alignment was at least 1 month (average, 5 months) following the initial botulinum injection. The results must be considered preliminary. However, when these results are compared with those of patients with congenital esotropia aligned by incisional surgery by age 2 years and examined with the same testing devices by this same investigator, botulinum alignment appears to be less effective than surgical alignment in establishing evidence for binocularity (P < 0.005). PMID:1494828

  20. Space Mirror Alignment System

    NASA Technical Reports Server (NTRS)

    Jau, Bruno M.; McKinney, Colin; Smythe, Robert F.; Palmer, Dean L.

    2011-01-01

    An optical alignment mirror mechanism (AMM) has been developed with angular positioning accuracy of +/-0.2 arcsec. This requires the mirror s linear positioning actuators to have positioning resolutions of +/-112 nm to enable the mirror to meet the angular tip/tilt accuracy requirement. Demonstrated capabilities are 0.1 arc-sec angular mirror positioning accuracy, which translates into linear positioning resolutions at the actuator of 50 nm. The mechanism consists of a structure with sets of cross-directional flexures that enable the mirror s tip and tilt motion, a mirror with its kinematic mount, and two linear actuators. An actuator comprises a brushless DC motor, a linear ball screw, and a piezoelectric brake that holds the mirror s position while the unit is unpowered. An interferometric linear position sensor senses the actuator s position. The AMMs were developed for an Astrometric Beam Combiner (ABC) optical bench, which is part of an interferometer development. Custom electronics were also developed to accommodate the presence of multiple AMMs within the ABC and provide a compact, all-in-one solution to power and control the AMMs.

  1. Alignment of the stellar spin with the orbits of a three-planet system.

    PubMed

    Sanchis-Ojeda, Roberto; Fabrycky, Daniel C; Winn, Joshua N; Barclay, Thomas; Clarke, Bruce D; Ford, Eric B; Fortney, Jonathan J; Geary, John C; Holman, Matthew J; Howard, Andrew W; Jenkins, Jon M; Koch, David; Lissauer, Jack J; Marcy, Geoffrey W; Mullally, Fergal; Ragozzine, Darin; Seader, Shawn E; Still, Martin; Thompson, Susan E

    2012-07-25

    The Sun's equator and the planets' orbital planes are nearly aligned, which is presumably a consequence of their formation from a single spinning gaseous disk. For exoplanetary systems this well-aligned configuration is not guaranteed: dynamical interactions may tilt planetary orbits, or stars may be misaligned with the protoplanetary disk through chaotic accretion , magnetic interactions or torques from neighbouring stars. Indeed, isolated 'hot Jupiters' are often misaligned and even orbiting retrograde. Here we report an analysis of transits of planets over starspots on the Sun-like star Kepler-30 (ref. 8), and show that the orbits of its three planets are aligned with the stellar equator. Furthermore, the orbits are aligned with one another to within a few degrees. This configuration is similar to that of our Solar System, and contrasts with the isolated hot Jupiters. The orderly alignment seen in the Kepler-30 system suggests that high obliquities are confined to systems that experienced disruptive dynamical interactions. Should this be corroborated by observations of other coplanar multi-planet systems, then star-disk misalignments would be ruled out as the explanation for the high obliquities of hot Jupiters, and dynamical interactions would be implicated as the origin of hot Jupiters.

  2. A shortcut to align 3D images captured from multiple views

    NASA Astrophysics Data System (ADS)

    Heng, Wei; Wang, Hao

    2008-11-01

    In order to get whole shape of an object, lots of parts of 3D images need to be captured from multiple views and aligned into a same 3D coordinate. That usually involves in both complex software process and expensive hardware system. In this paper, a shortcut approach is proposed to align 3D images captured from multiple views. Employing only a calibrated turntable, a single-view 3D camera can capture a sequence of 3D images of an object from different view angle one by one, then align them quickly and automatically. The alignment doesn't need any help from the operator. It can achieve good performances such as high accuracy, robust, rapidly capturing and low cost. The turntable calibration can be easily implemented by the single-view 3D camera. Fixed with the turntable, single-view 3D camera can calibrate the revolving-axis of the turntable just by measuring the positions of a little calibration-ball revolving with the turntable at several angles. Then system can get the coordinate transformation formula between multiple views of different revolving angle by a LMS algorithm. The formulae for calibration and alignment are given with the precision analysis. Experiments were performed and showed effective result to recover 3D objects.

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  4. Biocompatibility, alignment degree and mechanical properties of an electrospun chitosan-P(LLA-CL) fibrous scaffold.

    PubMed

    Chen, Feng; Su, Yan; Mo, Xiumei; He, Chuanglong; Wang, Hongsheng; Ikada, Yoshito

    2009-01-01

    Chitosan-poly(L-lactide-co-epsilon-caprolactone) (P(LLA-CL)) complex fibers, fibrous mats and a tubular scaffold have been obtained through electrospinning. Due to their high porosity, there were more porcine iliac artery endothelial cells (PIECs) attached to fiber mats than to tissue-culture plate (TCP) and coverslips. The cells could grow and spread well on nanofiber mats. There were many of native extracellular matrix (ECM)-like colloids above and under the surface of fibrous mats after cell culturing. The two-dimensional fast Fourier transform (2-D FFT) approach was used to analysis alignment degree of fibers collected on a rotary mandrel. The relations among mechanical properties, alignment degree, fiber diameter and rotary speed are discussed. Aligned fibers with various alignment degrees could be found through adjusting rotary speed. Fiber alignment was the variable most closely associated with the regulation of stress and strain. In this study, we show a feasible approach for producing scaffold with controllable mechanical property for soft tissue engineering through electrospinning.

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

    PubMed

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

    2006-03-01

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

  6. Aligned Nanotopography Promotes a Migratory State in Glioblastoma Multiforme Tumor Cells

    PubMed Central

    Beliveau, Alexander; Thomas, Gawain; Gong, Jiaxin; Wen, Qi; Jain, Anjana

    2016-01-01

    Glioblastoma multiforme (GBM) is an aggressive, Grade IV astrocytoma with a poor survival rate, primarily due to the GBM tumor cells migrating away from the primary tumor site along the nanotopography of white matter tracts and blood vessels. It is unclear whether this nanotopography influences the biomechanical properties (i.e. cytoskeletal stiffness) of GBM tumor cells. Although GBM tumor cells have an innate propensity to migrate, we believe this capability is enhanced due to the influence of nanotopography on the tumor cells’ biomechanical properties. In this study, we used an aligned nanofiber film that mimics the nanotopography in the tumor microenvironment to investigate the mechanical properties of GBM tumor cells in vitro. The data demonstrate that the cytoskeletal stiffness, cell traction stress, and focal adhesion area were significantly lower in the GBM tumor cells compared to healthy astrocytes. Moreover, the cytoskeletal stiffness was significantly reduced when cultured on aligned nanofiber films compared to smooth and randomly aligned nanofiber films. Gene expression analysis showed that tumor cells cultured on the aligned nanotopography upregulated key migratory genes and downregulated key proliferative genes. Therefore, our data suggest that the migratory potential is elevated when GBM tumor cells are migrating along aligned nanotopographical substrates. PMID:27189099

  7. Alignment of the stellar spin with the orbits of a three-planet system.

    PubMed

    Sanchis-Ojeda, Roberto; Fabrycky, Daniel C; Winn, Joshua N; Barclay, Thomas; Clarke, Bruce D; Ford, Eric B; Fortney, Jonathan J; Geary, John C; Holman, Matthew J; Howard, Andrew W; Jenkins, Jon M; Koch, David; Lissauer, Jack J; Marcy, Geoffrey W; Mullally, Fergal; Ragozzine, Darin; Seader, Shawn E; Still, Martin; Thompson, Susan E

    2012-07-26

    The Sun's equator and the planets' orbital planes are nearly aligned, which is presumably a consequence of their formation from a single spinning gaseous disk. For exoplanetary systems this well-aligned configuration is not guaranteed: dynamical interactions may tilt planetary orbits, or stars may be misaligned with the protoplanetary disk through chaotic accretion , magnetic interactions or torques from neighbouring stars. Indeed, isolated 'hot Jupiters' are often misaligned and even orbiting retrograde. Here we report an analysis of transits of planets over starspots on the Sun-like star Kepler-30 (ref. 8), and show that the orbits of its three planets are aligned with the stellar equator. Furthermore, the orbits are aligned with one another to within a few degrees. This configuration is similar to that of our Solar System, and contrasts with the isolated hot Jupiters. The orderly alignment seen in the Kepler-30 system suggests that high obliquities are confined to systems that experienced disruptive dynamical interactions. Should this be corroborated by observations of other coplanar multi-planet systems, then star-disk misalignments would be ruled out as the explanation for the high obliquities of hot Jupiters, and dynamical interactions would be implicated as the origin of hot Jupiters. PMID:22836999

  8. SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

    PubMed Central

    Zhu, Xiaoqian; Wu, Edward; Lee, Lap-Kei; Lin, Haoxiang; Zhu, Wenjuan; Cheung, David W.; Ting, Hing-Fung; Yiu, Siu-Ming; Peng, Shaoliang; Yu, Chang; Li, Yingrui; Li, Ruiqiang; Lam, Tak-Wah

    2013-01-01

    To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A. PMID:23741504

  9. Alignment technology for backside integration

    NASA Astrophysics Data System (ADS)

    Bauer, J.; Kulse, P.; Haak, U.; Old, G.; Scheuring, G.; Döbereiner, St.; Hillmann, F.; Brück, H.-J.; Kaynak, M.; Ehwald, K.-E.; Marschmeyer, St.; Birkholz, M.; Schulz, K.

    2011-03-01

    This paper presents a backside-to-frontside alignment technique for the backside processing of Si wafers. Integrated MEMS components like BiCMOS-embedded RF-MEMS switches require accurate (1-2μm) alignment. We demonstrate an alignment technique providing overlay values of less than 500 nm by using a backside alignment layer. The approach is enabled by a new non-contact wafer pre-alignment system of the Nikon Scanner S207D allowing precise loading (<5μm) of the wafer onto the exposure stage. Before starting the back-side MEMS process, the misalignment between frontside devices and backside alignment layer has to be measured. The alignment errors are applied as lithography overlay corrections to the backside MEMS process. For the specific application of deep Si etching (Bosch process), moreover, one has to consider the etch profile angle deviation across the wafer (tilting), which turned out in our experiments to amount up to 8 μm. During initial experiments with a Nikon i-line stepper NSR-2205 i- 11D the overlay has been corrected by the stepper offset parameters. These parameters have been obtained by summing up both the wafer and intra-field scaling errors caused by deep Si etching and backside-to-frontside alignment errors. Misalignments and tilting errors were all measured with a MueTec MT 3000 IR optical metrology system using overlay marks. The developed alignment technique is applied to BiCMOS-embedded MEMS devices, i.e. mm-wave RF switches and a viscosity sensor chip based on the IHP's high-speed SiGe technology. It turned out to be very promising for backside processed MEMS components with critical alignment requirements.

  10. OBSERVATIONS OF ENHANCED RADIATIVE GRAIN ALIGNMENT NEAR HD 97300

    SciTech Connect

    Andersson, B-G; Potter, S. B. E-mail: sbp@saao.ac.z

    2010-09-10

    We have obtained optical multi-band polarimetry toward sightlines through the Chamaeleon I cloud, particularly in the vicinity of the young B9/A0 star HD 97300. We show, in agreement with earlier studies, that the radiation field impinging on the cloud in the projected vicinity of the star is dominated by the flux from the star, as evidenced by a local enhancement in the grain heating. By comparing the differential grain heating with the differential change in the location of the peak of the polarization curve, we show that the grain alignment is enhanced by the increase in the radiation field. We also find a weak, but measurable, variation in the grain alignment with the relative angle between the radiation field anisotropy and the magnetic field direction. Such an anisotropy in the grain alignment is consistent with a unique prediction of modern radiative alignment torque theory and provides direct support for radiatively driven grain alignment.

  11. FlexSnap: Flexible Non-sequential Protein Structure Alignment

    PubMed Central

    2010-01-01

    Background Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins that have gone through conformational changes can be captured effectively if flexibility is considered. Topologically unrelated proteins that preserve secondary structure packing interactions can be detected if both flexibility and Sequential permutations are considered. We propose the FlexSnap algorithm for flexible non-topological protein structural alignment. Results The effectiveness of FlexSnap is demonstrated by measuring the agreement of its alignments with manually curated non-sequential structural alignments. FlexSnap showed competitive results against state-of-the-art algorithms, like DALI, SARF2, MultiProt, FlexProt, and FATCAT. Moreover on the DynDom dataset, FlexSnap reported longer alignments with smaller rmsd. Conclusions We have introduced FlexSnap, a greedy chaining algorithm that reports both sequential and non-sequential alignments and allows twists (hinges). We assessed the quality of the FlexSnap alignments by measuring its agreements with manually curated non-sequential alignments. On the FlexProt dataset, FlexSnap was competitive to state-of-the-art flexible alignment methods. Moreover, we demonstrated the benefits of introducing hinges by showing significant improvements in the alignments reported by FlexSnap for the structure pairs for which rigid alignment methods reported alignments with either low coverage or large rmsd. Availability An implementation of the FlexSnap algorithm will be made available online at http://www.cs.rpi.edu/~zaki/software/flexsnap. PMID:20047669

  12. Direct comparative study on the energy level alignments in unoccupied/occupied states of organic semiconductor/electrode interface by constructing in-situ photoemission spectroscopy and Ar gas cluster ion beam sputtering integrated analysis system

    SciTech Connect

    Yun, Dong-Jin Chung, JaeGwan; Kim, Yongsu; Park, Sung-Hoon; Kim, Seong-Heon; Heo, Sung

    2014-10-21

    Through the installation of electron gun and photon detector, an in-situ photoemission and damage-free sputtering integrated analysis system is completely constructed. Therefore, this system enables to accurately characterize the energy level alignments including unoccupied/occupied molecular orbital (LUMO/HOMO) levels at interface region of organic semiconductor/electrode according to depth position. Based on Ultraviolet Photoemission Spectroscopy (UPS), Inverse Photoemission Spectroscopy (IPES), and reflective electron energy loss spectroscopy, the occupied/unoccupied state of in-situ deposited Tris[4-(carbazol-9-yl)phenyl]amine (TCTA) organic semiconductors on Au (E{sub LUMO}: 2.51 eV and E{sub HOMO}: 1.35 eV) and Ti (E{sub LUMO}: 2.19 eV and E{sub HOMO}: 1.69 eV) electrodes are investigated, and the variation of energy level alignments according to work function of electrode (Au: 4.81 eV and Ti: 4.19 eV) is clearly verified. Subsequently, under the same analysis condition, the unoccupied/occupied states at bulk region of TCTA/Au structures are characterized using different Ar gas cluster ion beam (Ar GCIB) and Ar ion sputtering processes, respectively. While the Ar ion sputtering process critically distorts both occupied and unoccupied states in UPS/IPES spectra, the Ar GCIB sputtering process does not give rise to damage on them. Therefore, we clearly confirm that the in-situ photoemission spectroscopy in combination with Ar GCIB sputtering allows of investigating accurate energy level alignments at bulk/interface region as well as surface region of organic semiconductor/electrode structure.

