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

PubMed

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

2017-06-16

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

Virtualizing Specialized Software

ERIC Educational Resources Information Center

McSwain-Starrett, Lauren T.; Conley, Stephanie Scheer

2011-01-01

Student computing is now mobile. For college students across the nation, convenient access to information--anytime, anywhere, on demand--has become not only a priority, but a necessity. To successfully serve the needs of this current generation of students, colleges and universities must recognize the trend and align services accordingly.…

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

PubMed Central

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

2016-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

Teacher Efficacy Beliefs: A Case Study Investigation of Core Curriculum

ERIC Educational Resources Information Center

Brown, Natalie Marie

2017-01-01

The purpose of this qualitative case study was to understand how utilizing the Core Knowledge Sequence and aligned curricular resources influenced teachers' perceived self-efficacy for a sample of Arizona elementary charter school teachers. The sample for this study was a convenience sample of 15 elementary teachers, who were currently…

Microtomography imaging of an isolated plant fiber: a digital holographic approach.

PubMed

Malek, Mokrane; Khelfa, Haithem; Picart, Pascal; Mounier, Denis; Poilâne, Christophe

2016-01-20

This paper describes a method for optical projection tomography for the 3D in situ characterization of micrometric plant fibers. The proposed approach is based on digital holographic microscopy, the holographic capability being convenient to compensate for the runout of the fiber during rotations. The setup requires a telecentric alignment to prevent from the changes in the optical magnification, and calibration results show the very good experimental adjustment. Amplitude images are obtained from the set of recorded and digitally processed holograms. Refocusing of blurred images and correction of both runout and jitter are carried out to get appropriate amplitude images. The 3D data related to the plant fiber are computed from the set of images using a dedicated numerical processing. Experimental results exhibit the internal and external shapes of the plant fiber. These experimental results constitute the first attempt to obtain 3D data of flax fiber, about 12  μm×17  μm in apparent diameter, with a full-field optical tomography approach using light in the visible range.

Dynamic cholesteric liquid crystal superstructures photoaligned by one-step polarization holography

NASA Astrophysics Data System (ADS)

Li, Sen-Sen; Shen, Yuan; Chang, Zhen-Ni; Li, Wen-Song; Xu, Yan-Chao; Fan, Xing-Yu; Chen, Lu-Jian

2017-12-01

A convenient approach to modulate the fingerprint textures of methyl red (MR) doped cholesteric liquid crystals by asymmetric photoalignment in the green-light waveband is presented, resulting in the generation of voltage-controllable helical superstructures. The interaction between the MR molecules and the incident light polarization determines the initial twisted planar geometry, providing a multivariant control over the stripe directions of fingerprint textures by applying a proper electric field. The key factors for precise manipulation of fingerprint stripes in a predictable and rewritable manner are analyzed theoretically and investigated experimentally, which involves the alignment asymmetry, the ratio of cell gap to natural pitch length, and the chirality of chiral dopant. Dynamic periodic fingerprint textures in shapes of dashed curve and dashed line are further demonstrated by utilizing a facile one-step polarization holography process using two beams with orthogonal circular and orthogonal linear polarizations, respectively. It is believed that the practical approach described in this study would enrich the research contents of self-assembled hierarchical superstructures using soft liquid crystal building blocks.

Optimizing Health Care for Children with Spina Bifida

ERIC Educational Resources Information Center

Liptak, Gregory S.; El Samra, Ahmad

2010-01-01

The health care needs of children with spina bifida are complex. They need specialists, generalists, and an integrated system to deliver this complex care and to align and inform all the providers. Most research in spina bifida has been focused on narrow medical outcomes; it has been noncollaborative, based on small samples of convenience, with no…

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

DOE PAGES

Wang, Xu; Le, Anh -Thu; Yu, Chao; ...

2016-03-30

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

Erratum: Erratum to: Maximally symmetric two Higgs doublet model with natural standard model alignment

NASA Astrophysics Data System (ADS)

Bhupal Dev, P. S.; Pilaftsis, Apostolos

2015-11-01

Here we correct some typesetting errors in ref. [1]. These corrections have been implemented in the latest version of [1] on arXiv and the corrected equations have also been reproduced in ref. [2] for the reader's convenience. We clarify that all numerical results presented in ref. [1] remain unaffected by these typographic errors.

Leadership in Nursing Homes: Directors of Nursing Aligning Practice With Regulations.

PubMed

Siegel, Elena O; Bettega, Kristen; Bakerjian, Debra; Sikma, Suzanne

2018-06-01

Nursing homes use team nursing, with minimal RN presence, leaving the majority of direct care to licensed practical/vocational nurses (LPNs/LVNs) and unlicensed assistive personnel (UAP), including medication aides. The current article describes challenges faced by nursing home directors of nursing (DONs) leading and managing a team nursing approach, including consideration of scope of practice, delegation and supervision regulations, and related policy implications. A secondary data analysis was performed of qualitative data from a study to develop and test DON guidelines for delegation in nursing home practice. A convenience sample (N = 29) of current or previous DONs and other nursing home leaders with knowledge and expertise in the DON role participated in in-depth, guided interviews. The findings highlight a core concern to nursing licensure policy and regulation: knowledge and practice gaps related to scope of practice and delegation and supervision among DONs, RNs, and LPNs/LVNs, as well as administrators, and the role of nursing leaders in supporting appropriate delegation practices. The findings offer directions for research and practice in addressing challenges in aligning team nursing practices with regulatory standards as well as the related gaps in knowledge among DONs, administrators, and nursing staff. [Journal of Gerontological Nursing, 44(6), 10-14.]. Copyright 2018, SLACK Incorporated.

Generalizing, Extending, and Maximizing Nitrogen-15 Hyperpolarization Induced by Parahydrogen in Reversible Exchange

PubMed Central

2017-01-01

Signal Amplification by Reversible Exchange (SABRE) is a fast and convenient NMR hyperpolarization method that uses cheap and readily available para-hydrogen as a hyperpolarization source. SABRE can hyperpolarize protons and heteronuclei. Here we focus on the heteronuclear variant introduced as SABRE-SHEATH (SABRE in SHield Enables Alignment Transfer to Heteronuclei) and nitrogen-15 targets in particular. We show that 15N-SABRE works more efficiently and on a wider range of substrates than 1H-SABRE, greatly generalizing the SABRE approach. In addition, we show that nitrogen-15 offers significantly extended T1 times of up to 12 minutes. Long T1 times enable higher hyperpolarization levels but also hold the promise of hyperpolarized molecular imaging for several tens of minutes. Detailed characterization and optimization are presented, leading to nitrogen-15 polarization levels in excess of 10% on several compounds. PMID:28392884

Fast alignment-free sequence comparison using spaced-word frequencies.

PubMed

Leimeister, Chris-Andre; Boden, Marcus; Horwege, Sebastian; Lindner, Sebastian; Morgenstern, Burkhard

2014-07-15

Alignment-free methods for sequence comparison are increasingly used for genome analysis and phylogeny reconstruction; they circumvent various difficulties of traditional alignment-based approaches. In particular, alignment-free methods are much faster than pairwise or multiple alignments. They are, however, less accurate than methods based on sequence alignment. Most alignment-free approaches work by comparing the word composition of sequences. A well-known problem with these methods is that neighbouring word matches are far from independent. To reduce the statistical dependency between adjacent word matches, we propose to use 'spaced words', defined by patterns of 'match' and 'don't care' positions, for alignment-free sequence comparison. We describe a fast implementation of this approach using recursive hashing and bit operations, and we show that further improvements can be achieved by using multiple patterns instead of single patterns. To evaluate our approach, we use spaced-word frequencies as a basis for fast phylogeny reconstruction. Using real-world and simulated sequence data, we demonstrate that our multiple-pattern approach produces better phylogenies than approaches relying on contiguous words. Our program is freely available at http://spaced.gobics.de/. © The Author 2014. Published by Oxford University Press.

