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

PubMed

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

2015-01-01

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

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

PubMed

Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

2017-01-21

RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA comparison tools, RNApdist and RNAdistance, showcased that RNA-TVcurve can efficiently capture subtle relationships among RNAs for mutation detection and non-coding RNA classification. All the relevant results were shown in an intuitive graphical manner, and can be freely downloaded from this server. RNA-TVcurve, along with test examples and detailed documents, are available at: http://ml.jlu.edu.cn/tvcurve/ .

Parallel Implementation of MAFFT on CUDA-Enabled Graphics Hardware.

PubMed

Zhu, Xiangyuan; Li, Kenli; Salah, Ahmad; Shi, Lin; Li, Keqin

2015-01-01

Multiple sequence alignment (MSA) constitutes an extremely powerful tool for many biological applications including phylogenetic tree estimation, secondary structure prediction, and critical residue identification. However, aligning large biological sequences with popular tools such as MAFFT requires long runtimes on sequential architectures. Due to the ever increasing sizes of sequence databases, there is increasing demand to accelerate this task. In this paper, we demonstrate how graphic processing units (GPUs), powered by the compute unified device architecture (CUDA), can be used as an efficient computational platform to accelerate the MAFFT algorithm. To fully exploit the GPU's capabilities for accelerating MAFFT, we have optimized the sequence data organization to eliminate the bandwidth bottleneck of memory access, designed a memory allocation and reuse strategy to make full use of limited memory of GPUs, proposed a new modified-run-length encoding (MRLE) scheme to reduce memory consumption, and used high-performance shared memory to speed up I/O operations. Our implementation tested in three NVIDIA GPUs achieves speedup up to 11.28 on a Tesla K20m GPU compared to the sequential MAFFT 7.015.

On the Impact of Widening Vector Registers on Sequence Alignment

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

Daily, Jeffrey A.; Kalyanaraman, Anantharaman; Krishnamoorthy, Sriram

2016-09-22

Vector extensions, such as SSE, have been part of the x86 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. In this paper, we demonstrate that the trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based onmore » striped data layouts. We present a practically efficient SIMD implementation of a parallel scan based sequence alignment algorithm that can better exploit wider SIMD units. We conduct comprehensive workload and use case analyses to characterize the relative behavior of the striped and scan approaches and identify the best choice of algorithm based on input length and SIMD width.« less

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

PubMed

Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

2015-01-01

IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

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

Lee, Kyung Eun; Oh, Jung Jae; Yun, Taeyeong

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 withinmore » 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.« less

Using a color-coded ambigraphic nucleic acid notation to visualize conserved palindromic motifs within and across genomes

PubMed Central

2014-01-01

Background Ambiscript is a graphically-designed nucleic acid notation that uses symbol symmetries to support sequence complementation, highlight biologically-relevant palindromes, and facilitate the analysis of consensus sequences. Although the original Ambiscript notation was designed to easily represent consensus sequences for multiple sequence alignments, the notation’s black-on-white ambiguity characters are unable to reflect the statistical distribution of nucleotides found at each position. We now propose a color-augmented ambigraphic notation to encode the frequency of positional polymorphisms in these consensus sequences. Results We have implemented this color-coding approach by creating an Adobe Flash® application ( http://www.ambiscript.org) that shades and colors modified Ambiscript characters according to the prevalence of the encoded nucleotide at each position in the alignment. The resulting graphic helps viewers perceive biologically-relevant patterns in multiple sequence alignments by uniquely combining color, shading, and character symmetries to highlight palindromes and inverted repeats in conserved DNA motifs. Conclusion Juxtaposing an intuitive color scheme over the deliberate character symmetries of an ambigraphic nucleic acid notation yields a highly-functional nucleic acid notation that maximizes information content and successfully embodies key principles of graphic excellence put forth by the statistician and graphic design theorist, Edward Tufte. PMID:24447494

Architecture with GIDEON, A Program for Design in Structural DNA Nanotechnology

PubMed Central

Birac, Jeffrey J.; Sherman, William B.; Kopatsch, Jens; Constantinou, Pamela E.; Seeman, Nadrian C.

2012-01-01

We present geometry based design strategies for DNA nanostructures. The strategies have been implemented with GIDEON – a Graphical Integrated Development Environment for OligoNucleotides. GIDEON has a highly flexible graphical user interface that facilitates the development of simple yet precise models, and the evaluation of strains therein. Models are built on a simple model of undistorted B-DNA double-helical domains. Simple point and click manipulations of the model allow the minimization of strain in the phosphate-backbone linkages between these domains and the identification of any steric clashes that might occur as a result. Detailed analysis of 3D triangles yields clear predictions of the strains associated with triangles of different sizes. We have carried out experiments that confirm that 3D triangles form well only when their geometrical strain is less than 4% deviation from the estimated relaxed structure. Thus geometry-based techniques alone, without energetic considerations, can be used to explain general trends in DNA structure formation. We have used GIDEON to build detailed models of double crossover and triple crossover molecules, evaluating the non-planarity associated with base tilt and junction mis-alignments. Computer modeling using a graphical user interface overcomes the limited precision of physical models for larger systems, and the limited interaction rate associated with earlier, command-line driven software. PMID:16630733

Grade-Aligned Math Instruction for Secondary Students with Moderate Intellectual Disability

ERIC Educational Resources Information Center

Browder, Diane M.; Jimenez, Bree A.; Trela, Katherine

2012-01-01

The purpose of this study was to examine the effects of grade-aligned math instruction on math skill acquisition of four middle schools with moderate intellectual disability. Teachers were trained to follow a task analysis to teach grade-aligned math to middle school students using adapted math problem stories and graphic organizers. The teacher…

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2004-08-24

A process for producing a carbon foam heat sink is disclosed which obviates the need for conventional oxidative stabilization. The process employs mesophase or isotropic pitch and a simplified process using a single mold. The foam has a relatively uniform distribution of pore sizes and a highly aligned graphic structure in the struts. The foam material can be made into a composite which is useful in high temperature sandwich panels for both thermal and structural applications. The foam is encased and filled with a phase change material to provide a very efficient heat sink device.

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2007-01-02

A process for producing a carbon foam heat sink is disclosed which obviates the need for conventional oxidative stabilization. The process employs mesophase or isotropic pitch and a simplified process using a single mold. The foam has a relatively uniform distribution of pore sizes and a highly aligned graphic structure in the struts. The foam material can be made into a composite which is useful in high temperature sandwich panels for both thermal and structural applications. The foam is encased and filled with a phase change material to provide a very efficient heat sink device.

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2006-03-21

A process for producing a carbon foam heat sink is disclosed which obviates the need for conventional oxidative stabilization. The process employs mesophase or isotropic pitch and a simplified process using a single mold. The foam has a relatively uniform distribution of pore sizes and a highly aligned graphic structure in the struts. The foam material can be made into a composite which is useful in high temperature sandwich panels for both thermal and structural applications. The foam is encased and filled with a phase change material to provide a very efficient heat sink device.

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2002-01-01

A process for producing a carbon foam heat sink is disclosed which obviates the need for conventional oxidative stabilization. The process employs mesophase or isotropic pitch and a simplified process using a single mold. The foam has a relatively uniform distribution of pore sizes and a highly aligned graphic structure in the struts. The foam material can be made into a composite which is useful in high temperature sandwich panels for both thermal and structural applications. The foam is encased and filled with a phase change material to provide a very efficient heat sink device.

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2000-01-01

A process for producing a carbon foam heat sink is disclosed which obviates the need for conventional oxidative stabilization. The process employs mesophase or isotropic pitch and a simplified process using a single mold. The foam has a relatively uniform distribution of pore sizes and a highly aligned graphic structure in the struts. The foam material can be made into a composite which is useful in high temperature sandwich panels for both thermal and structural applications. The foam is encased and filled with a phase change material to provide a very efficient heat sink device.

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2007-01-23

A process for producing a carbon foam heat sink is disclosed which obviates the need for conventional oxidative stabilization. The process employs mesophase or isotropic pitch and a simplified process using a single mold. The foam has a relatively uniform distribution of pore sizes and a highly aligned graphic structure in the struts. The foam material can be made into a composite which is useful in high temperature sandwich panels for both thermal and structural applications. The foam is encased and filled with a phase change material to provide a very efficient heat sink device.

LABVIEW graphical user interface for precision multichannel alignment of Raman lidar at Jet Propulsion Laboratory, Table Mountain Facility.

PubMed

Aspey, R A; McDermid, I S; Leblanc, T; Howe, J W; Walsh, T D

2008-09-01

The Jet Propulsion Laboratory operates lidar systems at Table Mountain Facility (TMF), California (34.4 degrees N, 117.7 degrees W) and Mauna Loa Observatory, Hawaii (19.5 degrees N, 155.6 degrees W) under the framework of the Network for the Detection of Atmospheric Composition Change. To complement these systems a new Raman lidar has been developed at TMF with particular attention given to optimizing water vapor profile measurements up to the tropopause and lower stratosphere. The lidar has been designed for accuracies of 5% up to 12 km in the free troposphere and a detection capability of <5 ppmv. One important feature of the lidar is a precision alignment system using range resolved data from eight Licel transient recorders, allowing fully configurable alignment via a LABVIEW/C++ graphical user interface (GUI). This allows the lidar to be aligned on any channel while simultaneously displaying signals from other channels at configurable altitude/bin combinations. The general lidar instrumental setup and the details of the alignment control system, data acquisition, and GUI alignment software are described. Preliminary validation results using radiosonde and lidar intercomparisons are briefly presented.

Aligning the unalignable: bacteriophage whole genome alignments.

PubMed

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

2016-01-13

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

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

PubMed

Tajima, K

1988-11-01

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

PDBFlex: exploring flexibility in protein structures

PubMed Central

Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya; Rotkiewicz, Piotr; Jaroszewski, Lukasz; Godzik, Adam

2016-01-01

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. PMID:26615193

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

PubMed

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

2011-05-20

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

Automated Ontology Alignment with Fuselets for Community of Interest (COI) Integration

DTIC Science & Technology

2008-09-01

Search Example ............................................................................... 22 Figure 8 - Federated Search Example Revisited...integrating information from various sources through a single query. This is the traditional federated search problem, where the sources don’t...Figure 7 - Federated Search Example For the data sources in the graphic above, the ontologies align in a fairly straightforward manner

Sequence Similarity Presenter: a tool for the graphic display of similarities of long sequences for use in presentations.

PubMed

Fröhlich, K U

1994-04-01

A new method for the presentation of alignments of long sequences is described. The degree of identity for the aligned sequences is averaged for sections of a fixed number of residues. The resulting values are converted to shades of gray, with white corresponding to lack of identity and black corresponding to perfect identity. A sequence alignment is represented as a bar filled with varying shades of gray. The display is compact and allows for a fast and intuitive recognition of the distribution of regions with a high similarity. It is well suited for the presentation of alignments of long sequences, e.g. of protein superfamilies, in plenary lectures. The method is implemented as a HyperCard stack for Apple Macintosh computers. Several options for the modification of the output are available (e.g. background reduction, size of the summation window, consideration of amino acid similarity, inclusion of graphic markers to indicate specific domains). The output is a PostScript file which can be printed, imported as EPS or processed further with Adobe Illustrator.

An MHD Code for the Study of Magnetic Structures in the Solar Wind

NASA Technical Reports Server (NTRS)

Allred, J. C.; MacNeice, P. J.

2015-01-01

We have developed a 2.5D MHD code designed to study how the solar wind influences the evolution of transient events in the solar corona and inner heliosphere. The code includes thermal conduction, coronal heating and radiative cooling. Thermal conduction is assumed to be magnetic field-aligned in the inner corona and transitions to a collisionless formulation in the outer corona. We have developed a stable method to handle field-aligned conduction around magnetic null points. The inner boundary is placed in the upper transition region, and the mass flux across the boundary is determined from 1D field-aligned characteristics and a 'radiative energy balance' condition. The 2.5D nature of this code makes it ideal for parameter studies not yet possible with 3D codes. We have made this code publicly available as a tool for the community. To this end we have developed a graphical interface to aid in the selection of appropriate options and a graphical interface that can process and visualize the data produced by the simulation. As an example, we show a simulation of a dipole field stretched into a helmet streamer by the solar wind. Plasmoids periodically erupt from the streamer, and we perform a parameter study of how the frequency and location of these eruptions changed in response to different levels of coronal heating. As a further example, we show the solar wind stretching a compact multi-polar flux system. This flux system will be used to study breakout coronal mass ejections in the presence of the solar wind.

An image guidance system for positioning robotic cochlear implant insertion tools

NASA Astrophysics Data System (ADS)

Bruns, Trevor L.; Webster, Robert J.

2017-03-01

Cochlear implants must be inserted carefully to avoid damaging the delicate anatomical structures of the inner ear. This has motivated several approaches to improve the safety and efficacy of electrode array insertion by automating the process with specialized robotic or manual insertion tools. When such tools are used, they must be positioned at the entry point to the cochlea and aligned with the desired entry vector. This paper presents an image guidance system capable of accurately positioning a cochlear implant insertion tool. An optical tracking system localizes the insertion tool in physical space while a graphical user interface incorporates this with patient- specific anatomical data to provide error information to the surgeon in real-time. Guided by this interface, novice users successfully aligned the tool with an mean accuracy of 0.31 mm.

Structure-based Markov random field model for representing evolutionary constraints on functional sites.

PubMed

Jeong, Chan-Seok; Kim, Dongsup

2016-02-24

Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.

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

PubMed

Eernisse, D J

1992-04-01

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

Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System.

PubMed

Liu, Yu; Hong, Yang; Lin, Chun-Yuan; Hung, Che-Lun

2015-01-01

The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively.

Reduced graphene oxide and vertically aligned carbon nanotubes superhydrophilic films for supercapacitors devices

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

Zanin, H., E-mail: hudsonzanin@gmail.com; Departamento de Semicondutores, Instrumentos e Fotônica, Faculdade de Engenharia Elétrica e Computação, Universidade Estadual de Campinas, UNICAMP, Campinas 13083-970; Saito, E., E-mail: esaito135@gmail.com

2014-01-01

Graphical abstract: - Highlights: • Graphene nanosheets were produced onto wire rods. • RGO and VACNT-O were evaluated and compared as supercapacitor electrode. • RGO and VACNT-O have structural and electrochemical properties quite similars. • The materials present good specific capacitance, energy storage and power delivery. - Abstract: Reduced graphene oxide (RGO) and vertically aligned carbon nanotubes (VACNT) superhydrophilic films were prepared by chemical vapor deposition techniques for electrical energy storage investigations. These electrodes were characterized in terms of their material and electrochemical properties by scanning electron microscopy (SEM), surface wettability, Fourier transform infrared spectroscopy (FTIR), energy dispersive and Ramanmore » spectroscopies, cyclic voltammetry (CV) and galvanostatic charge–discharge. We observed several physical structural and electrochemical similarities between these carbon-based materials with particular attention to very good specific capacitance, ultra-high energy storage and fast power delivery. Our results showed that the main difference between specific capacitance values is attributed to pseudocapacitive contribution and high density of multiwall nanotubes tips. In this work we have tested a supercapacitor device using the VACNT electrodes.« less

Estimating Relative Positions of Outer-Space Structures

NASA Technical Reports Server (NTRS)

Balian, Harry; Breckenridge, William; Brugarolas, Paul

2009-01-01

A computer program estimates the relative position and orientation of two structures from measurements, made by use of electronic cameras and laser range finders on one structure, of distances and angular positions of fiducial objects on the other structure. The program was written specifically for use in determining errors in the alignment of large structures deployed in outer space from a space shuttle. The program is based partly on equations for transformations among the various coordinate systems involved in the measurements and on equations that account for errors in the transformation operators. It computes a least-squares estimate of the relative position and orientation. Sequential least-squares estimates, acquired at a measurement rate of 4 Hz, are averaged by passing them through a fourth-order Butterworth filter. The program is executed in a computer aboard the space shuttle, and its position and orientation estimates are displayed to astronauts on a graphical user interface.

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

PubMed Central

Manavski, Svetlin A; Valle, Giorgio

2008-01-01

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

The UCSC genome browser and associated tools

PubMed Central

Haussler, David; Kent, W. James

2013-01-01

The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting. PMID:22908213

The UCSC genome browser and associated tools.

PubMed

Kuhn, Robert M; Haussler, David; Kent, W James

2013-03-01

The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting.

Parametric inference for biological sequence analysis.

PubMed

Pachter, Lior; Sturmfels, Bernd

2004-11-16

One of the major successes in computational biology has been the unification, by using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied to these problems include hidden Markov models for annotation, tree models for phylogenetics, and pair hidden Markov models for alignment. A single algorithm, the sum-product algorithm, solves many of the inference problems that are associated with different statistical models. This article introduces the polytope propagation algorithm for computing the Newton polytope of an observation from a graphical model. This algorithm is a geometric version of the sum-product algorithm and is used to analyze the parametric behavior of maximum a posteriori inference calculations for graphical models.

Learning Layouts for Single-Page Graphic Designs.

PubMed

O'Donovan, Peter; Agarwala, Aseem; Hertzmann, Aaron

2014-08-01

This paper presents an approach for automatically creating graphic design layouts using a new energy-based model derived from design principles. The model includes several new algorithms for analyzing graphic designs, including the prediction of perceived importance, alignment detection, and hierarchical segmentation. Given the model, we use optimization to synthesize new layouts for a variety of single-page graphic designs. Model parameters are learned with Nonlinear Inverse Optimization (NIO) from a small number of example layouts. To demonstrate our approach, we show results for applications including generating design layouts in various styles, retargeting designs to new sizes, and improving existing designs. We also compare our automatic results with designs created using crowdsourcing and show that our approach performs slightly better than novice designers.

Brain maps 4.0—Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps

PubMed Central

2018-01-01

Abstract The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to “Google Maps” for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3‐D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. PMID:29277900

MICA: Multiple interval-based curve alignment

NASA Astrophysics Data System (ADS)

Mann, Martin; Kahle, Hans-Peter; Beck, Matthias; Bender, Bela Johannes; Spiecker, Heinrich; Backofen, Rolf

2018-01-01

MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments. Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data. The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA

An Overview of the National Shipbuilding Industrial Base,

DTIC Science & Technology

1982-04-01

increased use of modular construction. In the near future, laser welding and alignment, plasma cutting, air-cushion and water bearing materials handling...of computer graphics for design and lofting, laser alignment and welding , and robotization also will be adoptable by shipyards in the near future...introduced the "roll over" ship construction technique to maximize the use of down-hand welding with smooth production flow; modular construction

Acceleration of the Smith-Waterman algorithm using single and multiple graphics processors

NASA Astrophysics Data System (ADS)

Khajeh-Saeed, Ali; Poole, Stephen; Blair Perot, J.

2010-06-01

Finding regions of similarity between two very long data streams is a computationally intensive problem referred to as sequence alignment. Alignment algorithms must allow for imperfect sequence matching with different starting locations and some gaps and errors between the two data sequences. Perhaps the most well known application of sequence matching is the testing of DNA or protein sequences against genome databases. The Smith-Waterman algorithm is a method for precisely characterizing how well two sequences can be aligned and for determining the optimal alignment of those two sequences. Like many applications in computational science, the Smith-Waterman algorithm is constrained by the memory access speed and can be accelerated significantly by using graphics processors (GPUs) as the compute engine. In this work we show that effective use of the GPU requires a novel reformulation of the Smith-Waterman algorithm. The performance of this new version of the algorithm is demonstrated using the SSCA#1 (Bioinformatics) benchmark running on one GPU and on up to four GPUs executing in parallel. The results indicate that for large problems a single GPU is up to 45 times faster than a CPU for this application, and the parallel implementation shows linear speed up on up to 4 GPUs.

Bioinformatics and molecular modeling in glycobiology

PubMed Central

Schloissnig, Siegfried

2010-01-01

The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed. PMID:20364395

GapBlaster-A Graphical Gap Filler for Prokaryote Genomes.

PubMed

de Sá, Pablo H C G; Miranda, Fábio; Veras, Adonney; de Melo, Diego Magalhães; Soares, Siomar; Pinheiro, Kenny; Guimarães, Luis; Azevedo, Vasco; Silva, Artur; Ramos, Rommel T J

2016-01-01

The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer.

Streamline integration as a method for two-dimensional elliptic grid generation

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

Wiesenberger, M., E-mail: Matthias.Wiesenberger@uibk.ac.at; Held, M.; Einkemmer, L.

We propose a new numerical algorithm to construct a structured numerical elliptic grid of a doubly connected domain. Our method is applicable to domains with boundaries defined by two contour lines of a two-dimensional function. Furthermore, we can adapt any analytically given boundary aligned structured grid, which specifically includes polar and Cartesian grids. The resulting coordinate lines are orthogonal to the boundary. Grid points as well as the elements of the Jacobian matrix can be computed efficiently and up to machine precision. In the simplest case we construct conformal grids, yet with the help of weight functions and monitor metricsmore » we can control the distribution of cells across the domain. Our algorithm is parallelizable and easy to implement with elementary numerical methods. We assess the quality of grids by considering both the distribution of cell sizes and the accuracy of the solution to elliptic problems. Among the tested grids these key properties are best fulfilled by the grid constructed with the monitor metric approach. - Graphical abstract: - Highlights: • Construct structured, elliptic numerical grids with elementary numerical methods. • Align coordinate lines with or make them orthogonal to the domain boundary. • Compute grid points and metric elements up to machine precision. • Control cell distribution by adaption functions or monitor metrics.« less

DROIDS 1.20: A GUI-Based Pipeline for GPU-Accelerated Comparative Protein Dynamics.

PubMed

Babbitt, Gregory A; Mortensen, Jamie S; Coppola, Erin E; Adams, Lily E; Liao, Justin K

2018-03-13

Traditional informatics in comparative genomics work only with static representations of biomolecules (i.e., sequence and structure), thereby ignoring the molecular dynamics (MD) of proteins that define function in the cell. A comparative approach applied to MD would connect this very short timescale process, defined in femtoseconds, to one of the longest in the universe: molecular evolution measured in millions of years. Here, we leverage advances in graphics-processing-unit-accelerated MD simulation software to develop a comparative method of MD analysis and visualization that can be applied to any two homologous Protein Data Bank structures. Our open-source pipeline, DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations), works in conjunction with existing molecular modeling software to convert any Linux gaming personal computer into a "comparative computational microscope" for observing the biophysical effects of mutations and other chemical changes in proteins. DROIDS implements structural alignment and Benjamini-Hochberg-corrected Kolmogorov-Smirnov statistics to compare nanosecond-scale atom bond fluctuations on the protein backbone, color mapping the significant differences identified in protein MD with single-amino-acid resolution. DROIDS is simple to use, incorporating graphical user interface control for Amber16 MD simulations, cpptraj analysis, and the final statistical and visual representations in R graphics and UCSF Chimera. We demonstrate that DROIDS can be utilized to visually investigate molecular evolution and disease-related functional changes in MD due to genetic mutation and epigenetic modification. DROIDS can also be used to potentially investigate binding interactions of pharmaceuticals, toxins, or other biomolecules in a functional evolutionary context as well. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

PubMed Central

Budavari, Tamas; Langmead, Ben; Wheelan, Sarah J.; Salzberg, Steven L.; Szalay, Alexander S.

2015-01-01

When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU) hardware.We followed this approach in implementing a read aligner called Arioc that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found. We then carried out a read-by-read comparison of Arioc’s reported alignments with the alignments found by several leading read aligners. With simulated reads, Arioc has comparable or better accuracy than the other read aligners we tested. With human sequencing reads, Arioc demonstrates significantly greater throughput than the other aligners we evaluated across a wide range of sensitivity settings. The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license. PMID:25780763

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

PubMed

Paleo, Pierre; Pouyet, Emeline; Kieffer, Jérôme

2014-03-01

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

MACSIMS : multiple alignment of complete sequences information management system

PubMed Central

Thompson, Julie D; Muller, Arnaud; Waterhouse, Andrew; Procter, Jim; Barton, Geoffrey J; Plewniak, Frédéric; Poch, Olivier

2006-01-01

Background In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. Results MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. Conclusion MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at . PMID:16792820

Brain maps 4.0-Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps.

PubMed

Swanson, Larry W

2018-04-15

The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to "Google Maps" for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3-D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. © 2018 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

Markov Random Field Based Automatic Image Alignment for ElectronTomography

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

Moussavi, Farshid; Amat, Fernando; Comolli, Luis R.

2007-11-30

Cryo electron tomography (cryo-ET) is the primary method for obtaining 3D reconstructions of intact bacteria, viruses, and complex molecular machines ([7],[2]). It first flash freezes a specimen in a thin layer of ice, and then rotates the ice sheet in a transmission electron microscope (TEM) recording images of different projections through the sample. The resulting images are aligned and then back projected to form the desired 3-D model. The typical resolution of biological electron microscope is on the order of 1 nm per pixel which means that small imprecision in the microscope's stage or lenses can cause large alignment errors.more » To enable a high precision alignment, biologists add a small number of spherical gold beads to the sample before it is frozen. These beads generate high contrast dots in the image that can be tracked across projections. Each gold bead can be seen as a marker with a fixed location in 3D, which provides the reference points to bring all the images to a common frame as in the classical structure from motion problem. A high accuracy alignment is critical to obtain a high resolution tomogram (usually on the order of 5-15nm resolution). While some methods try to automate the task of tracking markers and aligning the images ([8],[4]), they require user intervention if the SNR of the image becomes too low. Unfortunately, cryogenic electron tomography (or cryo-ET) often has poor SNR, since the samples are relatively thick (for TEM) and the restricted electron dose usually results in projections with SNR under 0 dB. This paper shows that formulating this problem as a most-likely estimation task yields an approach that is able to automatically align with high precision cryo-ET datasets using inference in graphical models. This approach has been packaged into a publicly available software called RAPTOR-Robust Alignment and Projection estimation for Tomographic Reconstruction.« less

CHROMA: consensus-based colouring of multiple alignments for publication.

PubMed

Goodstadt, L; Ponting, C P

2001-09-01

CHROMA annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. The package is designed to be flexible and reliable, and has a simple-to-use graphical user interface running under Microsoft Windows. Both the executables and source code for CHROMA running under Windows and Linux (portable command-line only) are freely available at http://www.lg.ndirect.co.uk/chroma. Software enquiries should be directed to CHROMA@lg.ndirect.co.uk.

mcaGUI: microbial community analysis R-Graphical User Interface (GUI).

PubMed

Copeland, Wade K; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schütte, Ursel M E; Zhou, Xia; Williams, Christopher J; Forney, Larry J; Abdo, Zaid

2012-08-15

Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance tables and perform analyses specific to their needs. This GUI provides a flexible modular platform, expandable to include other statistical tools for microbial community analysis in the future. The mcaGUI package and source are freely available as part of Bionconductor at http://www.bioconductor.org/packages/release/bioc/html/mcaGUI.html

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

PubMed Central

Manconi, Andrea; Orro, Alessandro; Manca, Emanuele; Armano, Giuliano; Milanesi, Luciano

2014-01-01

Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads. PMID:24842718

R2R--software to speed the depiction of aesthetic consensus RNA secondary structures.

PubMed

Weinberg, Zasha; Breaker, Ronald R

2011-01-04

With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

Designing stereoscopic information visualization for 3D-TV: What can we can learn from S3D gaming?

NASA Astrophysics Data System (ADS)

Schild, Jonas; Masuch, Maic

2012-03-01

This paper explores graphical design and spatial alignment of visual information and graphical elements into stereoscopically filmed content, e.g. captions, subtitles, and especially more complex elements in 3D-TV productions. The method used is a descriptive analysis of existing computer- and video games that have been adapted for stereoscopic display using semi-automatic rendering techniques (e.g. Nvidia 3D Vision) or games which have been specifically designed for stereoscopic vision. Digital games often feature compelling visual interfaces that combine high usability with creative visual design. We explore selected examples of game interfaces in stereoscopic vision regarding their stereoscopic characteristics, how they draw attention, how we judge effect and comfort and where the interfaces fail. As a result, we propose a list of five aspects which should be considered when designing stereoscopic visual information: explicit information, implicit information, spatial reference, drawing attention, and vertical alignment. We discuss possible consequences, opportunities and challenges for integrating visual information elements into 3D-TV content. This work shall further help to improve current editing systems and identifies a need for future editing systems for 3DTV, e.g., live editing and real-time alignment of visual information into 3D footage.

Japanese MAGSAT Team

NASA Technical Reports Server (NTRS)

Fukushima, N. (Principal Investigator)

1982-01-01

CHRONINT and investigator B tapes as well as CHRONFIN data are being analyzed using a graphical display to illustrate X.Y,Z components as well as their residuals from the MGST (4/81) model. In addition to surveys of the vicinity of Japan, an aerial magnetic survey was conducted around Syowa Station in the Antarctic. Relative data collected by polar orbiting satellites are also being studied. Techniques used to separate external and internal fields from the vector data along the orbital paths; analysis of the frequency of the toroidal current in the equatorial ionosphere; investigation of the sudden storm commencement observed by MAGSAT; determination of the structure of field aligned currents associated with substorms; and calculation of the total electric current passing through the plane encircled by the MAGSAT orbit are discussed.

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

PubMed

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

2014-07-01

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

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

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

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

PubMed

Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

2015-01-01

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

GATA: A graphic alignment tool for comparative sequenceanalysis

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

Nix, David A.; Eisen, Michael B.

2005-01-01

Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dotmore » plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.« less

MMDB: Entrez’s 3D-structure database

PubMed Central

Wang, Yanli; Anderson, John B.; Chen, Jie; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Liebert, Cynthia A.; Madej, Thomas; Marchler, Gabriele H.; Marchler-Bauer, Aron; Panchenko, Anna R.; Shoemaker, Benjamin A.; Song, James S.; Thiessen, Paul A.; Yamashita, Roxanne A.; Bryant, Stephen H.

2002-01-01

Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez’s 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez’s search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez’s Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure. PMID:11752307

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

A Graphical Approach to Quantitative Structural Geology.

ERIC Educational Resources Information Center

De Paor, Declan G.

1986-01-01

Describes how computer graphic methods can be used in teaching structural geology. Describes the design of a graphics workstation for the Apple microcomputer. Includes a listing of commands used with software to plot structures in a digitized form. Argues for the establishment of computer laboratories for structural geology classes. (TW)

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

Wang Shumin; Tian Hongwei; Pei Yanhui

A novel hedgehog-like core/shell structure, consisting of a high density of vertically aligned graphene sheets and a thin graphene shell/a copper core (VGs-GS/CC), has been synthesized via a simple one-step synthesis route using radio-frequency plasma-enhanced chemical vapor deposition (RF-PECVD). Scanning and transmission electron microscopy investigations show that the morphology of this core/shell material could be controlled by deposition time. For a short deposition time, only multilayer graphene shell tightly surrounds the copper particle, while as the deposition time is relative long, graphene sheets extend from the surface of GS/CC. The GS can protect CC particles from oxidation. The growth mechanismmore » for the obtained GS/CC and VGs-GS/CC has been revealed. Compared to VGs, VGs-GS/CC material exhibits a better electron field emission property. This investigation opens a possibility for designing a core/shell structure of different carbon-metal hybrid materials for a wide variety of practical applications. - Graphical abstract: With increasing deposition time, graphene sheets extend from the surface of GS/CC, causing the multilayer graphene encapsulated copper to be converted into vertically aligned graphene sheets-graphene shell/copper core structure. Highlights: Black-Right-Pointing-Pointer A novel hedgehog-like core/shell structure has been synthesized. Black-Right-Pointing-Pointer The structure consists of vertical graphene sheets-graphene shell and copper core. Black-Right-Pointing-Pointer The morphology of VGs-GS/CC can be controlled by choosing a proper deposition time. Black-Right-Pointing-Pointer With increasing deposition time, graphene sheets extend from the surface of GS/CC. Black-Right-Pointing-Pointer VGs-GS/CC exhibits a better electron field emission property as compared with VGs.« less

Fine-tuning structural RNA alignments in the twilight zone.

PubMed

Bremges, Andreas; Schirmer, Stefanie; Giegerich, Robert

2010-04-30

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

Photo-Elicitation: Reflexivity on Method, Analysis, and Graphic Portraits

ERIC Educational Resources Information Center

Richard, Veronica M.; Lahman, Maria K. E.

2015-01-01

In this methodological discussion, the authors detail and reflect on the processes of using photo-elicitation interviewing as a way to align with positive qualitative methodologies, to gain access to participant beliefs and values, and to highlight participant voices through their choices of words and visuals. A review of the literature and an…

Top Ten Reasons To Use InDesign for Scholastic Media.

ERIC Educational Resources Information Center

Communication: Journalism Education Today, 2003

2003-01-01

Explains that Adobe InDesign 2.0 moves desktop to new possibilities because it combines the best of modern graphics techniques. Provides explanations of the following aspects of InDesign: drop shadow; align objects; define styles; type on a path; grids; accessible patterns; gradients; create outlines; indexing; and shows missing point. (PM)

Advanced computer graphic techniques for laser range finder (LRF) simulation

NASA Astrophysics Data System (ADS)

Bedkowski, Janusz; Jankowski, Stanislaw

2008-11-01

This paper show an advanced computer graphic techniques for laser range finder (LRF) simulation. The LRF is the common sensor for unmanned ground vehicle, autonomous mobile robot and security applications. The cost of the measurement system is extremely high, therefore the simulation tool is designed. The simulation gives an opportunity to execute algorithm such as the obstacle avoidance[1], slam for robot localization[2], detection of vegetation and water obstacles in surroundings of the robot chassis[3], LRF measurement in crowd of people[1]. The Axis Aligned Bounding Box (AABB) and alternative technique based on CUDA (NVIDIA Compute Unified Device Architecture) is presented.

LookSeq: a browser-based viewer for deep sequencing data.

PubMed

Manske, Heinrich Magnus; Kwiatkowski, Dominic P

2009-11-01

Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an overview of a genomic region to fine details such as heterogeneity within the sample. A specific problem, particularly if the sample is heterogeneous, is how to depict information about structural variation. LookSeq provides a simple graphical representation of paired sequence reads that is more revealing about potential insertions and deletions than are conventional methods.

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

PubMed

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

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

Novel low-cost 2D/3D switchable autostereoscopic system for notebook computers and other portable devices

NASA Astrophysics Data System (ADS)

Eichenlaub, Jesse B.

1995-03-01

Mounting a lenticular lens in front of a flat panel display is a well known, inexpensive, and easy way to create an autostereoscopic system. Such a lens produces half resolution 3D images because half the pixels on the LCD are seen by the left eye and half by the right eye. This may be acceptable for graphics, but it makes full resolution text, as displayed by common software, nearly unreadable. Very fine alignment tolerances normally preclude the possibility of removing and replacing the lens in order to switch between 2D and 3D applications. Lenticular lens based displays are therefore limited to use as dedicated 3D devices. DTI has devised a technique which removes this limitation, allowing switching between full resolution 2D and half resolution 3D imaging modes. A second element, in the form of a concave lenticular lens array whose shape is exactly the negative of the first lens, is mounted on a hinge so that it can be swung down over the first lens array. When so positioned the two lenses cancel optically, allowing the user to see full resolution 2D for text or numerical applications. The two lenses, having complementary shapes, naturally tend to nestle together and snap into perfect alignment when pressed together--thus obviating any need for user operated alignment mechanisms. This system represents an ideal solution for laptop and notebook computer applications. It was devised to meet the stringent requirements of a laptop computer manufacturer including very compact size, very low cost, little impact on existing manufacturing or assembly procedures, and compatibility with existing full resolution 2D text- oriented software as well as 3D graphics. Similar requirements apply to high and electronic calculators, several models of which now use LCDs for the display of graphics.

Fine-tuning structural RNA alignments in the twilight zone

PubMed Central

2010-01-01

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

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

PubMed Central

Wright, Imogen A.; Travers, Simon A.

2014-01-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Surface and deep structures in graphics comprehension.

PubMed

Schnotz, Wolfgang; Baadte, Christiane

2015-05-01

Comprehension of graphics can be considered as a process of schema-mediated structure mapping from external graphics on internal mental models. Two experiments were conducted to test the hypothesis that graphics possess a perceptible surface structure as well as a semantic deep structure both of which affect mental model construction. The same content was presented to different groups of learners by graphics from different perspectives with different surface structures but the same deep structure. Deep structures were complementary: major features of the learning content in one experiment became minor features in the other experiment, and vice versa. Text was held constant. Participants were asked to read, understand, and memorize the learning material. Furthermore, they were either instructed to process the material from the perspective supported by the graphic or from an alternative perspective, or they received no further instruction. After learning, they were asked to recall the learning content from different perspectives by completing graphs of different formats as accurately as possible. Learners' recall was more accurate if the format of recall was the same as the learning format which indicates surface structure influences. However, participants also showed more accurate recall when they remembered the content from a perspective emphasizing the deep structure, regardless of the graphics format presented before. This included better recall of what they had not seen than of what they really had seen before. That is, deep structure effects overrode surface effects. Depending on context conditions, stimulation of additional cognitive processing by instruction had partially positive and partially negative effects.

Iterative refinement of structure-based sequence alignments by Seed Extension

PubMed Central

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

2009-01-01

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

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

PubMed

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

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

Optimization of processing parameters on the controlled growth of ZnO nanorod arrays for the performance improvement of solid-state dye-sensitized solar cells

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

Lee, Yi-Mu, E-mail: ymlee@nuu.edu.t; Yang, Hsi-Wen

2011-03-15

High-transparency and high quality ZnO nanorod arrays were grown on the ITO substrates by a two-step chemical bath deposition (CBD) method. The effects of processing parameters including reaction temperature (25-95 {sup o}C) and solution concentration (0.01-0.1 M) on the crystal growth, alignment, optical and electrical properties were systematically investigated. It has been found that these process parameters are critical for the growth, orientation and aspect ratio of the nanorod arrays, showing different structural and optical properties. Experimental results reveal that the hexagonal ZnO nanorod arrays prepared under reaction temperature of 95 {sup o}C and solution concentration of 0.03 M possessmore » highest aspect ratio of {approx}21, and show the well-aligned orientation and optimum optical properties. Moreover the ZnO nanorod arrays based heterojunction electrodes and the solid-state dye-sensitized solar cells (SS-DSSCs) were fabricated with an improved optoelectrical performance. -- Graphical abstract: The ZnO nanorod arrays demonstrate well-alignment, high aspect ratio (L/D{approx}21) and excellent optical transmittance by low-temperature chemical bath deposition (CBD). Display Omitted Research highlights: > Investigate the processing parameters of CBD on the growth of ZnO nanorod arrays. > Optimization of CBD process parameters: 0.03 M solution concentration and reaction temperature of 95 {sup o}C. > The prepared ZnO samples possess well-alignment and high aspect ratio (L/D{approx}21). > An n-ZnO/p-NiO heterojunction: great rectifying behavior and low leakage current. > SS-DSSC has J{sub SC} of 0.31 mA/cm{sup 2} and V{sub OC} of 590 mV, and an improved {eta} of 0.059%.« less

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

PubMed Central

2011-01-01

Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file. PMID:21205310

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

PubMed

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

2005-12-15

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

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

PubMed

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

2015-09-03

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

Implementation of a parallel protein structure alignment service on cloud.

PubMed

Hung, Che-Lun; Lin, Yaw-Ling

2013-01-01

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

Implementation of a Parallel Protein Structure Alignment Service on Cloud

PubMed Central

Hung, Che-Lun; Lin, Yaw-Ling

2013-01-01

Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

Mathematical Self-Efficacy and Understanding: Using Geographic Information Systems to Mediate Urban High School Students' Real-World Problem Solving

ERIC Educational Resources Information Center

DeBay, Dennis J.

2013-01-01

To explore student mathematical self-efficacy and understanding of graphical data, this dissertation examines students solving real-world problems in their neighborhood, mediated by professional urban planning technologies. As states and schools are working on the alignment of the Common Core State Standards for Mathematics (CCSSM), traditional…

Accelerating adaptive inverse distance weighting interpolation algorithm on a graphics processing unit

PubMed Central

Xu, Liangliang; Xu, Nengxiong

2017-01-01

This paper focuses on designing and implementing parallel adaptive inverse distance weighting (AIDW) interpolation algorithms by using the graphics processing unit (GPU). The AIDW is an improved version of the standard IDW, which can adaptively determine the power parameter according to the data points’ spatial distribution pattern and achieve more accurate predictions than those predicted by IDW. In this paper, we first present two versions of the GPU-accelerated AIDW, i.e. the naive version without profiting from the shared memory and the tiled version taking advantage of the shared memory. We also implement the naive version and the tiled version using two data layouts, structure of arrays and array of aligned structures, on both single and double precision. We then evaluate the performance of parallel AIDW by comparing it with its corresponding serial algorithm on three different machines equipped with the GPUs GT730M, M5000 and K40c. The experimental results indicate that: (i) there is no significant difference in the computational efficiency when different data layouts are employed; (ii) the tiled version is always slightly faster than the naive version; and (iii) on single precision the achieved speed-up can be up to 763 (on the GPU M5000), while on double precision the obtained highest speed-up is 197 (on the GPU K40c). To benefit the community, all source code and testing data related to the presented parallel AIDW algorithm are publicly available. PMID:28989754

Accelerating adaptive inverse distance weighting interpolation algorithm on a graphics processing unit.