  13. Influence of Poly(L-Lactic Acid) Aligned Nanofibers on PC12 Differentiation.

    PubMed

    Yu, Yadong; Lü, Xiaoying; Ding, Fei

    2015-05-01

    The aim of this study was to unveil the mechanism by which aligned nanofibers influence neuronal differentiation. PC12 cells were seeded on three different poly(L-lactic acid) (PLLA) substrates (PLLA films (control), electrospun PLLA random nanofibers (RF) and electrospun PLLA aligned nanofibers (AF)). Subsequently, cellular experiments, cDNA microarrays and molecular biological approaches were employed to investigate the impacts of the different PLLA substrates on PC12 cell differentiation. Scanning electron microscope observation revealed that neurite outgrowth in the AF group was parallel to the direction of nanofiber alignment and that the filopodias at the neurite tips spread along the aligned nanofiber axis. Meanwhile, both neurite length and the expression of GAP43 (a neuronal differentiation marker gene) were higher in the AF group than those in the control and RF groups. These results suggested that the PLLA aligned nanofibers enhanced PC12 cell differentiation. cDNA microarray experiment revealed that 876 and 1937 genes had significantly changed expression in the RF and AF groups, respectively. Based on gene ontology analysis, 493 and 1193 differentially expressed genes involved in neuronal differentiation were found in the RF and AF groups, respectively. Pathway analysis showed that the PLLA aligned nanofibers mainly mediated their effects via integrin-mediated pathways. qRT-PCR and western blotting assays further confirmed that gene and protein expression levels in the integrin-mediated FAK-MEK-ERK pathway (e.g., Tln1, Mapk6, phosphorylated-ERK1/2) were enhanced by the PLLA aligned nanofibers. Both PC12 cell differentiation and the expressions of genes and proteins in the integrin-mediated FAK-MEK-ERK pathway were inhibited when integrins were blocked by the pentapeptide GRGDS. In addition, the Pafah1b-1 gene was found to be involved in PLLA aligned nanofibers' promotion of PC12 cell differentiation. Taken together, the results suggested that PLLA

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

    PubMed

    Ishii, Satoshi; Kadota, Koji; Senoo, Keishi

    2009-09-01

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

  15. Near-surface alignment of polymers in rubbed films

    NASA Astrophysics Data System (ADS)

    Toney, Michael F.; Russell, Thomas P.; Logan, J. Anthony; Kikuchi, Hirotsugu; Sands, James M.; Kumar, Sanat K.

    1995-04-01

    RUBBED polymer films (generally polyimides) are used in flat-panel displays to control the alignment of liquid crystals in contact with the polymer1-8, a phenomenon first discovered by Maugin1 in 1911. Buffing the film with a cloth produces liquid-crystal alignment in the rubbing direction. Several mechanisms have been proposed to explain this effect. The generation of microgrooves or scratches on the polymer surface during rubbing has led to the suggestion that alignment is the result of long-range elastic effects induced by these surface features3-5. Others have suggested that the polymer chains near the surface are aligned during rubbing and that these then serve as templates for liquid-crystal alignment6-13. Other studies 10-l2 have implied that both mechanisms might be operative. Here we present X-ray scattering measurements which show unambiguously that rubbing a polyimide film causes near-surface alignment of the polymer molecules. For a film 200 nm thick, most of the polymer chains within a thin surface region (about 5 nm thick) are aligned in the rubbing direction; for a 6-nm film essentially all of the chains are aligned within 20° of the rubbing direction. This marked orientation of the near-surface chains at temperatures far below the bulk glass transition temperature shows that the mechanical properties of the near-surface region differ significantly from those of the bulk polymer.

  16. Chromatographic peak alignment using derivative dynamic time warping.

    PubMed

    Bork, Christopher; Ng, Kenneth; Liu, Yinhan; Yee, Alex; Pohlscheidt, Michael

    2013-01-01

    Chromatogram overlays are frequently used to monitor inter-batch performance of bioprocess purification steps. However, the objective analysis of chromatograms is difficult due to peak shifts caused by variable phase durations or unexpected process holds. Furthermore, synchronization of batch process data may also be required prior to performing multivariate analysis techniques. Dynamic time warping was originally developed as a method for spoken word recognition, but shows potential in the objective analysis of time variant signals, such as manufacturing data. In this work we will discuss the application of dynamic time warping with a derivative weighting function to align chromatograms to facilitate process monitoring and fault detection. In addition, we will demonstrate the utility of this method as a preprocessing step for multivariate model development. PMID:23292764

  17. CMP-compatible alignment strategy

    NASA Astrophysics Data System (ADS)

    Rouchouze, Eric; Darracq, Jean-Michel; Gemen, Jack

    1997-07-01

    As semiconductor technology continues its way towards smaller geometries, CMP has gained acceptance as the planarization technique for interconnect layers. Its benefits are well known, especially in terms of imaging. However, one of its major drawbacks is to make difficult the alignment of interconnect layers, since a planarized alignment mark is less visible for the stepper's alignment system. Usual workarounds include the clearing of process layers from the alignment mark before exposing the product layer. Although these workarounds provide a temporary solution, they are too costly to be viable in a mass production environment. In this experiment, a non-zero alignment strategy using new mark designs has been tested on the backend layers of a 0.35 micrometers CMOS process. New mark designs have been evaluated, where the space part of the gratings has been filled with 'segments' of various width, the purpose being to minimize the planarization effect of the metallization process. For the selection of the best mark design, several criteria have been taken into account: the stepper's built-in alignment diagnostic software provides information on the quality of the alignment signal. The most important criterion is the product overlay measurement and its repeatability. Marks cross sections using a FIB/SEM tool give indications on the mark profile after metal deposition.

  18. Galaxy Alignments: Theory, Modelling & Simulations

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  19. Advanced Mask Aligner Lithography (AMALITH)

    NASA Astrophysics Data System (ADS)

    Voelkel, Reinhard; Vogler, Uwe; Bramati, Arianna

    2015-03-01

    Mask aligner lithography is very attractive for less-critical lithography layers and is widely used for LED, display, CMOS image sensor, micro-fluidics and MEMS manufacturing. Mask aligner lithography is also a preferred choice the semiconductor back-end for 3D-IC, TSV interconnects, advanced packaging (AdP) and wafer-level-packaging (WLP). Mask aligner lithography is a mature technique based on shadow printing and has not much changed since the 1980s. In shadow printing lithography a geometric pattern is transferred by free-space propagation from a photomask to a photosensitive layer on a wafer. The inherent simplicity of the pattern transfer offers ease of operation, low maintenance, moderate capital expenditure, high wafers-per-hour (WPH) throughput, and attractive cost-of-ownership (COO). Advanced mask aligner lithography (AMALITH) comprises different measures to improve shadow printing lithography beyond current limits. The key enabling technology for AMALITH is a novel light integrator systems, referred to as MO Exposure Optics® (MOEO). MOEO allows to fully control and shape the properties of the illumination light in a mask aligner. Full control is the base for accurate simulation and optimization of the shadow printing process (computational lithography). Now photolithography enhancement techniques like customized illumination, optical proximity correction (OPC), phase masks (AAPSM), half-tone lithography and Talbot lithography could be used in mask aligner lithography. We summarize the recent progress in advanced mask aligner lithography (AMALITH) and discuss possible measures to further improve shadow printing lithography.

  20. 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

  1. Aligning for Innovation - Alignment Strategy to Drive Innovation

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

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

  2. Design, Simulation and Testing of a Precision Alignment Frame for the Next Linear Collider

    SciTech Connect

    Fitsos, P

    2004-06-18

    An alignment frame is developed to support 3 Beam Position Monitors (BPM's) for detecting and ultimately aligning the electron beam from a linear accelerator. This report discusses the design details, preliminary modal analysis of the alignment frame as well as the addition of a metrology frame in the final phase of development.

  3. 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.

  4. 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.

  5. Multiple sequence alignment with DIALIGN.

    PubMed

    Morgenstern, Burkhard

    2014-01-01

    DIALIGN is a software tool for multiple sequence alignment by combining global and local alignment features. It composes multiple alignments from local pairwise sequence similarities. This approach is particularly useful to discover conserved functional regions in sequences that share only local homologies but are otherwise unrelated. An anchoring option allows to use external information and expert knowledge in addition to primary-sequence similarity alone. The latest version of DIALIGN optionally uses matches to the PFAM database to detect weak homologies. Various versions of the program are available through Göttingen Bioinformatics Compute Server (GOBICS) at http://www.gobics.de/department/software.

  6. Structural Alignment Sensor Feasibility Demonstration

    NASA Technical Reports Server (NTRS)

    Anderson, R. H.; Huang, C. C.; Hodor, J. R.

    1978-01-01

    A structural alignment sensor (SAS) was developed for use with large deployable antenna systems for contour measurement and/or active control. The SAS is a laser ranging system using frequency modulation and accurate phase measurement to determine distance. Work was done with a CO2 and HeNe laser. The capability of the SAS to measure antenna rib contours was studied over ranges of 50 meters to a resolution of 100 microns. Initial resolution data was taken with the CO2 system. This data shows that it will indeed meet the SAS requirements. The development of the HeNe system was initiated because it offers substantial improvement in size, weight, and power over the CO2 system. The final demonstration was made with the HeNe system and it too showed that the SAS requirements could be met with this alternate approach. The projection of these results to a conceptual design for a flight system and its application are described.

  7. Chemometric analysis of chromatographic fingerprints shows potential of Cyclopia maculata (Andrews) Kies for production of standardized extracts with high xanthone content.

    PubMed

    Schulze, Alexandra E; de Beer, Dalene; de Villiers, André; Manley, Marena; Joubert, Elizabeth

    2014-10-29

    Cyclopia species are used for the production of honeybush tea and food ingredient extracts associated with many health benefits. A species-specific high-performance liquid chromatography (HPLC) method for Cyclopia maculata, developed and validated, allowed quantification of the major compounds in extracts from "unfermented" and fermented C. maculata. Two xanthones were tentatively identified for the first time in a Cyclopia species, whereas an additional four compounds were tentatively identified for the first time in C. maculata. "Fermentation" (oxidation) decreased the content of all compounds, with the exception of vicenin-2. Similarity analysis of the chromatographic fingerprints of unfermented C. maculata aqueous extracts showed extremely low variation (r ≥ 0.97) between samples. Some differences between wild-harvested and cultivated seedling plants were, however, demonstrated using principal component analysis. Quantitative data of selected compounds confirmed the low level of variation, making this Cyclopia species ideal for the production of standardized food ingredient extracts.

  8. The Alignment of the Informal and Formal Organizational Supports for Reform: Implications for Improving Teaching in Schools

    ERIC Educational Resources Information Center

    Penuel, William R.; Riel, Margaret; Joshi, Aasha; Pearlman, Leslie; Kim, Chong Min; Frank, Kenneth A.

    2010-01-01

    Previous qualitative studies show that when the formal organization of a school and patterns of informal interaction are aligned, faculty and leaders in a school are better able to coordinate instructional change. This article combines social network analysis with interview data to analyze how well the formal and informal aspects of a school's…

  9. Simulation of exposure and alignment for nanoimprint lithography

    NASA Astrophysics Data System (ADS)

    Deng, Yunfei; Neureuther, Andrew R.

    2002-07-01

    Rigorous electromagnetic simulation with TEMPEST is used to examine the exposure and alignment processes for nano-imprint lithography with attenuating thin-film molds. Parameters in the design of topographical features of the nano-imprint system and material choices of the components are analyzed. The small feature size limits light transmission through the feature. While little can be done with auxiliary structures to attract light into small holes, the use of an absorbing material with a low real part of the refractive index such as silver helps mitigates the problem. Results on complementary alignment marks shows that the small transmission through the metal layer and the vertical separation of two alignment marks create the leakage equivalent to 1 nm misalignment but satisfactory alignment can be obtained by measuring alignment signals over a +/- 30 nm range.

  10. Alignment of atmospheric mineral dust due to electric field

    NASA Astrophysics Data System (ADS)

    Ulanowski, Z.; Bailey, J.; Lucas, P. W.; Hough, J. H.; Hirst, E.

    2007-12-01

    Optical polarimetry observations on La Palma, Canary Islands, during a Saharan dust episode show dichroic extinction indicating the presence of vertically aligned particles in the atmosphere. Modelling of the extinction together with particle orientation indicates that the alignment could have been due to an electric field of the order of 2 kV/m. Two alternative mechanisms for the origin of the field are examined: the effect of reduced atmospheric conductivity and charging of the dust layer, the latter effect being a more likely candidate. It is concluded that partial alignment may be a common feature of Saharan dust layers. The modelling indicates that the alignment can significantly alter dust optical depth. This "Venetian blind effect" may have decreased optical thickness in the vertical direction by as much as 10% for the case reported here. It is also possible that the alignment and the electric field modify dust transport.

  11. Field-free alignment in repetitively kicked nitrogen gas

    SciTech Connect

    Cryan, James P.; Bucksbaum, Philip H.; Coffee, Ryan N.