Ottawa Model of Implementation Leadership and Implementation Leadership Scale: mapping concepts for developing and evaluating theory-based leadership interventions.

PubMed

Gifford, Wendy; Graham, Ian D; Ehrhart, Mark G; Davies, Barbara L; Aarons, Gregory A

2017-01-01

Leadership in health care is instrumental to creating a supportive organizational environment and positive staff attitudes for implementing evidence-based practices to improve patient care and outcomes. The purpose of this study is to demonstrate the alignment of the Ottawa Model of Implementation Leadership (O-MILe), a theoretical model for developing implementation leadership, with the Implementation Leadership Scale (ILS), an empirically validated tool for measuring implementation leadership. A secondary objective is to describe the methodological process for aligning concepts of a theoretical model with an independently established measurement tool for evaluating theory-based interventions. Modified template analysis was conducted to deductively map items of the ILS onto concepts of the O-MILe. An iterative process was used in which the model and scale developers (n=5) appraised the relevance, conceptual clarity, and fit of each ILS items with the O-MILe concepts through individual feedback and group discussions until consensus was reached. All 12 items of the ILS correspond to at least one O-MILe concept, demonstrating compatibility of the ILS as a measurement tool for the O-MILe theoretical constructs. The O-MILe provides a theoretical basis for developing implementation leadership, and the ILS is a compatible tool for measuring leadership based on the O-MILe. Used together, the O-MILe and ILS provide an evidence- and theory-based approach for developing and measuring leadership for implementing evidence-based practices in health care. Template analysis offers a convenient approach for determining the compatibility of independently developed evaluation tools to test theoretical models.

Ottawa Model of Implementation Leadership and Implementation Leadership Scale: mapping concepts for developing and evaluating theory-based leadership interventions

PubMed Central

Gifford, Wendy; Graham, Ian D; Ehrhart, Mark G; Davies, Barbara L; Aarons, Gregory A

2017-01-01

Purpose Leadership in health care is instrumental to creating a supportive organizational environment and positive staff attitudes for implementing evidence-based practices to improve patient care and outcomes. The purpose of this study is to demonstrate the alignment of the Ottawa Model of Implementation Leadership (O-MILe), a theoretical model for developing implementation leadership, with the Implementation Leadership Scale (ILS), an empirically validated tool for measuring implementation leadership. A secondary objective is to describe the methodological process for aligning concepts of a theoretical model with an independently established measurement tool for evaluating theory-based interventions. Methods Modified template analysis was conducted to deductively map items of the ILS onto concepts of the O-MILe. An iterative process was used in which the model and scale developers (n=5) appraised the relevance, conceptual clarity, and fit of each ILS items with the O-MILe concepts through individual feedback and group discussions until consensus was reached. Results All 12 items of the ILS correspond to at least one O-MILe concept, demonstrating compatibility of the ILS as a measurement tool for the O-MILe theoretical constructs. Conclusion The O-MILe provides a theoretical basis for developing implementation leadership, and the ILS is a compatible tool for measuring leadership based on the O-MILe. Used together, the O-MILe and ILS provide an evidence- and theory-based approach for developing and measuring leadership for implementing evidence-based practices in health care. Template analysis offers a convenient approach for determining the compatibility of independently developed evaluation tools to test theoretical models. PMID:29355212

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.

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

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.

Optical Device for Converting a Laser Beam into Two Co-aligned but Oppositely Directed Beams

NASA Technical Reports Server (NTRS)

Jennings, Donald

2013-01-01

Optical systems consisting of a series of optical elements require alignment from the input end to the output end. The optical elements can be mirrors, lenses, sources, detectors, or other devices. Complex optical systems are often difficult to align from end-to-end because the alignment beam must be inserted at one end in order for the beam to traverse the entire optical path to the other end. The ends of the optical train may not be easily accessible to the alignment beam. Typically, when a series of optical elements is to be aligned, an alignment laser beam is inserted into the optical path with a pick-off mirror at one end of the series of elements. But it may be impossible to insert the beam at an end-point. It can be difficult to locate the pick-off mirror at the desired position because there is not enough space, there is no mounting surface, or the location is occupied by a source, detector, or other component. Alternatively, the laser beam might be inserted at an intermediate location (not at an end-point) and sent, first in one direction and then the other, to the opposite ends of the optical system for alignment. However, in this case, alignment must be performed in two directions and extra effort is required to co-align the two beams to make them parallel and coincident, i.e., to follow the same path as an end-to-end beam. An optical device has been developed that accepts a laser beam as input and produces two co-aligned, but counter-propagating beams. In contrast to a conventional alignment laser placed at one end of the optical path, this invention can be placed at a convenient position within the optical train and aligned to send its two beams simultaneously along precisely opposite paths that, taken together, trace out exactly the same path as the conventional alignment laser. This invention allows the user the freedom to choose locations within the optical train for placement of the alignment beam. It is also self-aligned by design and requires almost no adjustment.

Room Temperature Interband Cascade Lasers

DTIC Science & Technology

2010-01-01

interband cascade laser (ICL) [6]-[8] is particularly convenient, since the semimetallic band alignment between InAs and GaSb allows the electrons that...superlattice claddings and a non-ohmic part that may be associated with various band discontinuities in the structure . While the latter can probably be...made a radiative transition to the valence band to be transferred readily back to the conduction band via elastic or nearly elastic processes. Our

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

PubMed Central

Rampp, Markus; Soddemann, Thomas; Lederer, Hermann

2006-01-01

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’). PMID:16844980

Measurement of anchoring coefficient of homeotropically aligned nematic liquid crystal using a polarizing optical microscope in reflective mode

NASA Astrophysics Data System (ADS)

Baek, Sang-In; Kim, Sung-Jo; Kim, Jong-Hyun

2015-09-01

Although the homeotropic alignment of liquid crystals is widely used in LCD TVs, no easy method exists to measure its anchoring coefficient. In this study, we propose an easy and convenient measurement technique in which a polarizing optical microscope is used in the reflective mode with an objective lens having a low depth of focus. All measurements focus on the reflection of light near the interface between the liquid crystal and alignment layer. The change in the reflected light is measured by applying an electric field. We model the response of the director of the liquid crystal to the electric field and, thus, the change in reflectance. By adjusting the extrapolation length in the calculation, we match the experimental and calculated results and obtain the anchoring coefficient. In our experiment, the extrapolation lengths were 0.31 ± 0.04 μm, 0.32 ± 0.08 μm, and 0.23 ± 0.05 μm for lecithin, AL-64168, and SE-5662, respectively.

Calibration Issues and Operating System Requirements for Electron-Probe Microanalysis

NASA Technical Reports Server (NTRS)

Carpenter, P.