PubMed

Mei, Gang; Xu, Liangliang; Xu, Nengxiong

2017-09-01

This paper focuses on designing and implementing parallel adaptive inverse distance weighting (AIDW) interpolation algorithms by using the graphics processing unit (GPU). The AIDW is an improved version of the standard IDW, which can adaptively determine the power parameter according to the data points' spatial distribution pattern and achieve more accurate predictions than those predicted by IDW. In this paper, we first present two versions of the GPU-accelerated AIDW, i.e. the naive version without profiting from the shared memory and the tiled version taking advantage of the shared memory. We also implement the naive version and the tiled version using two data layouts, structure of arrays and array of aligned structures, on both single and double precision. We then evaluate the performance of parallel AIDW by comparing it with its corresponding serial algorithm on three different machines equipped with the GPUs GT730M, M5000 and K40c. The experimental results indicate that: (i) there is no significant difference in the computational efficiency when different data layouts are employed; (ii) the tiled version is always slightly faster than the naive version; and (iii) on single precision the achieved speed-up can be up to 763 (on the GPU M5000), while on double precision the obtained highest speed-up is 197 (on the GPU K40c). To benefit the community, all source code and testing data related to the presented parallel AIDW algorithm are publicly available.

Virtual tape measure for the operating microscope: system specifications and performance evaluation.

PubMed

Kim, M Y; Drake, J M; Milgram, P

2000-01-01

The Virtual Tape Measure for the Operating Microscope (VTMOM) was created to assist surgeons in making accurate 3D measurements of anatomical structures seen in the surgical field under the operating microscope. The VTMOM employs augmented reality techniques by combining stereoscopic video images with stereoscopic computer graphics, and functions by relying on an operator's ability to align a 3D graphic pointer, which serves as the end-point of the virtual tape measure, with designated locations on the anatomical structure being measured. The VTMOM was evaluated for its baseline and application performances as well as its application efficacy. Baseline performance was determined by measuring the mean error (bias) and standard deviation of error (imprecision) in measurements of non-anatomical objects. Application performance was determined by comparing the error in measuring the dimensions of aneurysm models with and without the VTMOM. Application efficacy was determined by comparing the error in selecting the appropriate aneurysm clip size with and without the VTMOM. Baseline performance indicated a bias of 0.3 mm and an imprecision of 0.6 mm. Application bias was 3.8 mm and imprecision was 2.8 mm for aneurysm diameter. The VTMOM did not improve aneurysm clip size selection accuracy. The VTMOM is a potentially accurate tool for use under the operating microscope. However, its performance when measuring anatomical objects is highly dependent on complex visual features of the object surfaces. Copyright 2000 Wiley-Liss, Inc.

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

PubMed

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

2013-07-01

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

An interactive graphics system to facilitate finite element structural analysis

NASA Technical Reports Server (NTRS)

Burk, R. C.; Held, F. H.

1973-01-01

The characteristics of an interactive graphics systems to facilitate the finite element method of structural analysis are described. The finite element model analysis consists of three phases: (1) preprocessing (model generation), (2) problem solution, and (3) postprocessing (interpretation of results). The advantages of interactive graphics to finite element structural analysis are defined.

User-Extensible Graphics Using Abstract Structure,

DTIC Science & Technology

1987-08-01

Flex 6 The Algol68 model of the graphical abstract structure 5 The creation of a PictureDefinition 6 The making of a picture from a PictureDefinition 7...data together with the operations that can be performed on that data. i 7! ś I _ § 4, The Alqol68 model of the graphical abstract structure Every

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

PubMed

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

2012-09-01

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.

PubMed

Chiapello, Hélène; Gendrault, Annie; Caron, Christophe; Blum, Jérome; Petit, Marie-Agnès; El Karoui, Meriem

2008-11-27

The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic.

Tips for better visual elements in posters and podium presentations.

PubMed

Zerwic, J J; Grandfield, K; Kavanaugh, K; Berger, B; Graham, L; Mershon, M

2010-08-01

The ability to effectively communicate through posters and podium presentations using appropriate visual content and style is essential for health care educators. To offer suggestions for more effective visual elements of posters and podium presentations. We present the experiences of our multidisciplinary publishing group, whose combined experiences and collaboration have provided us with an understanding of what works and how to achieve success when working on presentations and posters. Many others would offer similar advice, as these guidelines are consistent with effective presentation. FINDINGS/SUGGESTIONS: Certain visual elements should be attended to in any visual presentation: consistency, alignment, contrast and repetition. Presentations should be consistent in font size and type, line spacing, alignment of graphics and text, and size of graphics. All elements should be aligned with at least one other element. Contrasting light background with dark text (and vice versa) helps an audience read the text more easily. Standardized formatting lets viewers know when they are looking at similar things (tables, headings, etc.). Using a minimal number of colors (four at most) helps the audience more easily read text. For podium presentations, have one slide for each minute allotted for speaking. The speaker is also a visual element; one should not allow the audience's view of either the presentation or presenter to be blocked. Making eye contact with the audience also keeps them visually engaged. Health care educators often share information through posters and podium presentations. These tips should help the visual elements of presentations be more effective.

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

PubMed

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

2016-02-01

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

Structural re-alignment in an immunologic surface region of ricin A chain

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

Zemla, A T; Zhou, C E

2007-07-24

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connectingmore » the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.« less

Software Methodology Catalog. Second Edition. Revision

DTIC Science & Technology

1989-03-01

structured design involve characterization of the data flow through graphical representation, identification of the various transform elements, assembling...and graphical diagrams to facilitate communication within the team. The diagrams are consistent with the design language and can be automatically...organization, box structure graphics provide a visual means of client communication. These box structures are used during analysis and design to review

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

PubMed Central

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

2008-01-01

A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu. PMID:18304945

IMAT graphics manual

NASA Technical Reports Server (NTRS)

Stockwell, Alan E.; Cooper, Paul A.

1991-01-01

The Integrated Multidisciplinary Analysis Tool (IMAT) consists of a menu driven executive system coupled with a relational database which links commercial structures, structural dynamics and control codes. The IMAT graphics system, a key element of the software, provides a common interface for storing, retrieving, and displaying graphical information. The IMAT Graphics Manual shows users of commercial analysis codes (MATRIXx, MSC/NASTRAN and I-DEAS) how to use the IMAT graphics system to obtain high quality graphical output using familiar plotting procedures. The manual explains the key features of the IMAT graphics system, illustrates their use with simple step-by-step examples, and provides a reference for users who wish to take advantage of the flexibility of the software to customize their own applications.

Combining 3D structure of real video and synthetic objects

NASA Astrophysics Data System (ADS)

Kim, Man-Bae; Song, Mun-Sup; Kim, Do-Kyoon

1998-04-01

This paper presents a new approach of combining real video and synthetic objects. The purpose of this work is to use the proposed technology in the fields of advanced animation, virtual reality, games, and so forth. Computer graphics has been used in the fields previously mentioned. Recently, some applications have added real video to graphic scenes for the purpose of augmenting the realism that the computer graphics lacks in. This approach called augmented or mixed reality can produce more realistic environment that the entire use of computer graphics. Our approach differs from the virtual reality and augmented reality in the manner that computer- generated graphic objects are combined to 3D structure extracted from monocular image sequences. The extraction of the 3D structure requires the estimation of 3D depth followed by the construction of a height map. Graphic objects are then combined to the height map. The realization of our proposed approach is carried out in the following steps: (1) We derive 3D structure from test image sequences. The extraction of the 3D structure requires the estimation of depth and the construction of a height map. Due to the contents of the test sequence, the height map represents the 3D structure. (2) The height map is modeled by Delaunay triangulation or Bezier surface and each planar surface is texture-mapped. (3) Finally, graphic objects are combined to the height map. Because 3D structure of the height map is already known, Step (3) is easily manipulated. Following this procedure, we produced an animation video demonstrating the combination of the 3D structure and graphic models. Users can navigate the realistic 3D world whose associated image is rendered on the display monitor.

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

PubMed Central

Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

2014-01-01

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.

PubMed

Lajugie, Julien; Fourel, Nicolas; Bouhassira, Eric E

2015-01-01

Parallel visualization of multiple individual human genomes is a complex endeavor that is rapidly gaining importance with the increasing number of personal, phased and cancer genomes that are being generated. It requires the display of variants such as SNPs, indels and structural variants that are unique to specific genomes and the introduction of multiple overlapping gaps in the reference sequence. Here, we describe GenPlay Multi-Genome, an application specifically written to visualize and analyze multiple human genomes in parallel. GenPlay Multi-Genome is ideally suited for the comparison of allele-specific expression and functional genomic data obtained from multiple phased genomes in a graphical interface with access to multiple-track operation. It also allows the analysis of data that have been aligned to custom genomes rather than to a standard reference and can be used as a variant calling format file browser and as a tool to compare different genome assembly, such as hg19 and hg38. GenPlay is available under the GNU public license (GPL-3) from http://genplay.einstein.yu.edu. The source code is available at https://github.com/JulienLajugie/GenPlay. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Femoral articular shape and geometry. A three-dimensional computerized analysis of the knee.

PubMed

Siu, D; Rudan, J; Wevers, H W; Griffiths, P

1996-02-01

An average, three-dimensional anatomic shape and geometry of the distal femur were generated from x-ray computed tomography data of five fresh asymptomatic cadaver knees using AutoCAD (AutoDesk, Sausalito, CA), a computer-aided design and drafting software. Each femur model was graphically repositioned to a standardized orientation using a series of alignment templates and scaled to a nominal size of 85 mm in mediolateral and 73 mm in anteroposterior dimensions. An average generic shape of the distal femur was synthesized by combining these pseudosolid models and reslicing the composite structure at different elevations using clipping and smoothing techniques in interactive computer graphics. The resulting distal femoral geometry was imported into a computer-aided manufacturing system, and anatomic prototypes of the distal femur were produced. Quantitative geometric analyses of the generic femur in the coronal and transverse planes revealed definite condylar camber (3 degrees-6 degrees) and toe-in (8 degrees-10 degrees) with an oblique patellofemoral groove (15 degrees) with respect to the mechanical axis of the femur. In the sagittal plane, each condyle could be approximated by three concatenated circular arcs (anterior, distal, and posterior) with slope continuity and a single arc for the patellofemoral groove. The results of this study may have important implications in future femoral prosthesis design and clinical applications.

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

PubMed

Xu, Duo; Jaber, Yousef; Pavlidis, Pavlos; Gokcumen, Omer

2017-09-26

Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .

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

PubMed

Ibarra, Ignacio L; Melo, Francisco

2010-07-01

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

A new statistical framework to assess structural alignment quality using information compression

PubMed Central

Collier, James H.; Allison, Lloyd; Lesk, Arthur M.; Garcia de la Banda, Maria; Konagurthu, Arun S.

2014-01-01

Motivation: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field. Results: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field. Availability: http://lcb.infotech.monash.edu.au/I-value Contact: arun.konagurthu@monash.edu Supplementary information: Online supplementary data are available at http://lcb.infotech.monash.edu.au/I-value/suppl.html PMID:25161241

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.

PubMed

Wright, Imogen A; Travers, Simon A

2014-07-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Matt: local flexibility aids protein multiple structure alignment.

PubMed

Menke, Matthew; Berger, Bonnie; Cowen, Lenore

2008-01-01

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

A graphically oriented specification language for automatic code generation. GRASP/Ada: A Graphical Representation of Algorithms, Structure, and Processes for Ada, phase 1

NASA Technical Reports Server (NTRS)

Cross, James H., II; Morrison, Kelly I.; May, Charles H., Jr.; Waddel, Kathryn C.

1989-01-01

The first phase of a three-phase effort to develop a new graphically oriented specification language which will facilitate the reverse engineering of Ada source code into graphical representations (GRs) as well as the automatic generation of Ada source code is described. A simplified view of the three phases of Graphical Representations for Algorithms, Structure, and Processes for Ada (GRASP/Ada) with respect to three basic classes of GRs is presented. Phase 1 concentrated on the derivation of an algorithmic diagram, the control structure diagram (CSD) (CRO88a) from Ada source code or Ada PDL. Phase 2 includes the generation of architectural and system level diagrams such as structure charts and data flow diagrams and should result in a requirements specification for a graphically oriented language able to support automatic code generation. Phase 3 will concentrate on the development of a prototype to demonstrate the feasibility of this new specification language.

Electron microscope studies

NASA Astrophysics Data System (ADS)

Crewe, A. V.; Kapp, O. H.

1991-06-01

This year our laboratory has continued to make progress in the design of electron-optical systems, in the study of structure-function relationships of large multi-subunit proteins, in the development of new image processing software and in achieving a workable sub-angstrom STEM. We present an algebraic approach to the symmetrical Einzel (unipotential) lens wherein we simplify the analysis by specifying a field shape that meets some preferred set of boundary or other conditions and then calculate the fields. In a second study we generalize this approach to study of three element electrostatic lenses of which the symmetrical Einzel lens is a particular form. The purpose is to develop a method for assisting in the design of a lens for a particular purpose. In our biological work we study a stable and functional dodecameric complex of globin chains from the hemoglobin of Lumbricus terrestris. This is a complex lacking the 'linker' subunit first imaged in this lab and required for maintenance of the native structure. In addition, we do a complete work-up on the hemoglobin of the marine polychaete Eudistylia vancouverii, demonstrating the presence of a hierarchy of globin complexes. We demonstrate stable field-emission in the sub-angstrom STEM and the preliminary alignment of the beam. We continue our exploration of a algorithms for alignment of sequences of protein and DNA. Our computer facilities now include four second generation RISC workstations and we continue to take increasing advantage of the floating-point and graphical performance of these devices.

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

Crewe, A.V.; Kapp, O.H.

This year our laboratory has continued to make progress in the design of electron-optical systems, in the study of structure-function relationships of large multi-subunit proteins, in the development of new image processing software and in achieving a workable sub-angstrom STEM. We present an algebraic approach to the symmetrical Einzel (unipotential) lens wherein we simplify the analysis by specifying a field shape that meets some preferred set of boundary or other conditions and then calculate the fields. In a second study we generalize this approach to study of three element electrostatic lenses of which the symmetrical Einzel lens is a particularmore » form. The purpose is to develop a method for assisting in the design of a lens for a particular purpose. In our biological work we study a stable and functional dodecameric complex of globin chains from the hemoglobin of Lumbricus terrestris. This is a complex lacking the linker'' subunit first imaged in this lab and required for maintenance of the native structure. In addition, we do a complete work-up on the hemoglobin of the marine polychaete Eudistylia vancouverii demonstrating the presence of a hierarchy of globin complexes. We demonstrate stable field-emission in the sub-angstrom STEM and the preliminary alignment of the beam. We continue our exploration of a algorithms for alignment of sequences of protein and DNA. Our computer facilities now include four second generation RISC workstations and we continue to take increasing advantage of the floating-point and graphical performance of these devices.« less

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

Crewe, A.V.; Kapp, O.H.

This year our laboratory has continued to make progress in the design of electron-optical systems, in the study of structure-function relationships of large multi-subunit proteins, in the development of new image processing software and in achieving a workable sub-angstrom STEM. We present an algebraic approach to the symmetrical Einzel (unipotential) lens wherein we simplify the analysis by specifying a field shape that meets some preferred set of boundary or other conditions and then calculate the fields. In a second study we generalize this approach to study of three element electrostatic lenses of which the symmetrical Einzel lens is a particularmore » form. The purpose is to develop a method for assisting in the design of a lens for a particular purpose. In our biological work we study a stable and functional dodecameric complex of globin chains from the hemoglobin of Lumbricus terrestris. This is a complex lacking the ``linker`` subunit first imaged in this lab and required for maintenance of the native structure. In addition, we do a complete work-up on the hemoglobin of the marine polychaete Eudistylia vancouverii demonstrating the presence of a hierarchy of globin complexes. We demonstrate stable field-emission in the sub-angstrom STEM and the preliminary alignment of the beam. We continue our exploration of a algorithms for alignment of sequences of protein and DNA. Our computer facilities now include four second generation RISC workstations and we continue to take increasing advantage of the floating-point and graphical performance of these devices.« less

Diffraction phase microscopy realized with an automatic digital pinhole

NASA Astrophysics Data System (ADS)

Zheng, Cheng; Zhou, Renjie; Kuang, Cuifang; Zhao, Guangyuan; Zhang, Zhimin; Liu, Xu

2017-12-01

We report a novel approach to diffraction phase microscopy (DPM) with automatic pinhole alignment. The pinhole, which serves as a spatial low-pass filter to generate a uniform reference beam, is made out of a liquid crystal display (LCD) device that allows for electrical control. We have made DPM more accessible to users, while maintaining high phase measurement sensitivity and accuracy, through exploring low cost optical components and replacing the tedious pinhole alignment process with an automatic pinhole optical alignment procedure. Due to its flexibility in modifying the size and shape, this LCD device serves as a universal filter, requiring no future replacement. Moreover, a graphic user interface for real-time phase imaging has been also developed by using a USB CMOS camera. Experimental results of height maps of beads sample and live red blood cells (RBCs) dynamics are also presented, making this system ready for broad adaption to biological imaging and material metrology.

42: DESIGNING A DASHBOARD FOR EVALUATION THE BUSINESS-IT ALIGNMENT STRATEGIES IN HOSPITALS ORGANIZATIONS

PubMed Central

piri, Zakieh; Raef, Behnaz; moftian, Nazila; dehghani, Mohamad; khara, Rouhallah

2017-01-01

Background and aims Business-IT Alignment Evaluation is One of the most important issues that managers should monitor and make decisions about it. Dashboard software combines data and graphical indicators to deliver at-a-glance summaries of information for users to view the state of their business and quickly respond. The aim of this study was to design a dashboard to assess the business-IT alignment strategies for hospitals organizations in Tehran University of Medical Sciences. Methods This is a functional-developmental study. Initially, we searched related databases (PubMed and ProQuest) to determine the key performance indicators of business-IT alignment for selecting the best model for dashboard designing. After selecting the Luftman model, the key indicators were extracted for designing the dashboard model. In the next stage, an electronic questionnaire was designed based on extracted indicators. This questionnaire sends to Hospital managers and IT administrators. Collected data were analyzed by Excel 2015 and displayed in dashboard page. Results The number of key performance indicators was 39. After recognition the technical requirements the dashboard was designed in Excel. The overall business-IT alignment rate in hospitals was 3.12. Amir-aalam hospital has the highest business-IT alignment rate (3.55) and vali-asr hospital has the lowest business-IT alignment rat (2.80). Conclusion Using dashboard software improves the alignment and reduces the time and energy compared with doing this process manually.

The control data "GIRAFFE" system for interactive graphic finite element analysis

NASA Technical Reports Server (NTRS)

Park, S.; Brandon, D. M., Jr.

1975-01-01

The Graphical Interface for Finite Elements (GIRAFFE) general purpose interactive graphics application package was described. This system may be used as a pre/post processor for structural analysis computer programs. It facilitates the operations of creating, editing, or reviewing all the structural input/output data on a graphics terminal in a time-sharing mode of operation. An application program for a simple three-dimensional plate problem was illustrated.

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

PubMed

Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

2014-12-01

Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences. Graphical abstractA molecular fragment cheminformatics roadmap for mesoscopic simulation.

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

PubMed

Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

2018-02-15

Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align/. njyudj@njust.edu.cn or zhng@umich.edu. Supplementary data are available at Bioinformatics online.

Improving ontology matching with propagation strategy and user feedback

NASA Astrophysics Data System (ADS)

Li, Chunhua; Cui, Zhiming; Zhao, Pengpeng; Wu, Jian; Xin, Jie; He, Tianxu

2015-07-01

Markov logic networks which unify probabilistic graphical model and first-order logic provide an excellent framework for ontology matching. The existing approach requires a threshold to produce matching candidates and use a small set of constraints acting as filter to select the final alignments. We introduce novel match propagation strategy to model the influences between potential entity mappings across ontologies, which can help to identify the correct correspondences and produce missed correspondences. The estimation of appropriate threshold is a difficult task. We propose an interactive method for threshold selection through which we obtain an additional measurable improvement. Running experiments on a public dataset has demonstrated the effectiveness of proposed approach in terms of the quality of result alignment.

W-curve alignments for HIV-1 genomic comparisons.

PubMed

Cork, Douglas J; Lembark, Steven; Tovanabutra, Sodsai; Robb, Merlin L; Kim, Jerome H

2010-06-01

The W-curve was originally developed as a graphical visualization technique for viewing DNA and RNA sequences. Its ability to render features of DNA also makes it suitable for computational studies. Its main advantage in this area is utilizing a single-pass algorithm for comparing the sequences. Avoiding recursion during sequence alignments offers advantages for speed and in-process resources. The graphical technique also allows for multiple models of comparison to be used depending on the nucleotide patterns embedded in similar whole genomic sequences. The W-curve approach allows us to compare large numbers of samples quickly. We are currently tuning the algorithm to accommodate quirks specific to HIV-1 genomic sequences so that it can be used to aid in diagnostic and vaccine efforts. Tracking the molecular evolution of the virus has been greatly hampered by gap associated problems predominantly embedded within the envelope gene of the virus. Gaps and hypermutation of the virus slow conventional string based alignments of the whole genome. This paper describes the W-curve algorithm itself, and how we have adapted it for comparison of similar HIV-1 genomes. A treebuilding method is developed with the W-curve that utilizes a novel Cylindrical Coordinate distance method and gap analysis method. HIV-1 C2-V5 env sequence regions from a Mother/Infant cohort study are used in the comparison. The output distance matrix and neighbor results produced by the W-curve are functionally equivalent to those from Clustal for C2-V5 sequences in the mother/infant pairs infected with CRF01_AE. Significant potential exists for utilizing this method in place of conventional string based alignment of HIV-1 genomes, such as Clustal X. With W-curve heuristic alignment, it may be possible to obtain clinically useful results in a short time-short enough to affect clinical choices for acute treatment. A description of the W-curve generation process, including a comparison technique of aligning extremes of the curves to effectively phase-shift them past the HIV-1 gap problem, is presented. Besides yielding similar neighbor-joining phenogram topologies, most Mother and Infant C2-V5 sequences in the cohort pairs geometrically map closest to each other, indicating that W-curve heuristics overcame any gap problem.

The visual framing of graphics when used in preventative health digital news packages: exploring the use of a narrative structure as the message infrastructure.

PubMed

Sontag, Jennah M; Barnes, Spencer R

2017-09-26

Visual framing can improve health-message effectiveness. Narrative structure provides a template needed for determining how to frame visuals to maximise message effectiveness. Participants (N = 190) were assigned to a message condition determined by segments (establisher, initial, peak), graphic (static, animated) and cancer (lung, melanoma). ANOVAs revealed that melanoma was more believable than lung cancer with static graphics at the establisher and peak; narratives were more believable with animated graphics at the peak segment; melanoma elicited greater positive attitudes; graphics in the peak influenced greatest intentions. Animated graphics visually framed to emphasise information at the establisher and peak segments suggest maximum effectiveness.

Sequence Diversity Diagram for comparative analysis of multiple sequence alignments.

PubMed

Sakai, Ryo; Aerts, Jan

2014-01-01

The sequence logo is a graphical representation of a set of aligned sequences, commonly used to depict conservation of amino acid or nucleotide sequences. Although it effectively communicates the amount of information present at every position, this visual representation falls short when the domain task is to compare between two or more sets of aligned sequences. We present a new visual presentation called a Sequence Diversity Diagram and validate our design choices with a case study. Our software was developed using the open-source program called Processing. It loads multiple sequence alignment FASTA files and a configuration file, which can be modified as needed to change the visualization. The redesigned figure improves on the visual comparison of two or more sets, and it additionally encodes information on sequential position conservation. In our case study of the adenylate kinase lid domain, the Sequence Diversity Diagram reveals unexpected patterns and new insights, for example the identification of subgroups within the protein subfamily. Our future work will integrate this visual encoding into interactive visualization tools to support higher level data exploration tasks.

Tips for Better Visual Elements in Posters and Podium Presentations

PubMed Central

Zerwic, JJ; Grandfield, K; Kavanaugh, K; Berger, B; Graham, L; Mershon, M

2010-01-01

Context The ability to effectively communicate through posters and podium presentations using appropriate visual content and style is essential for health care educators. Objectives To offer suggestions for more effective visual elements of posters and podium presentations. Methods We present the experiences of our multidisciplinary publishing group, whose combined experiences and collaboration have provided us with an understanding of what works and how to achieve success when working on presentations and posters. Many others would offer similar advice, as these guidelines are consistent with effective presentation. Findings/Suggestions Certain visual elements should be attended to in any visual presentation: consistency, alignment, contrast and repetition. Presentations should be consistent in font size and type, line spacing, alignment of graphics and text, and size of graphics. All elements should be aligned with at least one other element. Contrasting light background with dark text (and vice versa) helps an audience read the text more easily. Standardized formatting lets viewers know when they are looking at similar things (tables, headings, etc.). Using a minimal number of colors (four at most) helps the audience more easily read text. For podium presentations, have one slide for each minute allotted for speaking. The speaker is also a visual element; one should not allow the audience’s view of either the presentation or presenter to be blocked. Making eye contact with the audience also keeps them visually engaged. Conclusions Health care educators often share information through posters and podium presentations. These tips should help the visual elements of presentations be more effective. PMID:20853236

Assurance Arguments for the Non-Graphically-Inclined: Two Approaches

NASA Technical Reports Server (NTRS)

Heavner, Emily; Holloway, C. Michael

2017-01-01

We introduce and discuss two approaches to presenting assurance arguments. One approach is based on a monograph structure, while the other is based on a tabular structure. In today's research and academic setting, assurance cases often use a graphical notation; however for people who are not graphically inclined, these notations can be difficult to read. This document proposes, outlines, explains, and presents examples of two non-graphical assurance argument notations that may be appropriate for non-graphically-inclined readers and also provide argument writers with freedom to add details and manipulate an argument in multiple ways.

Super miniaturization of film capacitor dielectrics

NASA Technical Reports Server (NTRS)

Lavene, B.

1981-01-01

The alignment of the stable electrical characteristics of film capacitors in the physical dimensions of ceramic and tantalum capacitors are discussed. The reliability of polycarbonate and mylar capacitors are described with respect to their compatibility with military specifications. Graphic illustrations are presented which show electrical and physical comparisons of film, ceramic, and tantalum capacitors. The major focus is on volumetric efficiency, weight reduction, and electrical stability.

Robust Gaussian Graphical Modeling via l1 Penalization

PubMed Central

Sun, Hokeun; Li, Hongzhe

2012-01-01

Summary Gaussian graphical models have been widely used as an effective method for studying the conditional independency structure among genes and for constructing genetic networks. However, gene expression data typically have heavier tails or more outlying observations than the standard Gaussian distribution. Such outliers in gene expression data can lead to wrong inference on the dependency structure among the genes. We propose a l1 penalized estimation procedure for the sparse Gaussian graphical models that is robustified against possible outliers. The likelihood function is weighted according to how the observation is deviated, where the deviation of the observation is measured based on its own likelihood. An efficient computational algorithm based on the coordinate gradient descent method is developed to obtain the minimizer of the negative penalized robustified-likelihood, where nonzero elements of the concentration matrix represents the graphical links among the genes. After the graphical structure is obtained, we re-estimate the positive definite concentration matrix using an iterative proportional fitting algorithm. Through simulations, we demonstrate that the proposed robust method performs much better than the graphical Lasso for the Gaussian graphical models in terms of both graph structure selection and estimation when outliers are present. We apply the robust estimation procedure to an analysis of yeast gene expression data and show that the resulting graph has better biological interpretation than that obtained from the graphical Lasso. PMID:23020775

Understanding of Relation Structures of Graphical Models by Lower Secondary Students

ERIC Educational Resources Information Center

van Buuren, Onne; Heck, André; Ellermeijer, Ton

2016-01-01

A learning path has been developed on system dynamical graphical modelling, integrated into the Dutch lower secondary physics curriculum. As part of the developmental research for this learning path, students' understanding of the relation structures shown in the diagrams of graphical system dynamics based models has been investigated. One of our…

Statistical inference of protein structural alignments using information and compression.

PubMed

Collier, James H; Allison, Lloyd; Lesk, Arthur M; Stuckey, Peter J; Garcia de la Banda, Maria; Konagurthu, Arun S

2017-04-01

Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power-the amount of lossless compression achieved to explain the protein coordinates using that alignment. We have implemented this approach in MMLigner , the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner 's alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Source code, binaries and an interactive web version are available at http://lcb.infotech.monash.edu.au/mmligner . arun.konagurthu@monash.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Interactive computer graphics system for structural sizing and analysis of aircraft structures

NASA Technical Reports Server (NTRS)

Bendavid, D.; Pipano, A.; Raibstein, A.; Somekh, E.

1975-01-01

A computerized system for preliminary sizing and analysis of aircraft wing and fuselage structures was described. The system is based upon repeated application of analytical program modules, which are interactively interfaced and sequence-controlled during the iterative design process with the aid of design-oriented graphics software modules. The entire process is initiated and controlled via low-cost interactive graphics terminals driven by a remote computer in a time-sharing mode.

ElecSus: Extension to arbitrary geometry magneto-optics

NASA Astrophysics Data System (ADS)

Keaveney, James; Adams, Charles S.; Hughes, Ifan G.

2018-03-01

We present a major update to ElecSus, a computer program and underlying model to calculate the electric susceptibility of an alkali-metal atomic vapour. Knowledge of the electric susceptibility of a medium is essential to predict its absorptive and dispersive properties. In this version we implement several changes which significantly extend the range of applications of ElecSus, the most important of which is support for non-axial magnetic fields (i.e. fields which are not aligned with the light propagation axis). Supporting this change requires a much more general approach to light propagation in the system, which we have now implemented. We exemplify many of these new applications by comparing ElecSus to experimental data. In addition, we have developed a graphical user interface front-end which makes the program much more accessible, and have improved on several other minor areas of the program structure.

Interactive computer graphics and its role in control system design of large space structures

NASA Technical Reports Server (NTRS)

Reddy, A. S. S. R.

1985-01-01

This paper attempts to show the relevance of interactive computer graphics in the design of control systems to maintain attitude and shape of large space structures to accomplish the required mission objectives. The typical phases of control system design, starting from the physical model such as modeling the dynamics, modal analysis, and control system design methodology are reviewed and the need of the interactive computer graphics is demonstrated. Typical constituent parts of large space structures such as free-free beams and free-free plates are used to demonstrate the complexity of the control system design and the effectiveness of the interactive computer graphics.

Well-aligned polycrystalline lanthanum silicate oxyapatite grown by reactive diffusion between solid La{sub 2}SiO{sub 5} and gases [SiO+1/2O{sub 2}

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

Fukuda, Koichiro, E-mail: fukuda.koichiro@nitech.ac.jp; Hasegawa, Ryo; Kitagawa, Takuya

2016-03-15

The c-axis-oriented polycrystalline lanthanum silicate oxyapatite, La{sub 9.48}(Si{sub 5.89}□{sub 0.11})O{sub 26} (□ denotes a vacancy in the Si site), was successfully prepared by the reactive diffusion between randomly grain-oriented La{sub 2}SiO{sub 5} polycrystal and [SiO+1/2O{sub 2}] gases at 1873 K in Ar atmosphere. The polycrystal was characterized using optical microscopy, scanning electron microscopy equipped with energy dispersive X-ray spectroscopy, micro-Raman spectroscopy, X-ray diffractometry, and impedance spectroscopy. The crystal structure (space group P6{sub 3}/m) showed the deficiency of Si site at ca. 1.9%. The bulk oxide-ion conductivity along the grain-alignment direction steadily increased from 9.2 × 10{sup −3} to 1.17 ×more » 10{sup −2} S/cm with increasing temperature from 923 to 1073 K. The activation energy of conduction was 0.23(2) eV. - Graphical abstract: We have successfully prepared the highly c-axis-oriented polycrystalline La{sub 9.48}(Si{sub 5.89}□{sub 0.11})O{sub 26} by the reactive diffusion between randomly grain-oriented La{sub 2}SiO{sub 5} polycrystal and [SiO + 1/2O{sub 2}] gases at 1873 K in Ar atmosphere. The crystal structure (space group P6{sub 3}/m) showed the deficiency of Si site of ca. 1.9%. - Highlights: • The c-axis-oriented polycrystalline La{sub 9.48}(Si{sub 5.89}□{sub 0.11})O{sub 26} is successfully prepared. • Crystal structure of La{sub 9.48}(Si{sub 5.89}□{sub 0.11})O{sub 26} is determined by single-crystal XRD. • The polycrystal shows relatively high oxide ion conductivity along the common c-axis. • Reactive diffusion is successfully used for the preparation of grain-aligned ceramics.« less

Graphic Display of Larger Sentence Dependency Structures.

ERIC Educational Resources Information Center

Craven, Timothy C.

1991-01-01

Outlines desirable qualities for graphic representation of sentence dependency structures in texts more than a few sentences in length. Several different display formats prototyped in the TEXNET experimental text structure management system are described, illustrated, and compared, and automatic structure manipulations are discussed. (36…

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

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

Comparing subjective contours for Kanizsa squares and linear edge alignments ('New York Titanic' figures).

PubMed

Gillam, Barbara; Marlow, Phillip J

2014-01-01

One current view is that subjective contours may involve high-level detection of a salient shape with back propagation to early visual areas where small receptive fields allow for scrutiny of relevant details. This idea applies to Kanizsa-type figures. However, Gillam and Chan (2002 Psychological Science, 13, 279-282) using figures based on Gillam's graphic 'New York Titanic' (Gillam, 1997 Thresholds: Limits of perception. New York: Arts Magazine) showed that strong subjective contours can be seen along the linearly aligned edges of a set of shapes if occlusion cues of 'extrinsic edge' and 'entropy contrast' are strong. Here we compared ratings of the strength of subjective contours along linear alignments with those seen in Kanizsa figures. The strongest subjective contour for a single set of linearly aligned shapes was similar in strength to the edges of a Kanizsa square (controlling for support ratio) despite the lack of a salient region. The addition of a second set of linearly aligned inducers consistent with a common surface increased subjective-contour strength, as did having four rather than two 'pacmen' in the Kanizsa figure, indicating a role for surface support. We argue that linear subjective contours allow for the investigation of certain occlusion cues and the interactions between them that are not easily explored with Kanizsa figures.

enoLOGOS: a versatile web tool for energy normalized sequence logos

PubMed Central

Workman, Christopher T.; Yin, Yutong; Corcoran, David L.; Ideker, Trey; Stormo, Gary D.; Benos, Panayiotis V.

2005-01-01

enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information content in this position. Currently, the available web servers are able to create logo images from a set of aligned sequences, but none of them generates weighted sequence logos directly from energy measurements or other sources. With the advent of high-throughput technologies for estimating the contact energy of different DNA sequences, tools that can create logos directly from binding affinity data are useful to researchers. enoLOGOS generates sequence logos from a variety of input data, including energy measurements, probability matrices, alignment matrices, count matrices and aligned sequences. Furthermore, enoLOGOS can represent the mutual information of different positions of the consensus sequence, a unique feature of this tool. Another web interface for our software, C2H2-enoLOGOS, generates logos for the DNA-binding preferences of the C2H2 zinc-finger transcription factor family members. enoLOGOS and C2H2-enoLOGOS are accessible over the web at . PMID:15980495

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.

PubMed

Sanchez Sorzano, Carlos Oscar; Alvarez-Cabrera, Ana Lucia; Kazemi, Mohsen; Carazo, Jose María; Jonić, Slavica

2016-04-26

Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta

PubMed Central

Kleffner, Robert; Flatten, Jeff; Leaver-Fay, Andrew; Baker, David; Siegel, Justin B.; Khatib, Firas; Cooper, Seth

2017-01-01

Abstract Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements. Foldit Standalone was built from the ground up with a custom rendering and event engine, configurable visualizations and interactions driven by Rosetta. Foldit Standalone contains, among other features: electron density and contact map visualizations, multiple sequence alignment tools for template-based modeling, rigid body transformation controls, RosettaScripts support and an embedded Lua interpreter. Availability and Implementation: Foldit Standalone is available for download at https://fold.it/standalone, under the Rosetta license, which is free for academic and non-profit users. It is implemented in cross-platform C ++ and binary executables are available for Windows, macOS and Linux. Contact: scooper@ccs.neu.edu PMID:28481970

StructAlign, a Program for Alignment of Structures of DNA-Protein Complexes.

PubMed

Popov, Ya V; Galitsyna, A A; Alexeevski, A V; Karyagina, A S; Spirin, S A

2015-11-01

Comparative analysis of structures of complexes of homologous proteins with DNA is important in the analysis of DNA-protein recognition. Alignment is a necessary stage of the analysis. An alignment is a matching of amino acid residues and nucleotides of one complex to residues and nucleotides of the other. Currently, there are no programs available for aligning structures of DNA-protein complexes. We present the program StructAlign, which should fill this gap. The program inputs a pair of complexes of DNA double helix with proteins and outputs an alignment of DNA chains corresponding to the best spatial fit of the protein chains.

Typography for Graphic Communication [and] Typographic Access Structures for Educational Texts [and] Graphic Aspects of Complex Texts: Typography as Macropunctuation.

ERIC Educational Resources Information Center

Waller, Robert

The three papers included in this report address typography for graphic communication, typographic access structures for educational texts, and typography as macropunctuation. The first paper considers the consequences of an aesthetic bias in the literature of typography, and identifies two misleading assumptions about textbooks; i.e., that print…

Silicon Graphics' IRIS InSight: An SGML Success Story.

ERIC Educational Resources Information Center

Glushko, Robert J.; Kershner, Ken

1993-01-01

Offers a case history of the development of the Silicon Graphics "IRIS InSight" system, a system for viewing on-line documentation using Standard Generalized Markup Language. Notes that SGML's explicit encoding of structure and separation of structure and presentation make possible structure-based search, alternative structural views of…

Iterative non-sequential protein structural alignment.

PubMed

Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

2009-06-01

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

Missing Data and Influential Sites: Choice of Sites for Phylogenetic Analysis Can Be As Important As Taxon Sampling and Model Choice

PubMed Central

Shavit Grievink, Liat; Penny, David; Holland, Barbara R.

2013-01-01

Phylogenetic studies based on molecular sequence alignments are expected to become more accurate as the number of sites in the alignments increases. With the advent of genomic-scale data, where alignments have very large numbers of sites, bootstrap values close to 100% and posterior probabilities close to 1 are the norm, suggesting that the number of sites is now seldom a limiting factor on phylogenetic accuracy. This provokes the question, should we be fussy about the sites we choose to include in a genomic-scale phylogenetic analysis? If some sites contain missing data, ambiguous character states, or gaps, then why not just throw them away before conducting the phylogenetic analysis? Indeed, this is exactly the approach taken in many phylogenetic studies. Here, we present an example where the decision on how to treat sites with missing data is of equal importance to decisions on taxon sampling and model choice, and we introduce a graphical method for illustrating this. PMID:23471508

Design and implementation of a hybrid MPI-CUDA model for the Smith-Waterman algorithm.

PubMed

Khaled, Heba; Faheem, Hossam El Deen Mostafa; El Gohary, Rania

2015-01-01

This paper provides a novel hybrid model for solving the multiple pair-wise sequence alignment problem combining message passing interface and CUDA, the parallel computing platform and programming model invented by NVIDIA. The proposed model targets homogeneous cluster nodes equipped with similar Graphical Processing Unit (GPU) cards. The model consists of the Master Node Dispatcher (MND) and the Worker GPU Nodes (WGN). The MND distributes the workload among the cluster working nodes and then aggregates the results. The WGN performs the multiple pair-wise sequence alignments using the Smith-Waterman algorithm. We also propose a modified implementation to the Smith-Waterman algorithm based on computing the alignment matrices row-wise. The experimental results demonstrate a considerable reduction in the running time by increasing the number of the working GPU nodes. The proposed model achieved a performance of about 12 Giga cell updates per second when we tested against the SWISS-PROT protein knowledge base running on four nodes.