    2009-12-15

    We demonstrate a high level of laser-induced transient alignment in room temperature and density N{sub 2} with a technique that avoids laser field ionization. Our measured alignment shows an improvement over previous one-pulse or two-pulse experimental alignment results and approaches the theoretical maximum value. We employ eight equally spaced ultrafast laser pulses with a separation that takes advantage of the periodic revivals for the ensemble of quantum rotors. Each successive pulse increases the transient alignment [(t)] and also moves the rotational population away from thermal equilibrium. These measurements are combined with simulations to determine the value of , the J-state distributions, and the functional dependencies of the alignment features.

  12. Visual attitude orientation and alignment system

    NASA Technical Reports Server (NTRS)

    Beam, R. A.; Morris, D. B.

    1967-01-01

    Active vehicle optical alignment aid and a passive vehicle three-dimensional alignment target ensure proper orientation and alignment plus control of the closure range and rate between two bodies, one in controlled motion and one at rest.

  13. Laser beam alignment apparatus and method

    DOEpatents

    Gruhn, Charles R.; Hammond, Robert B.

    1981-01-01

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

  14. Theory of grain alignment in molecular clouds

    NASA Technical Reports Server (NTRS)

    Roberge, Wayne G.

    1993-01-01

    Research accomplishments are presented and include the following: (1) mathematical theory of grain alignment; (2) super-paramagnetic alignment of molecular cloud grains; and (3) theory of grain alignment by ambipolar diffusion.

  15. Laser beam alignment apparatus and method

    DOEpatents

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

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

  16. Analysis of blood leukocytes in a naturally occurring immunodeficiency of pigs shows the defect is localized to B and T cells.

    PubMed

    Ewen, C L; Cino-Ozuna, A G; He, H; Kerrigan, M A; Dekkers, J C M; Tuggle, C K; Rowland, R R R; Wyatt, C R

    2014-12-15

    Severe combined immunodeficiency (SCID) is the result of a set of inherited genetic defects which render components of the immune response nonfunctional. In Arabian horses, Jack Russell terriers, and mice, the disorder is a consequence of the absence of T and B lymphocytes, while natural killer (NK) cell and other leukocyte populations remain intact. Preliminary analysis of a naturally acquired form of inherited SCID in a line of pigs showed several defects in the architecture and composition of secondary lymphoid organs. In this study, a quantitative assessment of lymphocyte populations in affected and normal littermates showed depleted T or B lymphocyte populations in affected pigs; however, NK cells and neutrophils were present in numbers comparable to unaffected littermates. The results indicate that the immune defect in pigs shares the same features as other SCID-affected species. PMID:25454085

  17. Concerning the alignment of modern telescopes: theory, practice, and tolerances illustrated by the ESO NTT

    NASA Astrophysics Data System (ADS)

    Wilson, Ray N.; Delabre, Bernard

    1997-01-01

    A recent paper by Bhatia (1995) suggest from calculations based on the optical geometry of the NTT that the zero-coma condition is a necessary but insufficient condition for the alignment of modern telescopes and that analysis of separate decenter effects is necessary to cope with decentering astigmatism aberrations near the field c enter. We show here that, while Bhatia's calculations are quite correct, their basis shows a misunderstanding of how the NTT was actually aligned and that this "passive" alignment was sufficiently good that the decentering astigmatism effects he indicates were negligible. More dangerous are the wide-field effects of decentering astigmatism discussed by McLeod (1996). However, we show that these effects, linear with field, are also negligible with the NTT alignment quality achieved, provided the correct effective shift of the astigmatic field center is allowed for int he active correction software. This is of great importance in the NTT because the image analyser operates at the edge of the field and the correct field astigmatism must be subtracted to give the necessary active correction at the mechanical field center. This approach is valid for the technical use of the edge field of an aplanatic (RC) telescope limited by field astigmatism. Decentering astigmatism will be much more critical at the field edge for anastigmatic telescopes is a wide field is also used for astronomical observation. (SECTION: Astronomical Instrumentation)

  18. Aligning Microtomography Analysis with Traditional Anatomy for a 3D Understanding of the Host-Parasite Interface – Phoradendron spp. Case Study

    PubMed Central

    Teixeira-Costa, Luíza; Ceccantini, Gregório C. T.

    2016-01-01

    The complex endophytic structure formed by parasitic plant species often represents a challenge in the study of the host-parasite interface. Even with the large amounts of anatomical slides, a three-dimensional comprehension of the structure may still be difficult to obtain. In the present study we applied the High Resolution X-ray Computed Tomography (HRXCT) analysis along with usual plant anatomy techniques in order to compare the infestation pattern of two mistletoe species of the genus Phoradendron. Additionally, we tested the use of contrasting solutions in order to improve the detection of the parasite’s endophytic tissue. To our knowledge, this is the first study to show the three-dimensional structure of host-mistletoe interface by using HRXCT technique. Results showed that Phoradendron perrottetii growing on the host Tapirira guianensis forms small woody galls with a restricted endophytic system. The sinkers were short and eventually grouped creating a continuous interface with the host wood. On the other hand, the long sinkers of P. bathyoryctum penetrate deeply into the wood of Cedrela fissilis branching in all directions throughout the woody gall area, forming a spread-out infestation pattern. The results indicate that the HRXCT is indeed a powerful approach to understand the endophytic system of parasitic plants. The combination of three-dimensional models of the infestation with anatomical analysis provided a broader understanding of the host-parasite connection. Unique anatomic features are reported for the sinkes of P. perrottetii, while the endophytic tissue of P. bathyoryctum conformed to general anatomy observed for other species of this genus. These differences are hypothesized to be related to the three-dimensional structure of each endophytic system and the communication stablished with the host.

  19. Aligning Microtomography Analysis with Traditional Anatomy for a 3D Understanding of the Host-Parasite Interface - Phoradendron spp. Case Study.

    PubMed

    Teixeira-Costa, Luíza; Ceccantini, Gregório C T

    2016-01-01

    The complex endophytic structure formed by parasitic plant species often represents a challenge in the study of the host-parasite interface. Even with the large amounts of anatomical slides, a three-dimensional comprehension of the structure may still be difficult to obtain. In the present study we applied the High Resolution X-ray Computed Tomography (HRXCT) analysis along with usual plant anatomy techniques in order to compare the infestation pattern of two mistletoe species of the genus Phoradendron. Additionally, we tested the use of contrasting solutions in order to improve the detection of the parasite's endophytic tissue. To our knowledge, this is the first study to show the three-dimensional structure of host-mistletoe interface by using HRXCT technique. Results showed that Phoradendron perrottetii growing on the host Tapirira guianensis forms small woody galls with a restricted endophytic system. The sinkers were short and eventually grouped creating a continuous interface with the host wood. On the other hand, the long sinkers of P. bathyoryctum penetrate deeply into the wood of Cedrela fissilis branching in all directions throughout the woody gall area, forming a spread-out infestation pattern. The results indicate that the HRXCT is indeed a powerful approach to understand the endophytic system of parasitic plants. The combination of three-dimensional models of the infestation with anatomical analysis provided a broader understanding of the host-parasite connection. Unique anatomic features are reported for the sinkes of P. perrottetii, while the endophytic tissue of P. bathyoryctum conformed to general anatomy observed for other species of this genus. These differences are hypothesized to be related to the three-dimensional structure of each endophytic system and the communication stablished with the host. PMID:27630661

  20. Aligning Microtomography Analysis with Traditional Anatomy for a 3D Understanding of the Host-Parasite Interface – Phoradendron spp. Case Study

    PubMed Central

    Teixeira-Costa, Luíza; Ceccantini, Gregório C. T.

    2016-01-01

    The complex endophytic structure formed by parasitic plant species often represents a challenge in the study of the host-parasite interface. Even with the large amounts of anatomical slides, a three-dimensional comprehension of the structure may still be difficult to obtain. In the present study we applied the High Resolution X-ray Computed Tomography (HRXCT) analysis along with usual plant anatomy techniques in order to compare the infestation pattern of two mistletoe species of the genus Phoradendron. Additionally, we tested the use of contrasting solutions in order to improve the detection of the parasite’s endophytic tissue. To our knowledge, this is the first study to show the three-dimensional structure of host-mistletoe interface by using HRXCT technique. Results showed that Phoradendron perrottetii growing on the host Tapirira guianensis forms small woody galls with a restricted endophytic system. The sinkers were short and eventually grouped creating a continuous interface with the host wood. On the other hand, the long sinkers of P. bathyoryctum penetrate deeply into the wood of Cedrela fissilis branching in all directions throughout the woody gall area, forming a spread-out infestation pattern. The results indicate that the HRXCT is indeed a powerful approach to understand the endophytic system of parasitic plants. The combination of three-dimensional models of the infestation with anatomical analysis provided a broader understanding of the host-parasite connection. Unique anatomic features are reported for the sinkes of P. perrottetii, while the endophytic tissue of P. bathyoryctum conformed to general anatomy observed for other species of this genus. These differences are hypothesized to be related to the three-dimensional structure of each endophytic system and the communication stablished with the host. PMID:27630661

  1. The Alignment effect of brightest cluster galaxies in the SDSS

    SciTech Connect

    Kim, R. S. J.; Annis, J.; Strauss, M. A.; Lupton, R. H.; Bahcall, N. A.; Gunn, J. E.; Kepner, J. V.; Postman, M.

    2001-10-01

    One of the most vital observational clues for unraveling the origin of Brightest Cluster Galaxies (BCG) is the observed alignment of the BCGs with their host cluster and its surroundings. We have examined the BCG-cluster alignment effect, using clusters of galaxies detected from the Sloan Digital Sky Survey (SDSS). We find that the BCGs are preferentially aligned with the principal axis of their hosts, to a much higher redshift (z >~ 0.3) than probed by previous studies (z <~ 0.1). The alignment effect strongly depends on the magnitude difference of the BCG and the second and third brightest cluster members: we find a strong alignment effect for the dominant BCGs, while less dominant BCGs do not show any departure from random alignment with respect to the cluster. We therefore claim that the alignment process originates from the same process that makes the BCG grow dominant, be it direct mergers in the early stage of cluster formation, or a later process that resembles the galactic cannibalism scenario. We do not find strong evidence for (or against) redshift evolution between 0alignment with redshift, richness and morphology of both the cluster and the BCG.

  2. Fixture for aligning motor assembly

    DOEpatents

    Shervington, Roger M.; Vaghani, Vallabh V.; Vanek, Laurence D.; Christensen, Scott A.

    2009-12-08

    An alignment fixture includes a rotor fixture, a stator fixture and a sensor system which measures a rotational displacement therebetween. The fixture precisely measures rotation of a generator stator assembly away from a NULL position referenced by a unique reference spline on the rotor shaft. By providing an adjustable location of the stator assembly within the housing, the magnetic axes within each generator shall be aligned to a predetermined and controlled tolerance between the generator interface mounting pin and the reference spline on the rotor shaft. Once magnetically aligned, each generator is essentially a line replaceable unit which may be readily mounted to any input of a multi-generator gearbox assembly with the assurance that the magnetic alignment will be within a predetermined tolerance.

  3. Well-pump alignment system

    DOEpatents

    Drumheller, D.S.

    1998-10-20

    An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump are disclosed, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping. 6 figs.

  4. Hippocampal gene expression analysis using the ORESTES methodology shows that homer 1a mRNA is upregulated in the acute period of the pilocarpine epilepsy model.

    PubMed

    Avedissian, Marcelo; Longo, Beatriz M; Jaqueta, Carolina B; Schnabel, Beatriz; Paiva, Paulo B; Mello, Luiz Eugênio A M; Briones, Marcelo R S

    2007-01-01

    In the study of temporal lobe epilepsy (TLE) the characterization of genes expressed in the hippocampus is of central importance for understanding their roles in epileptogenic mechanisms. Although several large-scale studies on TLE gene expression have been reported, precise assignment of individual genes associated with this syndrome is still debatable. Here we investigated differentially expressed genes by comparison of mRNAs from normal and epileptic rat hippocampus in the pilocarpine model of epilepsy. For this we used a powerful EST sequencing methodology, ORESTES (Open Reading frame Expressed Sequence Tags), which generates sequence datasets enriched for mRNAs open reading frames (ORFs) rather than simple 5' and 3' ends of mRNAs. Analysis of our sequences shows that ORESTES readily enables the identification of epilepsy associated ORFs. PFAM analysis of protein motifs present in our ORESTES epilepsy database revealed diverse important protein family domains, such as cytoskeletal, cell signaling and protein kinase domains, which could be involved in processes underlying epileptogenesis. More importantly, we show that the expression of homer 1a, known to be coupled to mGluR and NMDA synaptic transmission, is associated with pilocarpine induced status epilepticus (SE). The combined use of the pilocarpine model of epilepsy with the ORESTES technique can significantly contribute to the identification of specific genes and proteins related to TLE. This is the first study applying a large-scale method for rapid shotgun sequencing directed to ORFs in epilepsy research.

  5. Ion Implantation with Scanning Probe Alignment

    SciTech Connect

    Persaud, A.; Liddle, J.A.; Schenkel, T.; Bokor, J.; Ivanov, Tzv.; Rangelow, I.W.

    2005-07-12

    We describe a scanning probe instrument which integrates ion beams with the imaging and alignment function of a piezo-resistive scanning probe in high vacuum. The beam passes through several apertures and is finally collimated by a hole in the cantilever of the scanning probe. The ion beam spot size is limited by the size of the last aperture. Highly charged ions are used to show hits of single ions in resist, and we discuss the issues for implantation of single ions.

  6. BinAligner: a heuristic method to align biological networks

    PubMed Central

    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

  7. Alignment of Mathematics State-Level Standards and Assessments: The Role of Reviewer Agreement

    ERIC Educational Resources Information Center

    Webb, Noreen M.; Herman, Joan L.; Webb, Norman L.