2006-01-01

Instrument purchase requirements and dialogue with manufacturers have established hardware parameters for alignment, stability, and reproducibility, which have helped improve the precision and accuracy of electron microprobe analysis (EPMA). The development of correction algorithms and the accurate solution to quantitative analysis problems requires the minimization of systematic errors and relies on internally consistent data sets. Improved hardware and computer systems have resulted in better automation of vacuum systems, stage and wavelength-dispersive spectrometer (WDS) mechanisms, and x-ray detector systems which have improved instrument stability and precision. Improved software now allows extended automated runs involving diverse setups and better integrates digital imaging and quantitative analysis. However, instrumental performance is not regularly maintained, as WDS are aligned and calibrated during installation but few laboratories appear to check and maintain this calibration. In particular, detector deadtime (DT) data is typically assumed rather than measured, due primarily to the difficulty and inconvenience of the measurement process. This is a source of fundamental systematic error in many microprobe laboratories and is unknown to the analyst, as the magnitude of DT correction is not listed in output by microprobe operating systems. The analyst must remain vigilant to deviations in instrumental alignment and calibration, and microprobe system software must conveniently verify the necessary parameters. Microanalysis of mission critical materials requires an ongoing demonstration of instrumental calibration. Possible approaches to improvements in instrument calibration, quality control, and accuracy will be discussed. Development of a set of core requirements based on discussions with users, researchers, and manufacturers can yield documents that improve and unify the methods by which instruments can be calibrated. These results can be used to continue improvements of EPMA.

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

PubMed Central

Satija, Rahul; Novák, Ádám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-01-01

Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the α-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from PMID:19715598

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

PubMed

Satija, Rahul; Novák, Adám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-08-28

We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the alpha-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from http://www.stats.ox.ac.uk/~satija/BigFoot/

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment

PubMed Central

DeBlasio, Dan

2013-01-01

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

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.

Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene

PubMed Central

2017-01-01

The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data. We use a taxonomic gold standard to compare the accuracy of alignment-free phylogenetic inference with that of common microbiome-wide phylogenetic inference pipelines based on PyNAST and MUSCLE alignments with FastTree and RAxML. We re-simulate fecal communities from Human Microbiome Project data to evaluate the performance of the methods on datasets with properties of real data. Our comparisons show that alignment-free methods are not inferior to alignment-based methods in giving accurate and robust phylogenic trees. Moreover, consensus ensembles of alignment-free phylogenies are superior to those built from alignment-based methods in their ability to highlight community differences in low power settings. In addition, the overall running times of alignment-based and alignment-free phylogenetic inference are comparable. Taken together our empirical results suggest that alignment-free methods provide a viable approach for microbiome-wide phylogenetic inference. PMID:29136663

Incorporating evolution of transcription factor binding sites into annotated alignments.

PubMed

Bais, Abha S; Grossmann, Stefen; Vingron, Martin

2007-08-01

Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield "conserved TFBSs". Most current methods in this field adopt a multi-step approach that segregates the two aspects. Again, it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account. Although a plethora of approaches have been proposed for the prediction of conserved TFBSs, very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences. Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments. That is, alignments with parts annotated as gaplessly aligned TFBSs (pair-profile hits)are generated. Moreover,the pair- profile related parameters are derived in a sound statistical framework. In this article, we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework. We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models, previously used for modelling TFBS evolution. In a simulated setting, we provide a proof of concept that the approach works given the underlying assumptions,as compared to the original work. Finally, using a real dataset of experimentally verified binding sites in human-mouse sequence pairs,we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences, most comparative TFBS identification methods do not explicitly consider this.Additionally, prediction of conserved binding sites is carried out in a multi-step approach that segregates alignment from TFBS annotation. In this paper, we demonstrate how the simultaneous alignment and annotation approach of SimAnn can be further extended to incorporate TFBS evolutionary relationships. We study how alignments and binding site predictions interplay at varying evolutionary distances and for various profile qualities.

Fluid leakage through fractures in an impervious caprock embedded between two geologic aquifers

NASA Astrophysics Data System (ADS)

Selvadurai, A. P. S.

2012-06-01

The paper develops an analytical result for the flow through a single fracture under a hydraulic gradient between the two aquifer regions and takes into account permeability characteristics of all components of the system. Non-dimensional results are presented to illustrate the influence of the permeability mis-match between the two geologic formations and the permeability and geometry of the fracture on the flow rate through the fracture. The analytical result is then used to develop additional results for leakage through a swarm of vertically aligned hydraulically non-interacting fractures and a damaged region containing a densely spaced array of vertically aligned fractures and worm hole type features in the caprock. The work presents a convenient result for the estimation of leakage from storage formations in geoenvironmental applications.

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

PubMed

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

2017-09-18

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

Gas-Phase Functionalization of Macroscopic Carbon Nanotube Fiber Assemblies: Reaction Control, Electrochemical Properties, and Use for Flexible Supercapacitors.

PubMed

Iglesias, Daniel; Senokos, Evgeny; Alemán, Belén; Cabana, Laura; Navío, Cristina; Marcilla, Rebeca; Prato, Maurizio; Vilatela, Juan J; Marchesan, Silvia

2018-02-14

The assembly of aligned carbon nanotubes (CNTs) into fibers (CNTFs) is a convenient approach to exploit and apply the unique physico-chemical properties of CNTs in many fields. CNT functionalization has been extensively used for its implementation into composites and devices. However, CNTF functionalization is still in its infancy because of the challenges associated with preservation of CNTF morphology. Here, we report a thorough study of the gas-phase functionalization of CNTF assemblies using ozone which was generated in situ from a UV source. In contrast with liquid-based oxidation methods, this gas-phase approach preserves CNTF morphology, while notably increasing its hydrophilicity. The functionalized material is thoroughly characterized by Raman spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscopy, and scanning electron microscopy. Its newly acquired hydrophilicity enables CNTF electrochemical characterization in aqueous media, which was not possible for the pristine material. Through comparison of electrochemical measurements in aqueous electrolytes and ionic liquids, we decouple the effects of functionalization on pseudocapacitive reactions and quantum capacitance. The functionalized CNTF assembly is successfully used as an active material and a current collector in all-solid supercapacitor flexible devices with an ionic liquid-based polymer electrolyte.

The post-genomic era of biological network alignment.

PubMed

Faisal, Fazle E; Meng, Lei; Crawford, Joseph; Milenković, Tijana

2015-12-01

Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by genomic sequence alignment. Here, we review computational challenges behind the network alignment problem, existing approaches for solving the problem, ways of evaluating their alignment quality, and the approaches' biomedical applications. We discuss recent innovative efforts of improving the existing view of network alignment. We conclude with open research questions in comparative biological network research that could further our understanding of principles of life, evolution, disease, and therapeutics.

Investigating Conversational Dynamics: Interactive Alignment, Interpersonal Synergy, and Collective Task Performance

ERIC Educational Resources Information Center

Fusaroli, Riccardo; Tylén, Kristian

2016-01-01

This study investigates interpersonal processes underlying dialog by comparing two approaches, "interactive alignment" and "interpersonal synergy", and assesses how they predict collective performance in a joint task. While the interactive alignment approach highlights imitative patterns between interlocutors, the synergy…

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.

A construct analysis of meal convenience applied to military foods.

PubMed

Jaeger, Sara R; Cardello, Armand V

2007-07-01

The present research investigates the concept of food convenience within the institutional framework of military feeding. The approach views food-related convenience in terms of two broad dimensions: "type of convenience" and "timing of convenience." A discrete choice experiment was conducted with US military personnel (n=179) regarding their perceptions of the (in)convenience associated with the use and consumption of low-preparation, all-in-one, military meals (MREs-meals, ready-to-eat). The obtained data strongly suggest that perceived (in)convenience, time and effort are separate constructs. A food provisioning process perspective was captured in the "timing of convenience" dimension, and the contribution of different stages in the consumption process to the perceived convenience of the meal situation was empirically demonstrated. The latter result has important implications for the study of food convenience outside this specific population and context. As opposed to the product perspective that is currently predominant in the literature, it demonstrates the necessity of adopting a meal perspective in analysing food-related convenience.

Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection

DOE PAGES

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

2017-09-18

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

MANGO: a new approach to multiple sequence alignment.