Interactive navigation system for shock wave applications.

PubMed

Hagelauer, U; Russo, S; Gigliotti, S; de Durante, C; Corrado, E M

2001-01-01

The latest generation of shock wave lithotripters, with therapy heads mounted on articulated arms, have found widespread application in the treatment of orthopedic diseases. Currently, integration of an ultrasound probe in the therapy head is the dominant modality for positioning the shock wave focus on the treatment area. For orthopedic applications, however, X-ray imaging is often preferred. This article describes a new method to locate the therapy head of a lithotripter. In the first step, the surgeon positions the tissue to be treated at the isocenter of a C-arc. This is achieved using AP and 30-degree lateral projections, with corresponding horizontal and vertical movements of the patient under fluoroscopic guidance. These movements register the anatomic location in the coordinate system of the C-arc. In the second step, the therapy head is navigated to align the shock wave focus with the isocenter. Position data are reported from an optical tracker mounted on the X-ray system, which tracks an array of infrared LEDs on the therapy head. The accuracy of the tracking system was determined on a test bench, and was calculated to be 1.55 mm (RMS) for an angular movement of +/-15 degrees around a calibrated position. Free-hand navigation and precise alignment are performed with a single virtual reality display. The display is calculated by a computer system in real time, and uses graphical symbols to represent the shock wave path and isocenter. In an interactive process, the physician observes the display while navigating the therapy head towards the isocenter. Precise alignment is achieved by displaying an enlarged view of the intersecting graphical symbols. Results from the first tests on 100 patients demonstrate the feasibility of this approach in a clinical environment. Copyright 2001 Wiley-Liss, Inc.

Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment.

PubMed

Cao, Hu; Lu, Yonggang

2017-01-01

With the rapid growth of known protein 3D structures in number, how to efficiently compare protein structures becomes an essential and challenging problem in computational structural biology. At present, many protein structure alignment methods have been developed. Among all these methods, flexible structure alignment methods are shown to be superior to rigid structure alignment methods in identifying structure similarities between proteins, which have gone through conformational changes. It is also found that the methods based on aligned fragment pairs (AFPs) have a special advantage over other approaches in balancing global structure similarities and local structure similarities. Accordingly, we propose a new flexible protein structure alignment method based on variable-length AFPs. Compared with other methods, the proposed method possesses three main advantages. First, it is based on variable-length AFPs. The length of each AFP is separately determined to maximally represent a local similar structure fragment, which reduces the number of AFPs. Second, it uses local coordinate systems, which simplify the computation at each step of the expansion of AFPs during the AFP identification. Third, it decreases the number of twists by rewarding the situation where nonconsecutive AFPs share the same transformation in the alignment, which is realized by dynamic programming with an improved transition function. The experimental data show that compared with FlexProt, FATCAT, and FlexSnap, the proposed method can achieve comparable results by introducing fewer twists. Meanwhile, it can generate results similar to those of the FATCAT method in much less running time due to the reduced number of AFPs.

Accelerated probabilistic inference of RNA structure evolution

PubMed Central

Holmes, Ian

2005-01-01

Background Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. Results We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs) is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. Conclusion A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License. PMID:15790387

PASS2: an automated database of protein alignments organised as structural superfamilies.

PubMed

Bhaduri, Anirban; Pugalenthi, Ganesan; Sowdhamini, Ramanathan

2004-04-02

The functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The Protein Alignment organised as Structural Superfamily (PASS2) database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. An automated and updated version of PASS2 is, in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains have been grouped into 628 multi-member superfamilies and 566 single member superfamilies. Structure-based sequence alignments for the superfamilies have been obtained using COMPARER, while initial equivalencies have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aid annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 presents the phylogeny of its members both based on sequence and structural dissimilarities. Clustering of members allows us to understand diversification of the family members. The search engine has been improved for simpler browsing of the database. The database resolves alignments among the structural domains consisting of evolutionarily diverged set of sequences. Availability of reliable sequence alignments of distantly related proteins despite poor sequence identity and single-member superfamilies permit better sampling of structures in libraries for fold recognition of new sequences and for the understanding of protein structure-function relationships of individual superfamilies. PASS2 is accessible at http://www.ncbs.res.in/~faculty/mini/campass/pass2.html

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.

Alignment of dynamic networks.

PubMed

Vijayan, V; Critchlow, D; Milenkovic, T

2017-07-15

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

Alignment of dynamic networks

PubMed Central

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

2017-01-01

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

Overcoming Sequence Misalignments with Weighted Structural Superposition

PubMed Central

Khazanov, Nickolay A.; Damm-Ganamet, Kelly L.; Quang, Daniel X.; Carlson, Heather A.

2012-01-01

An appropriate structural superposition identifies similarities and differences between homologous proteins that are not evident from sequence alignments alone. We have coupled our Gaussian-weighted RMSD (wRMSD) tool with a sequence aligner and seed extension (SE) algorithm to create a robust technique for overlaying structures and aligning sequences of homologous proteins (HwRMSD). HwRMSD overcomes errors in the initial sequence alignment that would normally propagate into a standard RMSD overlay. SE can generate a corrected sequence alignment from the improved structural superposition obtained by wRMSD. HwRMSD’s robust performance and its superiority over standard RMSD are demonstrated over a range of homologous proteins. Its better overlay results in corrected sequence alignments with good agreement to HOMSTRAD. Finally, HwRMSD is compared to established structural alignment methods: FATCAT, SSM, CE, and Dalilite. Most methods are comparable at placing residue pairs within 2 Å, but HwRMSD places many more residue pairs within 1 Å, providing a clear advantage. Such high accuracy is essential in drug design, where small distances can have a large impact on computational predictions. This level of accuracy is also needed to correct sequence alignments in an automated fashion, especially for omics-scale analysis. HwRMSD can align homologs with low sequence identity and large conformational differences, cases where both sequence-based and structural-based methods may fail. The HwRMSD pipeline overcomes the dependency of structural overlays on initial sequence pairing and removes the need to determine the best sequence-alignment method, substitution matrix, and gap parameters for each unique pair of homologs. PMID:22733542

Relational, Structural, and Semantic Analysis of Graphical Representations and Concept Maps

ERIC Educational Resources Information Center

Ifenthaler, Dirk

2010-01-01

The demand for good instructional environments presupposes valid and reliable analytical instruments for educational research. This paper introduces the "SMD Technology" (Surface, Matching, Deep Structure), which measures relational, structural, and semantic levels of graphical representations and concept maps. The reliability and validity of the…

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

PubMed Central

2007-01-01

Background Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ constraints that reduce computation by restricting the alignments and/or structures (i.e. folds) that are permissible. In this paper, a new methodology is presented for the purpose of establishing alignment constraints based on nucleotide alignment and insertion posterior probabilities. Using a hidden Markov model, posterior probabilities of alignment and insertion are computed for all possible pairings of nucleotide positions from the two sequences. These alignment and insertion posterior probabilities are additively combined to obtain probabilities of co-incidence for nucleotide position pairs. A suitable alignment constraint is obtained by thresholding the co-incidence probabilities. The constraint is integrated with Dynalign, a free energy minimization algorithm for joint alignment and secondary structure prediction. The resulting method is benchmarked against the previous version of Dynalign and against other programs for pairwise RNA structure prediction. Results The proposed technique eliminates manual parameter selection in Dynalign and provides significant computational time savings in comparison to prior constraints in Dynalign while simultaneously providing a small improvement in the structural prediction accuracy. Savings are also realized in memory. In experiments over a 5S RNA dataset with average sequence length of approximately 120 nucleotides, the method reduces computation by a factor of 2. The method performs favorably in comparison to other programs for pairwise RNA structure prediction: yielding better accuracy, on average, and requiring significantly lesser computational resources. Conclusion Probabilistic analysis can be utilized in order to automate the determination of alignment constraints for pairwise RNA structure prediction methods in a principled fashion. These constraints can reduce the computational and memory requirements of these methods while maintaining or improving their accuracy of structural prediction. This extends the practical reach of these methods to longer length sequences. The revised Dynalign code is freely available for download. PMID:17445273

GuiTope: an application for mapping random-sequence peptides to protein sequences.

PubMed

Halperin, Rebecca F; Stafford, Phillip; Emery, Jack S; Navalkar, Krupa Arun; Johnston, Stephen Albert

2012-01-03

Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC) at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

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

PubMed Central

Castaño-Díez, Daniel

2017-01-01

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

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

PubMed

Castaño-Díez, Daniel

2017-06-01

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

GRASP/Ada: Graphical Representations of Algorithms, Structures, and Processes for Ada. The development of a program analysis environment for Ada: Reverse engineering tools for Ada, task 2, phase 3

NASA Technical Reports Server (NTRS)

Cross, James H., II

1991-01-01

The main objective is the investigation, formulation, and generation of graphical representations of algorithms, structures, and processes for Ada (GRASP/Ada). The presented task, in which various graphical representations that can be extracted or generated from source code are described and categorized, is focused on reverse engineering. The following subject areas are covered: the system model; control structure diagram generator; object oriented design diagram generator; user interface; and the GRASP library.

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

PubMed Central

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results. PMID:27493524

An Overview of Psycholinguistic Reading Theory.

ERIC Educational Resources Information Center

Hayes, Christopher G.

In the most adequate psycholinguistic model of the reading process the proficient silent reader decodes directly from graphic surface structure into deep structure, with no decoding into oral surface structure. Three cue systems used by all proficient readers include graphic cues (letters and words), syntactic cues (the grammatical arrangement of…

World Wide Web Page Design: A Structured Approach.

ERIC Educational Resources Information Center

Gregory, Gwen; Brown, M. Marlo

1997-01-01

Describes how to develop a World Wide Web site based on structured programming concepts. Highlights include flowcharting, first page design, evaluation, page titles, documenting source code, text, graphics, and browsers. Includes a template for HTML writers, tips for using graphics, a sample homepage, guidelines for authoring structured HTML, and…

NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.

PubMed

Nielsen, Morten; Andreatta, Massimo

2017-07-03

Peptides are extensively used to characterize functional or (linear) structural aspects of receptor-ligand interactions in biological systems, e.g. SH2, SH3, PDZ peptide-recognition domains, the MHC membrane receptors and enzymes such as kinases and phosphatases. NNAlign is a method for the identification of such linear motifs in biological sequences. The algorithm aligns the amino acid or nucleotide sequences provided as training set, and generates a model of the sequence motif detected in the data. The webserver allows setting up cross-validation experiments to estimate the performance of the model, as well as evaluations on independent data. Many features of the training sequences can be encoded as input, and the network architecture is highly customizable. The results returned by the server include a graphical representation of the motif identified by the method, performance values and a downloadable model that can be applied to scan protein sequences for occurrence of the motif. While its performance for the characterization of peptide-MHC interactions is widely documented, we extended NNAlign to be applicable to other receptor-ligand systems as well. Version 2.0 supports alignments with insertions and deletions, encoding of receptor pseudo-sequences, and custom alphabets for the training sequences. The server is available at http://www.cbs.dtu.dk/services/NNAlign-2.0. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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…

Vertically aligned nanostructure scanning probe microscope tips

DOEpatents

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

2006-12-19

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

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

PubMed

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

2013-09-01

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

A general graphical user interface for automatic reliability modeling

NASA Technical Reports Server (NTRS)

Liceaga, Carlos A.; Siewiorek, Daniel P.

1991-01-01

Reported here is a general Graphical User Interface (GUI) for automatic reliability modeling of Processor Memory Switch (PMS) structures using a Markov model. This GUI is based on a hierarchy of windows. One window has graphical editing capabilities for specifying the system's communication structure, hierarchy, reconfiguration capabilities, and requirements. Other windows have field texts, popup menus, and buttons for specifying parameters and selecting actions. An example application of the GUI is given.

Condensed Representation of Sentences in Graphic Displays of Text Structures.

ERIC Educational Resources Information Center

Craven, Timothy C.

1990-01-01

Discusses ways in which sentences may be represented in a condensed form in graphic displays of a sentence dependency structure. A prototype of a text structure management system, TEXNET, is described; a quantitative evaluation of automatic abbreviation schemes is presented; full-text compression is discussed; and additional research is suggested.…

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

PubMed

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

2006-08-15

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

MultiSETTER: web server for multiple RNA structure comparison.

PubMed

Čech, Petr; Hoksza, David; Svozil, Daniel

2015-08-12

Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

Writing English Script: An Overlooked Skill.

ERIC Educational Resources Information Center

Ball, Wendy E.

1986-01-01

An important component of second language programs is the skill of understanding and using the graphic structure of language involved. Inadequate handwriting, poor layout, and difficulties in reading are primary symptoms of students with a weak grasp of the graphic structure. (CB)

Information Technology (IT) Strategic Alignment: A Correlational Study between the Impact of IT Governance Structures and IT Strategic Alignment

ERIC Educational Resources Information Center

Asante, Keith K.

2010-01-01

This dissertation explored the extent to which Information Technology (IT) strategic alignment are impacted by IT governance structures. The study discusses several strategic alignment and IT governance literature that presents a gap in the literature domain. Subsequent studies researched issues surrounding why organizations are not able to align…

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

Lee, Sangkyu; Park, Hun; Paik, Ungyu

We have discovered a methodology to realize the fabrication of flexible metal oxide film using two-dimensional (2D) nanosheets. Atomic scale titanium oxide (TiO{sub x}) nanosheets were exfoliated from bulk TiO{sub x} powder that had a layered structure via the modified Sasaki’s method. The vacuum-assisted filtration generates films with laterally aligned TiO{sub x} nanosheets. The 2D sheet-like structure and hydrophilic nature of TiO{sub x} nanosheets enables the film consisting of TiO{sub x} nanosheets to be bendable. Also, we demonstrate the fabrication of electrochemical capacitors using this film. The mechanically flexible metal oxide film is expected to open up the possibility ofmore » fabricating flexible energy storage devices from 2D metal oxide nanosheets. - Graphical abstract: The modified Sasaki’s method, combined process of hydrothermal reaction and bulky ion exchange, enables to obtain TiO{sub x} monolayer nanosheets. The vacuum-assisted filtration generates bendable films with laterally aligned TiO{sub x} nanosheets. Also, we demonstrate the fabrication of electrochemical capacitors using this film. - Highlights: • TiO{sub x} single sheets, a novel 2-dimensional material, were exfoliated from bulk powders via the modified Sasaki’s method. • In our method, the acid treatment of TiO{sub x} bulk powders was simply modified by applying the hydrothermal reaction. • Then, the delamination procedures of large cation exchange were conducted following the method proposed by Sasaki et al. • Reassembly of TiO{sub x} sheets into flexible free-standing films was simply achieved via vacuum assisted filtration method. • TiO{sub x} films were used as a flexible supercapaictor electrode material.« less

Visualizing the anatomical-functional correlation of the human brain

NASA Astrophysics Data System (ADS)

Chang, YuKuang; Rockwood, Alyn P.; Reiman, Eric M.

1995-04-01

Three-dimensional tomographic images obtained from different modalities or from the same modality at different times provide complementary information. For example, while PET shows brain function, images from MRI identify anatomical structures. In this paper, we investigate the problem of displaying available information about structures and function together. Several steps are described to achieve our goal. These include segmentation of the data, registration, resampling, and display. Segmentation is used to identify brain tissue from surrounding tissues, especially in the MRI data. Registration aligns the different modalities as closely as possible. Resampling arises from the registration since two data sets do not usually correspond and the rendering method is most easily achieved if the data correspond to the same grid used in display. We combine several techniques to display the data. MRI data is reconstructed from 2D slices into 3D structures from which isosurfaces are extracted and represented by approximating polygonalizations. These are then displayed using standard graphics pipelines including shaded and transparent images. PET data measures the qualitative rates of cerebral glucose utilization or oxygen consumption. PET image is best displayed as a volume of luminous particles. The combination of both display methods allows the viewer to compare the functional information contained in the PET data with the anatomically more precise MRI data.

The Structure of Meaning--A Linguistic Description.

ERIC Educational Resources Information Center

Eisenhardt, Catheryn T.

Just as a reader must bring an experiential conceptual background to the printed page, so must he bring an ability to recognize the graphic cues that signal meaning. The graphic cues or structural meaning works as a system the description of which can be outlined in three parts as the vocabulary, the structure, and the sound. What has been…

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

PubMed Central

2010-01-01

Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid) obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used to reliably detect divergent regions via several scoring methods that provide different levels of selectivity. Its predictions have been verified by experimental means. Hence, it is expected that its usage will save researchers' time and ensure an objective selection of the best-possible divergent region when closely related sequences are analysed. AlignMiner is freely available at http://www.scbi.uma.es/alignminer. PMID:20525162

Structural identifiability of cyclic graphical models of biological networks with latent variables.

PubMed

Wang, Yulin; Lu, Na; Miao, Hongyu

2016-06-13

Graphical models have long been used to describe biological networks for a variety of important tasks such as the determination of key biological parameters, and the structure of graphical model ultimately determines whether such unknown parameters can be unambiguously obtained from experimental observations (i.e., the identifiability problem). Limited by resources or technical capacities, complex biological networks are usually partially observed in experiment, which thus introduces latent variables into the corresponding graphical models. A number of previous studies have tackled the parameter identifiability problem for graphical models such as linear structural equation models (SEMs) with or without latent variables. However, the limited resolution and efficiency of existing approaches necessarily calls for further development of novel structural identifiability analysis algorithms. An efficient structural identifiability analysis algorithm is developed in this study for a broad range of network structures. The proposed method adopts the Wright's path coefficient method to generate identifiability equations in forms of symbolic polynomials, and then converts these symbolic equations to binary matrices (called identifiability matrix). Several matrix operations are introduced for identifiability matrix reduction with system equivalency maintained. Based on the reduced identifiability matrices, the structural identifiability of each parameter is determined. A number of benchmark models are used to verify the validity of the proposed approach. Finally, the network module for influenza A virus replication is employed as a real example to illustrate the application of the proposed approach in practice. The proposed approach can deal with cyclic networks with latent variables. The key advantage is that it intentionally avoids symbolic computation and is thus highly efficient. Also, this method is capable of determining the identifiability of each single parameter and is thus of higher resolution in comparison with many existing approaches. Overall, this study provides a basis for systematic examination and refinement of graphical models of biological networks from the identifiability point of view, and it has a significant potential to be extended to more complex network structures or high-dimensional systems.

Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API.

PubMed

Ytow, Nozomi

2016-01-01

The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF's ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file.

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.

PubMed

Cer, Regina Z; Donohue, Duncan E; Mudunuri, Uma S; Temiz, Nuri A; Loss, Michael A; Starner, Nathan J; Halusa, Goran N; Volfovsky, Natalia; Yi, Ming; Luke, Brian T; Bacolla, Albino; Collins, Jack R; Stephens, Robert M

2013-01-01

The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance.

NUREBASE: database of nuclear hormone receptors.

PubMed

Duarte, Jorge; Perrière, Guy; Laudet, Vincent; Robinson-Rechavi, Marc

2002-01-01

Nuclear hormone receptors are an abundant class of ligand activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature of nuclear receptors, we have developed NUREBASE, a database containing protein and DNA sequences, reviewed protein alignments and phylogenies, taxonomy and annotations for all nuclear receptors. The reviewed NUREBASE is completed by NUREBASE_DAILY, automatically updated every 24 h. Both databases are organized under a client/server architecture, with a client written in Java which runs on any platform. This client, named FamFetch, integrates a graphical interface allowing selection of families, and manipulation of phylogenies and alignments. NUREBASE sequence data is also accessible through a World Wide Web server, allowing complex queries. All information on accessing and installing NUREBASE may be found at http://www.ens-lyon.fr/LBMC/laudet/nurebase.html.

WebLogo: A Sequence Logo Generator

PubMed Central

Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc; Brenner, Steven E.

2004-01-01

WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization. PMID:15173120

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

PubMed

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

2007-07-27

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

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta.

PubMed

Kleffner, Robert; Flatten, Jeff; Leaver-Fay, Andrew; Baker, David; Siegel, Justin B; Khatib, Firas; Cooper, Seth

2017-09-01

Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements. Foldit Standalone was built from the ground up with a custom rendering and event engine, configurable visualizations and interactions driven by Rosetta. Foldit Standalone contains, among other features: electron density and contact map visualizations, multiple sequence alignment tools for template-based modeling, rigid body transformation controls, RosettaScripts support and an embedded Lua interpreter. Foldit Standalone is available for download at https://fold.it/standalone , under the Rosetta license, which is free for academic and non-profit users. It is implemented in cross-platform C ++ and binary executables are available for Windows, macOS and Linux. scooper@ccs.neu.edu. © The Author(s) 2017. Published by Oxford University Press.

The Angular Power Spectrum of BATSE 3B Gamma-Ray Bursts

NASA Technical Reports Server (NTRS)

Tegmark, Max; Hartmann, Dieter H.; Briggs, Michael S.; Meegan, Charles A.

1996-01-01

We compute the angular power spectrum C(sub l) from the BATSE 3B catalog of 1122 gamma-ray bursts and find no evidence for clustering on any scale. These constraints bridge the entire range from small scales (which probe source clustering and burst repetition) to the largest scales (which constrain possible anisotropics from the Galactic halo or from nearby cosmological large-scale structures). We develop an analysis technique that takes the angular position errors into account. For specific clustering or repetition models, strong upper limits can be obtained down to scales l approx. equal to 30, corresponding to a couple of degrees on the sky. The minimum-variance burst weighting that we employ is visualized graphically as an all-sky map in which each burst is smeared out by an amount corresponding to its position uncertainty. We also present separate bandpass-filtered sky maps for the quadrupole term and for the multipole ranges l = 3-10 and l = 11-30, so that the fluctuations on different angular scales can be inspected separately for visual features such as localized 'hot spots' or structures aligned with the Galactic plane. These filtered maps reveal no apparent deviations from isotropy.

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

PubMed

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

2011-04-01

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

Interactive graphical computer-aided design system

NASA Technical Reports Server (NTRS)

Edge, T. M.

1975-01-01

System is used for design, layout, and modification of large-scale-integrated (LSI) metal-oxide semiconductor (MOS) arrays. System is structured around small computer which provides real-time support for graphics storage display unit with keyboard, slave display unit, hard copy unit, and graphics tablet for designer/computer interface.

Combinatorial evaluation of systems including decomposition of a system representation into fundamental cycles

DOEpatents

Oliveira, Joseph S [Richland, WA; Jones-Oliveira, Janet B [Richland, WA; Bailey, Colin G [Wellington, NZ; Gull, Dean W [Seattle, WA

2008-07-01

One embodiment of the present invention includes a computer operable to represent a physical system with a graphical data structure corresponding to a matroid. The graphical data structure corresponds to a number of vertices and a number of edges that each correspond to two of the vertices. The computer is further operable to define a closed pathway arrangement with the graphical data structure and identify each different one of a number of fundamental cycles by evaluating a different respective one of the edges with a spanning tree representation. The fundamental cycles each include three or more of the vertices.

The twilight zone of cis element alignments.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-02-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

The twilight zone of cis element alignments

PubMed Central

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-01-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein–DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein–DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments. PMID:23268451

Improved measurements of RNA structure conservation with generalized centroid estimators.

PubMed

Okada, Yohei; Saito, Yutaka; Sato, Kengo; Sakakibara, Yasubumi

2011-01-01

Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also bioinformatics. Secondary structures of ncRNAs are employed as a key feature of ncRNA analysis since biological functions of ncRNAs are deeply related to their secondary structures. Although the minimum free energy (MFE) structure of an RNA sequence is regarded as the most stable structure, MFE alone could not be an appropriate measure for identifying ncRNAs since the free energy is heavily biased by the nucleotide composition. Therefore, instead of MFE itself, several alternative measures for identifying ncRNAs have been proposed such as the structure conservation index (SCI) and the base pair distance (BPD), both of which employ MFE structures. However, these measurements are unfortunately not suitable for identifying ncRNAs in some cases including the genome-wide search and incur high false discovery rate. In this study, we propose improved measurements based on SCI and BPD, applying generalized centroid estimators to incorporate the robustness against low quality multiple alignments. Our experiments show that our proposed methods achieve higher accuracy than the original SCI and BPD for not only human-curated structural alignments but also low quality alignments produced by CLUSTAL W. Furthermore, the centroid-based SCI on CLUSTAL W alignments is more accurate than or comparable with that of the original SCI on structural alignments generated with RAF, a high quality structural aligner, for which twofold expensive computational time is required on average. We conclude that our methods are more suitable for genome-wide alignments which are of low quality from the point of view on secondary structures than the original SCI and BPD.

OAP- OFFICE AUTOMATION PILOT GRAPHICS DATABASE SYSTEM

NASA Technical Reports Server (NTRS)

Ackerson, T.

1994-01-01

The Office Automation Pilot (OAP) Graphics Database system offers the IBM PC user assistance in producing a wide variety of graphs and charts. OAP uses a convenient database system, called a chartbase, for creating and maintaining data associated with the charts, and twelve different graphics packages are available to the OAP user. Each of the graphics capabilities is accessed in a similar manner. The user chooses creation, revision, or chartbase/slide show maintenance options from an initial menu. The user may then enter or modify data displayed on a graphic chart. The cursor moves through the chart in a "circular" fashion to facilitate data entries and changes. Various "help" functions and on-screen instructions are available to aid the user. The user data is used to generate the graphics portion of the chart. Completed charts may be displayed in monotone or color, printed, plotted, or stored in the chartbase on the IBM PC. Once completed, the charts may be put in a vector format and plotted for color viewgraphs. The twelve graphics capabilities are divided into three groups: Forms, Structured Charts, and Block Diagrams. There are eight Forms available: 1) Bar/Line Charts, 2) Pie Charts, 3) Milestone Charts, 4) Resources Charts, 5) Earned Value Analysis Charts, 6) Progress/Effort Charts, 7) Travel/Training Charts, and 8) Trend Analysis Charts. There are three Structured Charts available: 1) Bullet Charts, 2) Organization Charts, and 3) Work Breakdown Structure (WBS) Charts. The Block Diagram available is an N x N Chart. Each graphics capability supports a chartbase. The OAP graphics database system provides the IBM PC user with an effective means of managing data which is best interpreted as a graphic display. The OAP graphics database system is written in IBM PASCAL 2.0 and assembler for interactive execution on an IBM PC or XT with at least 384K of memory, and a color graphics adapter and monitor. Printed charts require an Epson, IBM, OKIDATA, or HP Laser printer (or equivalent). Plots require the Tektronix 4662 Penplotter. Source code is supplied to the user for modification and customizing. Executables are also supplied for all twelve graphics capabilities. This system was developed in 1983, and Version 3.1 was released in 1986.

Mage: A Tool for Developing Interactive Instructional Graphics

ERIC Educational Resources Information Center

Pavkovic, Stephen F.

2005-01-01

Mage is a graphics program developed for visualization of three-dimensional structures of proteins and other macromolecules. An application of the Mage program is reported here for developing interactive instructional graphics files (kinemages) of much smaller scale. Examples are given illustrating features of VSEPR models, permanent dipoles,…

Pre-calculated protein structure alignments at the RCSB PDB website.

PubMed

Prlic, Andreas; Bliven, Spencer; Rose, Peter W; Bluhm, Wolfgang F; Bizon, Chris; Godzik, Adam; Bourne, Philip E

2010-12-01

With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user. A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org andreas@sdsc.edu; pbourne@ucsd.edu.

Four RNA families with functional transient structures

PubMed Central

Zhu, Jing Yun A; Meyer, Irmtraud M

2015-01-01

Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5′ flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5′ UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All transient and dominant structures are mapped to our new alignments introduced here. PMID:25751035

Four RNA families with functional transient structures.

PubMed

Zhu, Jing Yun A; Meyer, Irmtraud M

2015-01-01

Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5' flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5' UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All transient and dominant structures are mapped to our new alignments introduced here.

Alignment Pins for Assembling and Disassembling Structures

NASA Technical Reports Server (NTRS)

Campbell, Oliver C.

2008-01-01

Simple, easy-to-use, highly effective tooling has been devised for maintaining alignment of bolt holes in mating structures during assembly and disassembly of the structures. The tooling was originally used during removal of a body flap from the space shuttle Atlantis, in which misalignments during removal of the last few bolts could cause the bolts to bind in their holes. By suitably modifying the dimensions of the tooling components, the basic design of the tooling can readily be adapted to other structures that must be maintained in alignment. The tooling includes tapered, internally threaded alignment pins designed to fit in the bolt holes in one of the mating structures, plus a draw bolt and a cup that are used to install or remove each alignment pin. In preparation for disassembly of two mating structures, external supports are provided to prevent unintended movement of the structures. During disassembly of the structures, as each bolt that joins the structures is removed, an alignment pin is installed in its place. Once all the bolts have been removed and replaced with pins, the pins maintain alignment as the structures are gently pushed or pulled apart on the supports. In assembling the two structures, one reverses the procedure described above: pins are installed in the bolt holes, the structures are pulled or pushed together on the supports, then the pins are removed and replaced with bolts. The figure depicts the tooling and its use. To install an alignment pin in a bolt hole in a structural panel, the tapered end of the pin is inserted from one side of the panel, the cup is placed over the pin on the opposite side of the panel, the draw bolt is inserted through the cup and threaded into the pin, the draw bolt is tightened to pull the pin until the pin is seated firmly in the hole, then the draw bolt and cup are removed, leaving the pin in place. To remove an alignment pin, the cup is placed over the pin on the first-mentioned side of the panel, the draw bolt is inserted through the cup and threaded into the pin, then the draw bolt is tightened to pull the pin out of the hole.

Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.

PubMed

Brodie, Ryan; Smith, Alex J; Roper, Rachel L; Tcherepanov, Vasily; Upton, Chris

2004-07-14

With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools. A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs) to retrieve detailed annotation information about the aligned genomes or use information from text files. Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.

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

PubMed Central

Lee, Hui Sun; Im, Wonpil

2013-01-01

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

The Graphic Representation of Structure in Similarity/Dissimilarity Matrices: Alternative Methods.

ERIC Educational Resources Information Center

Rudnitsky, Alan N.

Three approaches to the graphic representation of similarity and dissimilarity matrices are compared and contrasted. Specifically, Kruskal's multidimensional scaling, Johnson's hierarchical clustering, and Waern's graphing techniques are employed to depict, in two dimensions, data representing the structure of a set of botanical concepts. Each of…

Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications

PubMed Central

Cvicek, Vaclav; Goddard, William A.; Abrol, Ravinder

2016-01-01

The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs. These residues can be used to make testable hypotheses about the structural basis of receptor function and about the molecular basis of disease-associated single nucleotide polymorphisms. PMID:27028541

Evolution of physician-hospital alignment models: a case study of comanagement.

PubMed

Sowers, Kevin W; Newman, Paul R; Langdon, Jeffrey C

2013-06-01

Recently, quality, financial, and regulatory demands have driven physicians to seek alignment opportunities with hospitals. The motivation for alignment on the part of physicians and hospitals is now accelerating because the new paradigm under healthcare reform requires an increased focus on improving quality, cost, and efficiency. We (1) identify the key drivers for physician-hospital alignment models; (2) summarize comanagement as a physician-hospital alignment model; and (3) explore a detailed case study of comanagement as an option to better align physicians with hospital goals on quality, safety, and outcomes. A Medline abstract review was performed that identified 45 references that discuss options for physician-hospital alignment. None of the articles identified provide a detailed example of successful alignment structures. A detailed case study of a successful comanagement alignment program is reviewed. The key drivers for alignment are inpatient growth rates, declining reimbursements, and the opportunity to improve quality, decrease costs, and increase efficiency. Two general strategies of alignment involve noneconomic and/or economic integration. In our example, comanagement with economic integration was chosen as the preferred structure for physician-hospital alignment. The choice of structure will vary depending on the existing relationships and governance of the hospital and the physicians in the targeted area of focus. The measure of success in building physician-hospital alignment is measured in improvements in care for the patient, reduced cost of care delivery, and improved relations between physicians and hospital leadership.

An adaptive structure data acquisition system using a graphical-based programming language

NASA Technical Reports Server (NTRS)

Baroth, Edmund C.; Clark, Douglas J.; Losey, Robert W.

1992-01-01

An example of the implementation of data fusion using a PC and a graphical programming language is discussed. A schematic of the data acquisition system and user interface panel for an adaptive structure test are presented. The computer programs (a series of icons 'wired' together) are also discussed. The way in which using graphical-based programming software to control a data acquisition system can simplify analysis of data, promote multidisciplinary interaction, and provide users a more visual key to understanding their data are shown.

Optimal Alignment of Structures for Finite and Periodic Systems.

PubMed

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

2017-10-10

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

User's manual for MacPASCO

NASA Technical Reports Server (NTRS)

Lucas, S. H.; Davis, R. C.

1992-01-01

A user's manual is presented for MacPASCO, which is an interactive, graphic, preprocessor for panel design. MacPASCO creates input for PASCO, an existing computer code for structural analysis and sizing of longitudinally stiffened composite panels. MacPASCO provides a graphical user interface which simplifies the specification of panel geometry and reduces user input errors. The user draws the initial structural geometry and reduces user input errors. The user draws the initial structural geometry on the computer screen, then uses a combination of graphic and text inputs to: refine the structural geometry; specify information required for analysis such as panel load and boundary conditions; and define design variables and constraints for minimum mass optimization. Only the use of MacPASCO is described, since the use of PASCO has been documented elsewhere.

Medical and Graphic Arts Unit; a Guide to Organizing a Medical and Graphic Arts Unit in Health Science Educational Institutions. Monograph 2.

ERIC Educational Resources Information Center

Smith, Herbert R., Jr.

This monograph describes the role of medical and graphic arts units within the comprehensive communications departments of health science educational institutions. Historical trends and contemporary practices are described. Suggestions are made for: organizational structure; services and activities; staff requirements; budget; facility…

Industrial Arts 7-9. Graphic Communications. Drafting. Graphic Arts.

ERIC Educational Resources Information Center

Manitoba Dept. of Education, Winnipeg.

This guide for industrial arts grades 7-9 provides teachers with a curriculum for the subject cluster of graphic communications. An "Overview" section presents the rationale, discusses how the content of the program is related to the developmental stages of the adolescent, describes the structure of the industrial arts program, and lists…

Predicting Flavonoid UGT Regioselectivity

PubMed Central

Jackson, Rhydon; Knisley, Debra; McIntosh, Cecilia; Pfeiffer, Phillip

2011-01-01

Machine learning was applied to a challenging and biologically significant protein classification problem: the prediction of avonoid UGT acceptor regioselectivity from primary sequence. Novel indices characterizing graphical models of residues were proposed and found to be widely distributed among existing amino acid indices and to cluster residues appropriately. UGT subsequences biochemically linked to regioselectivity were modeled as sets of index sequences. Several learning techniques incorporating these UGT models were compared with classifications based on standard sequence alignment scores. These techniques included an application of time series distance functions to protein classification. Time series distances defined on the index sequences were used in nearest neighbor and support vector machine classifiers. Additionally, Bayesian neural network classifiers were applied to the index sequences. The experiments identified improvements over the nearest neighbor and support vector machine classifications relying on standard alignment similarity scores, as well as strong correlations between specific subsequences and regioselectivities. PMID:21747849

VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.

PubMed

Fan, Long; Hui, Jerome H L; Yu, Zu Guo; Chu, Ka Hou

2014-07-01

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/. © 2014 John Wiley & Sons Ltd.

Optimization of sequence alignment for simple sequence repeat regions.

PubMed

Jighly, Abdulqader; Hamwieh, Aladdin; Ogbonnaya, Francis C

2011-07-20

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

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

The Digital Space Shuttle, 3D Graphics, and Knowledge Management

NASA Technical Reports Server (NTRS)

Gomez, Julian E.; Keller, Paul J.

2003-01-01

The Digital Shuttle is a knowledge management project that seeks to define symbiotic relationships between 3D graphics and formal knowledge representations (ontologies). 3D graphics provides geometric and visual content, in 2D and 3D CAD forms, and the capability to display systems knowledge. Because the data is so heterogeneous, and the interrelated data structures are complex, 3D graphics combined with ontologies provides mechanisms for navigating the data and visualizing relationships.

Silicon Alignment Pins: An Easy Way to Realize a Wafer-To-Wafer Alignment

NASA Technical Reports Server (NTRS)

Peralta, Alejandro (Inventor); Gill, John J. (Inventor); Toda, Risaku (Inventor); Lin, Robert H. (Inventor); Jung-Kubiak, Cecile (Inventor); Reck, Theodore (Inventor); Thomas, Bertrand (Inventor); Siles, Jose V. (Inventor); Lee, Choonsup (Inventor); Chattopadhyay, Goutam (Inventor)

2016-01-01

A silicon alignment pin is used to align successive layers of components made in semiconductor chips and/or metallic components to make easier the assembly of devices having a layered structure. The pin is made as a compressible structure which can be squeezed to reduce its outer diameter, have one end fit into a corresponding alignment pocket or cavity defined in a layer of material to be assembled into a layered structure, and then allowed to expand to produce an interference fit with the cavity. The other end can then be inserted into a corresponding cavity defined in a surface of a second layer of material that mates with the first layer. The two layers are in registry when the pin is mated to both. Multiple layers can be assembled to create a multilayer structure. Examples of such devices are presented.

GRAMPS: a graphics language interpreter for real-time, interactive, three-dimensional picture editing and animation

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

O'Donnell, T.J.; Olson, A.J.

1981-08-01

GRAMPS, a graphics language interpreter has been developed in FORTRAN 77 to be used in conjunction with an interactive vector display list processor (Evans and Sutherland Multi-Picture-System). Several of the features of the language make it very useful and convenient for real-time scene construction, manipulation and animation. The GRAMPS language syntax allows natural interaction with scene elements as well as easy, interactive assignment of graphics input devices. GRAMPS facilitates the creation, manipulation and copying of complex nested picture structures. The language has a powerful macro feature that enables new graphics commands to be developed and incorporated interactively. Animation may bemore » achieved in GRAMPS by two different, yet mutually compatible means. Picture structures may contain framed data, which consist of a sequence of fixed objects. These structures may be displayed sequentially to give a traditional frame animation effect. In addition, transformation information on picture structures may be saved at any time in the form of new macro commands that will transform these structures from one saved state to another in a specified number of steps, yielding an interpolated transformation animation effect. An overview of the GRAMPS command structure is given and several examples of application of the language to molecular modeling and animation are presented.« less

Programming Language Software For Graphics Applications

NASA Technical Reports Server (NTRS)

Beckman, Brian C.

1993-01-01

New approach reduces repetitive development of features common to different applications. High-level programming language and interactive environment with access to graphical hardware and software created by adding graphical commands and other constructs to standardized, general-purpose programming language, "Scheme". Designed for use in developing other software incorporating interactive computer-graphics capabilities into application programs. Provides alternative to programming entire applications in C or FORTRAN, specifically ameliorating design and implementation of complex control and data structures typifying applications with interactive graphics. Enables experimental programming and rapid development of prototype software, and yields high-level programs serving as executable versions of software-design documentation.

Structural and Functional Model of Organization of Geometric and Graphic Training of the Students

ERIC Educational Resources Information Center

Poluyanov, Valery B.; Pyankova, Zhanna A.; Chukalkina, Marina I.; Smolina, Ekaterina S.

2016-01-01

The topicality of the investigated problem is stipulated by the social need for training competitive engineers with a high level of graphical literacy; especially geometric and graphic training of students and its projected results in a competence-based approach; individual characteristics and interests of the students, as well as methodological…

A graphical vector autoregressive modelling approach to the analysis of electronic diary data

PubMed Central

2010-01-01

Background In recent years, electronic diaries are increasingly used in medical research and practice to investigate patients' processes and fluctuations in symptoms over time. To model dynamic dependence structures and feedback mechanisms between symptom-relevant variables, a multivariate time series method has to be applied. Methods We propose to analyse the temporal interrelationships among the variables by a structural modelling approach based on graphical vector autoregressive (VAR) models. We give a comprehensive description of the underlying concepts and explain how the dependence structure can be recovered from electronic diary data by a search over suitable constrained (graphical) VAR models. Results The graphical VAR approach is applied to the electronic diary data of 35 obese patients with and without binge eating disorder (BED). The dynamic relationships for the two subgroups between eating behaviour, depression, anxiety and eating control are visualized in two path diagrams. Results show that the two subgroups of obese patients with and without BED are distinguishable by the temporal patterns which influence their respective eating behaviours. Conclusion The use of the graphical VAR approach for the analysis of electronic diary data leads to a deeper insight into patient's dynamics and dependence structures. An increasing use of this modelling approach could lead to a better understanding of complex psychological and physiological mechanisms in different areas of medical care and research. PMID:20359333

Organizational Structure and Strategy. Symposium 30. [Concurrent Symposium Session at AHRD Annual Conference, 2000.