    2007-01-01

    This article examines the role of reviewer agreement in judgments about alignment between tests and standards. We used case data from three state alignment studies to explore how different approaches to incorporating reviewer agreement changes alignment conclusions. The three case studies showed varying degrees of reviewer agreement about…

  8. Strategies and tools for whole genome alignments

    SciTech Connect

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  9. A novel electrospun-aligned nanoyarn-reinforced nanofibrous scaffold for tendon tissue engineering.

    PubMed

    Yang, Chengwei; Deng, Guoying; Chen, Weiming; Ye, Xiaojian; Mo, Xiumei

    2014-10-01

    An electrospun-aligned nanoyarn-reinforced nanofibrous scaffold (NRS) was developed for tendon tissue engineering to improve mechanical strength and cell infiltration. The novel scaffold composed of aligned nanoyarns and random nanofibers was fabricated via electrospinning using a two-collector system. The aim of the present study was to investigate three different types of electrospun scaffolds (random nanofibrous scaffold, aligned nanofibrous scaffold and NRS) based on silk fibroin (SF) and poly(l-lactide-co-caprolactone) blends. Morphological analysis demonstrated that the NRS composed of aligned nanoyarns and randomly distributed nanofibers formed a 3D microstructure with relatively large pore sizes and high porosity. Biocompatibility analysis revealed that bone marrow-derived mesenchymal stem cells exhibited a higher proliferation rate when cultured on the NRS compared with the other scaffolds. The mechanical testing results indicated that the tensile properties of the NRS were reinforced in the direction parallel to the nanoyarns and satisfied the mechanical requirements for tendon repair. In addition, cell infiltration was significantly enhanced on the NRS. In conclusion, with its improved porosity and appropriate mechanical properties, the developed NRS shows promise for tendon tissue engineering applications.

  10. Alignment of Iron Nanoparticles in a Magnetic Field Due to Shape Anisotropy

    SciTech Connect

    Radhakrishnan, Balasubramaniam; Nicholson, Don M; Eisenbach, Markus; Ludtka, Gerard Michael; Rios, Orlando; Parish, Chad M

    2015-07-09

    During high magnetic field processing there is evidence for alignment of non-spherical metallic particles above the Curie temperature in alloys with negligible magneto-crystalline anisotropy. The main driving force for alignment is the magnetic shape anisotropy. Current understanding of the phenomenon is not adequate to quantify the effect of particle size, aspect ratio, temperature and the magnetic field on particle alignment. We demonstrate a Monte Carlo approach coupled with size scaling to show the conditions under which alignment is possible.

  11. An enhanced algorithm for multiple sequence alignment of protein sequences using genetic algorithm

    PubMed Central

    Kumar, Manish

    2015-01-01

    One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly crossover and mutation were defined and implemented with the proposed method in order to know the population evolution and quality of the sequence aligned. The proposed method is assessed with protein benchmark dataset, e.g., BALIBASE, by comparing the obtained results to those obtained with other alignment algorithms, e.g., SAGA, RBT-GA, PRRP, HMMT, SB-PIMA, CLUSTALX, CLUSTAL W, DIALIGN and PILEUP8 etc. Experiments on a wide range of data have shown that the proposed algorithm is much better (it terms of score) than previously proposed algorithms in its ability to achieve high alignment quality. PMID:27065770

  12. Improving scanner wafer alignment performance by target optimization

    NASA Astrophysics Data System (ADS)

    Leray, Philippe; Jehoul, Christiane; Socha, Robert; Menchtchikov, Boris; Raghunathan, Sudhar; Kent, Eric; Schoonewelle, Hielke; Tinnemans, Patrick; Tuffy, Paul; Belen, Jun; Wise, Rich

    2016-03-01

    In the process nodes of 10nm and below, the patterning complexity along with the processing and materials required has resulted in a need to optimize alignment targets in order to achieve the required precision, accuracy and throughput performance. Recent industry publications on the metrology target optimization process have shown a move from the expensive and time consuming empirical methodologies, towards a faster computational approach. ASML's Design for Control (D4C) application, which is currently used to optimize YieldStar diffraction based overlay (DBO) metrology targets, has been extended to support the optimization of scanner wafer alignment targets. This allows the necessary process information and design methodology, used for DBO target designs, to be leveraged for the optimization of alignment targets. In this paper, we show how we applied this computational approach to wafer alignment target design. We verify the correlation between predictions and measurements for the key alignment performance metrics and finally show the potential alignment and overlay performance improvements that an optimized alignment target could achieve.

  13. GraphCrunch 2: Software tool for network modeling, alignment and clustering

    PubMed Central

    2011-01-01

    Background Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. Results We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, Graph

  14. 223. FREQUENTLY REPRODUCED VIEW OF GWMP SHOWING VARIABLE WIDTH MEDIANS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    223. FREQUENTLY REPRODUCED VIEW OF GWMP SHOWING VARIABLE WIDTH MEDIANS WITH INDEPENDENT ALIGNMENTS FROM KEY BRIDGE LOOKING NORTHWEST, 1953. - George Washington Memorial Parkway, Along Potomac River from McLean to Mount Vernon, VA, Mount Vernon, Fairfax County, VA

  15. RFLP and AFLP analysis of inter- and intraspecific variation of Brassica rapa and B. napus shows that B. rapa is an important genetic resource for B. napus improvement.

    PubMed

    Liu, Ren-Hu; Meng, Jin-Ling

    2006-09-01

    Fingerprinting of 29 accessions of oilseed rape, including seven accessions of Brassica napus, and 22 accessions of B. rapa (B. campestris) from Europe, North America, and China was analyzed using RFLP and AFLP markers. In total, 1,477 polymorphic RFLP bands and 183 polymorphic AFLP bands from 166 enzyme-probe combinations and two pairs of AFLP primers, respectively, were scored for the 29 accessions. On average, RFLP analysis showed that the Arabidopsis EST probe detected more polymorphic bands in Brassica than the random genomic probe performed. More polymorphic RFLP markers were detected with the digestion of EcoR I or BamH I than HindIII. According to the number of bands amplified from each accession, the copy numbers of each gene in the genomes of B. rapa and B. napus were estimated. The average copy numbers in B. rapa of China, B. rapa of Europe, and B. napus, were 3.2, 3.1, and 2.9, respectively. Genetic distance based on the AFLP data was well correlated with that based on the RFLP data (r = 0.72, P<0.001), but 0.39 smaller on average. Genetic diversity analysis showed that Chinese B. rapa was more polymorphic than Chinese B. napus and European materials. Some European B. napus accessions were clustered into European B. rapa, which were distinctly different from Chinese B. napus. The larger variations of Chinese accessions of B. rapa suggest that they are valuable in oilseed rape breeding. Novel strategies to use intersubgenomic heterosis between genome of B. rapa (A(r)A(r)) and genome of B. napus (A(n)A(n)C(n)C(n)) were elucidated.

  16. Gene expression analysis of two extensively drug-resistant tuberculosis isolates show that two-component response systems enhance drug resistance.

    PubMed

    Yu, Guohua; Cui, Zhenling; Sun, Xian; Peng, Jinfu; Jiang, Jun; Wu, Wei; Huang, Wenhua; Chu, Kaili; Zhang, Lu; Ge, Baoxue; Li, Yao

    2015-05-01

    Global analysis of expression profiles using DNA microarrays was performed between a reference strain H37Rv and two clinical extensively drug-resistant isolates in response to three anti-tuberculosis drug exposures (isoniazid, capreomycin, and rifampicin). A deep analysis was then conducted using a combination of genome sequences of the resistant isolates, resistance information, and related public microarray data. Certain known resistance-associated gene sets were significantly overrepresented in upregulated genes in the resistant isolates relative to that observed in H37Rv, which suggested a link between resistance and expression levels of particular genes. In addition, isoniazid and capreomycin response genes, but not rifampicin, either obtained from published works or our data, were highly consistent with the differentially expressed genes of resistant isolates compared to those of H37Rv, indicating a strong association between drug resistance of the isolates and genes differentially regulated by isoniazid and capreomycin exposures. Based on these results, 92 genes of the studied isolates were identified as candidate resistance genes, 10 of which are known resistance-related genes. Regulatory network analysis of candidate resistance genes using published networks and literature mining showed that three two-component regulatory systems and regulator CRP play significant roles in the resistance of the isolates by mediating the production of essential envelope components. Finally, drug sensitivity testing indicated strong correlations between expression levels of these regulatory genes and sensitivity to multiple anti-tuberculosis drugs in Mycobacterium tuberculosis. These findings may provide novel insights into the mechanism underlying the emergence and development of drug resistance in resistant tuberculosis isolates and useful clues for further studies on this issue.

  17. Transcriptome analysis of human ageing in male skin shows mid-life period of variability and central role of NF-κB.

    PubMed

    Haustead, Daniel J; Stevenson, Andrew; Saxena, Vishal; Marriage, Fiona; Firth, Martin; Silla, Robyn; Martin, Lisa; Adcroft, Katharine F; Rea, Suzanne; Day, Philip J; Melton, Phillip; Wood, Fiona M; Fear, Mark W

    2016-01-01

    Age is well-known to be a significant factor in both disease pathology and response to treatment, yet the molecular changes that occur with age in humans remain ill-defined. Here, using transcriptome profiling of healthy human male skin, we demonstrate that there is a period of significantly elevated, transcriptome-wide expression changes occurring predominantly in middle age. Both pre and post this period, the transcriptome appears to undergo much smaller, linear changes with increasing age. Functional analysis of the transient changes in middle age suggest a period of heightened metabolic activity and cellular damage associated with NF-kappa-B and TNF signaling pathways. Through meta-analysis we also show the presence of global, tissue independent linear transcriptome changes with age which appear to be regulated by NF-kappa-B. These results suggest that aging in human skin is associated with a critical mid-life period with widespread transcriptome changes, both preceded and proceeded by a relatively steady rate of linear change in the transcriptome. The data provides insight into molecular changes associated with normal aging and will help to better understand the increasingly important pathological changes associated with aging. PMID:27229172

  18. Molecular analysis of transgenic melon plants showing virus resistance conferred by direct repeat of movement gene of Cucumber green mottle mosaic virus.

    PubMed

    Ali, Emran Md; Emran, Ali; Tabei, Yutaka; Kobayashi, Kappei; Yamaoka, Naoto; Nishiguchi, Masamichi

    2012-08-01

    Cucumber green mottle mosaic virus (CGMMV) is a major limiting factor in the production of melon plants worldwide. For effective control of this virus using the transgenic approach, the direct repeat of the movement protein gene of CGMMV was used for transforming melon plants by Agrobacterium tumefaciens. PCR and Southern blot analyses of T₃ confirmed that they carried the transgene. Northern blot analysis with total RNA showed that transgene transcript RNA as well as siRNA was observed in all plants tested. Separate leaves or individual plants were inoculated with CGMMV and subjected to ELISA and RNA blot analysis using the coat protein gene probe of the virus. Compared to nontransgenic control, these plants were shown to have high virus resistance. Furthermore, cytosine of the transgene DNA in the plants was methylated. Thus, these results reveal that the transgenic lines were highly resistant to the virus through RNA silencing. Key message High virus resistance was obtained in transgenic melon plants with direct repeat of movement protein gene of Cucumber green mottle mosaic tobamovirus through RNA silencing.

  19. Analysis of conservative tracer measurement results using the Frechet distribution at planted horizontal subsurface flow constructed wetlands filled with coarse gravel and showing the effect of clogging processes.

    PubMed

    Dittrich, Ernő; Klincsik, Mihály

    2015-11-01

    A mathematical process, developed in Maple environment, has been successful in decreasing the error of measurement results and in the precise calculation of the moments of corrected tracer functions. It was proved that with this process, the measured tracer results of horizontal subsurface flow constructed wetlands filled with coarse gravel (HSFCW-C) can be fitted more accurately than with the conventionally used distribution functions (Gaussian, Lognormal, Fick (Inverse Gaussian) and Gamma). This statement is true only for the planted HSFCW-Cs. The analysis of unplanted HSFCW-Cs needs more research. The result of the analysis shows that the conventional solutions (completely stirred series tank reactor (CSTR) model and convection-dispersion transport (CDT) model) cannot describe these types of transport processes with sufficient accuracy. These outcomes can help in developing better process descriptions of very difficult transport processes in HSFCW-Cs. Furthermore, a new mathematical process can be developed for the calculation of real hydraulic residence time (HRT) and dispersion coefficient values. The presented method can be generalized to other kinds of hydraulic environments.

  20. First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group.

    PubMed

    Pánek, Tomáš; Zadrobílková, Eliška; Walker, Giselle; Brown, Matthew W; Gentekaki, Eleni; Hroudová, Miluše; Kang, Seungho; Roger, Andrew J; Tice, Alexander K; Vlček, Čestmír; Čepička, Ivan

    2016-05-01

    Archamoebae is an understudied group of anaerobic free-living or endobiotic protists that constitutes the major anaerobic lineage of the supergroup Amoebozoa. Hitherto, the phylogeny of Archamoebae was based solely on SSU rRNA and actin genes, which did not resolve relationships among the main lineages of the group. Because of this uncertainty, several different scenarios had been proposed for the phylogeny of the Archamoebae. In this study, we present the first multigene phylogenetic analysis that includes members of Pelomyxidae, and Rhizomastixidae. The analysis clearly shows that Mastigamoebidae, Pelomyxidae and Rhizomastixidae form a clade of mostly free-living, amoeboid flagellates, here called Pelobiontida. The predominantly endobiotic and aflagellated Entamoebidae represents a separate, deep-branching lineage, Entamoebida. Therefore, two unique evolutionary events, horizontal transfer of the nitrogen fixation system from bacteria and transfer of the sulfate activation pathway to mitochondrial derivatives, predate the radiation of recent lineages of Archamoebae. The endobiotic lifestyle has arisen at least three times independently during the evolution of the group. We also present new ultrastructural data that clarifies the primary divergence among the family Mastigamoebidae which had previously been inferred from phylogenetic analyses based on SSU rDNA.