PubMed

Zhang, Zefeng; Lin, Hao; Li, Ming

2007-01-01

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

A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments.

PubMed

Robinson, Mark D; De Souza, David P; Keen, Woon Wai; Saunders, Eleanor C; McConville, Malcolm J; Speed, Terence P; Likić, Vladimir A

2007-10-29

Gas chromatography-mass spectrometry (GC-MS) is a robust platform for the profiling of certain classes of small molecules in biological samples. When multiple samples are profiled, including replicates of the same sample and/or different sample states, one needs to account for retention time drifts between experiments. This can be achieved either by the alignment of chromatographic profiles prior to peak detection, or by matching signal peaks after they have been extracted from chromatogram data matrices. Automated retention time correction is particularly important in non-targeted profiling studies. A new approach for matching signal peaks based on dynamic programming is presented. The proposed approach relies on both peak retention times and mass spectra. The alignment of more than two peak lists involves three steps: (1) all possible pairs of peak lists are aligned, and similarity of each pair of peak lists is estimated; (2) the guide tree is built based on the similarity between the peak lists; (3) peak lists are progressively aligned starting with the two most similar peak lists, following the guide tree until all peak lists are exhausted. When two or more experiments are performed on different sample states and each consisting of multiple replicates, peak lists within each set of replicate experiments are aligned first (within-state alignment), and subsequently the resulting alignments are aligned themselves (between-state alignment). When more than two sets of replicate experiments are present, the between-state alignment also employs the guide tree. We demonstrate the usefulness of this approach on GC-MS metabolic profiling experiments acquired on wild-type and mutant Leishmania mexicana parasites. We propose a progressive method to match signal peaks across multiple GC-MS experiments based on dynamic programming. A sensitive peak similarity function is proposed to balance peak retention time and peak mass spectra similarities. This approach can produce the optimal alignment between an arbitrary number of peak lists, and models explicitly within-state and between-state peak alignment. The accuracy of the proposed method was close to the accuracy of manually-curated peak matching, which required tens of man-hours for the analyzed data sets. The proposed approach may offer significant advantages for processing of high-throughput metabolomics data, especially when large numbers of experimental replicates and multiple sample states are analyzed.

Is multiple-sequence alignment required for accurate inference of phylogeny?

PubMed

Höhl, Michael; Ragan, Mark A

2007-04-01

The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available from http://www.bioinformatics.org.au (as Python package decaf+py). We show that most methods exhibit a higher overall reconstruction accuracy in the presence of high among-site rate variation. Under all conditions that we considered, variants of the pattern-based approach were significantly better than the other alignment-free methods. The new pattern-based variant achieved a speed-up of an order of magnitude in the distance calculation step, accompanied by a small loss of tree reconstruction accuracy. A method of Bayesian inference from k-mers did not improve on classical alignment-free (and distance-based) methods but may still offer other advantages due to its Bayesian nature. We found the optimal word length k of word-based methods to be stable across various data sets, and we provide parameter ranges for two different alphabets. The influence of these alphabets was analyzed to reveal a trade-off in reconstruction accuracy between long and short branches. We have mapped the phylogenetic accuracy for many alignment-free methods, among them several recently introduced ones, and increased our understanding of their behavior in response to biologically important parameters. In all experiments, the pattern-based approach emerged as superior, at the expense of higher resource consumption. Nonetheless, no alignment-free method that we examined recovers the correct phylogeny as accurately as does an approach based on maximum-likelihood distance estimates of multiply aligned sequences.

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

Electric fields and field-aligned currents in polar regions of the solar corona: 3-D MHD consideration

NASA Technical Reports Server (NTRS)

Pisanko, Yu. V.

1995-01-01

The calculation of the solar rotation electro-dynamical effects in the near-the-Sun solar wind seems more convenient from the non-inertial corotating reference frame. This implies some modification of the 3-D MHD equations generally on the base of the General Theory of Relativity. The paper deals with the search of stationary (in corotating non-inertial reference frame) solutions of the modified 3-D MHD equations for the in near-the-Sun high latitude sub-alfvenic solar wind. The solution is obtained requiring electric fields and field-aligned electric currents in the high latitude near-the-Sun solar wind. Various scenario are explored self-consistently via a number of numerical experiments. The analogy with the high latitude Earth's magnetosphere is used for the interpretation of the results. Possible observational manifestations are discussed.

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

The ties that bind: an integrative framework of physician-hospital alignment

PubMed Central

2011-01-01

Background Alignment between physicians and hospitals is of major importance to the health care sector. Two distinct approaches to align the medical staff with the hospital have characterized previous research. The first approach, economic integration, is rooted in the economic literature, in which alignment is realized by financial means. The second approach, noneconomic integration, represents a sociological perspective emphasizing the cooperative nature of their relationship. Discussion Empirical studies and management theory (agency theory and social exchange theory) are used to increase holistic understanding of physician hospital alignment. On the one hand, noneconomic integration is identified as a means to realize a cooperative relationship. On the other hand, economic integration is studied as a way to align financial incentives. The framework is developed around two key antecedent factors which play an important role in aligning the medical staff. First, provider financial risk bearing is identified as a driving force towards closer integration. Second, organizational trust is believed to be important in explaining the causal relation between noneconomic and economic integration. Summary Hospital financial risk bearing creates a greater need for closer cooperation with the medical staff and alignment of financial incentives. Noneconomic integration lies at the very basis of alignment. It contributes directly to alignment through the norm of reciprocity and indirectly by building trust with the medical staff, laying the foundation for alignment of financial incentives. PMID:21324128

The ties that bind: an integrative framework of physician-hospital alignment.

PubMed

Trybou, Jeroen; Gemmel, Paul; Annemans, Lieven

2011-02-15

Alignment between physicians and hospitals is of major importance to the health care sector. Two distinct approaches to align the medical staff with the hospital have characterized previous research. The first approach, economic integration, is rooted in the economic literature, in which alignment is realized by financial means. The second approach, noneconomic integration, represents a sociological perspective emphasizing the cooperative nature of their relationship. Empirical studies and management theory (agency theory and social exchange theory) are used to increase holistic understanding of physician hospital alignment. On the one hand, noneconomic integration is identified as a means to realize a cooperative relationship. On the other hand, economic integration is studied as a way to align financial incentives. The framework is developed around two key antecedent factors which play an important role in aligning the medical staff. First, provider financial risk bearing is identified as a driving force towards closer integration. Second, organizational trust is believed to be important in explaining the causal relation between noneconomic and economic integration. Hospital financial risk bearing creates a greater need for closer cooperation with the medical staff and alignment of financial incentives. Noneconomic integration lies at the very basis of alignment. It contributes directly to alignment through the norm of reciprocity and indirectly by building trust with the medical staff, laying the foundation for alignment of financial incentives.

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.

PubMed

Malhis, Nawar; Butterfield, Yaron S N; Ester, Martin; Jones, Steven J M

2009-01-01

A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new alignment approach (Slider) that reduces the alignment problem space by utilizing each read base's probabilities given in the prb files. Compared with other aligners, Slider has higher alignment accuracy and efficiency. In addition, given that Slider matches bases with probabilities other than the most probable, it significantly reduces the percentage of base mismatches. The result is that its SNP predictions are more accurate than other SNP prediction approaches used today that start from the most probable sequence, including those using base quality.

Using confidence intervals to evaluate the focus alignment of spectrograph detector arrays.