ERIC Educational Resources Information Center

2000

This packet contains four papers on organizational structure and strategy from a symposium on human resource development (HRD). The first paper, "Exploring Alignment: A Comparative Case Study of Alignment in Two Organizations" (Steven W. Semler), reports on a case study that compared the results of an alignment measurement instrument…

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models

PubMed Central

2014-01-01

Background Logos are commonly used in molecular biology to provide a compact graphical representation of the conservation pattern of a set of sequences. They render the information contained in sequence alignments or profile hidden Markov models by drawing a stack of letters for each position, where the height of the stack corresponds to the conservation at that position, and the height of each letter within a stack depends on the frequency of that letter at that position. Results We present a new tool and web server, called Skylign, which provides a unified framework for creating logos for both sequence alignments and profile hidden Markov models. In addition to static image files, Skylign creates a novel interactive logo plot for inclusion in web pages. These interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. Conclusion Skylign is available as a website, a scriptable web service with a RESTful interface, and as a software package for download. Skylign’s interactive logos are easily incorporated into a web page with just a few lines of HTML markup. Skylign may be found at http://skylign.org. PMID:24410852

First Year Engineering Graphics Curricula in Major Engineering Colleges.

ERIC Educational Resources Information Center

Meyers, Frederick D.

2000-01-01

Investigates the commonalities and differences of graphics programs among nine universities in the United States by analyzing the course structure and reviewing attendance and course syllabi. (Author/YDS)

Computer-Based Learning: Graphical Integration of Whole and Sectional Neuroanatomy Improves Long-Term Retention

PubMed Central

Naaz, Farah; Chariker, Julia H.; Pani, John R.

2013-01-01

A study was conducted to test the hypothesis that instruction with graphically integrated representations of whole and sectional neuroanatomy is especially effective for learning to recognize neural structures in sectional imagery (such as MRI images). Neuroanatomy was taught to two groups of participants using computer graphical models of the human brain. Both groups learned whole anatomy first with a three-dimensional model of the brain. One group then learned sectional anatomy using two-dimensional sectional representations, with the expectation that there would be transfer of learning from whole to sectional anatomy. The second group learned sectional anatomy by moving a virtual cutting plane through the three-dimensional model. In tests of long-term retention of sectional neuroanatomy, the group with graphically integrated representation recognized more neural structures that were known to be challenging to learn. This study demonstrates the use of graphical representation to facilitate a more elaborated (deeper) understanding of complex spatial relations. PMID:24563579

Automated batch fiducial-less tilt-series alignment in Appion using Protomo

PubMed Central

Noble, Alex J.; Stagg, Scott M.

2015-01-01

The field of electron tomography has benefited greatly from manual and semi-automated approaches to marker-based tilt-series alignment that have allowed for the structural determination of multitudes of in situ cellular structures as well as macromolecular structures of individual protein complexes. The emergence of complementary metal-oxide semiconductor detectors capable of detecting individual electrons has enabled the collection of low dose, high contrast images, opening the door for reliable correlation-based tilt-series alignment. Here we present a set of automated, correlation-based tilt-series alignment, contrast transfer function (CTF) correction, and reconstruction workflows for use in conjunction with the Appion/Leginon package that are primarily targeted at automating structure determination with cryogenic electron microscopy. PMID:26455557

Anisotropic piezoresistivity characteristics of aligned carbon nanotube-polymer nanocomposites

NASA Astrophysics Data System (ADS)

Sengezer, Engin C.; Seidel, Gary D.; Bodnar, Robert J.

2017-09-01

Dielectrophoresis under the application of AC electric fields is one of the primary fabrication techniques for obtaining aligned carbon nanotube (CNT)-polymer nanocomposites, and is used here to generate long range alignment of CNTs at the structural level. The degree of alignment of CNTs within this long range architecture is observed via polarized Raman spectroscopy so that its influence on the electrical conductivity and piezoresistive response in both the alignment and transverse to alignment directions can be assessed. Nanocomposite samples consisting of randomly oriented, well dispersed single-wall carbon nanotubes (SWCNTs) and of long range electric field aligned SWCNTs in a photopolymerizable monomer blend (urethane dimethacrylate and 1,6-hexanediol dimethacrylate) are quantitatively and qualitatively evaluated. Piezoresistive sensitivities in form of gauge factors were measured for randomly oriented, well dispersed specimens with 0.03, 0.1 and 0.5 wt% SWCNTs and compared with gauge factors in both the axial and transverse to SWCNT alignment directions for electric field aligned 0.03 wt% specimens under both quasi-static monotonic and cyclic tensile loading. Gauge factors in the axial direction were observed to be on the order of 2, while gauge factors in the transverse direction demonstrated a 5 fold increase with values on the order of 10 for aligned specimens. Based on Raman analysis, it is believed the higher sensitivity of the transverse direction is related to architectural evolution of misaligned bridging structures which connect alignment structures under load due to Poisson’s contraction.

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

PubMed Central

Kumar, Yadhu; Westram, Ralf; Kipfer, Peter; Meier, Harald; Ludwig, Wolfgang

2006-01-01

Background Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. Conclusion Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via . PMID:16672074

DR-TAMAS: Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures

PubMed Central

Irfanoglu, M. Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B.; Sadeghi, Neda; Thomas, Cibu P.; Pierpaoli, Carlo

2016-01-01

In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. PMID:26931817

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.

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.

Do adolescents with idiopathic scoliosis have body schema disorders? A cross-sectional study.

PubMed

Picelli, Alessandro; Negrini, Stefano; Zenorini, Andrea; Iosa, Marco; Paolucci, Stefano; Smania, Nicola

2016-01-01

To date etiology of adolescent idiopathic scoliosis appears complex and still remains unclear. A distorted body schema has been proposed to be a part of a sequence of pathological events in the development of adolescent idiopathic scoliosis. To investigate the awareness of trunk misalignment in adolescents with idiopathic scoliosis. Information about 44 adolescents with idiopathic scoliosis was collected as follows: age; sex; handedness; family history of scoliosis; back pain; sport practice; shoulder and waist line symmetry; leg length; dorsal kyphosis; back hump; rehabilitation; scoliotic curve; Risser sign. We evaluated awareness of trunk misalignment with a graphic table displaying pictures of progressively increasing scoliotic curves. Patients were asked to indicate which picture corresponded to their perceived own spinal alignment. Patients with thoracolumbar scoliosis overestimated their actual thoracic spine curve. Patients with thoracic-thoracolumbar scoliosis underestimated their actual thoracolumbar spine curve and overestimated their actual lumbar spine curve. Scoliotic curve > 15°, double curve, younger age, back pain, family history of scoliosis and lower Risser score related with a misperception of trunk alignment. Our results support the hypothesis that adolescents with idiopathic scoliosis have an altered corporeal awareness of their trunk alignment.

Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API

PubMed Central

2016-01-01

Abstract Background The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. New information A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF’s ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file. PMID:27932916

Scan for Motifs: a webserver for the analysis of post-transcriptional regulatory elements in the 3' untranslated regions (3' UTRs) of mRNAs.

PubMed

Biswas, Ambarish; Brown, Chris M

2014-06-08

Gene expression in vertebrate cells may be controlled post-transcriptionally through regulatory elements in mRNAs. These are usually located in the untranslated regions (UTRs) of mRNA sequences, particularly the 3'UTRs. Scan for Motifs (SFM) simplifies the process of identifying a wide range of regulatory elements on alignments of vertebrate 3'UTRs. SFM includes identification of both RNA Binding Protein (RBP) sites and targets of miRNAs. In addition to searching pre-computed alignments, the tool provides users the flexibility to search their own sequences or alignments. The regulatory elements may be filtered by expected value cutoffs and are cross-referenced back to their respective sources and literature. The output is an interactive graphical representation, highlighting potential regulatory elements and overlaps between them. The output also provides simple statistics and links to related resources for complementary analyses. The overall process is intuitive and fast. As SFM is a free web-application, the user does not need to install any software or databases. Visualisation of the binding sites of different classes of effectors that bind to 3'UTRs will facilitate the study of regulatory elements in 3' UTRs.

High-throughput flow alignment of barcoded hydrogel microparticles†

PubMed Central

Chapin, Stephen C.; Pregibon, Daniel C.

2010-01-01

Suspension (particle-based) arrays offer several advantages over conventional planar arrays in the detection and quantification of biomolecules, including the use of smaller sample volumes, more favorable probe-target binding kinetics, and rapid probe-set modification. We present a microfluidic system for the rapid alignment of multifunctional hydrogel microparticles designed to bear one or several biomolecule probe regions, as well as a graphical code to identify the embedded probes. Using high-speed imaging, we have developed and optimized a flow-through system that (1) allows for a high particle throughput, (2) ensures proper particle alignment for decoding and target quantification, and (3) can be reliably operated continuously without clogging. A tapered channel flanked by side focusing streams is used to orient the flexible, tablet-shaped particles into a well-ordered flow in the center of the channel. The effects of channel geometry, particle geometry, particle composition, particle loading density, and barcode design are explored to determine the best combination for eventual use in biological assays. Particles in the optimized system move at velocities of ~50 cm s−1 and with throughputs of ~40 particles s−1. Simple physical models and CFD simulations have been used to investigate flow behavior in the device. PMID:19823726

Desktop aligner for fabrication of multilayer microfluidic devices.

PubMed

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

2015-07-01

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

Desktop aligner for fabrication of multilayer microfluidic devices

PubMed Central

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

2015-01-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

CORAL: aligning conserved core regions across domain families.

PubMed

Fong, Jessica H; Marchler-Bauer, Aron

2009-08-01

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

Nanofiber alignment of a small diameter elastic electrospun scaffold

NASA Astrophysics Data System (ADS)

Patel, Jignesh

Cardiovascular disease is the leading cause of death in western countries with coronary heart disease making up 50% of these deaths. As a treatment option, tissue engineered grafts have great potential. Elastic scaffolds that mimic arterial extracellular matrix (ECM) may hold the key to creating viable vascular grafts. Electrospinning is a widely used scaffold fabrication technique to engineer tubular scaffolds. In this study, we investigated how the collector rotation speed altered the nanofiber alignment which may improve mechanical characteristics making the scaffold more suitable for arterial grafts. The scaffold was fabricated from a blend of PCL/Elastin. 2D Fast Fourier Transform (FFT) image processing tool and MatLab were used to quantitatively analyze nanofiber orientation at different collector speeds (13500 to 15500 rpm). Both Image J and MatLab showed graphical peaks indicating predominant fiber orientation angles. A collector speed of 15000 rpm was found to produce the best nanofiber alignment with narrow peaks at 90 and 270 degrees, and a relative amplitude of 200. This indicates a narrow distribution of circumferentially aligned nanofibers. Collector speeds below and above 15000 rpm caused a decrease in fiber alignment with a broader orientation distribution. Uniformity of fiber diameter was also measured. Of 600 measures from the 15000 rpm scaffolds, the fiber diameter range from 500 nm to 899 nm was most prevalent. This diameter range was slightly larger than native ECM which ranges from 50 nm to 500 nm. The second most prevalent diameter range had an average of 404 nm which is within the diameter range of collagen. This study concluded that with proper electrospinning technique and collector speed, it is possible to fabricate highly aligned small diameter elastic scaffolds. Image J 2D FFT results confirmed MatLab findings for the analyses of circumferentially aligned nanofibers. In addition, MatLab analyses simplified the FFT orientation data providing an accurate, user friendly orientation measurement tool.

Interactive graphic editing tools in bioluminescent imaging simulation

NASA Astrophysics Data System (ADS)

Li, Hui; Tian, Jie; Luo, Jie; Wang, Ge; Cong, Wenxiang

2005-04-01

It is a challenging task to accurately describe complicated biological tissues and bioluminescent sources in bioluminescent imaging simulation. Several graphic editing tools have been developed to efficiently model each part of the bioluminescent simulation environment and to interactively correct or improve the initial models of anatomical structures or bioluminescent sources. There are two major types of graphic editing tools: non-interactive tools and interactive tools. Geometric building blocks (i.e. regular geometric graphics and superquadrics) are applied as non-interactive tools. To a certain extent, complicated anatomical structures and bioluminescent sources can be approximately modeled by combining a sufficient large number of geometric building blocks with Boolean operators. However, those models are too simple to describe the local features and fine changes in 2D/3D irregular contours. Therefore, interactive graphic editing tools have been developed to facilitate the local modifications of any initial surface model. With initial models composed of geometric building blocks, interactive spline mode is applied to conveniently perform dragging and compressing operations on 2D/3D local surface of biological tissues and bioluminescent sources inside the region/volume of interest. Several applications of the interactive graphic editing tools will be presented in this article.

DspaceOgre 3D Graphics Visualization Tool

NASA Technical Reports Server (NTRS)

Jain, Abhinandan; Myin, Steven; Pomerantz, Marc I.

2011-01-01

This general-purpose 3D graphics visualization C++ tool is designed for visualization of simulation and analysis data for articulated mechanisms. Examples of such systems are vehicles, robotic arms, biomechanics models, and biomolecular structures. DspaceOgre builds upon the open-source Ogre3D graphics visualization library. It provides additional classes to support the management of complex scenes involving multiple viewpoints and different scene groups, and can be used as a remote graphics server. This software provides improved support for adding programs at the graphics processing unit (GPU) level for improved performance. It also improves upon the messaging interface it exposes for use as a visualization server.

Mapping the Space of Genomic Signatures

PubMed Central

Kari, Lila; Hill, Kathleen A.; Sayem, Abu S.; Karamichalis, Rallis; Bryans, Nathaniel; Davis, Katelyn; Dattani, Nikesh S.

2015-01-01

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to k (herein k = 9) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence alignment and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information. This method also correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal, the Denisovan, and the chimp), and that the sequence most different from it in this dataset belongs to a cucumber. PMID:26000734

Genetic Testing Registry

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Automated batch fiducial-less tilt-series alignment in Appion using Protomo.

PubMed

Noble, Alex J; Stagg, Scott M

2015-11-01

The field of electron tomography has benefited greatly from manual and semi-automated approaches to marker-based tilt-series alignment that have allowed for the structural determination of multitudes of in situ cellular structures as well as macromolecular structures of individual protein complexes. The emergence of complementary metal-oxide semiconductor detectors capable of detecting individual electrons has enabled the collection of low dose, high contrast images, opening the door for reliable correlation-based tilt-series alignment. Here we present a set of automated, correlation-based tilt-series alignment, contrast transfer function (CTF) correction, and reconstruction workflows for use in conjunction with the Appion/Leginon package that are primarily targeted at automating structure determination with cryogenic electron microscopy. Copyright © 2015 Elsevier Inc. All rights reserved.

What Can Causal Networks Tell Us about Metabolic Pathways?

PubMed Central

Blair, Rachael Hageman; Kliebenstein, Daniel J.; Churchill, Gary A.

2012-01-01

Graphical models describe the linear correlation structure of data and have been used to establish causal relationships among phenotypes in genetic mapping populations. Data are typically collected at a single point in time. Biological processes on the other hand are often non-linear and display time varying dynamics. The extent to which graphical models can recapitulate the architecture of an underlying biological processes is not well understood. We consider metabolic networks with known stoichiometry to address the fundamental question: “What can causal networks tell us about metabolic pathways?”. Using data from an Arabidopsis BaySha population and simulated data from dynamic models of pathway motifs, we assess our ability to reconstruct metabolic pathways using graphical models. Our results highlight the necessity of non-genetic residual biological variation for reliable inference. Recovery of the ordering within a pathway is possible, but should not be expected. Causal inference is sensitive to subtle patterns in the correlation structure that may be driven by a variety of factors, which may not emphasize the substrate-product relationship. We illustrate the effects of metabolic pathway architecture, epistasis and stochastic variation on correlation structure and graphical model-derived networks. We conclude that graphical models should be interpreted cautiously, especially if the implied causal relationships are to be used in the design of intervention strategies. PMID:22496633

The effects of a combination of text structure awareness and graphic postorganizers on recall and retention of science knowledge

NASA Astrophysics Data System (ADS)

Spiegel, George F., Jr.; Barufaldi, James P.

The purpose of this study was to determine the effectiveness of a self-regulated strategy on immediate recall and retention of science knowledge in community-college anatomy and physiology students who participated in a 14-hour (8 weeks) study skills class. The class emphasized the recognition of five common science textbook text structures (cause and effect, classification, enumeration, generalization, and sequence) and the construction of graphic postorganizers of the text structures. A pretest, two immediate posttests, and a retention posttest were used to measure recall and retention. Results indicated that on immediate posttests students who actively constructed graphic postorganizers of the test structure recalled significantly more content than did the control students who simply underlined, reread, or highlighted. On a 3-week retention posttest, those students in the study skills class retained significantly more of the material studied than did the control group of students.

ROCOPT: A user friendly interactive code to optimize rocket structural components

NASA Technical Reports Server (NTRS)

Rule, William K.

1989-01-01

ROCOPT is a user-friendly, graphically-interfaced, microcomputer-based computer program (IBM compatible) that optimizes rocket components by minimizing the structural weight. The rocket components considered are ring stiffened truncated cones and cylinders. The applied loading is static, and can consist of any combination of internal or external pressure, axial force, bending moment, and torque. Stress margins are calculated by means of simple closed form strength of material type equations. Stability margins are determined by approximate, orthotropic-shell, closed-form equations. A modified form of Powell's method, in conjunction with a modified form of the external penalty method, is used to determine the minimum weight of the structure subject to stress and stability margin constraints, as well as user input constraints on the structural dimensions. The graphical interface guides the user through the required data prompts, explains program options and graphically displays results for easy interpretation.

Diffeomorphic functional brain surface alignment: Functional demons.

PubMed

Nenning, Karl-Heinz; Liu, Hesheng; Ghosh, Satrajit S; Sabuncu, Mert R; Schwartz, Ernst; Langs, Georg

2017-08-01

Aligning brain structures across individuals is a central prerequisite for comparative neuroimaging studies. Typically, registration approaches assume a strong association between the features used for alignment, such as macro-anatomy, and the variable observed, such as functional activation or connectivity. Here, we propose to use the structure of intrinsic resting state fMRI signal correlation patterns as a basis for alignment of the cortex in functional studies. Rather than assuming the spatial correspondence of functional structures between subjects, we have identified locations with similar connectivity profiles across subjects. We mapped functional connectivity relationships within the brain into an embedding space, and aligned the resulting maps of multiple subjects. We then performed a diffeomorphic alignment of the cortical surfaces, driven by the corresponding features in the joint embedding space. Results show that functional alignment based on resting state fMRI identifies functionally homologous regions across individuals with higher accuracy than alignment based on the spatial correspondence of anatomy. Further, functional alignment enables measurement of the strength of the anatomo-functional link across the cortex, and reveals the uneven distribution of this link. Stronger anatomo-functional dissociation was found in higher association areas compared to primary sensory- and motor areas. Functional alignment based on resting state features improves group analysis of task based functional MRI data, increasing statistical power and improving the delineation of task-specific core regions. Finally, a comparison of the anatomo-functional dissociation between cohorts is demonstrated with a group of left and right handed subjects. Copyright © 2017 Elsevier Inc. All rights reserved.

Dali server update.

PubMed

Holm, Liisa; Laakso, Laura M

2016-07-08

The Dali server (http://ekhidna2.biocenter.helsinki.fi/dali) is a network service for comparing protein structures in 3D. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The Dali server has been running in various places for over 20 years and is used routinely by crystallographers on newly solved structures. The latest update of the server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. The combined structure-sequence alignment information is compressed to a stack of aligned sequence logos. In the stack, each structure is structurally aligned to the query protein and represented by a sequence logo. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

NASTRAN analysis of Tokamak vacuum vessel using interactive graphics

NASA Technical Reports Server (NTRS)

Miller, A.; Badrian, M.

1978-01-01

Isoparametric quadrilateral and triangular elements were used to represent the vacuum vessel shell structure. For toroidally symmetric loadings, MPCs were employed across model boundaries and rigid format 24 was invoked. Nonsymmetric loadings required the use of the cyclic symmetry analysis available with rigid format 49. NASTRAN served as an important analysis tool in the Tokamak design effort by providing a reliable means for assessing structural integrity. Interactive graphics were employed in the finite element model generation and in the post-processing of results. It was felt that model generation and checkout with interactive graphics reduced the modelling effort and debugging man-hours significantly.

Software engineering capability for Ada (GRASP/Ada Tool)

NASA Technical Reports Server (NTRS)

Cross, James H., II

1995-01-01

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped a new algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis has been on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada Source code. A new Motif compliant graphical user interface has been developed for the GRASP/Ada prototype.

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

PubMed

Neuwald, Andrew F

2009-08-01

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

Protein space: a natural method for realizing the nature of protein universe.

PubMed

Yu, Chenglong; Deng, Mo; Cheng, Shiu-Yuen; Yau, Shek-Chung; He, Rong L; Yau, Stephen S-T

2013-02-07

Current methods cannot tell us what the nature of the protein universe is concretely. They are based on different models of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requires manual intervention. Protein structural analysis also gives a direction for mapping the protein universe. Unfortunately, now only a minuscule fraction of proteins' 3-dimensional structures are known. Furthermore, the phylogenetic tree representations are not unique for any existing tree construction methods. Here we develop a novel method to realize the nature of protein universe. We show the protein universe can be realized as a protein space in 60-dimensional Euclidean space using a distance based on a normalized distribution of amino acids. Every protein is in one-to-one correspondence with a point in protein space, where proteins with similar properties stay close together. Thus the distance between two points in protein space represents the biological distance of the corresponding two proteins. We also propose a natural graphical representation for inferring phylogenies. The representation is natural and unique based on the biological distances of proteins in protein space. This will solve the fundamental question of how proteins are distributed in the protein universe. Copyright © 2012 Elsevier Ltd. All rights reserved.

The development of an engineering computer graphics laboratory

NASA Technical Reports Server (NTRS)

Anderson, D. C.; Garrett, R. E.

1975-01-01

Hardware and software systems developed to further research and education in interactive computer graphics were described, as well as several of the ongoing application-oriented projects, educational graphics programs, and graduate research projects. The software system consists of a FORTRAN 4 subroutine package, in conjunction with a PDP 11/40 minicomputer as the primary computation processor and the Imlac PDS-1 as an intelligent display processor. The package comprises a comprehensive set of graphics routines for dynamic, structured two-dimensional display manipulation, and numerous routines to handle a variety of input devices at the Imlac.

Effects of Training in Constructing Graphic Organizers on Disabled Readers' Summarization and Recognition of Expository Text Structure.

ERIC Educational Resources Information Center

Weisberg, Renee; Balajthy, Ernest

A study investigated the effects of training in the use of graphic organizers on the summarization strategies of disabled readers. Subjects, 21 disabled readers (with a mean age of 13 years, 7 months) from a reading clinic, received 5 hours of training in the use of graphic organizers to map expository passages. Instruction included training in…

PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

PubMed

Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

2015-10-01

There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.

PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps

PubMed Central

Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

2015-01-01

There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF2 fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF2 fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

National Center for Biotechnology Information

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

A statistical physics perspective on alignment-independent protein sequence comparison.

PubMed

Chattopadhyay, Amit K; Nasiev, Diar; Flower, Darren R

2015-08-01

Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly. Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from 'first passage probability distribution' to summarize statistics of ensemble averaged amino acid propensity values. In this article, we introduce and elaborate this approach. © The Author 2015. Published by Oxford University Press.

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

PubMed

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

2012-01-01

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

A Matlab user interface for the statistically assisted fluid registration algorithm and tensor-based morphometry

NASA Astrophysics Data System (ADS)

Yepes-Calderon, Fernando; Brun, Caroline; Sant, Nishita; Thompson, Paul; Lepore, Natasha

2015-01-01

Tensor-Based Morphometry (TBM) is an increasingly popular method for group analysis of brain MRI data. The main steps in the analysis consist of a nonlinear registration to align each individual scan to a common space, and a subsequent statistical analysis to determine morphometric differences, or difference in fiber structure between groups. Recently, we implemented the Statistically-Assisted Fluid Registration Algorithm or SAFIRA,1 which is designed for tracking morphometric differences among populations. To this end, SAFIRA allows the inclusion of statistical priors extracted from the populations being studied as regularizers in the registration. This flexibility and degree of sophistication limit the tool to expert use, even more so considering that SAFIRA was initially implemented in command line mode. Here, we introduce a new, intuitive, easy to use, Matlab-based graphical user interface for SAFIRA's multivariate TBM. The interface also generates different choices for the TBM statistics, including both the traditional univariate statistics on the Jacobian matrix, and comparison of the full deformation tensors.2 This software will be freely disseminated to the neuroimaging research community.

Hyperfine-Structure-Induced Depolarization of Impulsively Aligned I2 Molecules

NASA Astrophysics Data System (ADS)

Thomas, Esben F.; Søndergaard, Anders A.; Shepperson, Benjamin; Henriksen, Niels E.; Stapelfeldt, Henrik

2018-04-01

A moderately intense 450 fs laser pulse is used to create rotational wave packets in gas phase I2 molecules. The ensuing time-dependent alignment, measured by Coulomb explosion imaging with a delayed probe pulse, exhibits the characteristic revival structures expected for rotational wave packets but also a complex nonperiodic substructure and decreasing mean alignment not observed before. A quantum mechanical model attributes the phenomena to coupling between the rotational angular momenta and the nuclear spins through the electric quadrupole interaction. The calculated alignment trace agrees very well with the experimental results.

GKS. Minimal Graphical Kernel System C Binding

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

Simons, R.W.

1985-10-01

GKS (the Graphical Kernel System) is both an American National Standard (ANS) and an ISO international standard graphics package. It conforms to ANS X3.124-1985 and to the May 1985 draft proposal for the GKS C Language Binding standard under development by the X3H3 Technical Committee. This implementation includes level ma (the lowest level of the ANS) and some routines from level mb. The following graphics capabilities are supported: two-dimensional lines, markers, text, and filled areas; control over color, line type, and character height and alignment; multiple simultaneous workstations and multiple transformations; and locator and choice input. Tektronix 4014 and 4115more » terminals are supported, and support for other devices may be added. Since this implementation was developed under UNIX, it uses makefiles, C shell scripts, the ar library maintainer, editor scripts, and other UNIX utilities. Therefore, implementing it under another operating system may require considerable effort. Also included with GKS is the small plot package (SPP), a direct descendant of the WEASEL plot package developed at Sandia. SPP is built on the GKS; therefore, all of the capabilities of GKS are available. It is not necessary to use GKS functions, since entire plots can be produced using only SPP functions, but the addition of GKS will give the programmer added power and flexibility. SPP provides single-call plot commands, linear and logarithmic axis commands, control for optional plotting of tick marks and tick mark labels, and permits plotting of data with or without markers and connecting lines.« less

NASTRAN data generation of helicopter fuselages using interactive graphics. [preprocessor system for finite element analysis using IBM computer

NASA Technical Reports Server (NTRS)

Sainsbury-Carter, J. B.; Conaway, J. H.

1973-01-01

The development and implementation of a preprocessor system for the finite element analysis of helicopter fuselages is described. The system utilizes interactive graphics for the generation, display, and editing of NASTRAN data for fuselage models. It is operated from an IBM 2250 cathode ray tube (CRT) console driven by an IBM 370/145 computer. Real time interaction plus automatic data generation reduces the nominal 6 to 10 week time for manual generation and checking of data to a few days. The interactive graphics system consists of a series of satellite programs operated from a central NASTRAN Systems Monitor. Fuselage structural models including the outer shell and internal structure may be rapidly generated. All numbering systems are automatically assigned. Hard copy plots of the model labeled with GRID or elements ID's are also available. General purpose programs for displaying and editing NASTRAN data are included in the system. Utilization of the NASTRAN interactive graphics system has made possible the multiple finite element analysis of complex helicopter fuselage structures within design schedules.

Three-dimensional structural analysis using interactive graphics

NASA Technical Reports Server (NTRS)

Biffle, J.; Sumlin, H. A.

1975-01-01

The application of computer interactive graphics to three-dimensional structural analysis was described, with emphasis on the following aspects: (1) structural analysis, and (2) generation and checking of input data and examination of the large volume of output data (stresses, displacements, velocities, accelerations). Handling of three-dimensional input processing with a special MESH3D computer program was explained. Similarly, a special code PLTZ may be used to perform all the needed tasks for output processing from a finite element code. Examples were illustrated.

Structured Analysis of the Logistic Support Analysis (LSA) Task, ’Integrated Logistic Support (ILS) Assessment Maintenance Planning E-1 Element’ (APJ 966-204)

DTIC Science & Technology

1988-10-01

Structured Analysis involves building a logical (non-physical) model of a system, using graphic techniques which enable users, analysts, and designers to... Design uses tools, especially graphic ones, to render systems readily understandable. 8 Ř. Structured Design offers a set of strategies for...in the overall systems design process, and an overview of the assessment procedures, as well as a guide to the overall assessment. 20. DISTRIBUTION

A novel approach to multiple sequence alignment using hadoop data grids.

PubMed

Sudha Sadasivam, G; Baktavatchalam, G

2010-01-01

Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences.

Multi-subject Manifold Alignment of Functional Network Structures via Joint Diagonalization.

PubMed

Nenning, Karl-Heinz; Kollndorfer, Kathrin; Schöpf, Veronika; Prayer, Daniela; Langs, Georg

2015-01-01

Functional magnetic resonance imaging group studies rely on the ability to establish correspondence across individuals. This enables location specific comparison of functional brain characteristics. Registration is often based on morphology and does not take variability of functional localization into account. This can lead to a loss of specificity, or confounds when studying diseases. In this paper we propose multi-subject functional registration by manifold alignment via coupled joint diagonalization. The functional network structure of each subject is encoded in a diffusion map, where functional relationships are decoupled from spatial position. Two-step manifold alignment estimates initial correspondences between functionally equivalent regions. Then, coupled joint diagonalization establishes common eigenbases across all individuals, and refines the functional correspondences. We evaluate our approach on fMRI data acquired during a language paradigm. Experiments demonstrate the benefits in matching accuracy achieved by coupled joint diagonalization compared to previously proposed functional alignment approaches, or alignment based on structural correspondences.

Robot graphic simulation testbed

NASA Technical Reports Server (NTRS)

Cook, George E.; Sztipanovits, Janos; Biegl, Csaba; Karsai, Gabor; Springfield, James F.

1991-01-01

The objective of this research was twofold. First, the basic capabilities of ROBOSIM (graphical simulation system) were improved and extended by taking advantage of advanced graphic workstation technology and artificial intelligence programming techniques. Second, the scope of the graphic simulation testbed was extended to include general problems of Space Station automation. Hardware support for 3-D graphics and high processing performance make high resolution solid modeling, collision detection, and simulation of structural dynamics computationally feasible. The Space Station is a complex system with many interacting subsystems. Design and testing of automation concepts demand modeling of the affected processes, their interactions, and that of the proposed control systems. The automation testbed was designed to facilitate studies in Space Station automation concepts.

Network, system, and status software enhancements for the autonomously managed electrical power system breadboard. Volume 4: Graphical status display

NASA Technical Reports Server (NTRS)

Mckee, James W.

1990-01-01

This volume (4 of 4) contains the description, structured flow charts, prints of the graphical displays, and source code to generate the displays for the AMPS graphical status system. The function of these displays is to present to the manager of the AMPS system a graphical status display with the hot boxes that allow the manager to get more detailed status on selected portions of the AMPS system. The development of the graphical displays is divided into two processes; the creation of the screen images and storage of them in files on the computer, and the running of the status program which uses the screen images.

The use of interpractive graphic displays for interpretation of surface design parameters

NASA Technical Reports Server (NTRS)

Talcott, N. A., Jr.

1981-01-01

An interactive computer graphics technique known as the Graphic Display Data method has been developed to provide a convenient means for rapidly interpreting large amounts of surface design data. The display technique should prove valuable in such disciplines as aerodynamic analysis, structural analysis, and experimental data analysis. To demonstrate the system's features, an example is presented of the Graphic Data Display method used as an interpretive tool for radiation equilibrium temperature distributions over the surface of an aerodynamic vehicle. Color graphic displays were also examined as a logical extension of the technique to improve its clarity and to allow the presentation of greater detail in a single display.

The low-temperature structural behavior of sodium 1-carba-closo-decaborate: NaCB{sub 9}H{sub 10}

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

Wu, Hui, E-mail: hui.wu@nist.gov; Tang, Wan Si; Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742-2115

2016-11-15

Two ordered phases of the novel solid superionic conductor sodium 1-carba-closo-decaborate (NaCB{sub 9}H{sub 10}) were identified via synchrotron x-ray powder diffraction in combination with first-principles calculations and neutron vibrational spectroscopy. A monoclinic packing of the large ellipsoidal CB{sub 9}H{sub 10}{sup −} anions prevails at the lowest temperatures, but a first-order transformation to a slightly modified orthorhombic packing is largely complete by 240 K. The CB{sub 9}H{sub 10}{sup −} anion orientational alignments and Na{sup +} cation interstitial sitings in both phases are arranged so as to minimize the cation proximities to the uniquely more positive C-bonded H atoms of the anions.more » These results provide valuable structural information pertinent to understanding the relatively low-temperature, entropy-driven, order-disorder phase transition for this compound. - Graphical abstract: Ordered monoclinic and orthorhombic NaCB{sub 9}H{sub 10} phases were determined by XRD and DFT computations and corroborated by neutron vibrational spectroscopy. - Highlights: • Two T-dependent ordered structures of Na(1-CB{sub 9}H{sub 10}) were determined by XRD. • The lower-T monoclinic to higher-T orthorhombic transition occurs from 210 to 240 K. • The main structural differences involve changes in the canting of the CB{sub 9}H{sub 10}{sup −} anions. • DFT and neutron vibrational spectroscopy corroborate the lower-T monoclinic structure. • The results are important for understanding the nature of this superionic conductor.« less

Profex: a graphical user interface for the Rietveld refinement program BGMN.

PubMed

Doebelin, Nicola; Kleeberg, Reinhard

2015-10-01

Profex is a graphical user interface for the Rietveld refinement program BGMN . Its interface focuses on preserving BGMN 's powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems.

Profex: a graphical user interface for the Rietveld refinement program BGMN

PubMed Central

Doebelin, Nicola; Kleeberg, Reinhard

2015-01-01

Profex is a graphical user interface for the Rietveld refinement program BGMN. Its interface focuses on preserving BGMN’s powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems. PMID:26500466

A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors

NASA Astrophysics Data System (ADS)

Mestres, Jordi; Rohrer, Douglas C.; Maggiora, Gerald M.

1999-01-01

This article describes a molecular-field-based similarity method for aligning molecules by matching their steric and electrostatic fields and an application of the method to the alignment of three structurally diverse non-nucleoside HIV-1 reverse transcriptase inhibitors. A brief description of the method, as implemented in the program MIMIC, is presented, including a discussion of pairwise and multi-molecule similarity-based matching. The application provides an example that illustrates how relative binding orientations of molecules can be determined in the absence of detailed structural information on their target protein. In the particular system studied here, availability of the X-ray crystal structures of the respective ligand-protein complexes provides a means for constructing an 'experimental model' of the relative binding orientations of the three inhibitors. The experimental model is derived by using MIMIC to align the steric fields of the three protein P66 subunit main chains, producing an overlay with a 1.41 Å average rms distance between the corresponding Cα's in the three chains. The inter-chain residue similarities for the backbone structures show that the main-chain conformations are conserved in the region of the inhibitor-binding site, with the major deviations located primarily in the 'finger' and RNase H regions. The resulting inhibitor structure overlay provides an experimental-based model that can be used to evaluate the quality of the direct a priori inhibitor alignment obtained using MIMIC. It is found that the 'best' pairwise alignments do not always correspond to the experimental model alignments. Therefore, simply combining the best pairwise alignments will not necessarily produce the optimal multi-molecule alignment. However, the best simultaneous three-molecule alignment was found to reproduce the experimental inhibitor alignment model. A pairwise consistency index has been derived which gauges the quality of combining the pairwise alignments and aids in efficiently forming the optimal multi-molecule alignment analysis. Two post-alignment procedures are described that provide information on feature-based and field-based pharmacophoric patterns. The former corresponds to traditional pharmacophore models and is derived from the contribution of individual atoms to the total similarity. The latter is based on molecular regions rather than atoms and is constructed by computing the percent contribution to the similarity of individual points in a regular lattice surrounding the molecules, which when contoured and colored visually depict regions of highly conserved similarity. A discussion of how the information provided by each of the procedures is useful in drug design is also presented.

Structure and ionic conductivity of well-aligned polycrystalline sodium titanogallate grown by reactive diffusion

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

Hasegawa, Ryo; Okabe, Momoko; Asaka, Toru

We prepared the b-axis-oriented polycrystalline Na{sub 0.85}Ti{sub 0.51}Ga{sub 4.37}O{sub 8} (NTGO) embedded in Ga{sub 2}O{sub 3}-doped Na{sub 2}Ti{sub 4}O{sub 9} matrix using the reactive diffusion technique. When the sandwich-type Ga{sub 2}TiO{sub 5}/NaGaO{sub 2}/Ga{sub 2}TiO{sub 5} diffusion couple was heated at 1323 K for 24 h, the NTGO polycrystal was readily formed in the presence of a liquid phase. The resulting polycrystalline material was characterized by X-ray diffractometry, electron microscopy and impedance spectroscopy. We mechanically processed the annealed diffusion couple and obtained the thin-plate electrolyte consisting mostly of the grain-aligned NTGO polycrystal. The ionic conductivity (σ) of the electrolyte along themore » common b-axis direction steadily increased from 1.3×10{sup −4} to 7.3×10{sup −3} S/cm as the temperature increased from 573 to 1073 K. There was a slope change at ca. 792 K for the Arrhenius plot of σ; the activation energies were 0.39 eV above this temperature and 0.57 eV below it. The NTGO showed the crystal structure (space group C2/m) with substantial positional disordering of one of the two Ga sites. The Na{sup +} ions occupied ca. 43% of the Wyckoff position 4i site, the deficiency of which would contribute to the relatively high ionic conductivity along the b-axis. The reactive diffusion could be widely applicable as the novel technique to the preparation of grain-aligned ceramics of multi-component systems. - Graphical abstract: We have prepared the b-axis-oriented Na{sub 0.85}Ti{sub 0.51}Ga{sub 4.37}O{sub 8} polycrystal embedded in Ga{sub 2}O{sub 3}-doped Na{sub 2}Ti{sub 4}O{sub 9} matrix by the heat treatment of sandwich-type diffusion couple of Ga{sub 2}TiO{sub 5}/NaGaO{sub 2}/Ga{sub 2}TiO{sub 5}. The resulting Na{sub 0.85}Ti{sub 0.51}Ga{sub 4.37}O{sub 8} electrolyte showed the ionic conductivity ranging from 1.3×10{sup −4} S/cm at 573 K to 7.3×10{sup −3} S/cm at 1073 K. - Highlights: • The b-axis-oriented polycrystalline Na{sub 0.85}Ti{sub 0.51}Ga{sub 4.37}O{sub 8} is successfully prepared. • Crystal structure of Na{sub 0.85}Ti{sub 0.51}Ga{sub 4.37}O{sub 8} is determined by single-crystal XRD. • The polycrystal shows relatively high Na{sup +} ion conductivity along the common b-axis. • Reactive diffusion is successfully used for the preparation of grain-aligned ceramics.« less

DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures.

PubMed

Irfanoglu, M Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B; Sadeghi, Neda; Thomas, Cibu P; Pierpaoli, Carlo

2016-05-15

In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. Copyright © 2016 Elsevier Inc. All rights reserved.

Fall Department Head Report--Reporting Booklet 2.0 to the Massachusetts Division of Occupational Education (Fiscal Year Ending June 30, 1975) for Graphic Arts and Graphic Design.

ERIC Educational Resources Information Center

Management and Information System for Occupational Education, Winchester, MA.

The reporting booklet is required for the Census Data System (CDS) of the Management Information System for Occupational Education (MISOE); it contains the reporting forms which collect data that describe program structure and job-entry skill outcomes expected of program completors in the individual occupational education area of graphic arts and…

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

ERIC Educational Resources Information Center

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

2015-01-01

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

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

PubMed

Krissinel, E; Henrick, K

2004-12-01

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

A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

PubMed Central

Challis, Christopher J.; Schmidler, Scott C.