  1. Large Scale Genome Analysis Shows that the Epitopes for Broadly Cross-Reactive Antibodies Are Predominant in the Pandemic 2009 Influenza Virus A H1N1 Strain

    PubMed Central

    Lara-Ramírez, Edgar E.; Segura-Cabrera, Aldo; Salazar, Ma Isabel; Rodríguez-Pérez, Mario A.; Guo, Xianwu

    2013-01-01

    The past pandemic strain H1N1 (A (H1N1)pdm09) has now become a common component of current seasonal influenza viruses. It has changed the pre-existing immunity of the human population to succeeding infections. In the present study, a total of 14,210 distinct sequences downloaded from National Center for Biotechnology Information (NCBI) database were used for the analysis. The epitope compositions in A (H1N1)pdm09, classic seasonal strains, swine strains as well as highly virulent avian strain H5N1, identified with the aid of the Immune Epitope DataBase (IEDB), were compared at genomic level. The result showed that A (H1N1) pdm09 contains the 90% of B-cell epitopes for broadly cross-reactive antibodies (EBCA), which is in consonance with the recent reports on the experimental identification of new epitopes or antibodies for this virus and the binding tests with influenza virus protein HA of different subtypes. Our analysis supports that high proportional EBCA depends on the epitope pattern of A (H1N1)pdm09 virus. This study may be helpful for better understanding of A (H1N1)pdm09 and the production of new influenza vaccines. PMID:24257096

  2. Transcriptome analysis of human ageing in male skin shows mid-life period of variability and central role of NF-κB

    PubMed Central

    Haustead, Daniel J.; Stevenson, Andrew; Saxena, Vishal; Marriage, Fiona; Firth, Martin; Silla, Robyn; Martin, Lisa; Adcroft, Katharine F.; Rea, Suzanne; Day, Philip J.; Melton, Phillip; Wood, Fiona M.; Fear, Mark W.

    2016-01-01

    Age is well-known to be a significant factor in both disease pathology and response to treatment, yet the molecular changes that occur with age in humans remain ill-defined. Here, using transcriptome profiling of healthy human male skin, we demonstrate that there is a period of significantly elevated, transcriptome-wide expression changes occurring predominantly in middle age. Both pre and post this period, the transcriptome appears to undergo much smaller, linear changes with increasing age. Functional analysis of the transient changes in middle age suggest a period of heightened metabolic activity and cellular damage associated with NF-kappa-B and TNF signaling pathways. Through meta-analysis we also show the presence of global, tissue independent linear transcriptome changes with age which appear to be regulated by NF-kappa-B. These results suggest that aging in human skin is associated with a critical mid-life period with widespread transcriptome changes, both preceded and proceeded by a relatively steady rate of linear change in the transcriptome. The data provides insight into molecular changes associated with normal aging and will help to better understand the increasingly important pathological changes associated with aging. PMID:27229172

  3. Quantitative analysis of tissue deformation dynamics reveals three characteristic growth modes and globally aligned anisotropic tissue deformation during chick limb development

    PubMed Central

    Morishita, Yoshihiro; Kuroiwa, Atsushi; Suzuki, Takayuki

    2015-01-01

    Tissue-level characterization of deformation dynamics is crucial for understanding organ morphogenetic mechanisms, especially the interhierarchical links among molecular activities, cellular behaviors and tissue/organ morphogenetic processes. Limb development is a well-studied topic in vertebrate organogenesis. Nevertheless, there is still little understanding of tissue-level deformation relative to molecular and cellular dynamics. This is mainly because live recording of detailed cell behaviors in whole tissues is technically difficult. To overcome this limitation, by applying a recently developed Bayesian approach, we here constructed tissue deformation maps for chick limb development with high precision, based on snapshot lineage tracing using dye injection. The precision of the constructed maps was validated with a clear statistical criterion. From the geometrical analysis of the map, we identified three characteristic tissue growth modes in the limb and showed that they are consistent with local growth factor activity and cell cycle length. In particular, we report that SHH signaling activity changes dynamically with developmental stage and strongly correlates with the dynamic shift in the tissue growth mode. We also found anisotropic tissue deformation along the proximal-distal axis. Morphogenetic simulation and experimental studies suggested that this directional tissue elongation, and not local growth, has the greatest impact on limb shaping. This result was supported by the novel finding that anisotropic tissue elongation along the proximal-distal axis occurs independently of cell proliferation. Our study marks a pivotal point for multi-scale system understanding in vertebrate development. PMID:25858459

  4. Tevatron alignment issues 2003-2004

    SciTech Connect

    Volk, J.T.; Annala, J.; Elementi, L.; Gelfand, N.; Gollwitzer, K.E.; Greenwood, J.; Martens, M.; Moore, Craig D.; Nobrega, A.; Russell, A.D.; Shiltsev, V.; Stefanski, R.; Sager, T.; Syphers, M.J.; Wojcik, G.; /Fermilab

    2005-01-01

    It was observed during the early part of Run II that dipole corrector currents in the Tevatron were changing over time. Measurement of the roll for dipoles and quadrupoles confirmed that there was a slow and systematic movement of the magnets from their ideal position. A simple system using a digital protractor and laptop computer was developed to allow roll measurements of all dipoles and quadrupoles. These measurements showed that many magnets in the Tevatron had rolled more than 1 milliradian. To aid in magnet alignment a new survey network was built in the Tevatron tunnel. This network is based on the use of free centering laser tracker. During the measurement of the network coordinates for all dipole, quadrupole and corrector magnets were obtained. This paper discusses roll measurement techniques and data, the old and new Tevatron alignment network.

  5. Ultralight anisotropic foams from layered aligned carbon nanotube sheets

    NASA Astrophysics Data System (ADS)

    Faraji, Shaghayegh; L. Stano, Kelly; Yildiz, Ozkan; Li, Ang; Zhu, Yuntian; Bradford, Philip D.

    2015-10-01

    In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm-3, the foam structure is over 500 times less dense than bulk graphite. Microscopy revealed that PyC coated the junctions among CNTs, and also increased CNT surface roughness. These changes in the morphology explain the transition from inelastic behavior to foam-like recovery of the layered CNT sheet structure. Mechanical and thermal properties of the foams were tuned for different applications through variation of PyC deposition duration while dynamic mechanical analysis showed no change in mechanical properties over a large temperature range. Observation of a large and linear electrical resistance change during compression of the aligned CNT/carbon (ACNT/C) foams makes strain/pressure sensors a relevant application. The foams have high oil absorption capacities, up to 275 times their own weight, which suggests they may be useful in water treatment and oil spill cleanup. Finally, the ACNT/C foam's high porosity, surface area and stability allow for demonstration of the foams as catalyst support structures.In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm-3, the foam structure is over 500 times less dense than

  6. Unstable resonator alignment study using off-axis injection.

    PubMed

    Ferguson, T R; Ploor, M D

    1991-10-20

    A brief qualitative experiment and subsequent theoretical study provide new insight concerning off-axis injection of unstable resonators. Theoretical results for aligned resonators show that the regurgitated beam intensity distribution and direction of travel are sensitive to the size, tilt, and other parameters of the injected beam, to the coherence length and number of longitudinal modes of the injecting laser, to clipping and diffraction from apertures, and to resonator length tuning. It is concluded that visual observations of output asymmetries can be used to align the resonator to some degree, but precise alignment using measurement of output asymmetries by a detector array is questionable. PMID:20717200

  7. Cooperative liquid-crystal alignment generated by overlaid topography

    NASA Astrophysics Data System (ADS)

    Yi, Youngwoo; Maclennan, Joseph E.; Clark, Noel A.

    2011-05-01

    Nematic and smectic liquid crystals were introduced into μm-scale gaps between plates coated with polymer films nanoimprinted with parallel arrays of rectangular channels. Overlaying the channels on the two plates close enough at a slight angle produces a mosaic of alternating planar and homeotropic alignments and hybrid alignment, showing that complex liquid-crystal orientation patterns can be achieved by combining two simple topographic patterns. These alignment patterns are attributed to spatial variation of surface roughness and 3D topographic structure created by a sufficient proximity of the two patterns.

  8. Cooperative liquid-crystal alignment generated by overlaid topography.

    PubMed

    Yi, Youngwoo; Maclennan, Joseph E; Clark, Noel A

    2011-05-01

    Nematic and smectic liquid crystals were introduced into μm-scale gaps between plates coated with polymer films nanoimprinted with parallel arrays of rectangular channels. Overlaying the channels on the two plates close enough at a slight angle produces a mosaic of alternating planar and homeotropic alignments and hybrid alignment, showing that complex liquid-crystal orientation patterns can be achieved by combining two simple topographic patterns. These alignment patterns are attributed to spatial variation of surface roughness and 3D topographic structure created by a sufficient proximity of the two patterns. PMID:21728557

  9. Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.

    PubMed

    Ley, A C; Hardy, O J

    2013-04-01

    AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species. PMID:23398575

  10. Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.

    PubMed

    Ley, A C; Hardy, O J

    2013-04-01

    AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species.

  11. Automated quantification of one-dimensional nanostructure alignment on surfaces

    NASA Astrophysics Data System (ADS)

    Dong, Jianjin; Goldthorpe, Irene A.; Mohieddin Abukhdeir, Nasser

    2016-06-01

    A method for automated quantification of the alignment of one-dimensional (1D) nanostructures from microscopy imaging is presented. Nanostructure alignment metrics are formulated and shown to be able to rigorously quantify the orientational order of nanostructures within a two-dimensional domain (surface). A complementary image processing method is also presented which enables robust processing of microscopy images where overlapping nanostructures might be present. Scanning electron microscopy (SEM) images of nanowire-covered surfaces are analyzed using the presented methods and it is shown that past single parameter alignment metrics are insufficient for highly aligned domains. Through the use of multiple parameter alignment metrics, automated quantitative analysis of SEM images is shown to be possible and the alignment characteristics of different samples are able to be quantitatively compared using a similarity metric. The results of this work provide researchers in nanoscience and nanotechnology with a rigorous method for the determination of structure/property relationships, where alignment of 1D nanostructures is significant.

  12. Grain alignment: Role of radiative torques and paramagnetic relaxation

    NASA Astrophysics Data System (ADS)

    Lazarian, Alexander; Andersson, B.-G.; Hoang, Thiem

    2015-05-01

    Polarization arising from aligned dust grains presents a unique opportunity to study magnetic fields in the diffuse interstellar medium and molecular clouds. Polarization from circumstellar regions, accretion disks and comet atmospheres can also be related to aligned dust.To reliably trace magnetic fields quantitative theory of grain alignment is required. Formulating the theory that would correspond to observations was one of the longstanding problems in astrophysics. Lately this problem has been successfully addressed, and in this review we summarize some of the most important theoretical advances in the theory of grain alignment by radiative torques (RATs) that act on realistic irregular dust grains. We discuss an analytical model of RATs and the ways to make RAT alignment more efficient, e.g. through paramagnetic relaxation when grains have inclusions with strong magnetic response. For very small grains for which RAT alignment is inefficient, we also discuss paramagnetic relaxation and a process termed resonance relaxation. We provide an extensive analysis of the observational tests of grain alignment theory.

  13. Television Quiz Show Simulation

    ERIC Educational Resources Information Center

    Hill, Jonnie Lynn

    2007-01-01

    This article explores the simulation of four television quiz shows for students in China studying English as a foreign language (EFL). It discusses the adaptation and implementation of television quiz shows and how the students reacted to them.

  14. DIDA: Distributed Indexing Dispatched Alignment

    PubMed Central

    Mohamadi, Hamid; Vandervalk, Benjamin P; Raymond, Anthony; Jackman, Shaun D; Chu, Justin; Breshears, Clay P; Birol, Inanc

    2015-01-01

    One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through http://www.bcgsc.ca/platform/bioinfo/software/dida. The software is released under the British Columbia Cancer Agency License (BCCA), and is free for academic use. PMID:25923767

  15. Technology Alignment and Portfolio Prioritization (TAPP): Advanced Methods in Strategic Analysis, Technology Forecasting and Long Term Planning for Human Exploration and Operations, Advanced Exploration Systems and Advanced Concepts

    NASA Technical Reports Server (NTRS)

    Funaro, Gregory V.; Alexander, Reginald A.

    2015-01-01

    The Advanced Concepts Office (ACO) at NASA, Marshall Space Flight Center is expanding its current technology assessment methodologies. ACO is developing a framework called TAPP that uses a variety of methods, such as association mining and rule learning from data mining, structure development using a Technological Innovation System (TIS), and social network modeling to measure structural relationships. The role of ACO is to 1) produce a broad spectrum of ideas and alternatives for a variety of NASA's missions, 2) determine mission architecture feasibility and appropriateness to NASA's strategic plans, and 3) define a project in enough detail to establish an initial baseline capable of meeting mission objectives ACO's role supports the decision­-making process associated with the maturation of concepts for traveling through, living in, and understanding space. ACO performs concept studies and technology assessments to determine the degree of alignment between mission objectives and new technologies. The first step in technology assessment is to identify the current technology maturity in terms of a technology readiness level (TRL). The second step is to determine the difficulty associated with advancing a technology from one state to the next state. NASA has used TRLs since 1970 and ACO formalized them in 1995. The DoD, ESA, Oil & Gas, and DoE have adopted TRLs as a means to assess technology maturity. However, "with the emergence of more complex systems and system of systems, it has been increasingly recognized that TRL assessments have limitations, especially when considering [the] integration of complex systems." When performing the second step in a technology assessment, NASA requires that an Advancement Degree of Difficulty (AD2) method be utilized. NASA has used and developed or used a variety of methods to perform this step: Expert Opinion or Delphi Approach, Value Engineering or Value Stream, Analytical Hierarchy Process (AHP), Technique for the Order of

  16. Analysis of the mouse mutant Cloth-ears shows a role for the voltage-gated sodium channel Scn8a in peripheral neural hearing loss.