PubMed

Sawyer, Travis W; Hawkins, Kyle S; Damento, Michael

2017-06-20

High-resolution spectrographs extract detailed spectral information of a sample and are frequently used in astronomy, laser-induced breakdown spectroscopy, and Raman spectroscopy. These instruments employ dispersive elements such as prisms and diffraction gratings to spatially separate different wavelengths of light, which are then detected by a charge-coupled device (CCD) or complementary metal-oxide-semiconductor (CMOS) detector array. Precise alignment along the optical axis (focus position) of the detector array is critical to maximize the instrumental resolution; however, traditional approaches of scanning the detector through focus lack a quantitative measure of precision, limiting the repeatability and relying on one's experience. Here we propose a method to evaluate the focus alignment of spectrograph detector arrays by establishing confidence intervals to measure the alignment precision. We show that propagation of uncertainty can be used to estimate the variance in an alignment, thus providing a quantitative and repeatable means to evaluate the precision and confidence of an alignment. We test the approach by aligning the detector array of a prototype miniature echelle spectrograph. The results indicate that the procedure effectively quantifies alignment precision, enabling one to objectively determine when an alignment has reached an acceptable level. This quantitative approach also provides a foundation for further optimization, including automated alignment. Furthermore, the procedure introduced here can be extended to other alignment techniques that rely on numerically fitting data to a model, providing a general framework for evaluating the precision of alignment methods.

Ion-wake field inside a glass box.

PubMed

Chen, Mudi; Dropmann, Michael; Zhang, Bo; Matthews, Lorin S; Hyde, Truell W

2016-09-01

The confinement provided by a glass box is proving ideal for the formation of vertically aligned structures and a convenient method for controlling the number of dust particles comprising these dust structures as well as their sizes and shapes. In this paper, the electronic confinement of the glass box is mapped, and the particle interactions between the particle pairs inside the glass box are measured. The ion-wake field is shown to exist within the glass box, and its vertical and horizontal extents are measured.

How sterol tilt regulates properties and organization of lipid membranes and membrane insertions

PubMed Central

Khelashvili, George; Harries, Daniel

2013-01-01

Serving as a crucial component of mammalian cells, cholesterol critically regulates the functions of biomembranes. This review focuses on a specific property of cholesterol and other sterols: the tilt modulus χ that quantifies the energetic cost of tilting sterol molecules inside the lipid membrane. We show how χ is involved in determining properties of cholesterol-containing membranes, and detail a novel approach to quantify its value from atomistic molecular dynamics (MD) simulations. Specifically, we link χ with other structural, thermodynamic, and mechanical properties of cholesterol-containing lipid membranes, and delineate how this useful parameter can be obtained from the sterol tilt probability distributions derived from relatively small-scale unbiased MD simulations. We demonstrate how the tilt modulus quantitatively describes the aligning field that sterol molecules create inside the phospholipid bilayers, and we relate χ to the bending rigidity of the lipid bilayer through effective tilt and splay energy contributions to the elastic deformations. Moreover, we show how χ can conveniently characterize the “condensing effect” of cholesterol on phospholipids. Finally, we demonstrate the importance of this cholesterol aligning field to the proper folding and interactions of membrane peptides. Given the relative ease of obtaining the tilt modulus from atomistic simulations, we propose that χ can be routinely used to characterize the mechanical properties of sterol/lipid bilayers, and can also serve as a required fitting parameter in multi-scaled simulations of lipid membrane models to relate the different levels of coarse-grained details. PMID:23291283

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

PubMed

Sawyer, Travis W

2018-02-01

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

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

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

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

High-speed multiple sequence alignment on a reconfigurable platform.

PubMed

Oliver, Tim; Schmidt, Bertil; Maskell, Douglas; Nathan, Darran; Clemens, Ralf

2006-01-01

Progressive alignment is a widely used approach to compute multiple sequence alignments (MSAs). However, aligning several hundred sequences by popular progressive alignment tools requires hours on sequential computers. Due to the rapid growth of sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA.

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

Heuristics for multiobjective multiple sequence alignment.

PubMed

Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B

2016-07-15

Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity. Choosing only one parameter setting may provide an undesirable bias in further steps of the analysis and give too simplistic interpretations. In this work, we reformulate multiple sequence alignment from a multiobjective point of view. The goal is to generate several sequence alignments that represent a trade-off between maximizing the substitution score and minimizing the number of indels/gaps in the sum-of-pairs score function. This trade-off gives to the practitioner further information about the similarity of the sequences, from which she could analyse and choose the most plausible alignment. We introduce several heuristic approaches, based on local search procedures, that compute a set of sequence alignments, which are representative of the trade-off between the two objectives (substitution score and indels). Several algorithm design options are discussed and analysed, with particular emphasis on the influence of the starting alignment and neighborhood search definitions on the overall performance. A perturbation technique is proposed to improve the local search, which provides a wide range of high-quality alignments. The proposed approach is tested experimentally on a wide range of instances. We performed several experiments with sequences obtained from the benchmark database BAliBASE 3.0. To evaluate the quality of the results, we calculate the hypervolume indicator of the set of score vectors returned by the algorithms. The results obtained allow us to identify reasonably good choices of parameters for our approach. Further, we compared our method in terms of correctly aligned pairs ratio and columns correctly aligned ratio with respect to reference alignments. Experimental results show that our approaches can obtain better results than TCoffee and Clustal Omega in terms of the first ratio.

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

Orientational alignment in cavity quantum electrodynamics

NASA Astrophysics Data System (ADS)

Keeling, Jonathan; Kirton, Peter G.

2018-05-01

We consider the orientational alignment of dipoles due to strong matter-light coupling for a nonvanishing density of excitations. We compare various approaches to this problem in the limit of large numbers of emitters and show that direct Monte Carlo integration, mean-field theory, and large deviation methods match exactly in this limit. All three results show that orientational alignment develops in the presence of a macroscopically occupied polariton mode and that the dipoles asymptotically approach perfect alignment in the limit of high density or low temperature.

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

PubMed

Guzzi, Pietro Hiram; Milenkovic, Tijana

2018-05-01

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

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

DOE PAGES

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

2017-03-09

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

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

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

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

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

A parallel approach of COFFEE objective function to multiple sequence alignment

NASA Astrophysics Data System (ADS)

Zafalon, G. F. D.; Visotaky, J. M. V.; Amorim, A. R.; Valêncio, C. R.; Neves, L. A.; de Souza, R. C. G.; Machado, J. M.

2015-09-01

The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.

Multicolor, Fluorescent Supercapacitor Fiber.

PubMed

Liao, Meng; Sun, Hao; Zhang, Jing; Wu, Jingxia; Xie, Songlin; Fu, Xuemei; Sun, Xuemei; Wang, Bingjie; Peng, Huisheng

2017-10-05

Fiber-shaped supercapacitors have attracted broad attentions from both academic and industrial communities due to the demonstrated potentials as next-generation power modules. However, it is important while remains challenging to develop dark-environment identifiable supercapacitor fibers for enhancement on operation convenience and security in nighttime applications. Herein, a novel family of colorful fluorescent supercapacitor fibers has been produced from aligned multi-walled carbon nanotube sheets. Fluorescent dye particles are introduced and stably anchored on the surfaces of aligned multi-walled carbon nanotubes to prepare hybrid fiber electrodes with a broad range of colors from red to purple. The fluorescent component in the dye introduces fluorescent indication capability to the fiber, which is particularly promising for flexible and wearable devices applied in dark environment. In addition, the colorful fluorescent supercapacitor fibers also maintain high electrochemical performance under cyclic bending and charge-discharge processes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microchannel-electrode alignment and separation parameters comparison in microchip capillary electrophoresis by scanning electrochemical microscopy.