2012-01-01

We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein–Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution. PMID:22723302

The Visual Communication or Graphic Communication Dilemma

ERIC Educational Resources Information Center

Fecik, John T.

1975-01-01

The author reviews the history of communication and communications technology, considers differences between "visual communication" and "graphic communication," and comments on "seeds of revolution" in the industry. He offers four components of an educational structure or organization titled "graphic…

Parallel seed-based approach to multiple protein structure similarities detection

DOE PAGES

Chapuis, Guillaume; Le Boudic-Jamin, Mathilde; Andonov, Rumen; ...

2015-01-01

Finding similarities between protein structures is a crucial task in molecular biology. Most of the existing tools require proteins to be aligned in order-preserving way and only find single alignments even when multiple similar regions exist. We propose a new seed-based approach that discovers multiple pairs of similar regions. Its computational complexity is polynomial and it comes with a quality guarantee—the returned alignments have both root mean squared deviations (coordinate-based as well as internal-distances based) lower than a given threshold, if such exist. We do not require the alignments to be order preserving (i.e., we consider nonsequential alignments), which makesmore » our algorithm suitable for detecting similar domains when comparing multidomain proteins as well as to detect structural repetitions within a single protein. Because the search space for nonsequential alignments is much larger than for sequential ones, the computational burden is addressed by extensive use of parallel computing techniques: a coarse-grain level parallelism making use of available CPU cores for computation and a fine-grain level parallelism exploiting bit-level concurrency as well as vector instructions.« less

Evidence for Syntactic Alignment in Children with Autism

ERIC Educational Resources Information Center

Allen, Melissa L.; Haywood, Sarah; Rajendran, Gnanathusharan; Branigan, Holly

2011-01-01

We report an experiment that examined whether children with Autistic Spectrum Disorder (ASD) spontaneously converge, or align, syntactic structure with a conversational partner. Children with ASD were more likely to produce a passive structure to describe a picture after hearing their interlocutor use a passive structure to describe an unrelated…

Improving Robotic Operator Performance Using Augmented Reality

NASA Technical Reports Server (NTRS)

Maida, James C.; Bowen, Charles K.; Pace, John W.

2007-01-01

The Special Purpose Dexterous Manipulator (SPDM) is a two-armed robot that functions as an extension to the end effector of the Space Station Robotics Manipulator System (SSRMS), currently in use on the International Space Station (ISS). Crew training for the SPDM is accomplished using a robotic hardware simulator, which performs most of SPDM functions under normal static Earth gravitational forces. Both the simulator and SPDM are controlled from a standard robotic workstation using a laptop for the user interface and three monitors for camera views. Most operations anticipated for the SPDM involve the manipulation, insertion, and removal of any of several types of Orbital Replaceable Unit (ORU), modules which control various ISS functions. Alignment tolerances for insertion of the ORU into its receptacle are 0.25 inch and 0.5 degree from nominal values. The pre-insertion alignment task must be performed within these tolerances by using available video camera views of the intrinsic features of the ORU and receptacle, without special registration markings. Since optimum camera views may not be available, and dynamic orbital lighting conditions may limit periods of viewing, a successful ORU insertion operation may require an extended period of time. This study explored the feasibility of using augmented reality (AR) to assist SPDM operations. Geometric graphical symbols were overlaid on one of the workstation monitors to afford cues to assist the operator in attaining adequate pre-insertion ORU alignment. Twelve skilled subjects performed eight ORU insertion tasks using the simulator with and without the AR symbols in a repeated measures experimental design. Results indicated that using the AR symbols reduced pre-insertion alignment error for all subjects and reduced the time to complete pre-insertion alignment for most subjects.

CLAST: CUDA implemented large-scale alignment search tool.

PubMed

Yano, Masahiro; Mori, Hiroshi; Akiyama, Yutaka; Yamada, Takuji; Kurokawa, Ken

2014-12-11

Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing technologies.

Minerals and aligned collagen fibrils in tilapia fish scales: structural analysis using dark-field and energy-filtered transmission electron microscopy and electron tomography.

PubMed

Okuda, Mitsuhiro; Ogawa, Nobuhiro; Takeguchi, Masaki; Hashimoto, Ayako; Tagaya, Motohiro; Chen, Song; Hanagata, Nobutaka; Ikoma, Toshiyuki

2011-10-01

The mineralized structure of aligned collagen fibrils in a tilapia fish scale was investigated using transmission electron microscopy (TEM) techniques after a thin sample was prepared using aqueous techniques. Electron diffraction and electron energy loss spectroscopy data indicated that a mineralized internal layer consisting of aligned collagen fibrils contains hydroxyapatite crystals. Bright-field imaging, dark-field imaging, and energy-filtered TEM showed that the hydroxyapatite was mainly distributed in the hole zones of the aligned collagen fibrils structure, while needle-like materials composed of calcium compounds including hydroxyapatite existed in the mineralized internal layer. Dark-field imaging and three-dimensional observation using electron tomography revealed that hydroxyapatite and needle-like materials were mainly found in the matrix between the collagen fibrils. It was observed that hydroxyapatite and needle-like materials were preferentially distributed on the surface of the hole zones in the aligned collagen fibrils structure and in the matrix between the collagen fibrils in the mineralized internal layer of the scale.

TAIGA: Twente Advanced Interactive Graphic Authoring System. A New Concept in Computer Assisted Learning (CAL) and Educational Research. Doc 88-18.

ERIC Educational Resources Information Center

Pilot, A.

TAIGA (Twente Advanced Interactive Graphic Authoring system) is a system which can be used to develop instructional software. It is written in MS-PASCAL, and runs on computers that support MS-DOS. Designed to support the production of structured software, TAIGA has a hierarchical structure of three layers, each with a specific function, and each…

Graphic Somatography: Life Writing, Comics, and the Ethics of Care.

PubMed

DeFalco, Amelia

2016-09-01

This essay considers the ways in which graphic caregiving memoirs complicate the idealizing tendencies of ethics of care philosophy. The medium's "capacious" layering of words, images, temporalities, and perspectives produces "productive tensions. . . The words and images entwine, but never synthesize" (Chute 2010, 5). In graphic memoirs about care, this "capaciousness" allows for quick oscillation between the rewards and struggles of care work, representing ambiguous, even ambivalent attitudes toward care. Graphic memoirs effectively represent multiple perspectives without synthesis, part of a structural and thematic ambivalence that provides a provocative counterpart to the abstract idealism of ethics of care philosophy.

Aligning for accountable care: Strategic practices for change in accountable care organizations.

PubMed

Hilligoss, Brian; Song, Paula H; McAlearney, Ann Scheck

Alignment within accountable care organizations (ACOs) is crucial if these new entities are to achieve their lofty goals. However, the concept of alignment remains underexamined, and we know little about the work entailed in creating alignment. The aim of this study was to develop the concept of aligning by identifying and describing the strategic practices administrators use to align the structures, processes, and behaviors of their organizations and individual providers in pursuit of accountable care. We conducted 2-year qualitative case studies of four ACOs that have assumed full risk for the costs and quality of care for defined populations. Five strategic aligning practices were used by all four ACOs. Informing both aligns providers' understandings with the goals and value proposition of the ACO and aligns the providers' attention with the drivers of performance. Involving both aligns ACO leaders' understandings with the realities facing providers and aligns the policies of the ACO with the needs of providers. Enhancing both aligns the operations of individual provider practices with the operations of the ACO and aligns the trust of providers with the ACO. Motivating aligns what providers value with the goals of the ACO. Finally, evolving is a metapractice of learning and adapting that guides the execution of the other four practices. Our findings suggest that there are second-order cognitive (e.g., understandings and attention) and cultural (e.g., trust and values) levels of alignment, as well as a first-order operational level (organizational structures, processes, and incentives). A well-aligned organization may require ongoing repositioning at each of these levels, as well as attention to both cooperative and coordinative dimensions of alignment. Implications for research and practice are discussed.

Layered magnetic structures: Antiferromagnetic-type interlayer coupling and magnetoresistance due to antiparallel alignment

NASA Astrophysics Data System (ADS)

Grünberg, P.; Demokritov, S.; Fuss, A.; Vohl, M.; Wolf, J. A.

1991-04-01

Layered Fe/Cr structures are known to display antiferromagnetic-type interlayer coupling and a new magnetoresistance (MR) effect due to antiparallel magnetization alignment. The strength of the coupling is found to be similar in multilayered structures and in double layers. The oscillatory behavior of the coupling, previously found by Parkin, More, and Roche [Phys. Rev. Lett. 64, 2304 (1990)] on sputtered polycrystalline samples, is here confirmed for epitaxial samples, obtained by thermal evaporation. The new MR effect is interpreted as due to a spin-dependent scattering of the electrons at the Fe-Cr interfaces. The investigations have been extended to Fe/V, Fe/Mn, Fe/Cu, Co/Au, Co/Cr, and Co/Cu structures where the antiparallel alignment of the ferromagnetic layers is obtained via hysteresis effects. A MR effect due to antiparallel alignment, which is strong for Co/Au and Co/Cu but weak in the other cases, has been found.

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.

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.

PubMed

Tristão Ramos, Ravi José; de Azevedo Martins, Allan Cézar; da Silva Delgado, Gabrielle; Ionescu, Crina-Maria; Ürményi, Turán Peter; Silva, Rosane; Koca, Jaroslav

2017-11-15

CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss. CrocoBLAST is freely available online, with ample documentation (webchem.ncbr.muni.cz/Platform/App/CrocoBLAST). No installation or user registration is required. CrocoBLAST is implemented in C, while the graphical user interface is implemented in Java. CrocoBLAST is supported under Linux and Windows, and can be run under Mac OS X in a Linux virtual machine. jkoca@ceitec.cz. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

On-line surface inspection using cylindrical lens-based spectral domain low-coherence interferometry.

PubMed

Tang, Dawei; Gao, Feng; Jiang, X

2014-08-20

We present a spectral domain low-coherence interferometry (SD-LCI) method that is effective for applications in on-line surface inspection because it can obtain a surface profile in a single shot. It has an advantage over existing spectral interferometry techniques by using cylindrical lenses as the objective lenses in a Michelson interferometric configuration to enable the measurement of long profiles. Combined with a modern high-speed CCD camera, general-purpose graphics processing unit, and multicore processors computing technology, fast measurement can be achieved. By translating the tested sample during the measurement procedure, real-time surface inspection was implemented, which is proved by the large-scale 3D surface measurement in this paper. ZEMAX software is used to simulate the SD-LCI system and analyze the alignment errors. Two step height surfaces were measured, and the captured interferograms were analyzed using a fast Fourier transform algorithm. Both 2D profile results and 3D surface maps closely align with the calibrated specifications given by the manufacturer.

SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs

PubMed Central

Shaikh, Tanvir R; Gao, Haixiao; Baxter, William T; Asturias, Francisco J; Boisset, Nicolas; Leith, Ardean; Frank, Joachim

2009-01-01

This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Computation here is performed using the image-processing software SPIDER and can be managed using a graphical user interface, termed the SPIDER Reconstruction Engine. Two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines. Once an existing model is available, reference-based alignment can be used, a procedure that can be iterated. Also described is supervised classification, a method to look for homogeneous subsets when multiple known conformations of the molecule may coexist. PMID:19180078

MatchGUI: A Graphical MATLAB-Based Tool for Automatic Image Co-Registration

NASA Technical Reports Server (NTRS)

Ansar, Adnan I.

2011-01-01

MatchGUI software, based on MATLAB, automatically matches two images and displays the match result by superimposing one image on the other. A slider bar allows focus to shift between the two images. There are tools for zoom, auto-crop to overlap region, and basic image markup. Given a pair of ortho-rectified images (focused primarily on Mars orbital imagery for now), this software automatically co-registers the imagery so that corresponding image pixels are aligned. MatchGUI requires minimal user input, and performs a registration over scale and inplane rotation fully automatically

An Accurate Scalable Template-based Alignment Algorithm

PubMed Central

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

2013-01-01

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

Demonstrating Patterns in the Views Of Stakeholders Regarding Ethically-Salient Issues in Clinical Research: A Novel Use of Graphical Models in Empirical Ethics Inquiry.

PubMed

Kim, Jane Paik; Roberts, Laura Weiss

Empirical ethics inquiry works from the notion that stakeholder perspectives are necessary for gauging the ethical acceptability of human studies and assuring that research aligns with societal expectations. Although common, studies involving different populations often entail comparisons of trends that problematize the interpretation of results. Using graphical model selection - a technique aimed at transcending limitations of conventional methods - this report presents data on the ethics of clinical research with two objectives: (1) to display the patterns of views held by ill and healthy individuals in clinical research as a test of the study's original hypothesis and (2) to introduce graphical model selection as a key analytic tool for ethics research. In this IRB-approved, NIH-funded project, data were collected from 60 mentally ill and 43 physically ill clinical research protocol volunteers, 47 healthy protocol-consented participants, and 29 healthy individuals without research protocol experience. Respondents were queried on the ethical acceptability of research involving people with mental and physical illness (i.e., cancer, HIV, depression, schizophrenia, and post-traumatic stress disorder) and non-illness related sources of vulnerability (e.g., age, class, gender, ethnicity). Using a statistical algorithm, we selected graphical models to display interrelationships among responses to questions. Both mentally and physically ill protocol volunteers revealed a high degree of connectivity among ethically-salient perspectives. Healthy participants, irrespective of research protocol experience, revealed patterns of views that were not highly connected. Between ill and healthy protocol participants, the pattern of views is vastly different. Experience with illness was tied to dense connectivity, whereas healthy individuals expressed views with sparse connections. In offering a nuanced perspective on the interrelation of ethically relevant responses, graphical model selection has the potential to bring new insights to the field of ethics.

Applications of the pipeline environment for visual informatics and genomics computations

PubMed Central

2011-01-01

Background Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. Results This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. Conclusions The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power to a broad spectrum of informatics investigators - experienced developers and novice users, user with or without access to advanced computational-resources (e.g., Grid, data), as well as basic and translational scientists. The open development, validation and dissemination of computational networks (pipeline workflows) facilitates the sharing of knowledge, tools, protocols and best practices, and enables the unbiased validation and replication of scientific findings by the entire community. PMID:21791102

The protein structure prediction problem could be solved using the current PDB library

PubMed Central

Zhang, Yang; Skolnick, Jeffrey

2005-01-01

For single-domain proteins, we examine the completeness of the structures in the current Protein Data Bank (PDB) library for use in full-length model construction of unknown sequences. To address this issue, we employ a comprehensive benchmark set of 1,489 medium-size proteins that cover the PDB at the level of 35% sequence identity and identify templates by structure alignment. With homologous proteins excluded, we can always find similar folds to native with an average rms deviation (RMSD) from native of 2.5 Å with ≈82% alignment coverage. These template structures often contain a significant number of insertions/deletions. The tasser algorithm was applied to build full-length models, where continuous fragments are excised from the top-scoring templates and reassembled under the guide of an optimized force field, which includes consensus restraints taken from the templates and knowledge-based statistical potentials. For almost all targets (except for 2/1,489), the resultant full-length models have an RMSD to native below 6 Å (97% of them below 4 Å). On average, the RMSD of full-length models is 2.25 Å, with aligned regions improved from 2.5 Å to 1.88 Å, comparable with the accuracy of low-resolution experimental structures. Furthermore, starting from state-of-the-art structural alignments, we demonstrate a methodology that can consistently bring template-based alignments closer to native. These results are highly suggestive that the protein-folding problem can in principle be solved based on the current PDB library by developing efficient fold recognition algorithms that can recover such initial alignments. PMID:15653774

IMGT, the International ImMunoGeneTics database.

PubMed Central

Lefranc, M P; Giudicelli, V; Busin, C; Bodmer, J; Müller, W; Bontrop, R; Lemaitre, M; Malik, A; Chaume, D

1998-01-01

IMGT, the international ImMunoGeneTics database, is an integrated database specialising in Immunoglobulins (Ig), T cell Receptors (TcR) and Major Histocompatibility Complex (MHC) of all vertebrate species, created by Marie-Paule Lefranc, CNRS, Montpellier II University, Montpellier, France (lefranc@ligm.crbm.cnrs-mop.fr). IMGT includes three databases: LIGM-DB (for Ig and TcR), MHC/HLA-DB and PRIMER-DB (the last two in development). IMGT comprises expertly annotated sequences and alignment tables. LIGM-DB contains more than 23 000 Immunoglobulin and T cell Receptor sequences from 78 species. MHC/HLA-DB contains Class I and Class II Human Leucocyte Antigen alignment tables. An IMGT tool, DNAPLOT, developed for Ig, TcR and MHC sequence alignments, is also available. IMGT works in close collaboration with the EMBL database. IMGT goals are to establish a common data access to all immunogenetics data, including nucleotide and protein sequences, oligonucleotide primers, gene maps and other genetic data of Ig, TcR and MHC molecules, and to provide a graphical user friendly data access. IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas), therapeutical approaches (antibody engineering), genome diversity and genome evolution studies. IMGT is freely available at http://imgt.cnusc.fr:8104 PMID:9399859

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU.

PubMed

Zhang, Jing; Wang, Hao; Feng, Wu-Chun

2017-01-01

BLAST, short for Basic Local Alignment Search Tool, is a ubiquitous tool used in the life sciences for pairwise sequence search. However, with the advent of next-generation sequencing (NGS), whether at the outset or downstream from NGS, the exponential growth of sequence databases is outstripping our ability to analyze the data. While recent studies have utilized the graphics processing unit (GPU) to speedup the BLAST algorithm for searching protein sequences (i.e., BLASTP), these studies use coarse-grained parallelism, where one sequence alignment is mapped to only one thread. Such an approach does not efficiently utilize the capabilities of a GPU, particularly due to the irregularity of BLASTP in both execution paths and memory-access patterns. To address the above shortcomings, we present a fine-grained approach to parallelize BLASTP, where each individual phase of sequence search is mapped to many threads on a GPU. This approach, which we refer to as cuBLASTP, reorders data-access patterns and reduces divergent branches of the most time-consuming phases (i.e., hit detection and ungapped extension). In addition, cuBLASTP optimizes the remaining phases (i.e., gapped extension and alignment with trace back) on a multicore CPU and overlaps their execution with the phases running on the GPU.

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

PubMed

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

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

Cryo-EM Image Alignment Based on Nonuniform Fast Fourier Transform

PubMed Central

Yang, Zhengfan; Penczek, Pawel A.

2008-01-01

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

Alignments of Dark Matter Halos with Large-scale Tidal Fields: Mass and Redshift Dependence

NASA Astrophysics Data System (ADS)

Chen, Sijie; Wang, Huiyuan; Mo, H. J.; Shi, Jingjing

2016-07-01

Large-scale tidal fields estimated directly from the distribution of dark matter halos are used to investigate how halo shapes and spin vectors are aligned with the cosmic web. The major, intermediate, and minor axes of halos are aligned with the corresponding tidal axes, and halo spin axes tend to be parallel with the intermediate axes and perpendicular to the major axes of the tidal field. The strengths of these alignments generally increase with halo mass and redshift, but the dependence is only on the peak height, ν \\equiv {δ }{{c}}/σ ({M}{{h}},z). The scaling relations of the alignment strengths with the value of ν indicate that the alignment strengths remain roughly constant when the structures within which the halos reside are still in a quasi-linear regime, but decreases as nonlinear evolution becomes more important. We also calculate the alignments in projection so that our results can be compared directly with observations. Finally, we investigate the alignments of tidal tensors on large scales, and use the results to understand alignments of halo pairs separated at various distances. Our results suggest that the coherent structure of the tidal field is the underlying reason for the alignments of halos and galaxies seen in numerical simulations and in observations.

Quantum size and electric field modulations on electronic structures of SnS2/BN hetero-multilayers

NASA Astrophysics Data System (ADS)

Xia, Congxin; Zhang, Qian; Xiao, Wenbo; Du, Juan; Li, Xueping; Li, Jingbo

2018-05-01

Through first-principles calculations, we study the stability, band structures, band alignment, and interlayer charge transfer of SnS2/BN hetero-multilayers, considering quantum size and electric field effects. We find that SnS2/BN hetero-multilayers possess the characteristics of direct band structures and type-II band alignment. Moreover, increasing the BN layer number can decrease the band gap value and work function. Additionally, type-II can be tuned to type-I band alignment in the presence of an electric field. These results indicate that the SnS2/BN system is different from that of other BN-based hybrid materials, such as MoS2/BN with type-I band alignment, which is promising for optoelectronic device applications.

Active alignment/contact verification system

DOEpatents

Greenbaum, William M.

2000-01-01

A system involving an active (i.e. electrical) technique for the verification of: 1) close tolerance mechanical alignment between two component, and 2) electrical contact between mating through an elastomeric interface. For example, the two components may be an alumina carrier and a printed circuit board, two mating parts that are extremely small, high density parts and require alignment within a fraction of a mil, as well as a specified interface point of engagement between the parts. The system comprises pairs of conductive structures defined in the surfaces layers of the alumina carrier and the printed circuit board, for example. The first pair of conductive structures relate to item (1) above and permit alignment verification between mating parts. The second pair of conductive structures relate to item (2) above and permit verification of electrical contact between mating parts.

PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments.

PubMed

Caffrey, Daniel R; Dana, Paul H; Mathur, Vidhya; Ocano, Marco; Hong, Eun-Jong; Wang, Yaoyu E; Somaroo, Shyamal; Caffrey, Brian E; Potluri, Shobha; Huang, Enoch S

2007-10-11

By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue. Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition. PFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function.

The impact of visual sequencing of graphic symbols on the sentence construction output of children who have acquired language.

PubMed

Alant, Erna; du Plooy, Amelia; Dada, Shakila

2007-01-01

Although the sequence of graphic or pictorial symbols displayed on a communication board can have an impact on the language output of children, very little research has been conducted to describe this. Research in this area is particularly relevant for prioritising the importance of specific visual and graphic features in providing more effective and user-friendly access to communication boards. This study is concerned with understanding the impact ofspecific sequences of graphic symbol input on the graphic and spoken output of children who have acquired language. Forty participants were divided into two comparable groups. Each group was exposed to graphic symbol input with a certain word order sequence. The structure of input was either in typical English word order sequence Subject- Verb-Object (SVO) or in the word order sequence of Subject-Object-Verb (SOV). Both input groups had to answer six questions by using graphic output as well as speech. The findings indicated that there are significant differences in the PCS graphic output patterns of children who are exposed to graphic input in the SOV and SVO sequences. Furthermore, the output produced in the graphic mode differed considerably to the output produced in the spoken mode. Clinical implications of these findings are discussed

Communication Design Education: Could Nine Reflections Be Sufficient?

ERIC Educational Resources Information Center

van der Waarde, Karel; Vroombout, Maurits

2012-01-01

Situation: Graphic design education is subject to substantial changes. Changes in professional practice and higher education aggravate insecurities about the contents and structure of courses, assessment criteria, relations between practice, research and theory and teaching methods. Assumption: Graphic design education (visual communication design…

Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface.

PubMed

Berlin, Konstantin; Longhini, Andrew; Dayie, T Kwaku; Fushman, David

2013-12-01

To facilitate rigorous analysis of molecular motions in proteins, DNA, and RNA, we present a new version of ROTDIF, a program for determining the overall rotational diffusion tensor from single- or multiple-field nuclear magnetic resonance relaxation data. We introduce four major features that expand the program's versatility and usability. The first feature is the ability to analyze, separately or together, (13)C and/or (15)N relaxation data collected at a single or multiple fields. A significant improvement in the accuracy compared to direct analysis of R2/R1 ratios, especially critical for analysis of (13)C relaxation data, is achieved by subtracting high-frequency contributions to relaxation rates. The second new feature is an improved method for computing the rotational diffusion tensor in the presence of biased errors, such as large conformational exchange contributions, that significantly enhances the accuracy of the computation. The third new feature is the integration of the domain alignment and docking module for relaxation-based structure determination of multi-domain systems. Finally, to improve accessibility to all the program features, we introduced a graphical user interface that simplifies and speeds up the analysis of the data. Written in Java, the new ROTDIF can run on virtually any computer platform. In addition, the new ROTDIF achieves an order of magnitude speedup over the previous version by implementing a more efficient deterministic minimization algorithm. We not only demonstrate the improvement in accuracy and speed of the new algorithm for synthetic and experimental (13)C and (15)N relaxation data for several proteins and nucleic acids, but also show that careful analysis required especially for characterizing RNA dynamics allowed us to uncover subtle conformational changes in RNA as a function of temperature that were opaque to previous analysis.

bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System.

PubMed

Alexander, Nathan; Woetzel, Nils; Meiler, Jens

2011-02-01

Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.

On the typography of flight-deck documentation

NASA Technical Reports Server (NTRS)

Degani, Asaf

1992-01-01

Many types of paper documentation are employed on the flight-deck. They range from a simple checklist card to a bulky Aircraft Flight Manual (AFM). Some of these documentations have typographical and graphical deficiencies; yet, many cockpit tasks such as conducting checklists, way-point entry, limitations and performance calculations, and many more, require the use of these documents. Moreover, during emergency and abnormal situations, the flight crews' effectiveness in combating the situation is highly dependent on such documentation; accessing and reading procedures has a significant impact on flight safety. Although flight-deck documentation are an important (and sometimes critical) form of display in the modern cockpit, there is a dearth of information on how to effectively design these displays. The object of this report is to provide a summary of the available literature regarding the design and typographical aspects of printed matter. The report attempts 'to bridge' the gap between basic research about typography, and the kind of information needed by designers of flight-deck documentation. The report focuses on typographical factors such as type-faces, character height, use of lower- and upper-case characters, line length, and spacing. Some graphical aspects such as layout, color coding, fonts, and character contrast are also discussed. In addition, several aspects of cockpit reading conditions such as glare, angular alignment, and paper quality are addressed. Finally, a list of recommendations for the graphical design of flight-deck documentation is provided.

Analyzing Sliding Stability of Structures Using the Modified Computer Program GWALL. Revision,

DTIC Science & Technology

1983-11-01

R136 954 RNRLYZING SLIDING STRBILITY OF STRUCTURES USING THE i/i MODIFIED COMPUTER PRO..(U) ARMY ENGINEER WATERRYS EXPERIMENT STATION VICKSBURG MS...GWALL and/or the graphics software package, Graphics Compati- bility System (GCS). Input Features 4. GWALL is very easy to use because it allows the...Prepared Data File 9. Time-sharing computer systems do not always respond quickly to the userts commands, especially when there are many users

Generating a 2D Representation of a Complex Data Structure

NASA Technical Reports Server (NTRS)

James, Mark

2006-01-01

A computer program, designed to assist in the development and debugging of other software, generates a two-dimensional (2D) representation of a possibly complex n-dimensional (where n is an integer >2) data structure or abstract rank-n object in that other software. The nature of the 2D representation is such that it can be displayed on a non-graphical output device and distributed by non-graphical means.

ShelXle: a Qt graphical user interface for SHELXL.

PubMed

Hübschle, Christian B; Sheldrick, George M; Dittrich, Birger

2011-12-01

ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (F(o)) and difference density (F(o)-F(c)) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

The Gaussian Graphical Model in Cross-Sectional and Time-Series Data.

PubMed

Epskamp, Sacha; Waldorp, Lourens J; Mõttus, René; Borsboom, Denny

2018-04-16

We discuss the Gaussian graphical model (GGM; an undirected network of partial correlation coefficients) and detail its utility as an exploratory data analysis tool. The GGM shows which variables predict one-another, allows for sparse modeling of covariance structures, and may highlight potential causal relationships between observed variables. We describe the utility in three kinds of psychological data sets: data sets in which consecutive cases are assumed independent (e.g., cross-sectional data), temporally ordered data sets (e.g., n = 1 time series), and a mixture of the 2 (e.g., n > 1 time series). In time-series analysis, the GGM can be used to model the residual structure of a vector-autoregression analysis (VAR), also termed graphical VAR. Two network models can then be obtained: a temporal network and a contemporaneous network. When analyzing data from multiple subjects, a GGM can also be formed on the covariance structure of stationary means-the between-subjects network. We discuss the interpretation of these models and propose estimation methods to obtain these networks, which we implement in the R packages graphicalVAR and mlVAR. The methods are showcased in two empirical examples, and simulation studies on these methods are included in the supplementary materials.

DNA Nanotubes for NMR Structure Determination of Membrane Proteins

PubMed Central

Bellot, Gaëtan; McClintock, Mark A.; Chou, James J; Shih, William M.

2013-01-01

Structure determination of integral membrane proteins by solution NMR represents one of the most important challenges of structural biology. A Residual-Dipolar-Coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size, however, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for weak alignment of membrane proteins was severely limited. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400nm-long six-helix bundles each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, towards collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes via counter ions and small DNA binding molecules. This detergent-resistant liquid-crystal media offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility, and structural programmability. Production of sufficient nanotubes for 4–5 NMR experiments can be completed in one week by a single individual. PMID:23518667

Local-global alignment for finding 3D similarities in protein structures

DOEpatents

Zemla, Adam T [Brentwood, CA

2011-09-20

A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud[OPEN

PubMed Central

Merchant, Nirav

2016-01-01

Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today’s pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant’s Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. PMID:27020957

xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.

PubMed

Duvick, Jon; Standage, Daniel S; Merchant, Nirav; Brendel, Volker P

2016-04-01

Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today's pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant's Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. © 2016 American Society of Plant Biologists. All rights reserved.

Assessing the Moral Coherence and Moral Robustness of Social Systems: Proof of Concept for a Graphical Models Approach.

PubMed

Hoss, Frauke; London, Alex John

2016-12-01

This paper presents a proof of concept for a graphical models approach to assessing the moral coherence and moral robustness of systems of social interactions. "Moral coherence" refers to the degree to which the rights and duties of agents within a system are effectively respected when agents in the system comply with the rights and duties that are recognized as in force for the relevant context of interaction. "Moral robustness" refers to the degree to which a system of social interaction is configured to ensure that the interests of agents are effectively respected even in the face of noncompliance. Using the case of conscientious objection of pharmacists to filling prescriptions for emergency contraception as an example, we illustrate how a graphical models approach can help stakeholders identify structural weaknesses in systems of social interaction and evaluate the relative merits of alternate organizational structures. By illustrating the merits of a graphical models approach we hope to spur further developments in this area.

Representing and comparing protein structures as paths in three-dimensional space

PubMed Central

Zhi, Degui; Krishna, S Sri; Cao, Haibo; Pevzner, Pavel; Godzik, Adam

2006-01-01

Background Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction. Results We propose a structure comparison approach based on a simplified representation of proteins that describes its three-dimensional path by local curvature along the generalized backbone of the polypeptide. We have implemented a dynamic programming procedure that aligns curvatures of proteins by optimizing a defined sum turning angle deviation measure. Conclusion Although our procedure does not directly optimize global structural similarity as measured by RMSD, our benchmarking results indicate that it can surprisingly well recover the structural similarity defined by structure classification databases and traditional structure alignment programs. In addition, our program can recognize similarities between structures with extensive conformation changes that are beyond the ability of traditional structure alignment programs. We demonstrate the applications of procedure to several contexts of structure comparison. An implementation of our procedure, CURVE, is available as a public webserver. PMID:17052359

Formation of the Sun-aligned arc region and the void (polar slot) under the null-separator structure

NASA Astrophysics Data System (ADS)

Tanaka, T.; Obara, T.; Watanabe, M.; Fujita, S.; Ebihara, Y.; Kataoka, R.

2017-04-01

From the global magnetosphere-ionosphere coupling simulation, we examined the formation of the Sun-aligned arc region and the void (polar slot) under the northward interplanetary magnetic field (IMF) with negative By condition. In the magnetospheric null-separator structure, the separatrices generated from two null points and two separators divide the entire space into four types of magnetic region, i.e., the IMF, the northern open magnetic field, the southern open magnetic field, and the closed magnetic field. In the ionosphere, the Sun-aligned arc region and the void are reproduced in the distributions of simulated plasma pressure and field-aligned current. The outermost closed magnetic field lines on the boundary (separatrix) between the northern open magnetic field and the closed magnetic field are projected to the northern ionosphere at the boundary between the Sun-aligned arc region and the void, both on the morning and evening sides. The magnetic field lines at the plasma sheet inner edge are projected to the equatorward boundary of the oval. Therefore, the Sun-aligned arc region is on the closed magnetic field lines of the plasma sheet. In the plasma sheet, an inflated structure (bulge) is generated at the junction of the tilted plasma sheet in the far-to-middle tail and nontilted plasma sheet in the ring current region. In the Northern Hemisphere, the bulge is on the evening side wrapped by the outermost closed magnetic field lines that are connected to the northern evening ionosphere. This inflated structure (bulge) is associated with shear flows that cause the Sun-aligned arc.

Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments

PubMed Central

Wei, Jyh-Da; Cheng, Hui-Jun; Lin, Chun-Yuan; Ye, Jin; Yeh, Kuan-Yu

2017-01-01

High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1), which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs). Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform) was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform). Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments. PMID:28835734

Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments.

PubMed

Wei, Jyh-Da; Cheng, Hui-Jun; Lin, Chun-Yuan; Ye, Jin; Yeh, Kuan-Yu

2017-01-01

High-end graphics processing units (GPUs), such as NVIDIA Tesla/Fermi/Kepler series cards with thousands of cores per chip, are widely applied to high-performance computing fields in a decade. These desktop GPU cards should be installed in personal computers/servers with desktop CPUs, and the cost and power consumption of constructing a GPU cluster platform are very high. In recent years, NVIDIA releases an embedded board, called Jetson Tegra K1 (TK1), which contains 4 ARM Cortex-A15 CPUs and 192 Compute Unified Device Architecture cores (belong to Kepler GPUs). Jetson Tegra K1 has several advantages, such as the low cost, low power consumption, and high applicability, and it has been applied into several specific applications. In our previous work, a bioinformatics platform with a single TK1 (STK platform) was constructed, and this previous work is also used to prove that the Web and mobile services can be implemented in the STK platform with a good cost-performance ratio by comparing a STK platform with the desktop CPU and GPU. In this work, an embedded-based GPU cluster platform will be constructed with multiple TK1s (MTK platform). Complex system installation and setup are necessary procedures at first. Then, 2 job assignment modes are designed for the MTK platform to provide services for users. Finally, ClustalW v2.0.11 and ClustalWtk will be ported to the MTK platform. The experimental results showed that the speedup ratios achieved 5.5 and 4.8 times for ClustalW v2.0.11 and ClustalWtk, respectively, by comparing 6 TK1s with a single TK1. The MTK platform is proven to be useful for multiple sequence alignments.

High-harmonic spectroscopy of aligned molecules

NASA Astrophysics Data System (ADS)

Yun, Hyeok; Yun, Sang Jae; Lee, Gae Hwang; Nam, Chang Hee

2017-01-01

High harmonics emitted from aligned molecules driven by intense femtosecond laser pulses provide the opportunity to explore the structural information of molecules. The field-free molecular alignment technique is an expedient tool for investigating the structural characteristics of linear molecules. The underlying physics of field-free alignment, showing the characteristic revival structure specific to molecular species, is clearly explained from the quantum-phase analysis of molecular rotational states. The anisotropic nature of molecules is shown from the harmonic polarization measurement performed with spatial interferometry. The multi-orbital characteristics of molecules are investigated using high-harmonic spectroscopy, applied to molecules of N2 and CO2. In the latter case the two-dimensional high-harmonic spectroscopy, implemented using a two-color laser field, is applied to distinguish harmonics from different orbitals. Molecular high-harmonic spectroscopy will open a new route to investigate ultrafast dynamics of molecules.

Leveling the Playing Field: Graphical Aids on Mathematics Tests

ERIC Educational Resources Information Center

Jiménez, Albert M.; Nixon, Casey B.; Zepeda, Sally J.

2017-01-01

This research suggests that structural accommodation can be implemented during the construction phase of standardized mathematics examinations. Data from a racially diverse district in the United States are used to compare student performance on questions with and without graphical aids. Findings suggest that mathematics questions possessing…

Graphic Design in Educational Television.

ERIC Educational Resources Information Center

Clarke, Beverley

To help educational television (ETV) practitioners achieve maximum clarity, economy and purposiveness, the range of techniques of television graphics is explained. Closed-circuit and broadcast ETV are compared. The design process is discussed in terms of aspect ratio, line structure, cut off, screen size, tone scales, studio apparatus, and…

Method for alignment of microwires

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

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

2017-01-24

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

Designing an Advanced Instructional Design Advisor: Incorporating Visual Materials and Other Research Issues. Volume 4

DTIC Science & Technology

1991-12-01

property of graphics (such as concreteness) shared by other media that has benefitted performance. The exact componential aspect of a graphic...graphic will normally attempt to convey some substantive information, and it will do so using a "grammar" and "syntax" which are assumed to be shared ...and Ehrenfeucht (1982) specifically tried to equate content as well as structure between a narrative movie (The Unicorn in the Garden) and a text. They

Exact calculation of distributions on integers, with application to sequence alignment.

PubMed

Newberg, Lee A; Lawrence, Charles E

2009-01-01

Computational biology is replete with high-dimensional discrete prediction and inference problems. Dynamic programming recursions can be applied to several of the most important of these, including sequence alignment, RNA secondary-structure prediction, phylogenetic inference, and motif finding. In these problems, attention is frequently focused on some scalar quantity of interest, a score, such as an alignment score or the free energy of an RNA secondary structure. In many cases, score is naturally defined on integers, such as a count of the number of pairing differences between two sequence alignments, or else an integer score has been adopted for computational reasons, such as in the test of significance of motif scores. The probability distribution of the score under an appropriate probabilistic model is of interest, such as in tests of significance of motif scores, or in calculation of Bayesian confidence limits around an alignment. Here we present three algorithms for calculating the exact distribution of a score of this type; then, in the context of pairwise local sequence alignments, we apply the approach so as to find the alignment score distribution and Bayesian confidence limits.

Dimension towers of SICs. I. Aligned SICs and embedded tight frames

NASA Astrophysics Data System (ADS)

Appleby, Marcus; Bengtsson, Ingemar; Dumitru, Irina; Flammia, Steven

2017-11-01

Algebraic number theory relates SIC-POVMs in dimension d > 3 to those in dimension d(d - 2). We define a SIC in dimension d(d - 2) to be aligned to a SIC in dimension d if and only if the squares of the overlap phases in dimension d appear as a subset of the overlap phases in dimension d(d - 2) in a specified way. We give 19 (mostly numerical) examples of aligned SICs. We conjecture that given any SIC in dimension d, there exists an aligned SIC in dimension d(d - 2). In all our examples, the aligned SIC has lower dimensional equiangular tight frames embedded in it. If d is odd so that a natural tensor product structure exists, we prove that the individual vectors in the aligned SIC have a very special entanglement structure, and the existence of the embedded tight frames follows as a theorem. If d - 2 is an odd prime number, we prove that a complete set of mutually unbiased bases can be obtained by reducing an aligned SIC to this dimension.

Physically motivated global alignment method for electron tomography

DOE PAGES

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

2015-04-08

Electron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop amore » new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.« less

Technology Alignment and Portfolio Prioritization (TAPP)

NASA Technical Reports Server (NTRS)

Funaro, Gregory V.; Alexander, Reginald A.

2015-01-01

Technology Alignment and Portfolio Prioritization (TAPP) is a method being developed by the Advanced Concepts Office, at NASA Marshall Space Flight Center. The TAPP method expands on current technology assessment methods by incorporating the technological structure underlying technology development, e.g., organizational structures and resources, institutional policy and strategy, and the factors that motivate technological change. This paper discusses the methods ACO is currently developing to better perform technology assessments while taking into consideration Strategic Alignment, Technology Forecasting, and Long Term Planning.

fRMSDPred: Predicting Local RMSD Between Structural Fragments Using Sequence Information

DTIC Science & Technology

2007-04-04

machine learning approaches for estimating the RMSD value of a pair of protein fragments. These estimated fragment-level RMSD values can be used to construct the alignment, assess the quality of an alignment, and identify high-quality alignment segments. We present algorithms to solve this fragment-level RMSD prediction problem using a supervised learning framework based on support vector regression and classification that incorporates protein profiles, predicted secondary structure, effective information encoding schemes, and novel second-order pairwise exponential kernel

LenVarDB: database of length-variant protein domains.