    PubMed

    Mackenzie, F E; Parker, A; Parkinson, N J; Oliver, P L; Brooker, D; Underhill, P; Lukashkina, V A; Lukashkin, A N; Holmes, C; Brown, S D M

    2009-10-01

    Deafness is the most common sensory disorder in humans and the aetiology of genetic deafness is complex. Mouse mutants have been crucial in identifying genes involved in hearing. However, many deafness genes remain unidentified. Using N-ethyl N-nitrosourea (ENU) mutagenesis to generate new mouse models of deafness, we identified a novel semi-dominant mouse mutant, Cloth-ears (Clth). Cloth-ears mice show reduced acoustic startle response and mild hearing loss from approximately 30 days old. Auditory-evoked brainstem response (ABR) and distortion product otoacoustic emission (DPOAE) analyses indicate that the peripheral neural auditory pathway is impaired in Cloth-ears mice, but that cochlear function is normal. In addition, both Clth/Clth and Clth/+ mice display paroxysmal tremor episodes with behavioural arrest. Clth/Clth mice also show a milder continuous tremor during movement and rest. Longitudinal phenotypic analysis showed that Clth/+ and Clth/Clth mice also have complex defects in behaviour, growth, neurological and motor function. Positional cloning of Cloth-ears identified a point mutation in the neuronal voltage-gated sodium channel alpha-subunit gene, Scn8a, causing an aspartic acid to valine (D981V) change six amino acids downstream of the sixth transmembrane segment of the second domain (D2S6). Complementation testing with a known Scn8a mouse mutant confirmed that this mutation is responsible for the Cloth-ears phenotype. Our findings suggest a novel role for Scn8a in peripheral neural hearing loss and paroxysmal motor dysfunction. PMID:19737145

  17. Multi-point Analysis of Electrostatic Solitary Waves and Field Aligned Electrons Observed by Cluster in and Near the Auroral Current Regions

    NASA Astrophysics Data System (ADS)

    Pickett, J. S.; Forsyth, C.; Christopher, I.; Fazakerley, A. N.; Masson, A.; Marklund, G. T.; Georgescu, E.

    2011-12-01

    The four Cluster spacecraft have been transiting Earth's mid and upper auroral acceleration region (AAR) during parts of the year since late 2008. The Wideband Data (WBD) plasma wave receiver mounted on all four spacecraft obtains high time resolution, band-limited waveforms over a wide frequency range (100 Hz to 577 kHz). We present observations of Electrostatic Solitary Waves (ESWs) made by the WBD instrument simultaneously on more than one Cluster spacecraft in and near the auroral downward current region in the following two frequency bands: 100 Hz to 9.5 kHz and 700 Hz to 77 kHz. We examine and analyze these ESWs for similarities on different spacecraft, and investigate the conclusion, based on single spacecraft FAST satellite data, that fast ESWs (~1 ms duration) in this region are observed in conjunction with modulations in both upgoing and downgoing electrons, suggesting a current instability as the mechanism for generation of these ESWs. We also analyze and discuss the very short time duration ESWs (~20-30 microseconds) observed in the upward current region by the Cluster spacecraft. Such short time duration ESWs have not been previously reported in this region, although fast ESWs of ~300 microseconds duration have been reported using data from the FAST satellite. The Cluster PEACE electron data in this upward current region are examined to determine if there is a correlation of ESW detection with narrow, field-aligned downgoing beams as shown by the FAST results, suggesting ESW generation through a beam instability. The electron density and electric field data are also presented for some events in order to place the wave measurements into context with relation to the auroral density cavity and electric field configuration in and near the AAR.

  18. Global Alignment System for Large Genomic Sequencing

    2002-03-01

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

  19. Photosensitive Polymers for Liquid Crystal Alignment

    NASA Astrophysics Data System (ADS)

    Mahilny, U. V.; Stankevich, A. I.; Trofimova, A. V.; Muravsky, A. A.; Murauski, A. A.

    The peculiarities of alignment of liquid crystal (LC) materials by the layers of photocrosslinkable polymers with side benzaldehyde groups are considered. The investigation of mechanism of photostimulated alignment by rubbed benzaldehyde layer is performed. The methods of creation of multidomain aligning layers on the basis of photostimulated rubbing alignment are described.

  20. Assembly and alignment of infrared refractive system

    NASA Astrophysics Data System (ADS)

    Yang, Lin; Lin, Jian-chun; Wang, Ya-jing; Chen, Fan-sheng

    2013-09-01

    space changing along the optical axis were measured and determined the relative position of the two components. Finally, the integrated system was verified and results showed that alignment met the design requirement.

  1. Alignment method for parabolic trough solar concentrators

    DOEpatents

    Diver, Richard B.

    2010-02-23

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

  2. Combining Multiple Pairwise Structure-based Alignments

    SciTech Connect

    2014-11-12

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

  3. Superposition and alignment of labeled point clouds.

    PubMed

    Fober, Thomas; Glinca, Serghei; Klebe, Gerhard; Hüllermeier, Eyke

    2011-01-01

    Geometric objects are often represented approximately in terms of a finite set of points in three-dimensional euclidean space. In this paper, we extend this representation to what we call labeled point clouds. A labeled point cloud is a finite set of points, where each point is not only associated with a position in three-dimensional space, but also with a discrete class label that represents a specific property. This type of model is especially suitable for modeling biomolecules such as proteins and protein binding sites, where a label may represent an atom type or a physico-chemical property. Proceeding from this representation, we address the question of how to compare two labeled points clouds in terms of their similarity. Using fuzzy modeling techniques, we develop a suitable similarity measure as well as an efficient evolutionary algorithm to compute it. Moreover, we consider the problem of establishing an alignment of the structures in the sense of a one-to-one correspondence between their basic constituents. From a biological point of view, alignments of this kind are of great interest, since mutually corresponding molecular constituents offer important information about evolution and heredity, and can also serve as a means to explain a degree of similarity. In this paper, we therefore develop a method for computing pairwise or multiple alignments of labeled point clouds. To this end, we proceed from an optimal superposition of the corresponding point clouds and construct an alignment which is as much as possible in agreement with the neighborhood structure established by this superposition. We apply our methods to the structural analysis of protein binding sites.

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

    PubMed Central

    2015-01-01

    Background Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. Results We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. Conclusions We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes. PMID:26678826

  5. Grain Alignment in Starless Cores

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  6. Transformation and alignment in similarity.

    PubMed

    Hodgetts, Carl J; Hahn, Ulrike; Chater, Nick

    2009-10-01

    This paper contrasts two structural accounts of psychological similarity: structural alignment (SA) and Representational Distortion (RD). SA proposes that similarity is determined by how readily the structures of two objects can be brought into alignment; RD measures similarity by the complexity of the transformation that "distorts" one representation into the other. We assess RD by defining a simple coding scheme of psychological transformations for the experimental materials. In two experiments, this "concrete" version of RD provides compelling fits of the data and compares favourably with SA. Finally, stepping back from particular models, we argue that perceptual theory suggests that transformations and alignment processes should generally be viewed as complementary, in contrast to the current distinction in the literature. PMID:19720370

  7. Modeling of Field-Aligned Guided Echoes in the Plasmasphere

    NASA Technical Reports Server (NTRS)

    Fung, Shing F.; Green, James L.

    2004-01-01

    The conditions under which high frequency (f>>f(sub uh)) long-range extraordinary-mode discrete field-aligned echoes observed by the Radio Plasma Imager (RPI) on board the Imager for Magnetopause-to-Aurora Global Exploration (IMAGE) satellite in the plasmasphere are investigated by ray tracing modeling. Field-aligned discrete echoes are most commonly observed by RPI in the plasmasphere although they are also observed over the polar cap region. The plasmasphere field-aligned echoes appearing as multiple echo traces at different virtual ranges are attributed to signals reflected successively between conjugate hemispheres that propagate along or nearly along closed geomagnetic field lines. The ray tracing simulations show that field-aligned ducts with as little as 1% density perturbations (depletions) and less than 10 wavelengths wide can guide nearly field-aligned propagating high frequency X mode waves. Effective guidance of wave at a given frequency and wave normal angle (Psi) depends on the cross-field density scale of the duct, such that ducts with stronger density depletions need to be wider in order to maintain the same gradient of refractive index across the magnetic field. While signal guidance by field aligned density gradient without ducting is possible only over the polar region, conjugate field-aligned echoes that have traversed through the equatorial region are most likely guided by ducting.

  8. The Alignment Effect of Brightest Cluster Galaxies in the SDSS

    NASA Astrophysics Data System (ADS)

    Kim, R. S. J.; Sloan Digital Sky Survey Collaboration

    2001-12-01

    One of the most vital observational clues for unraveling the origin of Brightest Cluster Galaxies (BCG) is the observed alignment of the BCGs with their host cluster and its surroundings. We have examined the BCG-cluster alignment effect, using clusters of galaxies detected from the Sloan Digital Sky Survey (SDSS). We find that the BCGs are preferentially aligned with the principal axis of their hosts, to a much higher redshift (z > 0.3) than probed by previous studies (z < 0.1). The alignment effect strongly depends on the magnitude difference of the BCG and the second and third brightest cluster members: we find a strong alignment effect for the dominant BCGs, while less dominant BCGs do not show any departure from random alignment with respect to the cluster. We therefore claim that the alignment process originates from the same process that makes the BCG grow dominant, be it direct mergers in the early stage of cluster formation, or a later process that resembles the galactic cannibalism scenario. We discuss ways in which we can distinguish between the viable scenarios.

  9. 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.

  10. Alignment of bicelles studied with high-field magnetic birefringence and small-angle neutron scattering measurements.

    PubMed

    Liebi, Marianne; van Rhee, Peter G; Christianen, Peter C M; Kohlbrecher, Joachim; Fischer, Peter; Walde, Peter; Windhab, Erich J

    2013-03-12

    Birefringence measurements at high magnetic field strength of up to 33 T were used to detect magnetically induced alignment of bicelles composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), cholesterol, and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-diethylenetriaminepentaacetate (DMPE-DTPA) with complexed lanthanide ions. These birefringence measurements together with a small-angle neutron scattering (SANS) analysis in a magnetic field showed parallel alignment of the bicelles if the lanthanide was thulium (Tm(3+)), and perpendicular alignment with dysprosium (Dy(3+)). With the birefringence measurements, the order parameter S can be determined as a function of the magnetic field strength, if the magnetic alignment reaches saturation. Additional structural information can be obtained if the maximum induced birefringence is considered. The degree of alignment of the studied bicelles increased with decreasing temperature from 40 to 5 °C and showed a new bicellar structure comprising a transient hole formation at intermediate temperatures (20 °C) during heating from 5 to 40 °C.

  11. Amino acid δ13C analysis shows flexibility in the routing of dietary protein and lipids to the tissue of an omnivore.

    PubMed

    Newsome, Seth D; Wolf, Nathan; Peters, Jacob; Fogel, Marilyn L

    2014-11-01

    Stable-isotope analysis (SIA) has revolutionized animal ecology by providing time-integrated estimates of the use of resources and/or habitats. SIA is based on the premise that the isotopic composition of a consumer's tissues originates from its food, but is offset by trophic-discrimination (enrichment) factors controlled by metabolic processes associated with the assimilation of nutrients and the biosynthesis of tissues. Laboratory preparation protocols dictate that tissues both of consumers and of their potential prey be lipid-extracted prior to analysis, because (1) lipids have carbon isotope (δ(13)C) values that are lower by approximately 3-8‰ than associated proteins and (2) amino acids in consumers' proteinaceous tissues are assumed to be completely routed from dietary protein. In contrast, models of stable-isotope mixing assume that dietary macromolecules are broken into their elemental constituents from which non-essential amino acids are resynthesized to build tissues. Here, we show that carbon from non-protein dietary macromolecules, namely lipids, was used to synthesize muscle tissue in an omnivorous rodent (Mus musculus). We traced the influence of dietary lipids on the synthesis of consumers' tissues by inversely varying the dietary proportion of C4-based lipids and C3-based protein while keeping carbohydrate content constant in four dietary treatments, and analyzing the δ(13)C values of amino acids in mouse muscle after 4 months of feeding. The influence of dietary lipids on non-essential amino acids varied as function of biosynthetic pathway. The source of carbon in ketogenic amino acids synthesized through the Krebs cycle was highly sensitive to dietary lipid content, with significant increases of approximately 2-4‰ in Glutamate and Aspartate δ(13)C values from the 5% to 15% dietary lipid treatment. Glucogenic amino acids (Glycine and Serine) were less sensitive to dietary lipid, but increased by approximately 3-4‰ from the 25% to 40% lipid

  12. Measurements of magnetic field alignment

    SciTech Connect

    Kuchnir, M.; Schmidt, E.E.

    1987-11-06

    The procedure for installing Superconducting Super Collider (SSC) dipoles in their respective cryostats involves aligning the average direction of their field with the vertical to an accuracy of 0.5 mrad. The equipment developed for carrying on these measurements is described and the measurements performed on the first few prototypes SSC magnets are presented. The field angle as a function of position in these 16.6 m long magnets is a characteristic of the individual magnet with possible feedback information to its manufacturing procedure. A comparison of this vertical alignment characteristic with a magnetic field intensity (by NMR) characteristic for one of the prototypes is also presented. 5 refs., 7 figs.

  13. Alignment Tool For Inertia Welding

    NASA Technical Reports Server (NTRS)

    Snyder, Gary L.

    1991-01-01

    Compact, easy-to-use tool aligns drive bar of inertia welder over hole in stub. Ensures drive bar concentric to hole within 0.002 in. (0.051 mm.). Holds two batteries and light bulb. Electrical circuit completed, providing current to bulb when pin in contact with post. When pin centered in post hole, it does not touch post, and lamp turns off. Built for use in making repair welds on liquid-oxygen-injector posts in Space Shuttle main engine. Version having suitably modified dimensions used to facilitate alignment in other forests of post.

  14. XUV ionization of aligned molecules

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO2 molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  15. XUV ionization of aligned molecules

    SciTech Connect

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

    2011-11-15

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

  16. Alignment of cD-galaxies with their surroundings

    NASA Technical Reports Server (NTRS)

    Vankampen, Eelco; Rhee, George

    1990-01-01

    For a sample of 122 rich Abell clusters the authors find a strong correlation of the position angle (orientation) of the first-ranked galaxy and its parent cluster. This alignment effect is strongest for cD-galaxies. Formation scenarios for cD galaxies, like the merging scenario, must produce such a strong alignment effect. The authors show some N-body simulations done for this purpose.