PubMed

Wang, Kang; Xia, Xing-Hua

2006-03-31

The end of separation channel in a microchip was electrochemically mapped using the feedback imaging mode of scanning electrochemical microscopy (SECM). This method provides a convenient way for microchannel-electrode alignment in microchip capillary electrophoresis. Influence of electrode-to-channel positions on separation parameters in this capillary electrophoresis-electrochemical detection (CE-ED) was then investigated. For the trapezoid shaped microchannel, detection in the central area resulted in the best apparent separation efficiency and peak shape. In the electrode-to-channel distance ranging from 65 to 15mum, the limiting peak currents of dopamine increased with the decrease of the detection distance due to the limited diffusion and convection of the sample band. Results showed that radial position and axial distance of the detection electrode to microchannel was important for the improvement of separation parameters in CE amperometric detection.

Using the small alignment index chaos indicator to characterize the vibrational dynamics of a molecular system: LiNC-LiCN.

PubMed

Benitez, P; Losada, J C; Benito, R M; Borondo, F

2015-10-01

A study of the dynamical characteristics of the phase space corresponding to the vibrations of the LiNC-LiCN molecule using an analysis based on the small alignment index (SALI) is presented. SALI is a good indicator of chaos that can easily determine whether a given trajectory is regular or chaotic regardless of the dimensionality of the system, and can also provide a wealth of dynamical information when conveniently implemented. In two-dimensional (2D) systems SALI maps are computed as 2D phase space representations, where the SALI asymptotic values are represented in color scale. We show here how these maps provide full information on the dynamical phase space structure of the LiNC-LiCN system, even quantifying numerically the volume of the different zones of chaos and regularity as a function of the molecule excitation energy.

Classroom EFL Writing: The Alignment-Oriented Approach

ERIC Educational Resources Information Center

Haiyan, Miao; Rilong, Liu

2016-01-01

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

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees.

PubMed

Kück, Patrick; Meusemann, Karen; Dambach, Johannes; Thormann, Birthe; von Reumont, Björn M; Wägele, Johann W; Misof, Bernhard

2010-03-31

Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking should routinely be used to improve tree reconstructions. Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements.

Sampling considerations for disease surveillance in wildlife populations

USGS Publications Warehouse

Nusser, S.M.; Clark, W.R.; Otis, D.L.; Huang, L.

2008-01-01

Disease surveillance in wildlife populations involves detecting the presence of a disease, characterizing its prevalence and spread, and subsequent monitoring. A probability sample of animals selected from the population and corresponding estimators of disease prevalence and detection provide estimates with quantifiable statistical properties, but this approach is rarely used. Although wildlife scientists often assume probability sampling and random disease distributions to calculate sample sizes, convenience samples (i.e., samples of readily available animals) are typically used, and disease distributions are rarely random. We demonstrate how landscape-based simulation can be used to explore properties of estimators from convenience samples in relation to probability samples. We used simulation methods to model what is known about the habitat preferences of the wildlife population, the disease distribution, and the potential biases of the convenience-sample approach. Using chronic wasting disease in free-ranging deer (Odocoileus virginianus) as a simple illustration, we show that using probability sample designs with appropriate estimators provides unbiased surveillance parameter estimates but that the selection bias and coverage errors associated with convenience samples can lead to biased and misleading results. We also suggest practical alternatives to convenience samples that mix probability and convenience sampling. For example, a sample of land areas can be selected using a probability design that oversamples areas with larger animal populations, followed by harvesting of individual animals within sampled areas using a convenience sampling method.

Limiting Data Friction by Reducing Data Download Using Spatiotemporally Aligned Data Organization Through STARE

NASA Technical Reports Server (NTRS)

Kuo, Kwo-Sen; Rilee, Michael Lee

2017-01-01

Current data processing practice limits the volume and variety of relevant geoscience data that can practically be applied to important problems. File archives in centralized data centers are the principal means by which Earth Science data are accessed. This approach, however, requires laborious search, retrieval, and eventual customization/adaptation for the data to be used. Such fractionation makes it even more difficult to share outcomes, i.e. research artifacts and data products, hampering reusability and repeatability, since end users generally have their own research agenda and preferences as well as scarce resources. Thus, while finding and downloading data files from central data centers are already costly for end users working in their own field, using data products from other disciplines rapidly becomes prohibitive. This curtails scientific productivity, limits avenues of study, and endangers quality and reproducibility. The Spatio-Temporal Adaptive Resolution Encoding (STARE) is a unifying scheme that facilitates the indexing, access, and fusion of diverse Earth Science data. STARE implements an innovative encoding of geo-spatiotemporal information, originally developed for aligning datasets with diverse spatiotemporal characteristics in an array database. The spatial component of STARE recursively quadfurcates a root polyhedron, producing a hierarchical scheme for addressing geographic locations and regions. The temporal component of STARE uses conventional date-time units as an indexing hierarchy. The additional encoding of spatial and temporal resolution information in STARE enables comparisons and conditional selections across diverse datasets. Moreover, spatiotemporal set-operations, e.g. union and intersection, are mapped to efficient integer operations with STARE. Applied to existing data models (point, grid, spacecraft swath) and corresponding granules, STARE indexes provide a streamlined description usable as geo-spatiotemporal metadata. When coupled with large scale, distributed hardware and software, STARE-based data access reduces pre-analysis data preparation costs by offering a convenient means to align different datasets spatiotemporally without specialized effort in parallel computing or distributed data management.

Limiting Data Friction by Reducing Data Download Using Spatiotemporally Aligned Data Organization Through STARE

NASA Astrophysics Data System (ADS)

Kuo, K. S.; Rilee, M. L.

2017-12-01

Current data processing practice limits the volume and variety of relevant geoscience data that can practically be applied to important problems. File archives in centralized data centers are the principal means by which Earth Science data are accessed. This approach, however, requires laborious search, retrieval, and eventual customization/adaptation for the data to be used. Such fractionation makes it even more difficult to share outcomes, i.e. research artifacts and data products, hampering reusability and repeatability, since end users generally have their own research agenda and preferences as well as scarce resources. Thus, while finding and downloading data files from central data centers are already costly for end users working in their own field, using data products from other disciplines rapidly becomes prohibitive. This curtails scientific productivity, limits avenues of study, and endangers quality and reproducibility. The Spatio-Temporal Adaptive Resolution Encoding ( STARE ) is a unifying scheme that facilitates the indexing, access, and fusion of diverse Earth Science data. STARE implements an innovative encoding of geo-spatiotemporal information, originally developed for aligning datasets with diverse spatiotemporal characteristics in an array database. The spatial component of STARE recursively quadfurcates a root polyhedron, producing a hierarchical scheme for addressing geographic locations and regions. The temporal component of STARE uses conventional date-time units as an indexing hierarchy. The additional encoding of spatial and temporal resolution information in STARE enables comparisons and conditional selections across diverse datasets. Moreover, spatiotemporal set-operations, e.g. union and intersection, are mapped to efficient integer operations with STARE. Applied to existing data models (point, grid, spacecraft swath) and corresponding granules, STARE indexes provide a streamlined description usable as geo-spatiotemporal metadata. When coupled with large scale, distributed hardware and software, STARE-based data access reduces pre-analysis data preparation costs by offering a convenient means to align different datasets spatiotemporally without specialized effort in parallel computing or distributed data management.

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

PubMed

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

2015-01-01

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

Initial Navigation Alignment of Optical Instruments on GOES-R

NASA Astrophysics Data System (ADS)

Isaacson, P.; DeLuccia, F.; Reth, A. D.; Igli, D. A.; Carter, D.