PubMed

Mutt, Eshita; Mathew, Oommen K; Sowdhamini, Ramanathan

2014-01-01

Protein domains are functionally and structurally independent modules, which add to the functional variety of proteins. This array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. Length variations (indels) can introduce changes at structural, functional and interaction levels. LenVarDB (freely available at http://caps.ncbs.res.in/lenvardb/) traces these length variations, starting from structure-based sequence alignments in our Protein Alignments organized as Structural Superfamilies (PASS2) database, across 731 structural classification of proteins (SCOP)-based protein domain superfamilies connected to 2 730 625 sequence homologues. Alignment of sequence homologues corresponding to a structural domain is available, starting from a structure-based sequence alignment of the superfamily. Orientation of the length-variant (indel) regions in protein domains can be visualized by mapping them on the structure and on the alignment. Knowledge about location of length variations within protein domains and their visual representation will be useful in predicting changes within structurally or functionally relevant sites, which may ultimately regulate protein function. Non-technical summary: Evolutionary changes bring about natural changes to proteins that may be found in many organisms. Such changes could be reflected as amino acid substitutions or insertions-deletions (indels) in protein sequences. LenVarDB is a database that provides an early overview of observed length variations that were set among 731 protein families and after examining >2 million sequences. Indels are followed up to observe if they are close to the active site such that they can affect the activity of proteins. Inclusion of such information can aid the design of bioengineering experiments.

An alternative view of protein fold space.

PubMed

Shindyalov, I N; Bourne, P E

2000-02-15

Comparing and subsequently classifying protein structures information has received significant attention concurrent with the increase in the number of experimentally derived 3-dimensional structures. Classification schemes have focused on biological function found within protein domains and on structure classification based on topology. Here an alternative view is presented that groups substructures. Substructures are long (50-150 residue) highly repetitive near-contiguous pieces of polypeptide chain that occur frequently in a set of proteins from the PDB defined as structurally non-redundant over the complete polypeptide chain. The substructure classification is based on a previously reported Combinatorial Extension (CE) algorithm that provides a significantly different set of structure alignments than those previously described, having, for example, only a 40% overlap with FSSP. Qualitatively the algorithm provides longer contiguous aligned segments at the price of a slightly higher root-mean-square deviation (rmsd). Clustering these alignments gives a discreet and highly repetitive set of substructures not detectable by sequence similarity alone. In some cases different substructures represent all or different parts of well known folds indicative of the Russian doll effect--the continuity of protein fold space. In other cases they fall into different structure and functional classifications. It is too early to determine whether these newly classified substructures represent new insights into the evolution of a structural framework important to many proteins. What is apparent from on-going work is that these substructures have the potential to be useful probes in finding remote sequence homology and in structure prediction studies. The characteristics of the complete all-by-all comparison of the polypeptide chains present in the PDB and details of the filtering procedure by pair-wise structure alignment that led to the emergent substructure gallery are discussed. Substructure classification, alignments, and tools to analyze them are available at http://cl.sdsc.edu/ce.html.

OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals.

PubMed

Douzery, Emmanuel J P; Scornavacca, Celine; Romiguier, Jonathan; Belkhir, Khalid; Galtier, Nicolas; Delsuc, Frédéric; Ranwez, Vincent

2014-07-01

Comparative genomic studies extensively rely on alignments of orthologous sequences. Yet, selecting, gathering, and aligning orthologous exons and protein-coding sequences (CDS) that are relevant for a given evolutionary analysis can be a difficult and time-consuming task. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of orthologous genes in mammalian genomes using a phylogenetic framework. Since its first release in 2007, OrthoMaM has regularly evolved, not only to include newly available genomes but also to incorporate up-to-date software in its analytic pipeline. This eighth release integrates the 40 complete mammalian genomes available in Ensembl v73 and provides alignments, phylogenies, evolutionary descriptor information, and functional annotations for 13,404 single-copy orthologous CDS and 6,953 long exons. The graphical interface allows to easily explore OrthoMaM to identify markers with specific characteristics (e.g., taxa availability, alignment size, %G+C, evolutionary rate, chromosome location). It hence provides an efficient solution to sample preprocessed markers adapted to user-specific needs. OrthoMaM has proven to be a valuable resource for researchers interested in mammalian phylogenomics, evolutionary genomics, and has served as a source of benchmark empirical data sets in several methodological studies. OrthoMaM is available for browsing, query and complete or filtered downloads at http://www.orthomam.univ-montp2.fr/. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Understanding Global Change: A New Conceptual Framework To Guide Teaching About Planetary Systems And Both The Causes And Effects Of Changes In Those Systems

NASA Astrophysics Data System (ADS)

Levine, J.; Bean, J. R.

2016-12-01

Goals of the Next Generation Science Standards include understanding climate change and learning about ways to moderate the causes and mitigate the consequences of planetary-scale anthropogenic activities that interact synergistically to affect ecosystems and societies. The sheer number and scale of both causes and effects of global change can be daunting for teachers, and the lack of a clear conceptual framework for presenting this material usually leads educators (and textbooks) to present these phenomenon as a disjointed "laundry list." But an alternative approach is in the works. The Understanding Global Change web resource, currently under development at the UC Berkeley Museum of Paleontology, will provide educators with a conceptual framework, graphic models, lessons, and assessment templates for teaching NGSS-aligned, interdisciplinary, global change curricula. The core of this resource is an original informational graphic that presents and relates Earth's global systems, human and non-human factors that produce changes in those systems, and the effects of those changes that scientists can measure.

Evaluation of SMART sensor displays for multidimensional precision control of Space Shuttle remote manipulator

NASA Technical Reports Server (NTRS)

Bejczy, A. K.; Brown, J. W.; Lewis, J. L.

1982-01-01

An enhanced proximity sensor and display system was developed at the Jet Propulsion Laboratory (JPL) and tested on the full scale Space Shuttle Remote Manipulator at the Johnson Space Center (JSC) Manipulator Development Facility (MDF). The sensor system, integrated with a four-claw end effector, measures range error up to 6 inches, and pitch and yaw alignment errors within + or 15 deg., and displays error data on both graphic and numeric displays. The errors are referenced to the end effector control axes through appropriate data processing by a dedicated microcomputer acting on the sensor data in real time. Both display boxes contain a green lamp which indicates whether the combination of range, pitch and yaw errors will assure a successful grapple. More than 200 test runs were completed in early 1980 by three operators at JSC for grasping static and capturing slowly moving targets. The tests have indicated that the use of graphic/numeric displays of proximity sensor information improves precision control of grasp/capture range by more than a factor of two for both static and dynamic grapple conditions.

Structured grid technology to enable flow simulation in an integrated system environment

NASA Astrophysics Data System (ADS)

Remotigue, Michael Gerard

An application-driven Computational Fluid Dynamics (CFD) environment needs flexible and general tools to effectively solve complex problems in a timely manner. In addition, reusable, portable, and maintainable specialized libraries will aid in rapidly developing integrated systems or procedures. The presented structured grid technology enables the flow simulation for complex geometries by addressing grid generation, grid decomposition/solver setup, solution, and interpretation. Grid generation is accomplished with the graphical, arbitrarily-connected, multi-block structured grid generation software system (GUM-B) developed and presented here. GUM-B is an integrated system comprised of specialized libraries for the graphical user interface and graphical display coupled with a solid-modeling data structure that utilizes a structured grid generation library and a geometric library based on Non-Uniform Rational B-Splines (NURBS). A presented modification of the solid-modeling data structure provides the capability for arbitrarily-connected regions between the grid blocks. The presented grid generation library provides algorithms that are reliable and accurate. GUM-B has been utilized to generate numerous structured grids for complex geometries in hydrodynamics, propulsors, and aerodynamics. The versatility of the libraries that compose GUM-B is also displayed in a prototype to automatically regenerate a grid for a free-surface solution. Grid decomposition and solver setup is accomplished with the graphical grid manipulation and repartition software system (GUMBO) developed and presented here. GUMBO is an integrated system comprised of specialized libraries for the graphical user interface and graphical display coupled with a structured grid-tools library. The described functions within the grid-tools library reduce the possibility of human error during decomposition and setup for the numerical solver by accounting for boundary conditions and connectivity. GUMBO is linked with a flow solver interface, to the parallel UNCLE code, to provide load balancing tools and solver setup. Weeks of boundary condition and connectivity specification and validation has been reduced to hours. The UNCLE flow solver is utilized for the solution of the flow field. To accelerate convergence toward a quick engineering answer, a full multigrid (FMG) approach coupled with UNCLE, which is a full approximation scheme (FAS), is presented. The prolongation operators used in the FMG-FAS method are compared. The procedure is demonstrated on a marine propeller in incompressible flow. Interpretation of the solution is accomplished by vortex feature detection. Regions of "Intrinsic Swirl" are located by interrogating the velocity gradient tensor for complex eigenvalues. The "Intrinsic Swirl" parameter is visualized on a solution of a marine propeller to determine if any vortical features are captured. The libraries and the structured grid technology presented herein are flexible and general enough to tackle a variety of complex applications. This technology has significantly enabled the capability of the ERC personnel to effectively calculate solutions for complex geometries.

Preschool-aged children have difficulty constructing and interpreting simple utterances composed of graphic symbols.

PubMed

Sutton, Ann; Trudeau, Natacha; Morford, Jill; Rios, Monica; Poirier, Marie-Andrée

2010-01-01

Children who require augmentative and alternative communication (AAC) systems while they are in the process of acquiring language face unique challenges because they use graphic symbols for communication. In contrast to the situation of typically developing children, they use different modalities for comprehension (auditory) and expression (visual). This study explored the ability of three- and four-year-old children without disabilities to perform tasks involving sequences of graphic symbols. Thirty participants were asked to transpose spoken simple sentences into graphic symbols by selecting individual symbols corresponding to the spoken words, and to interpret graphic symbol utterances by selecting one of four photographs corresponding to a sequence of three graphic symbols. The results showed that these were not simple tasks for the participants, and few of them performed in the expected manner - only one in transposition, and only one-third of participants in interpretation. Individual response strategies in some cases lead to contrasting response patterns. Children at this age level have not yet developed the skills required to deal with graphic symbols even though they have mastered the corresponding spoken language structures.

G protein-coupled odorant receptors: From sequence to structure.

PubMed

de March, Claire A; Kim, Soo-Kyung; Antonczak, Serge; Goddard, William A; Golebiowski, Jérôme

2015-09-01

Odorant receptors (ORs) are the largest subfamily within class A G protein-coupled receptors (GPCRs). No experimental structural data of any OR is available to date and atomic-level insights are likely to be obtained by means of molecular modeling. In this article, we critically align sequences of ORs with those GPCRs for which a structure is available. Here, an alignment consistent with available site-directed mutagenesis data on various ORs is proposed. Using this alignment, the choice of the template is deemed rather minor for identifying residues that constitute the wall of the binding cavity or those involved in G protein recognition. © 2015 The Protein Society.

Energy Level Alignment at the Interface between Linear-Structured Benzenediamine Molecules and Au(111) Surface

NASA Astrophysics Data System (ADS)

Li, Guo; Rangel, Tonatiuh; Liu, Zhenfei; Cooper, Valentino; Neaton, Jeffrey

Using density functional theory with model self-energy corrections, we calculate the adsorption energetics and geometry, and the energy level alignment of benzenediamine (BDA) molecules adsorbed on Au(111) surfaces. Our calculations show that linear structures of BDA, stabilized via hydrogen bonds between amine groups, are energetically more favorable than monomeric phases. Moreover, our self-energy-corrected calculations of energy level alignment show that the highest occupied molecular orbital energy of the BDA linear structure is deeper relative to the Fermi level relative to the isolated monomer and agrees well with the values measured with photoemission spectroscopy. This work supported by DOE.

G protein-coupled odorant receptors: From sequence to structure

PubMed Central

de March, Claire A; Kim, Soo-Kyung; Antonczak, Serge; Goddard, William A; Golebiowski, Jérôme

2015-01-01

Odorant receptors (ORs) are the largest subfamily within class A G protein-coupled receptors (GPCRs). No experimental structural data of any OR is available to date and atomic-level insights are likely to be obtained by means of molecular modeling. In this article, we critically align sequences of ORs with those GPCRs for which a structure is available. Here, an alignment consistent with available site-directed mutagenesis data on various ORs is proposed. Using this alignment, the choice of the template is deemed rather minor for identifying residues that constitute the wall of the binding cavity or those involved in G protein recognition. PMID:26044705

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

PubMed

Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L

2011-06-02

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/.

Subsurface Mapping: A Question of Position and Interpretation

ERIC Educational Resources Information Center

Kellie, Andrew C.

2009-01-01

This paper discusses the character and challenges inherent in the graphical portrayal of features in subsurface mapping. Subsurface structures are, by their nature, hidden and must be mapped based on drilling and/or geophysical data. Efficient use of graphical techniques is central to effectively communicating the results of expensive exploration…

Chemistry for Kids: What Do Chemists Do? A Program for Grades 1-3.

ERIC Educational Resources Information Center

Umland, Jean B.

1985-01-01

Proposes a simple solution to the problem of expressing graphically absolute configuration, racemic character, and relative configuration in molecules. As demonstrated by several examples, the proposed convention brings added clarity and simplicity to structural drawings and renders graphic displays of chiral molecules as explicit and information…

Arrows: A Special Case of Graphic Communication.

ERIC Educational Resources Information Center

Hardin, Pris

The purpose of this paper is to examine arrow design in relation to the type of pointing, connecting, or processing involved. Three possible approaches to the investigation of arrows as graphic communication include research: by arrow function, relating message structure to arrow design, and linking user expectations to arrow design. The following…

The interaction between cations and anionic groups inducing SHG enhancement in a series of apatite-like crystals: A first-principles study

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

Jing, Qun; University of Chinese Academy of Sciences, Beijing 100049; Department of Physics, School of Science, Shihezi University, Shihezi 832000

2014-11-15

It is an interesting topic to reveal the origin of the SHG intensity enhancement after substitution from alkali and alkali-earth metal atoms to cadmium in a series of apatite-like borates KSr{sub 4}(BO{sub 3}){sub 3}, Ca{sub 5}(BO{sub 3}){sub 3}F, Cd{sub 5}(BO{sub 3}){sub 3}F. Combined with the first-principles method, SHG-density method and real-space atom-cutting method, the electronic structure, the optical properties and the contribution of respective ion and ion groups have been investigated. Second harmonic generation (SHG) responses are mainly attributed to BO{sub 3} groups with π conjugated configuration and their alignment framework. The contributions of A site are more important inmore » CaBOF and CdBOF compounds than in KSrBO. It is also demonstrated that the strong covalent interactions between the boron–oxygen groups and the cadmium atoms contribute the enhancement of SHG responses after substitution from alkali and alkali-earth metal atoms. - graphical abstract: Combined with the first-principles method, SHG-density method and real-space atom-cutting method, the enhancement of SHG response are attributed to the interaction between cadmium and BO{sub 3} groups. - Highlights: • SHG response on a series of apatite-like borates was studied by a SHG-density method. • SHG responses are mainly attributed to BO{sub 3} groups and their alignment framework. • The contributions of A site are more important in CaBOF and CdBOF than in KSrBO. • Covalent interaction between BO and Cd is responsible for SHG of CdBOF.« less

Unsupervised image matching based on manifold alignment.

PubMed

Pei, Yuru; Huang, Fengchun; Shi, Fuhao; Zha, Hongbin

2012-08-01

This paper challenges the issue of automatic matching between two image sets with similar intrinsic structures and different appearances, especially when there is no prior correspondence. An unsupervised manifold alignment framework is proposed to establish correspondence between data sets by a mapping function in the mutual embedding space. We introduce a local similarity metric based on parameterized distance curves to represent the connection of one point with the rest of the manifold. A small set of valid feature pairs can be found without manual interactions by matching the distance curve of one manifold with the curve cluster of the other manifold. To avoid potential confusions in image matching, we propose an extended affine transformation to solve the nonrigid alignment in the embedding space. The comparatively tight alignments and the structure preservation can be obtained simultaneously. The point pairs with the minimum distance after alignment are viewed as the matchings. We apply manifold alignment to image set matching problems. The correspondence between image sets of different poses, illuminations, and identities can be established effectively by our approach.

Rapid shear alignment of sub-10 nm cylinder-forming block copolymer films based on thermal expansion mismatch

NASA Astrophysics Data System (ADS)

Nicaise, Samuel M.; Gadelrab, Karim R.; G, Amir Tavakkoli K.; Ross, Caroline A.; Alexander-Katz, Alfredo; Berggren, Karl K.

2018-01-01

Directed self-assembly of block copolymers (BCPs) provided by shear-stress can produce aligned sub-10 nm structures over large areas for applications in integrated circuits, next-generation data storage, and plasmonic structures. In this work, we present a fast, versatile BCP shear-alignment process based on coefficient of thermal expansion mismatch of the BCP film, a rigid top coat and a substrate. Monolayer and bilayer cylindrical microdomains of poly(styrene-b-dimethylsiloxane) aligned preferentially in-plane and orthogonal to naturally-forming or engineered cracks in the top coat film, allowing for orientation control over 1 cm2 substrates. Annealing temperatures, up to 275 °C, provided low-defect alignment up to 2 mm away from cracks for rapid (<1 min) annealing times. Finite-element simulations of the stress as a function of annealing time, annealing temperature, and distance from cracks showed that shear stress during the cooling phase of the thermal annealing was critical for the observed microdomain alignment.

Statistical Significance of Optical Map Alignments

PubMed Central

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

2012-01-01

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

DNA nanotubes for NMR structure determination of membrane proteins.

PubMed

Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

2013-04-01

Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

Permanent bending and alignment of ZnO nanowires.

PubMed

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

2011-05-06

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

NASTRAN data generation and management using interactive graphics

NASA Technical Reports Server (NTRS)

Smootkatow, M.; Cooper, B. M.

1972-01-01

A method of using an interactive graphics device to generate a large portion of the input bulk data with visual checks of the structure and the card images is described. The generation starts from GRID and PBAR cards. The visual checks result from a three-dimensional display of the model in any rotated position. By detailing the steps, the time saving and cost effectiveness of this method may be judged, and its potential as a useful tool for the structural analyst may be established.

Image selection system. [computerized data storage and retrieval system

NASA Technical Reports Server (NTRS)

Knutson, M. A.; Hurd, D.; Hubble, L.; Kroeck, R. M.

1974-01-01

An image selection (ISS) was developed for the NASA-Ames Research Center Earth Resources Aircraft Project. The ISS is an interactive, graphics oriented, computer retrieval system for aerial imagery. An analysis of user coverage requests and retrieval strategies is presented, followed by a complete system description. Data base structure, retrieval processors, command language, interactive display options, file structures, and the system's capability to manage sets of selected imagery are described. A detailed example of an area coverage request is graphically presented.

Effects of Transfer to Real-World Subject Area Materials from Training in Graphic Organizers and Summarizing on Developmental College Readers' Comprehension of the Compare/Contrast Text Structure in Science Expository Text.

ERIC Educational Resources Information Center

Balajthy, Ernest; Weisberg, Renee

To determine whether less able readers could use the strategies they had been taught, a study investigated the transfer effects of training in the use of graphic organizers and summary writing on readers' recognition of the compare/contrast text structure. Subjects, 70 freshmen at a western New York state college of liberal arts and sciences in a…

Structured Analysis of the Logistics Support Analysis (LSA) Task, and Integrated Logistic Support (ILS) Element, ’Standardization and Interoperability (S and I)’.

DTIC Science & Technology

1988-11-01

system, using graphic techniques which enable users, analysts, and designers to get a clear and common picture of the system and how its parts fit...boxes into hierarchies suitable for computer implementation. ŗ. Structured Design uses tools, especially graphic ones, to render systems readily...LSA, PROCESSES, DATA FLOWS, DATA STORES, EX"RNAL ENTITIES, OVERALL SYSTEMS DESIGN PROCESS, over 19, ABSTRACT (Continue on reverse if necessary and

The hierarchical nature of the spin alignment of dark matter haloes in filaments

NASA Astrophysics Data System (ADS)

Aragon-Calvo, M. A.; Yang, Lin Forrest

2014-05-01

Dark matter haloes in cosmological filaments and walls have (in average) their spin vector aligned with their host structure. While haloes in walls are aligned with the plane of the wall independently of their mass, haloes in filaments present a mass-dependent two-regime orientation. Here, we show that the transition mass determining the change in the alignment regime (from parallel to perpendicular) depends on the hierarchical level in which the halo is located, reflecting the hierarchical nature of the Cosmic Web. By explicitly exposing the hierarchical structure of the Cosmic Web, we are able to identify the contributions of different components of the filament network to the alignment signal. We propose a unifying picture of angular momentum acquisition that is based on the results presented here and previous results found by other authors. In order to do a hierarchical characterization of the Cosmic Web, we introduce a new implementation of the multiscale morphology filter, the MMF-2, that significantly improves the identification of structures and explicitly describes their hierarchy. L36

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

PubMed

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

2008-09-01

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

Characterising RNA secondary structure space using information entropy

PubMed Central

2013-01-01

Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is, however, unclear how this probability distribution changes as a function of the input alignment. As prediction programs typically only return a single secondary structure, better characterisation of the underlying probability space of RNA secondary structures is of great interest. In this work, we show how to efficiently compute the information entropy of the probability distribution over RNA secondary structures produced for RNA alignments by a phylo-SCFG, and implement it for the PPfold model. We also discuss interpretations and applications of this quantity, including how it can clarify reasons for low prediction reliability scores. PPfold and its source code are available from http://birc.au.dk/software/ppfold/. PMID:23368905

Bayesian comparison of protein structures using partial Procrustes distance.

PubMed

Ejlali, Nasim; Faghihi, Mohammad Reza; Sadeghi, Mehdi

2017-09-26

An important topic in bioinformatics is the protein structure alignment. Some statistical methods have been proposed for this problem, but most of them align two protein structures based on the global geometric information without considering the effect of neighbourhood in the structures. In this paper, we provide a Bayesian model to align protein structures, by considering the effect of both local and global geometric information of protein structures. Local geometric information is incorporated to the model through the partial Procrustes distance of small substructures. These substructures are composed of β-carbon atoms from the side chains. Parameters are estimated using a Markov chain Monte Carlo (MCMC) approach. We evaluate the performance of our model through some simulation studies. Furthermore, we apply our model to a real dataset and assess the accuracy and convergence rate. Results show that our model is much more efficient than previous approaches.

ITG modes in the presence of inhomogeneous field-aligned flow

NASA Astrophysics Data System (ADS)

Sen, S.; McCarthy, D. R.; Lontano, M.; Lazzaro, E.; Honary, F.

2010-02-01

In a recent paper, Varischetti et al. (Plasma Phys. Contr. F. 2008, 50, 105008-1-15) have found that in a slab geometry the effect of the flow shear in the field-aligned parallel flow on the linear mode stability of the ion temperature gradient (ITG)-driven modes is not very prominent. They found that the flow shear also has a negligible effect on the mode characteristics. The work in this paper shows that the inclusion of flow curvature in the field-aligned flow can have a considerable effect on the mode stability; it can also change the mode structure so as to effect the mixing length transport in the core region of a fusion device. Flow shear, on the other hand, has indeed an insignificant role in the mode stability and mode structure. Inhomogeneous field-aligned flow should therefore still be considered for a viable candidate in controlling the ITG mode stability and mode structure.

Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.

PubMed

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.

Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis

PubMed Central

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit PMID:25816325

The display of molecular models with the Ames Interactive Modeling System (AIMS)

NASA Technical Reports Server (NTRS)

Egan, J. T.; Hart, J.; Burt, S. K.; Macelroy, R. D.

1982-01-01

A visualization of molecular models can lead to a clearer understanding of the models. Sophisticated graphics devices supported by minicomputers make it possible for the chemist to interact with the display of a very large model, altering its structure. In addition to user interaction, the need arises also for other ways of displaying information. These include the production of viewgraphs, film presentation, as well as publication quality prints of various models. To satisfy these needs, the display capability of the Ames Interactive Modeling System (AIMS) has been enhanced to provide a wide range of graphics and plotting capabilities. Attention is given to an overview of the AIMS system, graphics hardware used by the AIMS display subsystem, a comparison of graphics hardware, the representation of molecular models, graphics software used by the AIMS display subsystem, the display of a model obtained from data stored in molecule data base, a graphics feature for obtaining single frame permanent copy displays, and a feature for producing multiple frame displays.

Support for fast comprehension of ICU data: visualization using metaphor graphics.

PubMed

Horn, W; Popow, C; Unterasinger, L

2001-01-01

The time-oriented analysis of electronic patient records on (neonatal) intensive care units is a tedious and time-consuming task. Graphic data visualization should make it easier for physicians to assess the overall situation of a patient and to recognize essential changes over time. Metaphor graphics are used to sketch the most relevant parameters for characterizing a patient's situation. By repetition of the graphic object in 24 frames the situation of the ICU patient is presented in one display, usually summarizing the last 24 h. VIE-VISU is a data visualization system which uses multiples to present the change in the patient's status over time in graphic form. Each multiple is a highly structured metaphor graphic object. Each object visualizes important ICU parameters from circulation, ventilation, and fluid balance. The design using multiples promotes a focus on stability and change. A stable patient is recognizable at first sight, continuous improvement or worsening condition are easy to analyze, drastic changes in the patient's situation get the viewers attention immediately.

Fast 3D shape screening of large chemical databases through alignment-recycling

PubMed Central

Fontaine, Fabien; Bolton, Evan; Borodina, Yulia; Bryant, Stephen H

2007-01-01

Background Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes. Results Using a dataset of more than one million PubChem compounds of limited size (< 28 heavy atoms) and flexibility (< 6 rotatable bonds), we obtained a set of a few thousand diverse structures covering entirely the 3D shape space of the conformers of the dataset. Transformation matrices gathered from the overlays between these diverse structures and the 3D conformer dataset allowed us to drastically (100-fold) reduce the CPU time required for shape overlay. The alignment-recycling heuristic produces results consistent with de novo alignment calculation, with better than 80% hit list overlap on average. Conclusion Overlay-based 3D methods are computationally demanding when searching large databases. Alignment-recycling reduces the CPU time to perform shape similarity searches by breaking the alignment problem into three steps: selection of diverse shapes to describe the database shape-space; overlay of the database conformers to the diverse shapes; and non-optimized overlay of query and database conformers using common reference shapes. The precomputation, required by the first two steps, is a significant cost of the method; however, once performed, querying is two orders of magnitude faster. Extensions and variations of this methodology, for example, to handle more flexible and larger small-molecules are discussed. PMID:17880744

Electric-Field-Induced Alignment of Block Copolymer/Nanoparticle Blends

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

Liedel, Clemens; Schindler, Kerstin; Pavan, Mariela J.

External electric fi elds readily align birefringent block-copolymer mesophases. In this study the effect of gold nanoparticles on the electric-fi eld-induced alignment of a lamellae-forming polystyrene- block -poly(2-vinylpyridine) copolymer is assessed. Nanoparticles are homogeneously dispersed in the styrenic phase and promote the quantitative alignment of lamellar domains by substantially lowering the critical field strength above which alignment proceeds. The results suggest that the electric-fi eldassisted alignment of nanostructured block copolymer/nanoparticle composites may offer a simple way to greatly mitigate structural and orientational defects of such fi lms under benign experimental conditions.

Photoshop tips and tricks every facial plastic surgeon should know.

PubMed

Hamilton, Grant S

2010-05-01

Postprocessing of patient photographs is an important skill for the facial plastic surgeon. Postprocessing is intended to optimize the image, not change the surgical result. This article refers to use of Photoshop CS3 (Adobe Systems Incorporated, San Jose, CA, USA) for descriptions, but any recent version of Photoshop is sufficiently similar. Topics covered are types of camera, shooting formats, color balance, alignment of preoperative and postoperative photographs, and preparing figures for publication. Each section presents step-by-step guidance and instructions along with a graphic depiction of the computer screen and Photoshop tools under discussion. Copyright 2010 Elsevier Inc. All rights reserved.

Impact of Information Technology Governance Structures on Strategic Alignment

ERIC Educational Resources Information Center

Gordon, Fitzroy R.

2013-01-01

This dissertation is a study of the relationship between Information Technology (IT) strategic alignment and IT governance structure within the organization. This dissertation replicates Asante (2010) among a different population where the prior results continue to hold, the non-experimental approach explored two research questions but include two…

Structural alignment sensor. [laser applications and interferometry

NASA Technical Reports Server (NTRS)

Davis, L.; Buholz, N. E.; Gillard, C. W.; Huang, C. C.; Wells, W. M., III

1978-01-01

Comparative Michelson interferometers are discussed as well as the operating range potential of a structural alignment sensor (SAS) which requires only one laser mode. Schematics are presented for the distance measurement logic, the basic SAS system, the SAS optical layout, the coarse measurement signal processor, and the measured range resolution.

Rclick: a web server for comparison of RNA 3D structures.

PubMed

Nguyen, Minh N; Verma, Chandra

2015-03-15

RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Our server Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. Our server also recognizes conformational changes between structures. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server for comparison of RNA, RNA-protein complexes and RNA-ligand structures. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Filament Winding Multifunctional Carbon Nanotube Composites of Various Dimensionality

NASA Astrophysics Data System (ADS)

Wells, Brian David

Carbon nanotubes (CNT) have been long considered an optimal material for composites due to their high strength, high modulus, and electrical/thermal conductivity. These composite materials have the potential to be used in the aerospace, computer, automotive, medical industry as well as many others. The nano dimensions of these structures make controlled alignment and distribution difficult using many production techniques. An area that shows promise for controlled alignment is the formation of CNT yarns. Different approaches have been used to create yarns with various winding angles and diameters. CNTs resemble traditional textile fiber structures due to their one-dimensional dimensions, axial strength and radial flexibility. One difference is, depending on the length, CNTs can have aspect ratios that far exceed those of traditional textile fibers. This can complicate processing techniques and cause agglomeration which prevents optimal structures from being created. However, with specific aspect ratios and spatial distributions a specific type of CNT, vertically aligned spinnable carbon nanotubes (VASCNTs), have interesting properties that allow carbon nanotubes to be drawn from an array in a continuous aligned web. This dissertation examines the feasibility of combining VASCNTs with another textile manufacturing process, filament winding, to create structures with various levels of dimensionality. While yarn formation with CNTs has been largely studied, there has not been significant work studying the use of VASCNTs to create composite materials. The studies that have been produces revolve around mixing CNTs into epoxy or creating uni-directional wound structures. In this dissertation VASCNTs are used to create filament wound materials with various degrees of alignment. These structures include 1 dimensional coatings applied to non-conductive polymer monofilaments, two dimensional multifunctional adhesive films, and three dimensional hybrid-nano composites. The angle of alignment between the individual CNTs relative to the overall structure was used to affect the electrical properties in all of these structures and the mechanical properties of the adhesive films and hybrid-nano composites. Varying the concentration of CNT was also found to have a significant effect on the electrical and mechanical properties. The variable properties that can be created with these production techniques allow users to engineer the structure to match the desired property.

A sophisticated cad tool for the creation of complex models for electromagnetic interaction analysis

NASA Astrophysics Data System (ADS)

Dion, Marc; Kashyap, Satish; Louie, Aloisius

1991-06-01

This report describes the essential features of the MS-DOS version of DIDEC-DREO, an interactive program for creating wire grid, surface patch, and cell models of complex structures for electromagnetic interaction analysis. It uses the device-independent graphics library DIGRAF and the graphics kernel system HALO, and can be executed on systems with various graphics devices. Complicated structures can be created by direct alphanumeric keyboard entry, digitization of blueprints, conversion form existing geometric structure files, and merging of simple geometric shapes. A completed DIDEC geometric file may then be converted to the format required for input to a variety of time domain and frequency domain electromagnetic interaction codes. This report gives a detailed description of the program DIDEC-DREO, its installation, and its theoretical background. Each available interactive command is described. The associated program HEDRON which generates simple geometric shapes, and other programs that extract the current amplitude data from electromagnetic interaction code outputs, are also discussed.

Investigation of MAGSAT and TRIAD magnetometer data to provide corrective information on high-lattitude external fields

NASA Technical Reports Server (NTRS)

Potemra, T. A. (Principal Investigator); Sugiura, M.; Zanettic, L. J.

1982-01-01

Disturbances in the MAGSAT magnetometer data set due to high latitude phenomena were evaluated. Much of the categorization of disturbances due to Birkeland currents, ionospheric Hall currents, fine structure and wave phenomena was done with the MAGSAT data catalog. A color graphics technique was developed for the display of disturbances from multiple orbits, from which one can infer a 'global-image' of the current systems of the auroral zone. The MAGSAT 4/81 magnetic field model appears to represent the Earth's main field at high latitudes very well for the epoch 1980. MAGSAT's low altitude allows analysis of disturbances in the magnetometer data due to ionospheric electrojet currents. These current distributions were modeled properly for single events as a precursor to the inference of the Birkeland current system. MAGSAT's orbit was approximately shared with that of the Navy/APL TRIAD satellite. This allowed space-time studies of the magnetic disturbance signatures to be performed, the result being an approximately 75% agreement in, as well as high frequency of, signatures due to Birkeland currents. Thus the field-aligned currents are a steady-state participant in the Earth's magnetospheric current system.

Sockeye: A 3D Environment for Comparative Genomics

PubMed Central

Montgomery, Stephen B.; Astakhova, Tamara; Bilenky, Mikhail; Birney, Ewan; Fu, Tony; Hassel, Maik; Melsopp, Craig; Rak, Marcin; Robertson, A. Gordon; Sleumer, Monica; Siddiqui, Asim S.; Jones, Steven J.M.

2004-01-01

Comparative genomics techniques are used in bioinformatics analyses to identify the structural and functional properties of DNA sequences. As the amount of available sequence data steadily increases, the ability to perform large-scale comparative analyses has become increasingly relevant. In addition, the growing complexity of genomic feature annotation means that new approaches to genomic visualization need to be explored. We have developed a Java-based application called Sockeye that uses three-dimensional (3D) graphics technology to facilitate the visualization of annotation and conservation across multiple sequences. This software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization. PMID:15123592

The Inorganic Illustrator: A 3-D Graphical Supplement for Inorganic and Bioinorganic Chemistry Courses Distributed on CD-ROM

NASA Astrophysics Data System (ADS)

Childs, Scott L.; Hagen, Karl S.

1996-10-01

The visualization of molecular and solid state chemical structures in three dimensions is a particularly difficult problem for students to overcome when the primary means of communication is the two-dimensional world of textbooks, blackboards, and overhead projector screens. Recent editions of popular textbooks in organic, inorganic, and biochemistry have included stereoviews of molecules to aid the student, and stereoviews of crystal structures have been used in inorganic chemistry publications for many years. These are powerful aids for visualizing complex molecules, but with the exception of the biochemistry text mentioned above, they are limited to single, static images generally in black and white. Molecular model kits are routinely used very effectively in organic chemistry but their utility in inorganic chemistry is limited to all but the most simple molecules encountered. Now that personal computers are generally accessible and multimedia tools are starting to make an appearance in chemistry lecture halls (1), we can make our inorganic and bioinorganic chemistry and crystallography lectures come alive with the aid of the computer-based resources, which are the essence of this project. As part of this project we are accumulating a database of representative crystal structures of main group molecules, coordination complexes, organometallic compounds, small metalloproteins, bioinorganic model complexes, clusters, and solid state materials in Chem3D Plus format to be viewed with Chem3D Viewer, which is free software from Cambridge Scientific Computing. We are also generating a library of high-quality graphic images of these same molecules and structures using Cerius2 package from Molecular Simulations. These include polyhedral representations of clusters and solid state structures (see Fig. 1). Figure 1. Representation of the user interface: the title page and an example of polyhedral and ball-and-stick representation of an octanuclear iron-oxo cluster. The files of solid state structures will not be limited to single unit cells that are common in textbooks, but will present multiple cells such that the extended lattice of the material is evident. Navigation through these resources is through a unique open hypertext-based interface using Authorware, which allows the user to create complex applications that support movies, animation, and other graphics seamlessly. Chem3D Viewer is a powerful program that allows not only multiple visualization modes, but also the detailed analysis of both bonded and nonbonded distances and angles. This is particularly useful for recognizing symmetry elements within molecules, as the student can precisely align atoms along the screen's Cartesian axes or within its planes and subsequently rotate the molecules about the axes at precise angles. We are developing stand-alone interactive tutorials to assign point groups to molecules and clusters. In addition, tutorials are being developed that show how the Chem3D Viewer software can be most effectively used in a classroom setting for lectures or for home or lab use by the students. The Inorganic Illustrator will be made available to the education community for the cost of materials plus shipping and handling. Acknowledgment We would like to thank the NSF for financial support through the Division of Undergraduate Education Course and Curriculum Program (DUE-CCD 9455567). Literature Cited 1. Illman, D. L. Chem. Eng. News 1994, 72(May 9), 34.

Flexible and Lightweight Pressure Sensor Based on Carbon Nanotube/Thermoplastic Polyurethane-Aligned Conductive Foam with Superior Compressibility and Stability.

PubMed

Huang, Wenju; Dai, Kun; Zhai, Yue; Liu, Hu; Zhan, Pengfei; Gao, Jiachen; Zheng, Guoqiang; Liu, Chuntai; Shen, Changyu

2017-12-06

Flexible and lightweight carbon nanotube (CNT)/thermoplastic polyurethane (TPU) conductive foam with a novel aligned porous structure was fabricated. The density of the aligned porous material was as low as 0.123 g·cm -3 . Homogeneous dispersion of CNTs was achieved through the skeleton of the foam, and an ultralow percolation threshold of 0.0023 vol % was obtained. Compared with the disordered foam, mechanical properties of the aligned foam were enhanced and the piezoresistive stability of the flexible foam was improved significantly. The compression strength of the aligned TPU foam increases by 30.7% at the strain of 50%, and the stress of the aligned foam is 22 times that of the disordered foam at the strain of 90%. Importantly, the resistance variation of the aligned foam shows a fascinating linear characteristic under the applied strain until 77%, which would benefit the application of the foam as a desired pressure sensor. During multiple cyclic compression-release measurements, the aligned conductive CNT/TPU foam represents excellent reversibility and reproducibility in terms of resistance. This nice capability benefits from the aligned porous structure composed of ladderlike cells along the orientation direction. Simultaneously, the human motion detections, such as walk, jump, squat, etc. were demonstrated by using our flexible pressure sensor. Because of the lightweight, flexibility, high compressibility, excellent reversibility, and reproducibility of the conductive aligned foam, the present study is capable of providing new insights into the fabrication of a high-performance pressure sensor.

Preparation of Nanocomposite Plasmonic Films Made from Cellulose Nanocrystals or Mesoporous Silica Decorated with Unidirectionally Aligned Gold Nanorods.

PubMed

Campbell, Michael G; Liu, Qingkun; Sanders, Aric; Evans, Julian S; Smalyukh, Ivan I

2014-04-11

Using liquid crystalline self-assembly of cellulose nanocrystals, we achieve long-range alignment of anisotropic metal nanoparticles in colloidal nanocrystal dispersions that are then used to deposit thin structured films with ordering features highly dependent on the deposition method. These hybrid films are comprised of gold nanorods unidirectionally aligned in a matrix that can be made of ordered cellulose nanocrystals or silica nanostructures obtained by using cellulose-based nanostructures as a replica. The ensuing long-range alignment of gold nanorods in both cellulose-based and nanoporous silica films results in a polarization-sensitive surface plasmon resonance. The demonstrated device-scale bulk nanoparticle alignment may enable engineering of new material properties arising from combining the orientational ordering of host nanostructures and properties of the anisotropic plasmonic metal nanoparticles. Our approach may also allow for scalable fabrication of plasmonic polarizers and nanoporous silica structures with orientationally ordered anisotropic plasmonic nanoinclusions.

Magnetic field effect for cellulose nanofiber alignment

NASA Astrophysics Data System (ADS)

Kim, Jaehwan; Chen, Yi; Kang, Kwang-Sun; Park, Young-Bin; Schwartz, Mark

2008-11-01

Regenerated cellulose formed into cellulose nanofibers under strong magnetic field and aligned perpendicularly to the magnetic field. Well-aligned microfibrils were found as the exposure time of the magnetic field increased. Better alignment and more crystalline structure of the cellulose resulted in the increased decomposition temperature of the material. X-ray crystallograms showed that crystallinity index of the cellulose increased as the exposure time of the magnetic field increased.

Interactive Alignment of Multisyllabic Stress Patterns in a Second Language Classroom

ERIC Educational Resources Information Center

Trofimovich, Pavel; McDonough, Kim; Foote, Jennifer A.