  17. Survey, alignment, and beam stability at the Advanced Light Source

    SciTech Connect

    Krebs, G.F.

    1997-10-01

    This paper describes survey and alignment at the Lawrence Berkeley Laboratories Advanced Light Source (ALS) accelerators from 1993 to 1997. The ALS is a third generation light source requiring magnet alignment to within 150 microns. To accomplish this, a network of monuments was established and maintained. Monthly elevation surveys show the movement of the floor over time. Inclinometers have recently been employed to give real time information about magnet, vacuum tank and magnet girder motion in the ALS storage ring.

  18. Alignment of cD-galaxies with their surroundings

    NASA Astrophysics Data System (ADS)

    van Kampen, Eelco; Rhee, George

    1990-11-01

    For a sample of 122 rich Abell clusters the authors find a strong correlation of the position angle (orientation) of the first-ranked galaxy and its parent cluster. This alignment effect is strongest for cD-galaxies. Formation scenarios for cD galaxies, like the merging scenario, must produce such a strong alignment effect. The authors show some N-body simulations done for this purpose.

  19. Genome-wide analysis of AP2/ERF family genes from Lotus corniculatus shows LcERF054 enhances salt tolerance.

    PubMed

    Sun, Zhan-Min; Zhou, Mei-Liang; Xiao, Xing-Guo; Tang, Yi-Xiong; Wu, Yan-Min

    2014-09-01

    Lotus corniculatus is used in agriculture as a main forage plant. Members of the Apetala2/ethylene response factor (AP2/ERF) family play important roles in regulating gene expression in response to many forms of stress, including drought and salt. Here, starting from database of the L. corniculatus var. japonicus genome, we identified 127 AP2/ERF genes by insilico cloning method. The phylogeny, gene structures, and putative conserved motifs in L. corniculatus var. japonicus ERF proteins were analyzed. Based on the number of AP2/ERF domains and the function of the genes, 127 AP2/ERF genes from L. corniculatus var. japonicus were classified into five subfamilies named the AP2, dehydration-responsive element binding factor (DREB), ERF, RAV, and a soloist. Outside the AP2/ERF domain, many L. corniculatus var. japonicus-specific conserved motifs were detected. Expression profile analysis of AP2/ERF genes by quantitative real-time PCR revealed that 19 LcERF genes, including LcERF054 (KJ004728), were significantly induced by salt stress. The results showed that the LcERF054 gene encodes a nuclear transcription activator. Overexpression of LcERF054 in Arabidopsis enhanced the tolerances to salt stress, showed higher germination ratio of seeds, and had elevated levels of relative moisture contents, soluble sugars, proline, and lower levels of malondialdehyde under stress conditions compared to wild-type plants. The expression of hyperosmotic salinity response genes COR15A, LEA4-5, P5CS1, and RD29A was found to be elevated in the LcERF054-overexpressing Arabidopsis plants compared to wild type. These results revealed that the LcERF genes play important roles in L. corniculatus cv Leo under salt stress and that LcERFs are attractive engineering targets in applied efforts to improve abiotic stress tolerances in L. corniculatus cv Leo or other crops. PMID:24777608

  20. Genome-wide methylation analysis in vestibular schwannomas shows putative mechanisms of gene expression modulation and global hypomethylation at the HOX gene cluster.

    PubMed

    Torres-Martín, Miguel; Lassaletta, Luis; de Campos, Jose M; Isla, Alberto; Pinto, Giovanny R; Burbano, Rommel R; Melendez, Bárbara; Castresana, Javier S; Rey, Juan A

    2015-04-01

    Schwannomas are tumors that develop from Schwann cells in the peripheral nerves and commonly arise from the vestibular nerve. Vestibular schwannomas can present unilaterally and sporadically or bilaterally when the tumor is associated with neurofibromatosis Type 2 (NF2) syndrome. The molecular hallmark of the disease is biallelic inactivation of the NF2 gene. The epigenetic signature of schwannomas remains poorly understood and is mostly limited to DNA methylation of the NF2 gene, whose altered expression due to epigenetic factors in this tumor is controversial. In this study, we tested the genomewide DNA methylation pattern of schwannomas to shed light on this epigenetic alteration in these particular tumors. The methodology used includes Infinium Human Methylation 450K BeadChip microarrays in a series of 36 vestibular schwannomas, 4 nonvestibular schwannomas, and 5 healthy nerves. Our results show a trend toward hypomethylation in schwannomas. Furthermore, homeobox (HOX) genes, located at four clusters in the genome, displayed hypomethylation in several CpG sites in the vestibular schwannomas but not in the nonvestibular schwannomas. Several microRNA (miRNA) and protein-coding genes were also found to be hypomethylated at promoter regions and were confirmed as upregulated by expression analysis; including miRNA-21, Met Proto-Oncogene (MET), and PMEPA1. We also detected methylation patterns that might be involved in alternative transcripts of several genes such as NRXN1 or MBP, which would increase the complexity of the methylation and expression patterns. Overall, our results show specific epigenetic signatures in several coding genes and miRNAs that could potentially be used as therapeutic targets. PMID:25533176

  1. Genome-wide analysis of AP2/ERF family genes from Lotus corniculatus shows LcERF054 enhances salt tolerance.

    PubMed

    Sun, Zhan-Min; Zhou, Mei-Liang; Xiao, Xing-Guo; Tang, Yi-Xiong; Wu, Yan-Min

    2014-09-01

    Lotus corniculatus is used in agriculture as a main forage plant. Members of the Apetala2/ethylene response factor (AP2/ERF) family play important roles in regulating gene expression in response to many forms of stress, including drought and salt. Here, starting from database of the L. corniculatus var. japonicus genome, we identified 127 AP2/ERF genes by insilico cloning method. The phylogeny, gene structures, and putative conserved motifs in L. corniculatus var. japonicus ERF proteins were analyzed. Based on the number of AP2/ERF domains and the function of the genes, 127 AP2/ERF genes from L. corniculatus var. japonicus were classified into five subfamilies named the AP2, dehydration-responsive element binding factor (DREB), ERF, RAV, and a soloist. Outside the AP2/ERF domain, many L. corniculatus var. japonicus-specific conserved motifs were detected. Expression profile analysis of AP2/ERF genes by quantitative real-time PCR revealed that 19 LcERF genes, including LcERF054 (KJ004728), were significantly induced by salt stress. The results showed that the LcERF054 gene encodes a nuclear transcription activator. Overexpression of LcERF054 in Arabidopsis enhanced the tolerances to salt stress, showed higher germination ratio of seeds, and had elevated levels of relative moisture contents, soluble sugars, proline, and lower levels of malondialdehyde under stress conditions compared to wild-type plants. The expression of hyperosmotic salinity response genes COR15A, LEA4-5, P5CS1, and RD29A was found to be elevated in the LcERF054-overexpressing Arabidopsis plants compared to wild type. These results revealed that the LcERF genes play important roles in L. corniculatus cv Leo under salt stress and that LcERFs are attractive engineering targets in applied efforts to improve abiotic stress tolerances in L. corniculatus cv Leo or other crops.

  2. Partial face recognition: alignment-free approach.

    PubMed

    Liao, Shengcai; Jain, Anil K; Li, Stan Z

    2013-05-01

    Numerous methods have been developed for holistic face recognition with impressive performance. However, few studies have tackled how to recognize an arbitrary patch of a face image. Partial faces frequently appear in unconstrained scenarios, with images captured by surveillance cameras or handheld devices (e.g., mobile phones) in particular. In this paper, we propose a general partial face recognition approach that does not require face alignment by eye coordinates or any other fiducial points. We develop an alignment-free face representation method based on Multi-Keypoint Descriptors (MKD), where the descriptor size of a face is determined by the actual content of the image. In this way, any probe face image, holistic or partial, can be sparsely represented by a large dictionary of gallery descriptors. A new keypoint descriptor called Gabor Ternary Pattern (GTP) is also developed for robust and discriminative face recognition. Experimental results are reported on four public domain face databases (FRGCv2.0, AR, LFW, and PubFig) under both the open-set identification and verification scenarios. Comparisons with two leading commercial face recognition SDKs (PittPatt and FaceVACS) and two baseline algorithms (PCA+LDA and LBP) show that the proposed method, overall, is superior in recognizing both holistic and partial faces without requiring alignment.

  3. Shear adhesion strength of aligned electrospun nanofibers.

    PubMed

    Najem, Johnny F; Wong, Shing-Chung; Ji, Guang

    2014-09-01

    Inspiration from nature such as insects' foot hairs motivates scientists to fabricate nanoscale cylindrical solids that allow tens of millions of contact points per unit area with material substrates. In this paper, we present a simple yet robust method for fabricating directionally sensitive shear adhesive laminates. By using aligned electrospun nylon-6, we create dry adhesives, as a succession of our previous work on measuring adhesion energies between two single free-standing electrospun polymer fibers in cross-cylinder geometry, randomly oriented membranes and substrate, and peel forces between aligned fibers and substrate. The synthetic aligned cylindrical solids in this study are electrically insulating and show a maximal Mode II shear adhesion strength of 27 N/cm(2) on a glass slide. This measured value, for the purpose of comparison, is 270% of that reported from gecko feet. The Mode II shear adhesion strength, based on a commonly known "dead-weight" test, is 97-fold greater than the Mode I (normal) adhesion strength of the same. The data indicate a strong shear binding on and easy normal lifting off. Anisotropic adhesion (Mode II/Mode I) is pronounced. The size and surface boundary effects, crystallinity, and bending stiffness of fibers are used to understand these electrospun nanofibers, which vastly differ from otherwise known adhesive technologies. The anisotropic strength distribution is attributed to a decreasing fiber diameter and an optimized laminate thickness, which, in turn, influences the bending stiffness and solid-state "wettability" of points of contact between nanofibers and surface asperities.

  4. Alignment limit of the NMSSM Higgs sector

    DOE PAGES

    Carena, Marcela; Haber, Howard E.; Low, Ian; Shah, Nausheen R.; Wagner, Carlos E. M.

    2016-02-17

    The Next-to-Minimal Supersymmetric extension of the Standard Model (NMSSM) with a Higgs boson of mass 125 GeV can be compatible with stop masses of order of the electroweak scale, thereby reducing the degree of fine-tuning necessary to achieve electroweak symmetry breaking. Moreover, in an attractive region of the NMSSM parameter space, corresponding to the \\alignment limit" in which one of the neutral Higgs fields lies approximately in the same direction in field space as the doublet Higgs vacuum expectation value, the observed Higgs boson is predicted to have Standard- Model-like properties. We derive analytical expressions for the alignment conditions andmore » show that they point toward a more natural region of parameter space for electroweak symmetry breaking, while allowing for perturbativity of the theory up to the Planck scale. Additionally, the alignment limit in the NMSSM leads to a well defined spectrum in the Higgs and Higgsino sectors, and yields a rich and interesting Higgs boson phenomenology that can be tested at the LHC. Here, we discuss the most promising channels for discovery and present several benchmark points for further study.« less

  5. Partial face recognition: alignment-free approach.

    PubMed

    Liao, Shengcai; Jain, Anil K; Li, Stan Z

    2013-05-01

    Numerous methods have been developed for holistic face recognition with impressive performance. However, few studies have tackled how to recognize an arbitrary patch of a face image. Partial faces frequently appear in unconstrained scenarios, with images captured by surveillance cameras or handheld devices (e.g., mobile phones) in particular. In this paper, we propose a general partial face recognition approach that does not require face alignment by eye coordinates or any other fiducial points. We develop an alignment-free face representation method based on Multi-Keypoint Descriptors (MKD), where the descriptor size of a face is determined by the actual content of the image. In this way, any probe face image, holistic or partial, can be sparsely represented by a large dictionary of gallery descriptors. A new keypoint descriptor called Gabor Ternary Pattern (GTP) is also developed for robust and discriminative face recognition. Experimental results are reported on four public domain face databases (FRGCv2.0, AR, LFW, and PubFig) under both the open-set identification and verification scenarios. Comparisons with two leading commercial face recognition SDKs (PittPatt and FaceVACS) and two baseline algorithms (PCA+LDA and LBP) show that the proposed method, overall, is superior in recognizing both holistic and partial faces without requiring alignment. PMID:23520259

  6. Image Guidance During Head-and-Neck Cancer Radiation Therapy: Analysis of Alignment Trends With In-Room Cone-Beam Computed Tomography Scans

    SciTech Connect

    Zumsteg, Zachary; DeMarco, John; Lee, Steve P.; Steinberg, Michael L.; Lin, Chun Shu; McBride, William; Lin, Kevin; Wang, Pin-Chieh; Kupelian, Patrick; Lee, Percy

    2012-06-01

    Purpose: On-board cone-beam computed tomography (CBCT) is currently available for alignment of patients with head-and-neck cancer before radiotherapy. However, daily CBCT is time intensive and increases the overall radiation dose. We assessed the feasibility of using the average couch shifts from the first several CBCTs to estimate and correct for the presumed systematic setup error. Methods and Materials: 56 patients with head-and-neck cancer who received daily CBCT before intensity-modulated radiation therapy had recorded shift values in the medial-lateral, superior-inferior, and anterior-posterior dimensions. The average displacements in each direction were calculated for each patient based on the first five or 10 CBCT shifts and were presumed to represent the systematic setup error. The residual error after this correction was determined by subtracting the calculated shifts from the shifts obtained using daily CBCT. Results: The magnitude of the average daily residual three-dimensional (3D) error was 4.8 {+-} 1.4 mm, 3.9 {+-} 1.3 mm, and 3.7 {+-} 1.1 mm for uncorrected, five CBCT corrected, and 10 CBCT corrected protocols, respectively. With no image guidance, 40.8% of fractions would have been >5 mm off target. Using the first five CBCT shifts to correct subsequent fractions, this percentage decreased to 19.0% of all fractions delivered and decreased the percentage of patients with average daily 3D errors >5 mm from 35.7% to 14.3% vs. no image guidance. Using an average of the first 10 CBCT shifts did not significantly improve this outcome. Conclusions: Using the first five CBCT shift measurements as an estimation of the systematic setup error improves daily setup accuracy for a subset of patients with head-and-neck cancer receiving intensity-modulated radiation therapy and primarily benefited those with large 3D correction vectors (>5 mm). Daily CBCT is still necessary until methods are developed that more accurately determine which patients may benefit from

  7. SWAMP+: multiple subsequence alignment using associative massive parallelism

    SciTech Connect

    Steinfadt, Shannon Irene; Baker, Johnnie W

    2010-10-18

    A new parallel algorithm SWAMP+ incorporates the Smith-Waterman sequence alignment on an associative parallel model known as ASC. It is a highly sensitive parallel approach that expands traditional pairwise sequence alignment. This is the first parallel algorithm to provide multiple non-overlapping, non-intersecting subsequence alignments with the accuracy of Smith-Waterman. The efficient algorithm provides multiple alignments similar to BLAST while creating a better workflow for the end users. The parallel portions of the code run in O(m+n) time using m processors. When m = n, the algorithmic analysis becomes O(n) with a coefficient of two, yielding a linear speedup. Implementation of the algorithm on the SIMD ClearSpeed CSX620 confirms this theoretical linear speedup with real timings.