2016-12-01

The GOES-R satellite is the first in NOAA's next-generation series of geostationary weather satellites. In addition to a number of space weather sensors, it will carry two principal optical earth-observing instruments, the Advanced Baseline Imager (ABI) and the Geostationary Lightning Mapper (GLM). During launch, currently scheduled for November of 2016, the alignment of these optical instruments is anticipated to shift from that measured during pre-launch characterization. While both instruments have image navigation and registration (INR) processing algorithms to enable automated geolocation of the collected data, the launch-derived misalignment may be too large for these approaches to function without an initial adjustment to calibration parameters. The parameters that may require adjustment are for Line of Sight Motion Compensation (LMC), and the adjustments will be estimated on orbit during the post-launch test (PLT) phase. We have developed approaches to estimate the initial alignment errors for both ABI and GLM image products. Our approaches involve comparison of ABI and GLM images collected during PLT to a set of reference ("truth") images using custom image processing tools and other software (the INR Performance Assessment Tool Set, or "IPATS") being developed for other INR assessments of ABI and GLM data. IPATS is based on image correlation approaches to determine offsets between input and reference images, and these offsets are the fundamental input to our estimate of the initial alignment errors. Initial testing of our alignment algorithms on proxy datasets lends high confidence that their application will determine the initial alignment errors to within sufficient accuracy to enable the operational INR processing approaches to proceed in a nominal fashion. We will report on the algorithms, implementation approach, and status of these initial alignment tools being developed for the GOES-R ABI and GLM instruments.

Neural nets for aligning optical components in harsh environments: Beam smoothing spatial filter as an example

NASA Technical Reports Server (NTRS)

Decker, Arthur J.; Krasowski, Michael J.

1991-01-01

The goal is to develop an approach to automating the alignment and adjustment of optical measurement, visualization, inspection, and control systems. Classical controls, expert systems, and neural networks are three approaches to automating the alignment of an optical system. Neural networks were chosen for this project and the judgements that led to this decision are presented. Neural networks were used to automate the alignment of the ubiquitous laser-beam-smoothing spatial filter. The results and future plans of the project are presented.

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.

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.

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.

PubMed

Kuraku, Shigehiro; Zmasek, Christian M; Nishimura, Osamu; Katoh, Kazutaka

2013-07-01

We report a new web server, aLeaves (http://aleaves.cdb.riken.jp/), for homologue collection from diverse animal genomes. In molecular comparative studies involving multiple species, orthology identification is the basis on which most subsequent biological analyses rely. It can be achieved most accurately by explicit phylogenetic inference. More and more species are subjected to large-scale sequencing, but the resultant resources are scattered in independent project-based, and multi-species, but separate, web sites. This complicates data access and is becoming a serious barrier to the comprehensiveness of molecular phylogenetic analysis. aLeaves, launched to overcome this difficulty, collects sequences similar to an input query sequence from various data sources. The collected sequences can be passed on to the MAFFT sequence alignment server (http://mafft.cbrc.jp/alignment/server/), which has been significantly improved in interactivity. This update enables to switch between (i) sequence selection using the Archaeopteryx tree viewer, (ii) multiple sequence alignment and (iii) tree inference. This can be performed as a loop until one reaches a sensible data set, which minimizes redundancy for better visibility and handling in phylogenetic inference while covering relevant taxa. The work flow achieved by the seamless link between aLeaves and MAFFT provides a convenient online platform to address various questions in zoology and evolutionary biology.

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity

PubMed Central

Kuraku, Shigehiro; Zmasek, Christian M.; Nishimura, Osamu; Katoh, Kazutaka

2013-01-01

We report a new web server, aLeaves (http://aleaves.cdb.riken.jp/), for homologue collection from diverse animal genomes. In molecular comparative studies involving multiple species, orthology identification is the basis on which most subsequent biological analyses rely. It can be achieved most accurately by explicit phylogenetic inference. More and more species are subjected to large-scale sequencing, but the resultant resources are scattered in independent project-based, and multi-species, but separate, web sites. This complicates data access and is becoming a serious barrier to the comprehensiveness of molecular phylogenetic analysis. aLeaves, launched to overcome this difficulty, collects sequences similar to an input query sequence from various data sources. The collected sequences can be passed on to the MAFFT sequence alignment server (http://mafft.cbrc.jp/alignment/server/), which has been significantly improved in interactivity. This update enables to switch between (i) sequence selection using the Archaeopteryx tree viewer, (ii) multiple sequence alignment and (iii) tree inference. This can be performed as a loop until one reaches a sensible data set, which minimizes redundancy for better visibility and handling in phylogenetic inference while covering relevant taxa. The work flow achieved by the seamless link between aLeaves and MAFFT provides a convenient online platform to address various questions in zoology and evolutionary biology. PMID:23677614

Improving scanner wafer alignment performance by target optimization

NASA Astrophysics Data System (ADS)

Leray, Philippe; Jehoul, Christiane; Socha, Robert; Menchtchikov, Boris; Raghunathan, Sudhar; Kent, Eric; Schoonewelle, Hielke; Tinnemans, Patrick; Tuffy, Paul; Belen, Jun; Wise, Rich

2016-03-01

In the process nodes of 10nm and below, the patterning complexity along with the processing and materials required has resulted in a need to optimize alignment targets in order to achieve the required precision, accuracy and throughput performance. Recent industry publications on the metrology target optimization process have shown a move from the expensive and time consuming empirical methodologies, towards a faster computational approach. ASML's Design for Control (D4C) application, which is currently used to optimize YieldStar diffraction based overlay (DBO) metrology targets, has been extended to support the optimization of scanner wafer alignment targets. This allows the necessary process information and design methodology, used for DBO target designs, to be leveraged for the optimization of alignment targets. In this paper, we show how we applied this computational approach to wafer alignment target design. We verify the correlation between predictions and measurements for the key alignment performance metrics and finally show the potential alignment and overlay performance improvements that an optimized alignment target could achieve.

Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

DOE PAGES

Tian, Wenhong; Samatova, Nagiza F.

2013-01-01

A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based onmore » a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium , E. coli K12 and C. crescenttus , we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.« less

BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.

PubMed

Worley, K C; Wiese, B A; Smith, R F

1995-09-01

BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search-launcher/launcher.html > ).

Entrainment and motor emulation approaches to joint action: Alternatives or complementary approaches?

PubMed

Colling, Lincoln J; Williamson, Kellie

2014-01-01

Joint actions, such as music and dance, rely crucially on the ability of two, or more, agents to align their actions with great temporal precision. Within the literature that seeks to explain how this action alignment is possible, two broad approaches have appeared. The first, what we term the entrainment approach, has sought to explain these alignment phenomena in terms of the behavioral dynamics of the system of two agents. The second, what we term the emulator approach, has sought to explain these alignment phenomena in terms of mechanisms, such as forward and inverse models, that are implemented in the brain. They have often been pitched as alternative explanations of the same phenomena; however, we argue that this view is mistaken, because, as we show, these two approaches are engaged in distinct, and not mutually exclusive, explanatory tasks. While the entrainment approach seeks to uncover the general laws that govern behavior the emulator approach seeks to uncover mechanisms. We argue that is possible to do both and that the entrainment approach must pay greater attention to the mechanisms that support the behavioral dynamics of interest. In short, the entrainment approach must be transformed into a neuroentrainment approach by adopting a mechanistic view of explanation and by seeking mechanisms that are implemented in the brain.