2014-01-01

The current study explored the occurrence of stress pattern alignment during peer interaction in a second language (L2) classroom. Interactive alignment is a sociocognitive phenomenon in which interlocutors reuse each other's expressions, structures, and pronunciation patterns during conversation. Students (N = 41) enrolled in a…

3D flexible alignment using 2D maximum common substructure: dependence of prediction accuracy on target-reference chemical similarity.

PubMed

Kawabata, Takeshi; Nakamura, Haruki

2014-07-28

A protein-bound conformation of a target molecule can be predicted by aligning the target molecule on the reference molecule obtained from the 3D structure of the compound-protein complex. This strategy is called "similarity-based docking". For this purpose, we develop the flexible alignment program fkcombu, which aligns the target molecule based on atomic correspondences with the reference molecule. The correspondences are obtained by the maximum common substructure (MCS) of 2D chemical structures, using our program kcombu. The prediction performance was evaluated using many target-reference pairs of superimposed ligand 3D structures on the same protein in the PDB, with different ranges of chemical similarity. The details of atomic correspondence largely affected the prediction success. We found that topologically constrained disconnected MCS (TD-MCS) with the simple element-based atomic classification provides the best prediction. The crashing potential energy with the receptor protein improved the performance. We also found that the RMSD between the predicted and correct target conformations significantly correlates with the chemical similarities between target-reference molecules. Generally speaking, if the reference and target compounds have more than 70% chemical similarity, then the average RMSD of 3D conformations is <2.0 Å. We compared the performance with a rigid-body molecular alignment program based on volume-overlap scores (ShaEP). Our MCS-based flexible alignment program performed better than the rigid-body alignment program, especially when the target and reference molecules were sufficiently similar.

Use cases and DEMO: aligning functional features of ICT-infrastructure to business processes.

PubMed

Maij, E; Toussaint, P J; Kalshoven, M; Poerschke, M; Zwetsloot-Schonk, J H M

2002-11-12

The proper alignment of functional features of the ICT-infrastructure to business processes is a major challenge in health care organisations. This alignment takes into account that the organisational structure not only shapes the ICT-infrastructure, but that the inverse also holds. To solve the alignment problem, relevant features of the ICT-infrastructure should be derived from the organisational structure and the influence of this envisaged ICT to the work practices should be pointed out. The objective of our study was to develop a method to solve this alignment problem. In a previous study we demonstrated the appropriateness of the business process modelling methodology Dynamic Essential Modelling of Organizations (DEMO). A proven and widely used modelling language for expressing functional features is Unified Modelling Language (UML). In the context of a specific case study at the University Medical Centre Utrecht in the Netherlands we investigated if the combined use of DEMO and UML could solve the alignment problem. The study demonstrated that the DEMO models were suited as a starting point in deriving system functionality by using the use case concept of UML. Further, the case study demonstrated that in using this approach for the alignment problem, insight is gained into the mutual influence of ICT-infrastructure and organisation structure: (a) specification of independent, re-usable components-as a set of related functionalities-is realised, and (b) a helpful representation of the current and future work practice is provided for in relation to the envisaged ICT support.

Development and application of an algorithm to compute weighted multiple glycan alignments.

PubMed

Hosoda, Masae; Akune, Yukie; Aoki-Kinoshita, Kiyoko F

2017-05-01

A glycan consists of monosaccharides linked by glycosidic bonds, has branches and forms complex molecular structures. Databases have been developed to store large amounts of glycan-binding experiments, including glycan arrays with glycan-binding proteins. However, there are few bioinformatics techniques to analyze large amounts of data for glycans because there are few tools that can handle the complexity of glycan structures. Thus, we have developed the MCAW (Multiple Carbohydrate Alignment with Weights) tool that can align multiple glycan structures, to aid in the understanding of their function as binding recognition molecules. We have described in detail the first algorithm to perform multiple glycan alignments by modeling glycans as trees. To test our tool, we prepared several data sets, and as a result, we found that the glycan motif could be successfully aligned without any prior knowledge applied to the tool, and the known recognition binding sites of glycans could be aligned at a high rate amongst all our datasets tested. We thus claim that our tool is able to find meaningful glycan recognition and binding patterns using data obtained by glycan-binding experiments. The development and availability of an effective multiple glycan alignment tool opens possibilities for many other glycoinformatics analysis, making this work a big step towards furthering glycomics analysis. http://www.rings.t.soka.ac.jp. kkiyoko@soka.ac.jp. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.

PubMed

Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

2016-01-01

Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).

gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances

PubMed Central

Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

2016-01-01

Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos). PMID:27846272

The effect of visuals on non-native English students' learning of the basic principles and laws of motion

NASA Astrophysics Data System (ADS)

Yang, Quan

2001-10-01

This study, involving 154 undergraduate college students in China, was conducted to determine whether the surface structure of visual graphics affect content learning when the learner was a non-native English speaker and learning took place in a non-English speaking environment. Instruction with concrete animated graphics resulted in significantly higher achievement, when compared to instruction with concrete static, abstract static, abstract animated graphics or text only without any graphical illustrations. It was also found, unexpectedly, the text-only instruction resulted in the second best achievement, significantly higher than instruction with concrete static, abstract static, and abstract animated graphics. In addition, there was a significant interaction with treatment and test item, which indicated that treatment effects on graphic-specific items differed from those on definitional items. Additional findings indicated that relation to graphics directly or indirectly from the text that students studied had little impact on their performance in the posttests. Further, 51% of the participants indicated that they relied on some graphical images to answer the test questions and 19% relied heavily on graphics when completing the tests. In conclusion, concrete graphics when combined with animation played a significant role in enhancing ESL student performance and enabled the students to achieve the best learning outcomes as compared to abstract animated, concrete static, and abstract static graphics. This result suggested a significant innovation in the design and development of ESL curriculum in computer-based instruction, which would enable ESL students to perform better and achieve the expected outcomes in content area learning.

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.

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.

Computer Graphics in Research: Some State -of-the-Art Systems

ERIC Educational Resources Information Center

Reddy, R.; And Others

1975-01-01

A description is given of the structure and functional characteristics of three types of interactive computer graphic systems, developed by the Department of Computer Science at Carnegie-Mellon; a high-speed programmable display capable of displaying 50,000 short vectors, flicker free; a shaded-color video display for the display of gray-scale…

Solving Additive Problems at Pre-Elementary School Level with the Support of Graphical Representation

ERIC Educational Resources Information Center

Selva, Ana Coelho Vieira; Falcao, Jorge Tarcisio da Rocha; Nunes, Terezinha

2005-01-01

This research offers empirical evidence of the importance of supplying diverse symbolic representations in order to support concept development in mathematics. Graphical representation can be a helpful symbolic tool for concept development in the conceptual field of additive structures. Nevertheless, this symbolic tool has specific difficulties…

Computer-Based Learning: Graphical Integration of Whole and Sectional Neuroanatomy Improves Long-Term Retention

ERIC Educational Resources Information Center

Naaz, Farah; Chariker, Julia H.; Pani, John R.

2014-01-01

A study was conducted to test the hypothesis that instruction with graphically integrated representations of whole and sectional neuroanatomy is especially effective for learning to recognize neural structures in sectional imagery (such as magnetic resonance imaging [MRI]). Neuroanatomy was taught to two groups of participants using computer…

A Prototype HTML Training System for Graphic Communication Majors

ERIC Educational Resources Information Center

Runquist, Roger L.

2010-01-01

This design research demonstrates a prototype content management system capable of training graphic communication students in the creation of basic HTML web pages. The prototype serve as a method of helping students learn basic HTML structure and commands earlier in their academic careers. Exposure to the concepts of web page creation early in…

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing

PubMed Central

2014-01-01

Background RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by high throughput sequencers. Results We developed a standalone tool with graphic user interface (GUI)-based analytic modules, known as eRNA. The capacity of performing parallel processing and sample management facilitates large data analyses by maximizing hardware usage and freeing users from tediously handling sequencing data. The module miRNA identification” includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting. The module “mRNA identification” includes GUIs for reference sequences, genome mapping, transcript assembling, and differential expression. The module “Target screening” provides expression profiling analyses and graphic visualization. The module “Self-testing” offers the directory setups, sample management, and a check for third-party package dependency. Integration of other GUIs including Bowtie, miRDeep2, and miRspring extend the program’s functionality. Conclusions eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory. PMID:24593312

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.

PubMed

Yuan, Tiezheng; Huang, Xiaoyi; Dittmar, Rachel L; Du, Meijun; Kohli, Manish; Boardman, Lisa; Thibodeau, Stephen N; Wang, Liang

2014-03-05

RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by high throughput sequencers. We developed a standalone tool with graphic user interface (GUI)-based analytic modules, known as eRNA. The capacity of performing parallel processing and sample management facilitates large data analyses by maximizing hardware usage and freeing users from tediously handling sequencing data. The module miRNA identification" includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting. The module "mRNA identification" includes GUIs for reference sequences, genome mapping, transcript assembling, and differential expression. The module "Target screening" provides expression profiling analyses and graphic visualization. The module "Self-testing" offers the directory setups, sample management, and a check for third-party package dependency. Integration of other GUIs including Bowtie, miRDeep2, and miRspring extend the program's functionality. eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory.

A Novel Partial Sequence Alignment Tool for Finding Large Deletions

PubMed Central

Aruk, Taner; Ustek, Duran; Kursun, Olcay

2012-01-01

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method. PMID:22566777

A new graph-based method for pairwise global network alignment

PubMed Central

Klau, Gunnar W

2009-01-01

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

DSSR-enhanced visualization of nucleic acid structures in Jmol

PubMed Central

Hanson, Robert M.

2017-01-01

Abstract Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). PMID:28472503

Abnormal arrangement of a collagen/apatite extracellular matrix orthogonal to osteoblast alignment is constructed by a nanoscale periodic surface structure.

PubMed

Matsugaki, Aira; Aramoto, Gento; Ninomiya, Takafumi; Sawada, Hiroshi; Hata, Satoshi; Nakano, Takayoshi

2015-01-01

Morphological and directional alteration of cells is essential for structurally appropriate construction of tissues and organs. In particular, osteoblast alignment is crucial for the realization of anisotropic bone tissue microstructure. In this article, the orientation of a collagen/apatite extracellular matrix (ECM) was established by controlling osteoblast alignment using a surface geometry with nanometer-sized periodicity induced by laser ablation. Laser irradiation induced self-organized periodic structures (laser-induced periodic surface structures; LIPSS) with a spatial period equal to the wavelength of the incident laser on the surface of biomedical alloys of Ti-6Al-4V and Co-Cr-Mo. Osteoblast orientation was successfully induced parallel to the grating structure. Notably, both the fibrous orientation of the secreted collagen matrix and the c-axis of the produced apatite crystals were orientated orthogonal to the cell direction. To the best of our knowledge, this is the first report demonstrating that bone tissue anisotropy is controllable, including the characteristic organization of a collagen/apatite composite orthogonal to the osteoblast orientation, by controlling the cell alignment using periodic surface geometry. Copyright © 2014 Elsevier Ltd. All rights reserved.

Pharmaceutical structure montages as catalysts for design and discovery.

PubMed

Njarðarson, Jon T

2012-05-01

Majority of pharmaceuticals are small molecule organic compounds. Their structures are most effectively described and communicated using the graphical language of organic chemistry. A few years ago we decided to harness this powerful language to create new educational tools that could serve well for data mining and as catalysts for discovery. The results were the Top 200 drug posters, which we have posted online for everyone to enjoy and update yearly. This article details the origin and motivation for our design and highlights the value of this graphical format by presenting and analyzing a new pharmaceutical structure montage (poster) focused on US FDA approved drugs in 2011.

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

PubMed Central

2012-01-01

Background Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. Results The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Conclusions Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family. PMID:22793672

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

PubMed

Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl

2012-07-13

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

Poly(vinyl alcohol)/cellulose nanofibril hybrid aerogels with an aligned microtubular porous structure and their composites with polydimethylsiloxane

Treesearch

Tianliang Zhai; Qifeng Zheng; Zhiyong Cai; Lih-Sheng Turng; Hesheng Xia; Shaoqin Gong

2015-01-01

Superhydrophobic poly(vinyl alcohol) (PVA)/ cellulose nanofibril (CNF) aerogels with a unidirectionally aligned microtubular porous structure were prepared using a unidirectional freeze-drying process, followed by the thermal chemical vapor deposition of methyltrichlorosilane. The silanized aerogels were characterized using various techniques including scanning...

Transformation Education: A Vehicle for Structuring Group Care Organizations to Increase Service Quality and Effectiveness

ERIC Educational Resources Information Center

Ross, Andrew L.

2007-01-01

Transformation Education, an organizational philosophy and operating system, is designed to increase service quality and effectiveness of group care through aligning its organizational structure with its purpose. This alignment is achieved through creating a culture designed to dispense transformation rather than treatment. The author presents how…

On an Additive Semigraphoid Model for Statistical Networks With Application to Pathway Analysis.

PubMed

Li, Bing; Chun, Hyonho; Zhao, Hongyu

2014-09-01

We introduce a nonparametric method for estimating non-gaussian graphical models based on a new statistical relation called additive conditional independence, which is a three-way relation among random vectors that resembles the logical structure of conditional independence. Additive conditional independence allows us to use one-dimensional kernel regardless of the dimension of the graph, which not only avoids the curse of dimensionality but also simplifies computation. It also gives rise to a parallel structure to the gaussian graphical model that replaces the precision matrix by an additive precision operator. The estimators derived from additive conditional independence cover the recently introduced nonparanormal graphical model as a special case, but outperform it when the gaussian copula assumption is violated. We compare the new method with existing ones by simulations and in genetic pathway analysis.

Prediction of β-turns in proteins from multiple alignment using neural network

PubMed Central

Kaur, Harpreet; Raghava, Gajendra Pal Singh

2003-01-01

A neural network-based method has been developed for the prediction of β-turns in proteins by using multiple sequence alignment. Two feed-forward back-propagation networks with a single hidden layer are used where the first-sequence structure network is trained with the multiple sequence alignment in the form of PSI-BLAST–generated position-specific scoring matrices. The initial predictions from the first network and PSIPRED-predicted secondary structure are used as input to the second structure-structure network to refine the predictions obtained from the first net. A significant improvement in prediction accuracy has been achieved by using evolutionary information contained in the multiple sequence alignment. The final network yields an overall prediction accuracy of 75.5% when tested by sevenfold cross-validation on a set of 426 nonhomologous protein chains. The corresponding Qpred, Qobs, and Matthews correlation coefficient values are 49.8%, 72.3%, and 0.43, respectively, and are the best among all the previously published β-turn prediction methods. The Web server BetaTPred2 (http://www.imtech.res.in/raghava/betatpred2/) has been developed based on this approach. PMID:12592033

[Communication prostheses and behavioral alignment in hospital leaflets].

PubMed

Vasconcellos-Silva, Paulo Roberto; Rivera, Francisco Javier Uribe; Rozemberg, Brani

2003-08-01

Review was made of publications that describe experience with printed material distributed to the lay public in hospital institutions. From the 146 leaflets examined, those aimed at professionals or disabled people, thus leaving 75 papers that illustrate the present pattern for the rationality behind the production, use and evaluation of this type of resource. In a general manner, such leaflets invest in the power of "ideal printed information" to align behavior with the hospital's biomedical agenda. The underlying rationality that permeates them perceives the "perfect information package" as one that efficiently describes its technical content for the purpose of unidirectional persuasion, is up-to-date in relation to readability scales and embellished by graphic design, and emphasizes the priorities defined by the professionals. Such "communication prostheses" should be capable of electronic validation by means of software suitable for proportioning the "doses" to the subject matter. Information as a drug, cognitivism, the lack of research on message reception and the need for communicative action for the deconstruction of systems of closed thinking within the hospital environment have been discussed.

Seismic anisotropy in the Earth's innermost inner core: Testing structural models against mineral physics predictions

DOE PAGES

Romanowicz, Barbara; Cao, Aimin; Godwal, Budhiram; ...

2016-01-06

Using an updated data set of ballistic PKIKP travel time data at antipodal distances, we test different models of anisotropy in the Earth's innermost inner core (IMIC) and obtain significantly better fits for a fast axis aligned with Earth's rotation axis, rather than a quasi-equatorial direction, as proposed recently. Reviewing recent results on the single crystal structure and elasticity of iron at core conditions, we find that an hcp structure with the fast c axis parallel to Earth's rotation is more likely but a body-centered cubic structure with the [111] axis aligned in that direction results in very similar predictionsmore » for seismic anisotropy. These models are therefore not distinguishable based on current seismological data. In addition, to match the seismological observations, the inferred strength of anisotropy in the IMIC (6–7%) implies almost perfect alignment of iron crystals, an intriguing, albeit unlikely situation, especially in the presence of heterogeneity, which calls for further studies. Fast axis of anisotropy in the central part of the inner core aligned with Earth's axis of rotation Lastly, the structure of iron in the inner core is most likely hcp, not bcc Not currently possible to distinguish between hcp and bcc structures from seismic observations« less

Protein local structure alignment under the discrete Fréchet distance.

PubMed

Zhu, Binhai

2007-12-01

Protein structure alignment is a fundamental problem in computational and structural biology. While there has been lots of experimental/heuristic methods and empirical results, very few results are known regarding the algorithmic/complexity aspects of the problem, especially on protein local structure alignment. A well-known measure to characterize the similarity of two polygonal chains is the famous Fréchet distance, and with the application of protein-related research, a related discrete Fréchet distance has been used recently. In this paper, following the recent work of Jiang et al. we investigate the protein local structural alignment problem using bounded discrete Fréchet distance. Given m proteins (or protein backbones, which are 3D polygonal chains), each of length O(n), our main results are summarized as follows: * If the number of proteins, m, is not part of the input, then the problem is NP-complete; moreover, under bounded discrete Fréchet distance it is NP-hard to approximate the maximum size common local structure within a factor of n(1-epsilon). These results hold both when all the proteins are static and when translation/rotation are allowed. * If the number of proteins, m, is a constant, then there is a polynomial time solution for the problem.

GeneSilico protein structure prediction meta-server.

PubMed

Kurowski, Michal A; Bujnicki, Janusz M

2003-07-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta.

GeneSilico protein structure prediction meta-server

PubMed Central

Kurowski, Michal A.; Bujnicki, Janusz M.

2003-01-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta. PMID:12824313

Interspecific variation in mitochondrial serine transfer RNA (UCN) in Euptychiina butterflies (Lepidoptera: Satyrinae): structure and alignment.

PubMed

Marín, Mario Alejandro; López, Andrés; Uribe, Sandra Inés

2012-06-01

The nucleotide variation and structural patterns of mitochondrial RNA molecule have been proposed as useful tools in molecular systematics; however, their usefulness is always subject to a proper assessment of homology in the sequence alignment. The present study describes the secondary structure of mitochondrial tRNA for the amino acid serine (UCN) on 13 Euptychiina species and the evaluation of its potential use for evolutionary studies in this group of butterflies. The secondary structure of tRNAs showed variation among the included species except between Hermeuptychia sp1 and sp2. Variation was concentrated in the ribotimidina-pseudouridine-cystosine (TψC), dihydrouridine (DHU) and variable loops and in the DHU and TψC arms. These results suggest this region as a potential marker useful for taxonomic differentiation of species in this group and also confirm the importance of including information from the secondary structure of tRNA to optimize the alignments.

Constant field gradient planar coupled cavity structure

DOEpatents

Kang, Y.W.; Kustom, R.L.

1999-07-27

A cavity structure is disclosed having at least two opposing planar housing members spaced apart to accommodate the passage of a particle beam through the structure between the members. Each of the housing members have a plurality of serially aligned hollows defined therein, and also passages, formed in the members, which interconnect serially adjacent hollows to provide communication between the hollows. The opposing planar housing members are spaced and aligned such that the hollows in one member cooperate with corresponding hollows in the other member to form a plurality of resonant cavities aligned along the particle beam within the cavity structure. To facilitate the obtaining of a constant field gradient within the cavity structure, the passages are configured so as to be incrementally narrower in the direction of travel of the particle beam. In addition, the spacing distance between the opposing housing members is configured to be incrementally smaller in the direction of travel of the beam. 16 figs.

Constant field gradient planar coupled cavity structure

DOEpatents

Kang, Yoon W.; Kustom, Robert L.

1999-01-01

A cavity structure having at least two opposing planar housing members spaced apart to accommodate the passage of a particle beam through the structure between the members. Each of the housing members have a plurality of serially aligned hollows defined therein, and also passages, formed in the members, which interconnect serially adjacent hollows to provide communication between the hollows. The opposing planar housing members are spaced and aligned such that the hollows in one member cooperate with corresponding hollows in the other member to form a plurality of resonant cavities aligned along the particle beam within the cavity structure. To facilitate the obtaining of a constant field gradient within the cavity structure, the passages are configured so as to be incrementally narrower in the direction of travel of the particle beam. In addition, the spacing distance between the opposing housing members is configured to be incrementally smaller in the direction of travel of the beam.

NGL Viewer: a web application for molecular visualization

PubMed Central

Rose, Alexander S.; Hildebrand, Peter W.

2015-01-01

The NGL Viewer (http://proteinformatics.charite.de/ngl) is a web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is also unaffected by the retirement of third-party plug-ins like Flash and Java Applets. Generally, the web application offers comprehensive molecular visualization through a graphical user interface so that life scientists can easily access and profit from available structural data. It supports common structural file-formats (e.g. PDB, mmCIF) and a variety of molecular representations (e.g. ‘cartoon, spacefill, licorice’). Moreover, the viewer can be embedded in other web sites to provide specialized visualizations of entries in structural databases or results of structure-related calculations. PMID:25925569

FASMA: a service to format and analyze sequences in multiple alignments.

PubMed

Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

2007-12-01

Multiple sequence alignments are successfully applied in many studies for under- standing the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http://bioinformatica.isa.cnr.it/FASMA/.

Making Macroscopic Assemblies of Aligned Carbon Nanotubes

NASA Technical Reports Server (NTRS)

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

Design and fabrication of advanced fiber alignment structures for field-installable fiber connectors

NASA Astrophysics Data System (ADS)

Van Erps, Jürgen; Vervaeke, Michael; Sánchez Martínez, Alberto; Beri, Stefano; Debaes, Christof; Watté, Jan; Thienpont, Hugo

2012-06-01

Fiber-To-The-Home (FTTH) networks have been adopted as a potential replacement of traditional electrical connections for the 'last mile' transmission of information at bandwidths over 1Gb/s. However, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field-installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. Novel low-cost structures for bare fiber alignment with outstanding positioning accuracies are strongly desired as they would allow reducing loss beyond the level achievable with ferrule-bore systems. However, the realization of such alignment system is challenging as it should provide sufficient force to position the fiber with sub-micron accuracy required in positioning the fiber. In this contribution we propose, design and prototype a bare-fiber alignment system which makes use of deflectable/compressible micro-cantilevers. Such cantilevers behave as springs and provide self-centering functionality to the structure. Simulations of the mechanical properties of the cantilevers are carried out in order to get an analytical approximation and a mathematical model of the spring constant and stress in the structure. Elastic constants of the order of 104 to 105N/m are found out to be compatible with a proof stress of 70 MPa. Finally a first self-centering structure is prototyped in PMMA using our Deep Proton Writing technology. The spring constants of the fabricated cantilevers are in the range of 4 to 6 × 104N/m and the stress is in the range 10 to 20 MPa. These self-centering structures have the potential to become the basic building blocks for a new generation of field-installable connectors.

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

PubMed Central

Haas, Brian J; Salzberg, Steven L; Zhu, Wei; Pertea, Mihaela; Allen, Jonathan E; Orvis, Joshua; White, Owen; Buell, C Robin; Wortman, Jennifer R

2008-01-01

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation. PMID:18190707

Communication: Gas-phase structural isomer identification by Coulomb explosion of aligned molecules

NASA Astrophysics Data System (ADS)

Burt, Michael; Amini, Kasra; Lee, Jason W. L.; Christiansen, Lars; Johansen, Rasmus R.; Kobayashi, Yuki; Pickering, James D.; Vallance, Claire; Brouard, Mark; Stapelfeldt, Henrik

2018-03-01

The gas-phase structures of four difluoroiodobenzene and two dihydroxybromobenzene isomers were identified by correlating the emission angles of atomic fragment ions created, following femtosecond laser-induced Coulomb explosion. The structural determinations were facilitated by confining the most polarizable axis of each molecule to the detection plane prior to the Coulomb explosion event using one-dimensional laser-induced adiabatic alignment. For a molecular target consisting of two difluoroiodobenzene isomers, each constituent structure could additionally be singled out and distinguished.

Health System Creation and Integration at a Health Sciences University: A Five-Year Follow-up.

PubMed

Slade, Catherine P; Azziz, Ricardo; Levin, Steven; Caughman, Gretchen B; Hefner, David S; Halbur, Kimberly V; Tingen, Martha S; James, Susan

Shifting healthcare market forces and regulation have exerted near-constant pressure on U.S. academic health centers (AHCs) attempting to successfully execute their traditional tripartite mission. A governance structure and organizational alignment that works well under one set of conditions is rarely optimal when conditions change. Thus, the degree and type of alignment of an AHC's clinical, educational, and faculty practice organizations have changed regularly within the sector, typically landing near one end or the other on a continuum from fully aligned with centralized governance to largely independent with separate governance. The authors examine the case of Georgia Regents University and Health System in this context. In step with industry trends, the institution's governance structure swung from fully aligned/centralized governance in the early 1990s to essentially separate and decentralized by 2000. In 2010, the Georgia Regents University organizations achieved rapid realignment by creating a governance structure of sufficient strength and flexibility to absorb and adjust to continuing external upheaval. The hospitals, clinics, and physician-faculty practice group were combined into one integrated health system, then aligned with the university to form the state's only public AHC under aligned, but distinct, corporate and management structures. The years since reorganization have seen significant growth in patient volumes and complexity, improved service quality, and enhanced faculty physician satisfaction, while also significantly increasing economic contributions from the health system to the academic mission. This case study offers observations and lessons learned that may be useful to other higher education institutions considering reorganization.

Incremental Ontology-Based Extraction and Alignment in Semi-structured Documents

NASA Astrophysics Data System (ADS)

Thiam, Mouhamadou; Bennacer, Nacéra; Pernelle, Nathalie; Lô, Moussa

SHIRIis an ontology-based system for integration of semi-structured documents related to a specific domain. The system’s purpose is to allow users to access to relevant parts of documents as answers to their queries. SHIRI uses RDF/OWL for representation of resources and SPARQL for their querying. It relies on an automatic, unsupervised and ontology-driven approach for extraction, alignment and semantic annotation of tagged elements of documents. In this paper, we focus on the Extract-Align algorithm which exploits a set of named entity and term patterns to extract term candidates to be aligned with the ontology. It proceeds in an incremental manner in order to populate the ontology with terms describing instances of the domain and to reduce the access to extern resources such as Web. We experiment it on a HTML corpus related to call for papers in computer science and the results that we obtain are very promising. These results show how the incremental behaviour of Extract-Align algorithm enriches the ontology and the number of terms (or named entities) aligned directly with the ontology increases.

CCP4i2: the new graphical user interface to the CCP4 program suite.

PubMed

Potterton, Liz; Agirre, Jon; Ballard, Charles; Cowtan, Kevin; Dodson, Eleanor; Evans, Phil R; Jenkins, Huw T; Keegan, Ronan; Krissinel, Eugene; Stevenson, Kyle; Lebedev, Andrey; McNicholas, Stuart J; Nicholls, Robert A; Noble, Martin; Pannu, Navraj S; Roth, Christian; Sheldrick, George; Skubak, Pavol; Turkenburg, Johan; Uski, Ville; von Delft, Frank; Waterman, David; Wilson, Keith; Winn, Martyn; Wojdyr, Marcin

2018-02-01

The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition, CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures.

An interactive NASTRAN preprocessor. [graphic display of undeformed structure using CDC 6000 series computer

NASA Technical Reports Server (NTRS)

Smith, W. W.

1973-01-01

A Langley Research Center version of NASTRAN Level 15.1.0 designed to provide the analyst with an added tool for debugging massive NASTRAN input data is described. The program checks all NASTRAN input data cards and displays on a CRT the graphic representation of the undeformed structure. In addition, the program permits the display and alteration of input data and allows reexecution without physically resubmitting the job. Core requirements on the CDC 6000 computer are approximately 77,000 octal words of central memory.

Der Aufbau mentaler Modelle durch bildliche Darstellungen: Eine experimentalle Studie uber die Bedeutung der Merkmalsdimensionen Elaboriertheit und Strukturierheit im Sachunterricht der Grundschule (The Development of Mental Processes through Graphic Representation with Diverging Degrees of Elaboration and Structurization: An Experimental Study Carried Out in Elementary Science Instruction in Primary School).

ERIC Educational Resources Information Center

Martschinke, Sabine

1996-01-01

Examines types of graphical representation as to their suitability for knowledge acquisition in primary grades. Uses the concept of mental models to clarify the relationship between external presentation and internal representation of knowledge. Finds that students who learned with highly elaborated and highly structured pictures displayed the…

GPU Acceleration of DSP for Communication Receivers.

PubMed

Gunther, Jake; Gunther, Hyrum; Moon, Todd

2017-09-01

Graphics processing unit (GPU) implementations of signal processing algorithms can outperform CPU-based implementations. This paper describes the GPU implementation of several algorithms encountered in a wide range of high-data rate communication receivers including filters, multirate filters, numerically controlled oscillators, and multi-stage digital down converters. These structures are tested by processing the 20 MHz wide FM radio band (88-108 MHz). Two receiver structures are explored: a single channel receiver and a filter bank channelizer. Both run in real time on NVIDIA GeForce GTX 1080 graphics card.

[Application of the technique of analytical structure of project for the sub-project of websites catalog of the Virtual Health Library-Nursing].

PubMed

dos, Santos Luís Augusto; Marin, Heimar de Fátima; Marques, Isaac Rosa; Cunha, Isabel Cristina Kowal Olm

2007-01-01

This work intents, in a didactic form, to explain the benefits of use of a technique of project management, named Work Breakdown Structure: a graphical tool to identify the main results to be developed in a project. The real examples are applied to a sub-project of the Virtual Library in Health in Nursing (BVS-Enfermagem) to development of the Sites Catalogs. The benefits of graphical visualization for a major agreement between professionals of different expertise are presented.

Reverse freeze casting: a new method for fabricating highly porous titanium scaffolds with aligned large pores.

PubMed

Yook, Se-Won; Jung, Hyun-Do; Park, Chang-Hoon; Shin, Kwan-Ha; Koh, Young-Hag; Estrin, Yuri; Kim, Hyoun-Ee

2012-07-01

Highly porous titanium with aligned large pores up to 500 μm in size, which is suitable for scaffold applications, was successfully fabricated using the reverse freeze casting method. In this process we have newly developed, the Ti powders migrated spontaneously along the pre-aligned camphene boundaries at a temperature of 45.5°C and formed a titanium-camphene mixture with an aligned structure; this was followed by freeze drying and sintering. As the casting time increased from 24 to 48 h, the initial columnar structures turned into lamellar structures, with the porosity decreasing from 69 to 51%. This reduction in porosity caused the compressive yield strength to increase from 121 to 302 MPa, with an elastic modulus of the samples being in the range of 2-5 GPa. In addition, it was demonstrated that reverse freeze casting can also be successfully applied to various other raw powders, suggesting that the method developed in this work opens up new avenues for the production of a range of porous metallic and ceramic scaffolds with highly aligned pores. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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

DOE PAGES

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

2017-02-21

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

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Geometrical appearance and spatial arrangement of structural blocks of the Malan loess in NW China: implications for the formation of loess columns

NASA Astrophysics Data System (ADS)

Li, Yanrong; Zhang, Tao; Zhang, Yongbo; Xu, Qiang

2018-06-01

Loess, as one of the main Quaternary deposits, covers approximately 6% of the land surface of the Earth. Although loess is loose and fragile, loess columns are popular and they can stand stably for hundreds of years, thereby forming a spectacular landform. The formation of such special column-shaped soil structures is puzzling, and the underlying fundamentals remain unclear. The present study focuses on quantifying and examining the geometrical shape and spatial alignment of structural blocks of the Malan loess at different locations in the Loess Plateau of China. The structural blocks under investigation include clay- and silt-sized particles, aggregates, fragments, lumps, and columns, which vary in size from microns to tens of meters. Regardless of their size, the structural blocks of the Malan loess are found to be similar in shape, i.e., elongated with a length-to-width ratio of approximately 2.6. The aggregates, fragments, lumps, columns, and macropores between aggregates exhibit strong concentration in the vertical or subvertical alignment. These phenomena imply that the Malan loess is anisotropic and it is composed of a combination of vertically aligned strong units and vertically aligned weak segments. Based on this, "vertiloess" structure is proposed to denote this combination. The vertiloess structure prevents horizontal erosion, but favors spalling, peeling, toppling, falling and cracking-sliding of vertical loess pieces, thereby forming loess columns.

Alignment hierarchies: engineering architecture from the nanometre to the micrometre scale.

PubMed

Kureshi, Alvena; Cheema, Umber; Alekseeva, Tijna; Cambrey, Alison; Brown, Robert

2010-12-06

Natural tissues are built of metabolites, soluble proteins and solid extracellular matrix components (largely fibrils) together with cells. These are configured in highly organized hierarchies of structure across length scales from nanometre to millimetre, with alignments that are dominated by anisotropies in their fibrillar matrix. If we are to successfully engineer tissues, these hierarchies need to be mimicked with an understanding of the interaction between them. In particular, the movement of different elements of the tissue (e.g. molecules, cells and bulk fluids) is controlled by matrix structures at distinct scales. We present three novel systems to introduce alignment of collagen fibrils, cells and growth factor gradients within a three-dimensional collagen scaffold using fluid flow, embossing and layering of construct. Importantly, these can be seen as different parts of the same hierarchy of three-dimensional structure, as they are all formed into dense collagen gels. Fluid flow aligns collagen fibrils at the nanoscale, embossed topographical features provide alignment cues at the microscale and introducing layered configuration to three-dimensional collagen scaffolds provides microscale- and mesoscale-aligned pathways for protein factor delivery as well as barriers to confine protein diffusion to specific spatial directions. These seemingly separate methods can be employed to increase complexity of simple extracellular matrix scaffolds, providing insight into new approaches to directly fabricate complex physical and chemical cues at different hierarchical scales, similar to those in natural tissues.

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

Chao, Tzu-Ling; Yang, Chen-I., E-mail: ciyang@thu.edu.tw

The preparations and properties of three new homochiral three-dimensional (3D) coordination polymers, [M(D-cam)(pyz)(H{sub 2}O){sub 2}]{sub n} (M=Co (1) and Ni (2); D-H{sub 2}cam=(+) D-camphoric acid; pyz=pyrazine) and [Mn{sub 2}(D-cam){sub 2}(H{sub 2}O){sub 2}] (3), under solvothermal conditions is described. Single-crystal X-ray diffraction analyses revealed that all of compounds are homochiral 3D structure. 1 and 2 are isostructural and crystallize in the trigonal space group P3{sub 2}21, while 3 crystallizes in monoclinic space group P2{sub 1}. The structure of 1 and 2 consists of metal-D-cam helical chains which are pillared with pyrazine ligands into a 3D framework structure and 3 features amore » 3D homochiral framework involving one-dimensional manganese-carboxylate chains that are aligned parallel to the b axis. Magnetic susceptibility data of all compounds were collected. The findings indicate that μ{sub 2}-pyrazine dominate weak antiferromagnetic coupling within 1 and 2, while 3 exhibits antiferromagnetic behavior through the carboxylate groups of D-cam ligand. -- Graphical abstract: The preparations and properties of three new homochiral three-dimensional (3D) coordination polymers, [M(D-cam)(pyz)(H{sub 2}O){sub 2}]{sub n} (M=Co (1) and Ni (2); D-H{sub 2}cam=(+) D-camphoric acid; pyz=pyrazine) and [Mn{sub 2}(D-cam){sub 2}(H{sub 2}O){sub 2}] (3), under solvothermal conditions is described. Single-crystal X-ray diffraction analyses revealed that all of compounds are homochiral 3D structure. 1 and 2 are isostructural and crystallize in the trigonal space group P3{sub 2}21, while 3 crystallizes in monoclinic space group P2{sub 1}. The structure of 1 and 2 consists of metal-D-cam helical chains which are pillared with pyrazine ligands into a 3D framework structure and 3 features a 3D homochiral framework involving one-dimensional manganese-carboxylate chains that are aligned parallel to the b axis. Magnetic susceptibility data of all compounds were collected. The findings indicate that μ{sub 2}-pyrazine dominate weak antiferromagnetic coupling within 1 and 2, while 3 exhibits antiferromagnetic behavior through the carboxylate groups of D-cam ligand. Highlights: • Three homochiral 3D coordination polymers were synthesized. • 1 and 2 are 3D structure with metal-D-cam helical chains pillared by pyrazine. • 3 shows a 3D homochiral framework involving 1D manganese-carboxylate chains. • Magnetic data analysis indicates that 1–3 exhibit weak antiferromagnetic coupling.« less

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.

PubMed

Pervouchine, Dmitri D

2018-06-15

The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the “first-align-then-fold” principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite “first-fold-then-align” approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA⁻RNA interactions across the transcriptome.

A computer graphics program for general finite element analyses

NASA Technical Reports Server (NTRS)

Thornton, E. A.; Sawyer, L. M.

1978-01-01

Documentation for a computer graphics program for displays from general finite element analyses is presented. A general description of display options and detailed user instructions are given. Several plots made in structural, thermal and fluid finite element analyses are included to illustrate program options. Sample data files are given to illustrate use of the program.

Batch Computed Tomography Analysis of Projectiles

DTIC Science & Technology

2016-05-01

error calculation. Projectiles are then grouped together according to the similarity of their components. Also discussed is graphical- cluster analysis...ballistic, armor, grouping, clustering 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF...Fig. 10 Graphical structure of 15 clusters of the jacket/core radii profiles with plots of the profiles contained within each cluster . The size of

Applications of Computer Graphics in Engineering

NASA Technical Reports Server (NTRS)

1975-01-01

Various applications of interactive computer graphics to the following areas of science and engineering were described: design and analysis of structures, configuration geometry, animation, flutter analysis, design and manufacturing, aircraft design and integration, wind tunnel data analysis, architecture and construction, flight simulation, hydrodynamics, curve and surface fitting, gas turbine engine design, analysis, and manufacturing, packaging of printed circuit boards, spacecraft design.

Structural alignment of protein descriptors - a combinatorial model.

PubMed

Antczak, Maciej; Kasprzak, Marta; Lukasiak, Piotr; Blazewicz, Jacek

2016-09-17

Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures are nowadays a main premise for understanding the latter. However, computationally derived 3D models often exhibit deviations from the native structure. A way to confirm a model is a comparison with other structures. The structural alignment of a pair of proteins can be defined with the use of a concept of protein descriptors. The protein descriptors are local substructures of protein molecules, which allow us to divide the original problem into a set of subproblems and, consequently, to propose a more efficient algorithmic solution. In the literature, one can find many applications of the descriptors concept that prove its usefulness for insight into protein 3D structures, but the proposed approaches are presented rather from the biological perspective than from the computational or algorithmic point of view. Efficient algorithms for identification and structural comparison of descriptors can become crucial components of methods for structural quality assessment as well as tertiary structure prediction. In this paper, we propose a new combinatorial model and new polynomial-time algorithms for the structural alignment of descriptors. The model is based on the maximum-size assignment problem, which we define here and prove that it can be solved in polynomial time. We demonstrate suitability of this approach by comparison with an exact backtracking algorithm. Besides a simplification coming from the combinatorial modeling, both on the conceptual and complexity level, we gain with this approach high quality of obtained results, in terms of 3D alignment accuracy and processing efficiency. All the proposed algorithms were developed and integrated in a computationally efficient tool descs-standalone, which allows the user to identify and structurally compare descriptors of biological molecules, such as proteins and RNAs. Both PDB (Protein Data Bank) and mmCIF (macromolecular Crystallographic Information File) formats are supported. The proposed tool is available as an open source project stored on GitHub ( https://github.com/mantczak/descs-standalone ).

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.