  8. Eco-genomic analysis of the poleward range expansion of the wasp spider Argiope bruennichi shows rapid adaptation and genomic admixture.

    PubMed

    Krehenwinkel, Henrik; Rödder, Dennis; Tautz, Diethard

    2015-12-01

    Poleward range expansions are commonly attributed to global change, but could alternatively be driven by rapid evolutionary adaptation. A well-documented example of a range expansion during the past decades is provided by the European wasp spider Argiope bruennichi. Using ecological niche modeling, thermal tolerance experiments and a genome-wide analysis of gene expression divergence, we show that invasive populations have adapted to novel climatic conditions in the course of their expansion. Their climatic niche shift is mirrored in an increased cold tolerance and a population-specific and functionally differentiated gene expression response. We generated an Argiope reference genome sequence and used population genome resequencing to assess genomic changes associated with the new climatic adaptations. We find clear genetic differentiation and a significant admixture with alleles from East Asian populations in the invasive Northern European populations. Population genetic modeling suggests that at least some of these introgressing alleles have contributed to the new adaptations during the expansion. Our results thus confirm the notion that range expansions are not a simple consequence of climate change, but are accompanied by fast genetic changes and adaptations that may be fuelled through admixture between long separated lineages. PMID:26183328

  9. Genome-wide transcriptional analysis of Drosophila larvae infected by entomopathogenic nematodes shows involvement of complement, recognition and extracellular matrix proteins.

    PubMed

    Arefin, Badrul; Kucerova, Lucie; Dobes, Pavel; Markus, Robert; Strnad, Hynek; Wang, Zhi; Hyrsl, Pavel; Zurovec, Michal; Theopold, Ulrich

    2014-01-01

    Heterorhabditis bacteriophora is an entomopathogenic nematode (EPN) which infects its host by accessing the hemolymph where it releases endosymbiotic bacteria of the species Photorhabdus luminescens. We performed a genome-wide transcriptional analysis of the Drosophila response to EPN infection at the time point at which the nematodes reached the hemolymph either via the cuticle or the gut and the bacteria had started to multiply. Many of the most strongly induced genes have been implicated in immune responses in other infection models. Mapping of the complete set of differentially regulated genes showed the hallmarks of a wound response, but also identified a large fraction of EPN-specific transcripts. Several genes identified by transcriptome profiling or their homologues play protective roles during nematode infections. Genes that positively contribute to controlling nematobacterial infections encode: a homolog of thioester-containing complement protein 3, a basement membrane component (glutactin), a recognition protein (GNBP-like 3) and possibly several small peptides. Of note is that several of these genes have not previously been implicated in immune responses.

  10. Linking concepts in the ecology and evolution of invasive plants: network analysis shows what has been most studied and identifies knowledge gaps

    PubMed Central

    Vanderhoeven, Sonia; Brown, Cynthia S; Tepolt, Carolyn K; Tsutsui, Neil D; Vanparys, Valérie; Atkinson, Sheryl; Mahy, Grégory; Monty, Arnaud

    2010-01-01

    In recent decades, a growing number of studies have addressed connections between ecological and evolutionary concepts in biologic invasions. These connections may be crucial for understanding the processes underlying invaders’ success. However, the extent to which scientists have worked on the integration of the ecology and evolution of invasive plants is poorly documented, as few attempts have been made to evaluate these efforts in invasion biology research. Such analysis can facilitate recognize well-documented relationships and identify gaps in our knowledge. In this study, we used a network-based method for visualizing the connections between major aspects of ecology and evolution in the primary research literature. Using the family Poaceae as an example, we show that ecological concepts were more studied and better interconnected than were evolutionary concepts. Several possible connections were not documented at all, representing knowledge gaps between ecology and evolution of invaders. Among knowledge gaps, the concepts of plasticity, gene flow, epigenetics and human influence were particularly under-connected. We discuss five possible research avenues to better understand the relationships between ecology and evolution in the success of Poaceae, and of alien plants in general. PMID:25567919

  11. Linking concepts in the ecology and evolution of invasive plants: network analysis shows what has been most studied and identifies knowledge gaps.

    PubMed

    Vanderhoeven, Sonia; Brown, Cynthia S; Tepolt, Carolyn K; Tsutsui, Neil D; Vanparys, Valérie; Atkinson, Sheryl; Mahy, Grégory; Monty, Arnaud

    2010-03-01

    In recent decades, a growing number of studies have addressed connections between ecological and evolutionary concepts in biologic invasions. These connections may be crucial for understanding the processes underlying invaders' success. However, the extent to which scientists have worked on the integration of the ecology and evolution of invasive plants is poorly documented, as few attempts have been made to evaluate these efforts in invasion biology research. Such analysis can facilitate recognize well-documented relationships and identify gaps in our knowledge. In this study, we used a network-based method for visualizing the connections between major aspects of ecology and evolution in the primary research literature. Using the family Poaceae as an example, we show that ecological concepts were more studied and better interconnected than were evolutionary concepts. Several possible connections were not documented at all, representing knowledge gaps between ecology and evolution of invaders. Among knowledge gaps, the concepts of plasticity, gene flow, epigenetics and human influence were particularly under-connected. We discuss five possible research avenues to better understand the relationships between ecology and evolution in the success of Poaceae, and of alien plants in general.

  12. Fine-tuning regression forests votes for object alignment in the wild.

    PubMed

    Yang, Heng; Patras, Ioannis

    2015-02-01

    In this paper, we propose a object alignment method that detects the landmarks of an object in 2D images. In the regression forests (RFs) framework, observations (patches) that are extracted at several image locations cast votes for the localization of several landmarks. We propose to refine the votes before accumulating them into the Hough space, by sieving and/or aggregating. In order to filter out false positive votes, we pass them through several sieves, each associated with a discrete or continuous latent variable. The sieves filter out votes that are not consistent with the latent variable in question, something that implicitly enforces global constraints. In order to aggregate the votes when necessary, we adjusts on-the-fly a proximity threshold by applying a classifier on middle-level features extracted from voting maps for the object landmark in question. Moreover, our method is able to predict the unreliability of an individual object landmark. This information can be useful for subsequent object analysis like object recognition. Our contributions are validated for two object alignment tasks, face alignment and car alignment, on data sets with challenging images collected in the wild, i.e., the Labeled Face in the Wild, the Annotated Facial Landmarks in the Wild, and the street scene car data set. We show that with the proposed approach, and without explicitly introducing shape models, we obtain performance superior or close to the state of the art for both tasks.

  13. Effects of physical exertion on trans-tibial prosthesis users' ability to accommodate alignment perturbations

    PubMed Central

    Fiedler, Goeran; Slavens, Brooke A; O'Connor, Kristian M; Smith, Roger O; Hafner, Brian J

    2015-01-01

    Background It has long been reported that a range of prosthesis alignments is acceptable in trans-tibial prosthetics. This range was shown to be smaller when walking on uneven surfaces. It has also been argued that findings on gait with prostheses that were obtained under laboratory conditions are limited in their applicability to real-life environments. Objectives This study investigated the hypothesis that efforts to compensate for suboptimal alignments by active users of trans-tibial prostheses become less effective when levels of physical exertion increase. Study design A 2 × 2 repeated-measures analysis of variance was conducted to compare the effects of physical exertion and subtle alignment perturbations on gait with trans-tibial prostheses. Methods The gait of eight subjects with trans-tibial amputation was analyzed when walking with two different prosthesis alignments and two different physical exertion levels. The main and interaction effects were statistically evaluated. Results Bilateral step length symmetry and measures of step variability within the same leg were found to be affected by the intervention. There was no significant effect on index variables that combined kinematic or kinetic measures. Conclusion Findings showed that persons with trans-tibial prostheses responded heterogeneously to the interventions. For most variables, the research hypothesis could not be confirmed. PMID:25138114

  14. Intrinsic alignments in redMaPPer clusters - I. Central galaxy alignments and angular segregation of satellites

    NASA Astrophysics Data System (ADS)

    Huang, Hung-Jin; Mandelbaum, Rachel; Freeman, Peter E.; Chen, Yen-Chi; Rozo, Eduardo; Rykoff, Eli; Baxter, Eric J.

    2016-08-01

    The shapes of cluster central galaxies are not randomly oriented, but rather exhibit coherent alignments with the shapes of their parent clusters as well as with the surrounding large-scale structures. In this work, we aim to identify the galaxy and cluster quantities that most strongly predict the central galaxy alignment phenomenon among a large parameter space with a sample of 8237 clusters and 94817 members within 0.1 < z < 0.35, based on the redMaPPer cluster catalog constructed from the Sloan Digital Sky Survey. We first quantify the alignment between the projected central galaxy shapes and the distribution of member satellites, to understand what central galaxy and cluster properties most strongly correlate with these alignments. Next, we investigate the angular segregation of satellites with respect to their central galaxy major axis directions, to identify the satellite properties that most strongly predict their angular segregation. We find that central galaxies are more aligned with their member galaxy distributions in clusters that are more elongated and have higher richness, and for central galaxies with larger physical size, higher luminosity and centering probability, and redder color. Satellites with redder color, higher luminosity, located closer to the central galaxy, and with smaller ellipticity show a stronger angular segregation toward their central galaxy major axes. Finally, we provide physical explanations for some of the identified correlations, and discuss the connection to theories of central galaxy alignments, the impact of primordial alignments with tidal fields, and the importance of anisotropic accretion.

  15. Segmented Ultralight Pre-Aligned Rotor for Extreme-Scale Wind Turbines

    SciTech Connect

    Loth, E.; Steele, A.; Ichter, B.; Selig, M.; Moriarty, P.

    2012-01-01

    To alleviate the mass-scaling issues associated with conventional upwind rotors of extreme-scale turbines, a downwind rotor concept is proposed which employs fixed blade curvature based on force alignment at rated conditions. For a given peak stress constraint, the reduction in downwind cantilever loads allows reduced shell and spar thickness, and thus a reduced blade mass as compared with a conventional upwind rotor, especially as rotor sizes approach extreme-scales. To quantify this mass reduction, a Finite Element Analysis was conducted for a 10 MW rated rotor based on the NREL offshore 5 MW baseline wind turbine. The results show that this 'pre-alignment' yields a net downstream deflection of 32 deg, a downward hub-pitch angle of 6 deg, a 20% increase in blade length (to maintain the same radius as the conventional blade), and a net mass savings of about 50% through decreased shell and spar thicknesses. The pre-alignment may also allow a more straightforward and efficient segmentation of the blade since shear stresses near joints are substantially reduced. Segmenting, in turn, can dramatically reduce costs associated with fabrication, transport and assembly for extreme-scale off-shore systems. The pre-aligned geometric curvature can also help alleviate tower wake effects on the blades since blade tips (where shadow effects can be most problematic) are shifted downstream where the tower wake is weaker. In addition, the portion of the tower that is upstream of the blade tips can be faired with an externally-rotating aerodynamic shroud. Furthermore, the downwind rotor can allow a floating off-shore tri-pod platform to reduce tower weight and yaw-control requirements. A simple economic analysis of the segmented ultralight pre-aligned rotor (SUPAR) concept suggests that the overall system cost savings can be as much as 25%, indicating that more detailed (numerical and experimental) investigations are warranted.

  16. A Holographic Road Show.

    ERIC Educational Resources Information Center

    Kirkpatrick, Larry D.; Rugheimer, Mac

    1979-01-01

    Describes the viewing sessions and the holograms of a holographic road show. The traveling exhibits, believed to stimulate interest in physics, include a wide variety of holograms and demonstrate several physical principles. (GA)

  17. Aligning Assessments for COSMA Accreditation

    ERIC Educational Resources Information Center

    Laird, Curt; Johnson, Dennis A.; Alderman, Heather

    2015-01-01

    Many higher education sport management programs are currently in the process of seeking accreditation from the Commission on Sport Management Accreditation (COSMA). This article provides a best-practice method for aligning student learning outcomes with a sport management program's mission and goals. Formative and summative assessment procedures…

  18. Aligned natural inflation with modulations

    NASA Astrophysics Data System (ADS)

    Choi, Kiwoon; Kim, Hyungjin

    2016-08-01

    The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  19. Laser-Beam-Alignment Controller

    NASA Technical Reports Server (NTRS)

    Krasowski, M. J.; Dickens, D. E.

    1995-01-01

    In laser-beam-alignment controller, images from video camera compared to reference patterns by fuzzy-logic pattern comparator. Results processed by fuzzy-logic microcontroller, which sends control signals to motor driver adjusting lens and pinhole in spatial filter.

  20. Tonal Alignment in Irish Dialects

    ERIC Educational Resources Information Center

    Dalton, Martha; Ni Chasaide, Ailbhe

    2005-01-01

    A comparison of the contour alignment of nuclear and initial prenuclear accents was carried out for the Irish dialects of Gaoth Dobhair in Ulster (GD-U) and Cois Fharraige in Connaught (CF-C). This was done across conditions where the number of unstressed syllables following the nuclear and preceding the initial prenuclear accents was varied from…