PubMed

Dowsey, Andrew W; Dunn, Michael J; Yang, Guang-Zhong

2008-04-01

The quest for high-throughput proteomics has revealed a number of challenges in recent years. Whilst substantial improvements in automated protein separation with liquid chromatography and mass spectrometry (LC/MS), aka 'shotgun' proteomics, have been achieved, large-scale open initiatives such as the Human Proteome Organization (HUPO) Brain Proteome Project have shown that maximal proteome coverage is only possible when LC/MS is complemented by 2D gel electrophoresis (2-DE) studies. Moreover, both separation methods require automated alignment and differential analysis to relieve the bioinformatics bottleneck and so make high-throughput protein biomarker discovery a reality. The purpose of this article is to describe a fully automatic image alignment framework for the integration of 2-DE into a high-throughput differential expression proteomics pipeline. The proposed method is based on robust automated image normalization (RAIN) to circumvent the drawbacks of traditional approaches. These use symbolic representation at the very early stages of the analysis, which introduces persistent errors due to inaccuracies in modelling and alignment. In RAIN, a third-order volume-invariant B-spline model is incorporated into a multi-resolution schema to correct for geometric and expression inhomogeneity at multiple scales. The normalized images can then be compared directly in the image domain for quantitative differential analysis. Through evaluation against an existing state-of-the-art method on real and synthetically warped 2D gels, the proposed analysis framework demonstrates substantial improvements in matching accuracy and differential sensitivity. High-throughput analysis is established through an accelerated GPGPU (general purpose computation on graphics cards) implementation. Supplementary material, software and images used in the validation are available at http://www.proteomegrid.org/rain/.

Enhanced Lighting Techniques and Augmented Reality to Improve Human Task Performance

NASA Technical Reports Server (NTRS)

Maida, James C.; Bowen, Charles K.; Pace, John W.

2005-01-01

One of the most versatile tools designed for use on the International Space Station (ISS) is the Special Purpose Dexterous Manipulator (SPDM) robot. Operators for this system are trained at NASA Johnson Space Center (JSC) using a robotic simulator, the Dexterous Manipulator Trainer (DMT), which performs most SPDM functions under normal static Earth gravitational forces. The SPDM is controlled from a standard Robotic Workstation. A key feature of the SPDM and DMT is the Force/Moment Accommodation (FMA) system, which limits the contact forces and moments acting on the robot components, on its payload, an Orbital Replaceable Unit (ORU), and on the receptacle for the ORU. The FMA system helps to automatically alleviate any binding of the ORU as it is inserted or withdrawn from a receptacle, but it is limited in its correction capability. A successful ORU insertion generally requires that the reference axes of the ORU and receptacle be aligned to within approximately 0.25 inch and 0.5 degree of nominal values. The only guides available for the operator to achieve these alignment tolerances are views from any available video cameras. No special registration markings are provided on the ORU or receptacle, so the operator must use their intrinsic features in the video display to perform the pre-insertion alignment task. Since optimum camera views may not be available, and dynamic orbital lighting conditions may limit viewing periods, long times are anticipated for performing some ORU insertion or extraction operations. This study explored the feasibility of using augmented reality (AR) to assist with SPDM operations. Geometric graphical symbols were overlaid on the end effector (EE) camera view to afford cues to assist the operator in attaining adequate pre-insertion ORU alignment.

Structural zooming research and development of an interactive computer graphical interface for stress analysis of cracks

NASA Technical Reports Server (NTRS)

Gerstle, Walter

1989-01-01

Engineering problems sometimes involve the numerical solution of boundary value problems over domains containing geometric feature with widely varying scales. Often, a detailed solution is required at one or more of these features. Small details in large structures may have profound effects upon global performance. Conversely, large-scale conditions may effect local performance. Many man-hours and CPU-hours are currently spent in modeling such problems. With the structural zooming technique, it is now possible to design an integrated program which allows the analyst to interactively focus upon a small region of interest, to modify the local geometry, and then to obtain highly accurate responses in that region which reflect both the properties of the overall structure and the local detail. A boundary integral equation analysis program, called BOAST, was recently developed for the stress analysis of cracks. This program can accurately analyze two-dimensional linear elastic fracture mechanics problems with far less computational effort than existing finite element codes. An interactive computer graphical interface to BOAST was written. The graphical interface would have several requirements: it would be menu-driven, with mouse input; all aspects of input would be entered graphically; the results of a BOAST analysis would be displayed pictorially but also the user would be able to probe interactively to get numerical values of displacement and stress at desired locations within the analysis domain; the entire procedure would be integrated into a single, easy to use package; and it would be written using calls to the graphic package called HOOPS. The program is nearing completion. All of the preprocessing features are working satisfactorily and were debugged. The postprocessing features are under development, and rudimentary postprocessing should be available by the end of the summer. The program was developed and run on a VAX workstation, and must be ported to the SUN workstation. This activity is currently underway.

Community detection in sequence similarity networks based on attribute clustering

DOE PAGES

Chowdhary, Janamejaya; Loeffler, Frank E.; Smith, Jeremy C.

2017-07-24

Networks are powerful tools for the presentation and analysis of interactions in multi-component systems. A commonly studied mesoscopic feature of networks is their community structure, which arises from grouping together similar nodes into one community and dissimilar nodes into separate communities. Here in this paper, the community structure of protein sequence similarity networks is determined with a new method: Attribute Clustering Dependent Communities (ACDC). Sequence similarity has hitherto typically been quantified by the alignment score or its expectation value. However, pair alignments with the same score or expectation value cannot thus be differentiated. To overcome this deficiency, the method constructs,more » for pair alignments, an extended alignment metric, the link attribute vector, which includes the score and other alignment characteristics. Rescaling components of the attribute vectors qualitatively identifies a systematic variation of sequence similarity within protein superfamilies. The problem of community detection is then mapped to clustering the link attribute vectors, selection of an optimal subset of links and community structure refinement based on the partition density of the network. ACDC-predicted communities are found to be in good agreement with gold standard sequence databases for which the "ground truth" community structures (or families) are known. ACDC is therefore a community detection method for sequence similarity networks based entirely on pair similarity information. A serial implementation of ACDC is available from https://cmb.ornl.gov/resources/developments« less

Binocular contrast-gain control for natural scenes: Image structure and phase alignment.

PubMed

Huang, Pi-Chun; Dai, Yu-Ming

2018-05-01

In the context of natural scenes, we applied the pattern-masking paradigm to investigate how image structure and phase alignment affect contrast-gain control in binocular vision. We measured the discrimination thresholds of bandpass-filtered natural-scene images (targets) under various types of pedestals. Our first experiment had four pedestal types: bandpass-filtered pedestals, unfiltered pedestals, notch-filtered pedestals (which enabled removal of the spatial frequency), and misaligned pedestals (which involved rotation of unfiltered pedestals). Our second experiment featured six types of pedestals: bandpass-filtered, unfiltered, and notch-filtered pedestals, and the corresponding phase-scrambled pedestals. The thresholds were compared for monocular, binocular, and dichoptic viewing configurations. The bandpass-filtered pedestal and unfiltered pedestals showed classic dipper shapes; the dipper shapes of the notch-filtered, misaligned, and phase-scrambled pedestals were weak. We adopted a two-stage binocular contrast-gain control model to describe our results. We deduced that the phase-alignment information influenced the contrast-gain control mechanism before the binocular summation stage and that the phase-alignment information and structural misalignment information caused relatively strong divisive inhibition in the monocular and interocular suppression stages. When the pedestals were phase-scrambled, the elimination of the interocular suppression processing was the most convincing explanation of the results. Thus, our results indicated that both phase-alignment information and similar image structures cause strong interocular suppression. Copyright © 2018 Elsevier Ltd. All rights reserved.

Collective motion of active Brownian particles with polar alignment.

PubMed

Martín-Gómez, Aitor; Levis, Demian; Díaz-Guilera, Albert; Pagonabarraga, Ignacio

2018-04-04

We present a comprehensive computational study of the collective behavior emerging from the competition between self-propulsion, excluded volume interactions and velocity-alignment in a two-dimensional model of active particles. We consider an extension of the active brownian particles model where the self-propulsion direction of the particles aligns with the one of their neighbors. We analyze the onset of collective motion (flocking) in a low-density regime (10% surface area) and show that it is mainly controlled by the strength of velocity-alignment interactions: the competition between self-propulsion and crowding effects plays a minor role in the emergence of flocking. However, above the flocking threshold, the system presents a richer pattern formation scenario than analogous models without alignment interactions (active brownian particles) or excluded volume effects (Vicsek-like models). Depending on the parameter regime, the structure of the system is characterized by either a broad distribution of finite-sized polar clusters or the presence of an amorphous, highly fluctuating, large-scale traveling structure which can take a lane-like or band-like form (and usually a hybrid structure which is halfway in between both). We establish a phase diagram that summarizes collective behavior of polar active brownian particles and propose a generic mechanism to describe the complexity of the large-scale structures observed in systems of repulsive self-propelled particles.

Evolutionary profiles from the QR factorization of multiple sequence alignments

PubMed Central

Sethi, Anurag; O'Donoghue, Patrick; Luthey-Schulten, Zaida

2005-01-01

We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS. PMID:15741270

Community detection in sequence similarity networks based on attribute clustering

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

Chowdhary, Janamejaya; Loeffler, Frank E.; Smith, Jeremy C.

Networks are powerful tools for the presentation and analysis of interactions in multi-component systems. A commonly studied mesoscopic feature of networks is their community structure, which arises from grouping together similar nodes into one community and dissimilar nodes into separate communities. Here in this paper, the community structure of protein sequence similarity networks is determined with a new method: Attribute Clustering Dependent Communities (ACDC). Sequence similarity has hitherto typically been quantified by the alignment score or its expectation value. However, pair alignments with the same score or expectation value cannot thus be differentiated. To overcome this deficiency, the method constructs,more » for pair alignments, an extended alignment metric, the link attribute vector, which includes the score and other alignment characteristics. Rescaling components of the attribute vectors qualitatively identifies a systematic variation of sequence similarity within protein superfamilies. The problem of community detection is then mapped to clustering the link attribute vectors, selection of an optimal subset of links and community structure refinement based on the partition density of the network. ACDC-predicted communities are found to be in good agreement with gold standard sequence databases for which the "ground truth" community structures (or families) are known. ACDC is therefore a community detection method for sequence similarity networks based entirely on pair similarity information. A serial implementation of ACDC is available from https://cmb.ornl.gov/resources/developments« less

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures.

PubMed

Goldenberg, Ofir; Erez, Elana; Nimrod, Guy; Ben-Tal, Nir

2009-01-01

ConSurf-DB is a repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using standard methods. The evolutionary conservation of each amino acid position in the alignment was calculated using the Rate4Site algorithm, implemented in the ConSurf web server. The algorithm takes into account the phylogenetic relations between the aligned proteins and the stochastic nature of the evolutionary process explicitly. Rate4Site assigns a conservation level for each position in the multiple sequence alignment using an empirical Bayesian inference. Visual inspection of the conservation patterns on the 3D structure often enables the identification of key residues that comprise the functionally important regions of the protein. The repository is updated with the latest PDB entries on a monthly basis and will be rebuilt annually. ConSurf-DB is available online at http://consurfdb.tau.ac.il/

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures

PubMed Central

Goldenberg, Ofir; Erez, Elana; Nimrod, Guy; Ben-Tal, Nir

2009-01-01

ConSurf-DB is a repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using standard methods. The evolutionary conservation of each amino acid position in the alignment was calculated using the Rate4Site algorithm, implemented in the ConSurf web server. The algorithm takes into account the phylogenetic relations between the aligned proteins and the stochastic nature of the evolutionary process explicitly. Rate4Site assigns a conservation level for each position in the multiple sequence alignment using an empirical Bayesian inference. Visual inspection of the conservation patterns on the 3D structure often enables the identification of key residues that comprise the functionally important regions of the protein. The repository is updated with the latest PDB entries on a monthly basis and will be rebuilt annually. ConSurf-DB is available online at http://consurfdb.tau.ac.il/ PMID:18971256

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

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

2013-06-18

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

High performance ultracapacitors with carbon nanomaterials and ionic liquids

DOEpatents

Lu, Wen; Henry, Kent Douglas

2012-10-09

The present invention is directed to the use of carbon nanotubes and/or electrolyte structures in various electrochemical devices, such as ultracapacitors having an ionic liquid electrolyte. The carbon nanotubes are preferably aligned carbon nanotubes. Compared to randomly entangled carbon nanotubes, aligned carbon nanotubes can have better defined pore structures and higher specific surface areas.

FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web.

PubMed

Shapiro, Jessica; Brutlag, Douglas

2004-07-01

The FoldMiner web server (http://foldminer.stanford.edu/) provides remote access to methods for protein structure alignment and unsupervised motif discovery. FoldMiner is unique among such algorithms in that it improves both the motif definition and the sensitivity of a structural similarity search by combining the search and motif discovery methods and using information from each process to enhance the other. In a typical run, a query structure is aligned to all structures in one of several databases of single domain targets in order to identify its structural neighbors and to discover a motif that is the basis for the similarity among the query and statistically significant targets. This process is fully automated, but options for manual refinement of the results are available as well. The server uses the Chime plugin and customized controls to allow for visualization of the motif and of structural superpositions. In addition, we provide an interface to the LOCK 2 algorithm for rapid alignments of a query structure to smaller numbers of user-specified targets.

Pattern formation of frictional fingers in a gravitational potential

NASA Astrophysics Data System (ADS)

Eriksen, Jon Alm; Toussaint, Renaud; Mâløy, Knut Jørgen; Flekkøy, Eirik; Galland, Olivier; Sandnes, Bjørnar

2018-01-01

Aligned finger structures, with a characteristic width, emerge during the slow drainage of a liquid-granular mixture in a tilted Hele-Shaw cell. A transition from vertical to horizontal alignment of the finger structures is observed as the tilting angle and the granular density are varied. An analytical model is presented, demonstrating that the alignment properties are the result of the competition between fluctuating granular stresses and the hydrostatic pressure. The dynamics is reproduced in simulations. We also show how the system explains patterns observed in nature, created during the early stages of a dike formation.

Method for vacuum fusion bonding

DOEpatents

Ackler, Harold D.; Swierkowski, Stefan P.; Tarte, Lisa A.; Hicks, Randall K.

2001-01-01

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 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.

Organic Xenobiotics

NASA Astrophysics Data System (ADS)

Coleman, William F.

2005-02-01

Fully manipulable (Chime) versions of these molecules appear below. These and other molecules are available at Only@ JCE Online . Figure 1. Atrazine molecule. Interactive Chime-based structure (top); static structure graphic (bottom).

Synthesis and orientation of barium hexaferrite ceramics by magnetic alignment

NASA Astrophysics Data System (ADS)

Autissier, Denis

1990-01-01

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

Empirical comparison study of approximate methods for structure selection in binary graphical models.

PubMed

Viallon, Vivian; Banerjee, Onureena; Jougla, Eric; Rey, Grégoire; Coste, Joel

2014-03-01

Looking for associations among multiple variables is a topical issue in statistics due to the increasing amount of data encountered in biology, medicine, and many other domains involving statistical applications. Graphical models have recently gained popularity for this purpose in the statistical literature. In the binary case, however, exact inference is generally very slow or even intractable because of the form of the so-called log-partition function. In this paper, we review various approximate methods for structure selection in binary graphical models that have recently been proposed in the literature and compare them through an extensive simulation study. We also propose a modification of one existing method, that is shown to achieve good performance and to be generally very fast. We conclude with an application in which we search for associations among causes of death recorded on French death certificates. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mikado: A graphic program

NASA Astrophysics Data System (ADS)

Secretan, Y.

A discussion of the modular program Mikado is presented. Mikado was developed with the goal of creating a flexible graphic tool to display and help analyze the results of finite element fluid flow computations. Mikado works on unstructured meshes, with elements of mixed geometric type, but also offers the possibility of using structured meshes. The program can be operated by both menu and mouse (interactive), or by command file (batch). Mikado is written in FORTRAN, except for a few system dependent subroutines which are in C. It runs presently on Silicon Graphics' workstations and could be easily ported to the IBM-RISC System/6000 family of workstations.

GRASP/Ada (Graphical Representations of Algorithms, Structures, and Processes for Ada): The development of a program analysis environment for Ada. Reverse engineering tools for Ada, task 1, phase 2

NASA Technical Reports Server (NTRS)

Cross, James H., II

1990-01-01

The study, formulation, and generation of structures for Ada (GRASP/Ada) are discussed in this second phase report of a three phase effort. Various graphical representations that can be extracted or generated from source code are described and categorized with focus on reverse engineering. The overall goal is to provide the foundation for a CASE (computer-aided software design) environment in which reverse engineering and forward engineering (development) are tightly coupled. Emphasis is on a subset of architectural diagrams that can be generated automatically from source code with the control structure diagram (CSD) included for completeness.

DSSR-enhanced visualization of nucleic acid structures in Jmol.

PubMed

Hanson, Robert M; Lu, Xiang-Jun

2017-07-03

Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

PubMed

Burger, Melanie C

2015-01-01

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server.

PubMed

Abriata, Luciano A; Bovigny, Christophe; Dal Peraro, Matteo

2016-06-17

Protein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically interpreted coarsely, restricting detailed analyses to positions of extremely high or low variability or dubbed important beforehand based on existing knowledge about active sites, interaction surfaces, (de)stabilizing mutations, etc. Our new webserver PsychoProt (freely available without registration at http://psychoprot.epfl.ch or at http://lucianoabriata.altervista.org/psychoprot/index.html ) helps to detect, quantify, and sequence/structure map the biophysical and biochemical traits that shape amino acid preferences throughout a protein as determined by deep-sequencing of saturated mutational libraries or from large alignments of naturally occurring variants. We exemplify how PsychoProt helps to (i) unveil protein structure-function relationships from experiments and from alignments that are consistent with structures according to coevolution analysis, (ii) recall global information about structural and functional features and identify hitherto unknown constraints to variation in alignments, and (iii) point at different sources of variation among related experimental datasets or between experimental and alignment-based data. Remarkably, metabolic costs of the amino acids pose strong constraints to variability at protein surfaces in nature but not in the laboratory. This and other differences call for caution when extrapolating results from in vitro experiments to natural scenarios in, for example, studies of protein evolution. We show through examples how PsychoProt can be a useful tool for the broad communities of structural biology and molecular evolution, particularly for studies about protein modeling, evolution and design.

Arc Second Alignment of International X-Ray Observatory Mirror Segments in a Fixed Structure

NASA Technical Reports Server (NTRS)

Evans, Tyler C.; Chan, Kai-Wing

2009-01-01

The optics for the International X-Ray Observatory (IXO) require alignment and integration of about fourteen thousand thin mirror segments to achieve the mission goal of 3.0 square meters of effective area at 1.25 keV with an angular resolution of five arc seconds. These mirror segments are 0.4mm thick, and 200 to 400mm in size, which makes it hard not to impart distortion at the subarc second level. This paper outlines the precise alignment, verification testing, and permanent bonding techniques developed at NASA's Goddard Space Flight Center (GSFC). These techniques are used to overcome the challenge of transferring thin mirror segments from a temporary mount to a fixed structure with arc second alignment and minimal figure distortion. Recent advances in technology development in addition to the automation of several processes have produced significant results. This paper will highlight the recent advances in alignment, testing, and permanent bonding techniques as well as the results they have produced.

Passively aligned multichannel fiber-pigtailing of planar integrated optical waveguides

NASA Astrophysics Data System (ADS)

Kremmel, Johannes; Lamprecht, Tobias; Crameri, Nino; Michler, Markus

2017-02-01

A silicon device to simplify the coupling of multiple single-mode fibers to embedded single-mode waveguides has been developed. The silicon device features alignment structures that enable a passive alignment of fibers to integrated waveguides. For passive alignment, precisely machined V-grooves on a silicon device are used and the planar lightwave circuit board features high-precision structures acting as a mechanical stop. The approach has been tested for up to eight fiber-to-waveguide connections. The alignment approach, the design, and the fabrication of the silicon device as well as the assembly process are presented. The characterization of the fiber-to-waveguide link reveals total coupling losses of (0.45±0.20 dB) per coupling interface, which is significantly lower than the values reported in earlier works. Subsequent climate tests reveal that the coupling losses remain stable during thermal cycling but increases significantly during an 85°C/85 Rh-test. All applied fabrication and bonding steps have been performed using standard MOEMS fabrication and packaging processes.

Arc-Second Alignment of International X-Ray Observatory Mirror Segments in a Fixed Structure

NASA Technical Reports Server (NTRS)

Evans, Tyler C.; Chan, Kai-Wing; Saha, Timo T.

2010-01-01

The optics for the International X-Ray Observatory (IXO) require alignment and integration of about fourteen thousand thin mirror segments to achieve the mission goal of 3.0 square meters of effective area at 1.25 keV with an angular resolution of five arc-seconds. These mirror segments are 0.4 mm thick, and 200 to 400 mm in size, which makes it hard not to impart distortion at the subare- second level. This paper outlines the precise alignment, verification testing, and permanent bonding techniques developed at NASA's Goddard Space Flight Center (GSFC). These techniques are used to overcome the challenge of transferring thin mirror segments from a temporary mount to a fixed structure with arc-second alignment and minimal figure distortion. Recent advances in technology development in addition to the automation of several processes have produced significant results. This paper will highlight the recent advances in alignment, testing, and permanent bonding techniques as well as the results they have produced.

Fabrication and material properties of fibrous PHBV scaffolds depending on the cross-ply angle for tissue engineering.

PubMed

Kim, Yang-Hee; Min, Young-Ki; Lee, Byong-Taek

2012-11-01

Fibrous PHBV cross-ply scaffolds were fabricated using the electrospinning technique. The electrospun fibers were arranged depending on angles of alignment, which were 180°, 90°, 60°, and 45°. The stress and strain values of the fibrous PHBV cross-ply scaffolds increased as the cross-ply angle increased. At 180°, the strength and strain values of the fibers depended on tensile loading directions. At an alignment of 90°, the PHBV scaffolds had a stress value of 3.5 MPa, which was more than two times higher than the random structure. The cell morphology and proliferation of L-929 cells was strongly dependant on the fiber alignment and the best results were observed when the angle alignment was high. The results of this study showed that the cross-ply structure of the PHBV scaffold affected not only the cell adhesion and spreading properties but also dictated the mechanical properties, which were dependent on the angles of alignment.

PhyreStorm: A Web Server for Fast Structural Searches Against the PDB.

PubMed

Mezulis, Stefans; Sternberg, Michael J E; Kelley, Lawrence A

2016-02-22

The identification of structurally similar proteins can provide a range of biological insights, and accordingly, the alignment of a query protein to a database of experimentally determined protein structures is a technique commonly used in the fields of structural and evolutionary biology. The PhyreStorm Web server has been designed to provide comprehensive, up-to-date and rapid structural comparisons against the Protein Data Bank (PDB) combined with a rich and intuitive user interface. It is intended that this facility will enable biologists inexpert in bioinformatics access to a powerful tool for exploring protein structure relationships beyond what can be achieved by sequence analysis alone. By partitioning the PDB into similar structures, PhyreStorm is able to quickly discard the majority of structures that cannot possibly align well to a query protein, reducing the number of alignments required by an order of magnitude. PhyreStorm is capable of finding 93±2% of all highly similar (TM-score>0.7) structures in the PDB for each query structure, usually in less than 60s. PhyreStorm is available at http://www.sbg.bio.ic.ac.uk/phyrestorm/. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

A Facile Method to Fabricate Anisotropic Hydrogels with Perfectly Aligned Hierarchical Fibrous Structures.

PubMed

Mredha, Md Tariful Islam; Guo, Yun Zhou; Nonoyama, Takayuki; Nakajima, Tasuku; Kurokawa, Takayuki; Gong, Jian Ping

2018-03-01

Natural structural materials (such as tendons and ligaments) are comprised of multiscale hierarchical architectures, with dimensions ranging from nano- to macroscale, which are difficult to mimic synthetically. Here a bioinspired, facile method to fabricate anisotropic hydrogels with perfectly aligned multiscale hierarchical fibrous structures similar to those of tendons and ligaments is reported. The method includes drying a diluted physical hydrogel in air by confining its length direction. During this process, sufficiently high tensile stress is built along the length direction to align the polymer chains and multiscale fibrous structures (from nano- to submicro- to microscale) are spontaneously formed in the bulk material, which are well-retained in the reswollen gel. The method is useful for relatively rigid polymers (such as alginate and cellulose), which are susceptible to mechanical signal. By controlling the drying with or without prestretching, the degree of alignment, size of superstructures, and the strength of supramolecular interactions can be tuned, which sensitively influence the strength and toughness of the hydrogels. The mechanical properties are comparable with those of natural ligaments. This study provides a general strategy for designing hydrogels with highly ordered hierarchical structures, which opens routes for the development of many functional biomimetic materials for biomedical applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Von Dreele, Robert

One of the goals in developing GSAS-II was to expand from the capabilities of the original General Structure Analysis System (GSAS) which largely encompassed just structure refinement and post refinement analysis. GSAS-II has been written almost entirely in Python loaded with graphics, GUI and mathematical packages (matplotlib, pyOpenGL, wxpython, numpy and scipy). Thus, GSAS-II has a fully developed modern GUI as well as extensive graphical display of data and results. However, the structure and operation of Python has required new approaches to many of the algorithms used in crystal structure analysis. The extensions beyond GSAS include image calibration/integration as wellmore » as peak fitting and unit cell indexing for powder data which are precursors for structure solution. Structure solution within GSAS-II begins with either Pawley or LeBail extracted structure factors from powder data or those measured in a single crystal experiment. Both charge flipping and Monte Carlo-Simulated Annealing techniques are available; the former can be applied to (3+1) incommensurate structures as well as conventional 3D structures.« less

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution.

PubMed

Xia, Xuhua

2018-06-01

DAMBE is a comprehensive software package for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. New functions include imputing missing distances and phylogeny simultaneously (paving the way to build large phage and transposon trees), new bootstrapping/jackknifing methods for PhyPA (phylogenetics from pairwise alignments), and an improved function for fast and accurate estimation of the shape parameter of the gamma distribution for fitting rate heterogeneity over sites. Previous method corrects multiple hits for each site independently. DAMBE's new method uses all sites simultaneously for correction. DAMBE, featuring a user-friendly graphic interface, is freely available from http://dambe.bio.uottawa.ca (last accessed, April 17, 2018).

Tablet—next generation sequence assembly visualization

PubMed Central

Milne, Iain; Bayer, Micha; Cardle, Linda; Shaw, Paul; Stephen, Gordon; Wright, Frank; Marshall, David

2010-01-01

Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine. Availability: Tablet is freely available for Microsoft Windows, Apple Mac OS X, Linux and Solaris. Fully bundled installers can be downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit versions. Contact: tablet@scri.ac.uk PMID:19965881

Tactile Data Entry System

NASA Technical Reports Server (NTRS)

Adams, Richard J.

2015-01-01

The patent-pending Glove-Enabled Computer Operations (GECO) design leverages extravehicular activity (EVA) glove design features as platforms for instrumentation and tactile feedback, enabling the gloves to function as human-computer interface devices. Flexible sensors in each finger enable control inputs that can be mapped to any number of functions (e.g., a mouse click, a keyboard strike, or a button press). Tracking of hand motion is interpreted alternatively as movement of a mouse (change in cursor position on a graphical user interface) or a change in hand position on a virtual keyboard. Programmable vibro-tactile actuators aligned with each finger enrich the interface by creating the haptic sensations associated with control inputs, such as recoil of a button press.

Comparative genome analysis in the integrated microbial genomes (IMG) system.

PubMed

Markowitz, Victor M; Kyrpides, Nikos C

2007-01-01

Comparative genome analysis is critical for the effective exploration of a rapidly growing number of complete and draft sequences for microbial genomes. The Integrated Microbial Genomes (IMG) system (img.jgi.doe.gov) has been developed as a community resource that provides support for comparative analysis of microbial genomes in an integrated context. IMG allows users to navigate the multidimensional microbial genome data space and focus their analysis on a subset of genes, genomes, and functions of interest. IMG provides graphical viewers, summaries, and occurrence profile tools for comparing genes, pathways, and functions (terms) across specific genomes. Genes can be further examined using gene neighborhoods and compared with sequence alignment tools.

WebLogo

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

Crooks, Gavin E.

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. Sequesnce logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richermore » and more precise description of, for example, a binding site, than would a consensus sequence.« less

Graphic kinematics, visual virtual work and elastographics

PubMed Central

Konstantatou, Marina; Athanasopoulos, Georgios; Hannigan, Laura

2017-01-01

In this paper, recent progress in graphic statics is combined with Williot displacement diagrams to create a graphical description of both statics and kinematics for two- and three-dimensional pin-jointed trusses. We begin with reciprocal form and force diagrams. The force diagram is dissected into its component cells which are then translated relative to each other. This defines a displacement diagram which is topologically equivalent to the form diagram (the structure). The various contributions to the overall Virtual Work appear as parallelograms (for two-dimensional trusses) or parallelopipeds (for three-dimensional trusses) that separate the force and the displacement pieces. Structural mechanisms can be identified by translating the force cells such that their shared faces slide across each other without separating. Elastic solutions can be obtained by choosing parallelograms or parallelopipeds of the appropriate aspect ratio. Finally, a new type of ‘elastographic’ diagram—termed a deformed Maxwell–Williot diagram (two-dimensional) or a deformed Rankine–Williot diagram (three-dimensional)—is presented which combines the deflected structure with the forces carried by its members. PMID:28573030

Mechanisms of lamellar collagen formation in connective tissues.

PubMed

Ghazanfari, Samaneh; Khademhosseini, Ali; Smit, Theodoor H

2016-08-01

The objective of tissue engineering is to regenerate functional tissues. Engineering functional tissues requires an understanding of the mechanisms that guide the formation and evolution of structure in the extracellular matrix (ECM). In particular, the three-dimensional (3D) collagen fiber arrangement is important as it is the key structural determinant that provides mechanical integrity and biological function. In this review, we survey the current knowledge on collagen organization mechanisms that can be applied to create well-structured functional lamellar tissues and in particular intervertebral disc and cornea. Thus far, the mechanisms behind the formation of cross-aligned collagen fibers in the lamellar structures is not fully understood. We start with cell-induced collagen alignment and strain-stabilization behavior mechanisms which can explain a single anisotropically aligned collagen fiber layer. These mechanisms may explain why there is anisotropy in a single layer in the first place. However, they cannot explain why a consecutive collagen layer is laid down with an alternating alignment. Therefore, we explored another mechanism, called liquid crystal phasing. While dense concentrations of collagen show such behavior, there is little evidence that the conditions for liquid crystal phasing are actually met in vivo. Instead, lysyl aldehyde-derived collagen cross-links have been found essential for correct lamellar matrix deposition. Furthermore, we suggest that supra-cellular (tissue-level) shear stress may be instrumental in the alignment of collagen fibers. Understanding the potential mechanisms behind the lamellar collagen structure in connective tissues will lead to further improvement of the regeneration strategies of functional complex lamellar tissues. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

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

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

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 Triangularmore » 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.« less

AlignMe—a membrane protein sequence alignment web server

PubMed Central

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

2014-01-01

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

Structure and Characterization of Vertically Aligned Single-Walled Carbon Nanotube Bundles

DOE PAGES

Márquez, Francisco; López, Vicente; Morant, Carmen; ...

2010-01-01

Arrmore » ays of vertically aligned single-walled carbon nanotube bundles, SWCNTs, have been synthesized by simple alcohol catalytic chemical vapor deposition process, carried out at 800 ° C . The formed SWCNTs are organized in small groups perpendicularly aligned and attached to the substrate. These small bundles show a constant diameter of ca. 30 nm and are formed by the adhesion of no more than twenty individual SWCNTs perfectly aligned along their length.« less

Sequence-similar, structure-dissimilar protein pairs in the PDB.

PubMed

Kosloff, Mickey; Kolodny, Rachel

2008-05-01

It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which "redundant" structures have been removed, based on a sequence-based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence-similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence-based structural superpositions and geometry-based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence-based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry-based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence-based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry-based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We have established a data base of sequence-similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm).

Transactions and Answer Judging in Multimedia Instruction: A Way to Transact with Features Appearing in Video and Graphic Images.

ERIC Educational Resources Information Center

Casey, Carl

1992-01-01

Discussion of transactions in computer-based instruction for ill-structured and visual domains focuses on two transactions developed for meteorology training that provide the capability to interact with video and graphic images at a very detailed level. Potential applications for the transactions are suggested, and early evaluation reports are…

CCP4i2: the new graphical user interface to the CCP4 program suite

PubMed Central

Potterton, Liz; Ballard, Charles; Dodson, Eleanor; Evans, Phil R.; Keegan, Ronan; Krissinel, Eugene; Stevenson, Kyle; Lebedev, Andrey; McNicholas, Stuart J.; Noble, Martin; Pannu, Navraj S.; Roth, Christian; Sheldrick, George; Skubak, Pavol; Uski, Ville

2018-01-01

The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition, CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures. PMID:29533233

Merging Literature, Visual Art and Physics: Teaching Through Comics

NASA Astrophysics Data System (ADS)

Thompson, R.

2012-12-01

Comics have been around as a form of entertainment for decades. They are often as seen as one of the distracting vices of kids (and adults!), but comics and their more adult version, the graphic novel, are increasingly valued as a legitimate genre of both literature and visual. The APS Outreach Department has teamed up with the APS graphics department to create a series of comics, one featuring Nikola Tesla and his battles with the evil Thomas Edison, and four about laser the APS original super hero Spectra and her continuing battles with such villains as nefarious Miss Alignment and bumbling General Relativity. These comics have struck a delicate balance between education and entertainment being well received by both the comic book and education communities. By creating a compelling comic story that has correct physics, it is possible to use this under-appreciated medium to excite middle-school students who might otherwise be turned off by traditional teaching methods. In merging physics with the art of comics it is crucial to make sure first and foremost that the students enjoy the story and that they feel a connection to the characters. Students are thus hooked and once they are drawn in, the learning happens automatically.

1, 2, 3, 4: infusing quantitative literacy into introductory biology.

PubMed

Speth, Elena Bray; Momsen, Jennifer L; Moyerbrailean, Gregory A; Ebert-May, Diane; Long, Tammy M; Wyse, Sara; Linton, Debra

2010-01-01

Biology of the twenty-first century is an increasingly quantitative science. Undergraduate biology education therefore needs to provide opportunities for students to develop fluency in the tools and language of quantitative disciplines. Quantitative literacy (QL) is important for future scientists as well as for citizens, who need to interpret numeric information and data-based claims regarding nearly every aspect of daily life. To address the need for QL in biology education, we incorporated quantitative concepts throughout a semester-long introductory biology course at a large research university. Early in the course, we assessed the quantitative skills that students bring to the introductory biology classroom and found that students had difficulties in performing simple calculations, representing data graphically, and articulating data-driven arguments. In response to students' learning needs, we infused the course with quantitative concepts aligned with the existing course content and learning objectives. The effectiveness of this approach is demonstrated by significant improvement in the quality of students' graphical representations of biological data. Infusing QL in introductory biology presents challenges. Our study, however, supports the conclusion that it is feasible in the context of an existing course, consistent with the goals of college biology education, and promotes students' development of important quantitative skills.

Topologically Micropatterned Collagen and Poly(ε-caprolactone) Struts Fabricated Using the Poly(vinyl alcohol) Fibrillation/Leaching Process To Develop Efficiently Engineered Skeletal Muscle Tissue.

PubMed

Kim, Minseong; Kim, WonJin; Kim, GeunHyung

2017-12-20

Optimally designed three-dimensional (3D) biomedical scaffolds for skeletal muscle tissue regeneration pose significant research challenges. Currently, most studies on scaffolds focus on the two-dimensional (2D) surface structures that are patterned in the micro-/nanoscales with various repeating sizes and shapes to induce the alignment of myoblasts and myotube formation. The 2D patterned surface clearly provides effective analytical results of pattern size and shape of the myoblast alignment and differentiation. However, it is inconvenient in terms of the direct application for clinical usage due to the limited thickness and 3D shapeability. Hence, the present study suggests an innovative hydrogel or synthetic structure that consists of uniaxially surface-patterned cylindrical struts for skeleton muscle regeneration. The alignment of the pattern on the hydrogel (collagen) and poly(ε-caprolactone) struts was attained with the fibrillation of poly(vinyl alcohol) and the leaching process. Various cell culture results indicate that the C2C12 cells on the micropatterned collagen structure were fully aligned, and that a significantly high level of myotube formation was achieved when compared to the collagen structures that were not treated with the micropatterning process.

Atomistic cluster alignment method for local order mining in liquids and glasses

NASA Astrophysics Data System (ADS)

Fang, X. W.; Wang, C. Z.; Yao, Y. X.; Ding, Z. J.; Ho, K. M.

2010-11-01

An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the “order mining” idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65 , and Zr36Ni64 ). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.

Moire interferometry patterns for rotational alignment of structures

NASA Astrophysics Data System (ADS)

Heidari, Esmaeil; Harding, Kevin

2016-08-01

In some manufacturing applications the alignment of fine structures formed on the surface of a part such as micro-scribed patterns on solar panels can be critical to the panel performance. Variations in pattern uniformity may degrade the efficiency of the solar panel if the pattern deviates significantly from designed parameters. This paper will explore the use of moire patterns to interpret the angular alignment of such structures on 3 dimensional non-planar shapes. The moire interferometry pattern creates a beat between the scribed pattern and a reference pattern that is a function of both the shape of the part as well as the shape of the scribed pattern. Both the part shape variations and the patterns of interest are typically much smaller than can be seen visually. Similar challenges exist when inspecting specular models or testing low quality optics. The moire effect allows small displacements to be measured from patterns that are well below the resolution of the camera systems that are used to view the patterns. Issues such as the separation of the shape of the part from the alignment of the fine structure as well as resolution and robustness of the technique will be explored in this paper.

First-principles study on the ferrimagnetic half-metallic Mn{sub 2}FeAs alloy

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

Qi, Santao; Zhang, Chuan-Hui, E-mail: zhangch@ustb.edu.cn; Chen, Bao

2015-05-15

Mn-based full-Heusler alloys are kinds of promising candidates for new half-metallic materials. Basing on first principles, the electronic structures and magnetic properties of the Mn{sub 2}FeAs full-Heusler alloy have been investigated in detail. The Hg{sub 2}CuTi-type Mn{sub 2}FeAs compound obeys the Slater-Pauling rule, while the anti-parallel alignment atomic magnetic moments of Mn locating at different sites indicate it a ferrimagnetic alloy. The calculated spin-down bands behave half-metallic character, exhibiting a direct gap of 0.46 eV with a 100% spin polarization at the Fermi level. More studies show the compound would maintain half-metallic nature in a large range of variational latticemore » constants. We expect that our calculated results may trigger Mn{sub 2}FeAs applying in the future spintronics field. - Graphical abstract: The d orbitals of Mn and Fe atoms split into multi-degenerated levels which create new bonding and nonbonding states. These exchange splitting shift the Fermi level to origin band gap.▪ - Highlights: • The electronic structure and magnetic properties of Mn{sub 2}FeAs full-Heusler alloy were studied. • A total magnetic moment of 3μ{sub B} was obtained for Mn{sub 2}FeAs alloy, following the SP rule M{sub t}=Z{sub t}−24. • The origin of ferrimagnetism and half-metallic character in Mn{sub 2}FeAs were discussed.« less

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

Mahamdioua, N., E-mail: mahamdioua.nabil@gmail.com; Amira, A.; Altintas, S.P.

We present structural, magnetic and electrical properties of the polycrystalline A-site-deficient yttrium doped double layered manganites La{sub 1.2−x}□{sub 0.2}Y{sub x}Ca{sub 1.6}Mn{sub 2}O{sub 7} (x=0.2, 0.3 and 0.4) prepared by a solid state reaction method. The samples crystallize in the tetragonal structure with the space group I4/mmm. Doping with Y decreases the cell parameters and causes a decrease of the metal-insulator transition temperature. The same evolution with doping is also seen for the deduced Curie temperature from susceptibility curves which present a clear paramagnetic-ferromagnetic transition. The significant positive intrinsic magnetoresistance, shown in all samples, reaches 85% at 122 K under 7more » T for 0.3 doped sample and can be attributed to the suppression of spin fluctuations via aligning the spins under external magnetic field, while the extrinsic one is attributed to the inter-grain spin-polarized tunneling across the grain boundaries. The simulation of the resistivity curves in the entire temperature range show that the percolation model is suitable to fit our results. The applied magnetic field increases the density of states near the Fermi level, which is in accordance with the observed decrease of resistivity. - Graphical abstract: Resistivity and magnetoresistance of La{sub 1.2−x}□{sub 0.2}Y{sub x}Ca{sub 1.6}Mn{sub 2}O{sub 7} (x=0.2, 0.3, 0.4). Solid lines correspond to the fitting results. Display Omitted.« less