Multi-Scale CNT-Based Reinforcing Polymer Matrix Composites for Lightweight Structures

NASA Technical Reports Server (NTRS)

Eberly, Daniel; Ou, Runqing; Karcz, Adam; Skandan, Ganesh; Mather, Patrick; Rodriguez, Erika

2013-01-01

Reinforcing critical areas in carbon polymer matrix composites (PMCs), also known as fiber reinforced composites (FRCs), is advantageous for structural durability. Since carbon nanotubes (CNTs) have extremely high tensile strength, they can be used as a functional additive to enhance the mechanical properties of FRCs. However, CNTs are not readily dispersible in the polymer matrix, which leads to lower than theoretically predicted improvement in mechanical, thermal, and electrical properties of CNT composites. The inability to align CNTs in a polymer matrix is also a known issue. The feasibility of incorporating aligned CNTs into an FRC was demonstrated using a novel, yet commercially viable nanofiber approach, termed NRMs (nanofiber-reinforcing mats). The NRM concept of reinforcement allows for a convenient and safe means of incorporating CNTs into FRC structural components specifically where they are needed during the fabrication process. NRMs, fabricated through a novel and scalable process, were incorporated into FRC test panels using layup and vacuum bagging techniques, where alternating layers of the NRM and carbon prepreg were used to form the reinforced FRC structure. Control FRC test panel coupons were also fabricated in the same manner, but comprised of only carbon prepreg. The FRC coupons were machined to size and tested for flexural, tensile, and compression properties. This effort demonstrated that FRC structures can be fabricated using the NRM concept, with an increased average load at break during flexural testing versus that of the control. The NASA applications for the developed technologies are for lightweight structures for in-space and launch vehicles. In addition, the developed technologies would find use in NASA aerospace applications such as rockets, aircraft, aircraft/spacecraft propulsion systems, and supporting facilities. The reinforcing aspect of the technology will allow for more efficient joining of fiber composite parts, thus offering additional weight savings. More robust structures capable of withstanding micrometeoroid and space debris impacts will be possible with the enhanced mechanical properties imparted by the aligned CNTs incorporated into the fiber composite structure, as well as the potential for improved electrical and thermal properties. The materials fabrication approach developed in the present effort is a platform for customer applications where additional reinforcement is required or would be beneficial, especially in FRC structures and component parts. Depending upon the specific customer application, the NRM could be tailored to the specific matrix resin and desired property enhancement.

Sentence alignment using feed forward neural network.

PubMed

Fattah, Mohamed Abdel; Ren, Fuji; Kuroiwa, Shingo

2006-12-01

Parallel corpora have become an essential resource for work in multi lingual natural language processing. However, sentence aligned parallel corpora are more efficient than non-aligned parallel corpora for cross language information retrieval and machine translation applications. In this paper, we present a new approach to align sentences in bilingual parallel corpora based on feed forward neural network classifier. A feature parameter vector is extracted from the text pair under consideration. This vector contains text features such as length, punctuate score, and cognate score values. A set of manually prepared training data has been assigned to train the feed forward neural network. Another set of data was used for testing. Using this new approach, we could achieve an error reduction of 60% over length based approach when applied on English-Arabic parallel documents. Moreover this new approach is valid for any language pair and it is quite flexible approach since the feature parameter vector may contain more/less or different features than that we used in our system such as lexical match feature.

Identifying Natural Alignments Between Ambulatory Surgery Centers and Local Health Systems: Building Broader Communities of Surgical Care.

PubMed

Funk, Russell J; Owen-Smith, Jason; Landon, Bruce E; Birkmeyer, John D; Hollingsworth, John M

2017-02-01

To develop and compare methods for identifying natural alignments between ambulatory surgery centers (ASCs) and hospitals that anchor local health systems. Using all-payer data from Florida's State Ambulatory Surgery and Inpatient Databases (2005-2009), we developed 3 methods for identifying alignments between ASCS and hospitals. The first, a geographic proximity approach, used spatial data to assign an ASC to its nearest hospital neighbor. The second, a predominant affiliation approach, assigned an ASC to the hospital with which it shared a plurality of surgeons. The third, a network community approach, linked an ASC with a larger group of hospitals held together by naturally occurring physician networks. We compared each method in terms of its ability to capture meaningful and stable affiliations and its administrative simplicity. Although the proximity approach was simplest to implement and produced the most durable alignments, ASC surgeon's loyalty to the assigned hospital was low with this method. The predominant affiliation and network community approaches performed better and nearly equivalently on these metrics, capturing more meaningful affiliations between ASCs and hospitals. However, the latter's alignments were least durable, and it was complex to administer. We describe 3 methods for identifying natural alignments between ASCs and hospitals, each with strengths and weaknesses. These methods will help health system managers identify ASCs with which to partner. Moreover, health services researchers and policy analysts can use them to study broader communities of surgical care.

Extending the enterprise evolution contextualisation model

NASA Astrophysics Data System (ADS)

de Vries, Marné; van der Merwe, Alta; Gerber, Aurona

2017-07-01

Enterprise engineering (EE) emerged as a new discipline to encourage comprehensive and consistent enterprise design. Since EE is multidisciplinary, various researchers study enterprises from different perspectives, which resulted in a plethora of applicable literature and terminology, but without shared meaning. Previous research specifically focused on the fragmentation of knowledge for designing and aligning the information and communication technology (ICT) subsystem of the enterprise in order to support the business organisation subsystem of the enterprise. As a solution for this fragmented landscape, a business-IT alignment model (BIAM) was developed inductively from existing business-IT alignment approaches. Since most of the existing alignment frameworks addressed the alignment between the ICT subsystem and the business organisation subsystem, BIAM also focused on the alignment between these two subsystems. Yet, the emerging EE discipline intends to address a broader scope of design, evident in the existing approaches that incorporate a broader scope of design/alignment/governance. A need was identified to address the knowledge fragmentation of the EE knowledge base by adapting BIAM to an enterprise evolution contextualisation model (EECM), to contextualise a broader set of approaches, as identified by Lapalme. The main contribution of this article is the incremental development and evaluation of EECM. We also present guiding indicators/prerequisites for applying EECM as a contextualisation tool.

Sensitive Technique For Detecting Alignment Of Seed Laser

NASA Technical Reports Server (NTRS)

Barnes, Norman P.

1994-01-01

Frequency response near resonance measured. Improved technique for detection and quantification of alignment of injection-seeding laser with associated power-oscillator laser proposed. Particularly useful in indicating alignment at spectral purity greater than 98 percent because it becomes more sensitive as perfect alignment approached. In addition, implemented relatively easily, without turning on power-oscillator laser.

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

SPHINX--an algorithm for taxonomic binning of metagenomic sequences.

PubMed

Mohammed, Monzoorul Haque; Ghosh, Tarini Shankar; Singh, Nitin Kumar; Mande, Sharmila S

2011-01-01

Compared with composition-based binning algorithms, the binning accuracy and specificity of alignment-based binning algorithms is significantly higher. However, being alignment-based, the latter class of algorithms require enormous amount of time and computing resources for binning huge metagenomic datasets. The motivation was to develop a binning approach that can analyze metagenomic datasets as rapidly as composition-based approaches, but nevertheless has the accuracy and specificity of alignment-based algorithms. This article describes a hybrid binning approach (SPHINX) that achieves high binning efficiency by utilizing the principles of both 'composition'- and 'alignment'-based binning algorithms. Validation results with simulated sequence datasets indicate that SPHINX is able to analyze metagenomic sequences as rapidly as composition-based algorithms. Furthermore, the binning efficiency (in terms of accuracy and specificity of assignments) of SPHINX is observed to be comparable with results obtained using alignment-based algorithms. A web server for the SPHINX algorithm is available at http://metagenomics.atc.tcs.com/SPHINX/.

Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.

PubMed

Galpert, Deborah; Fernández, Alberto; Herrera, Francisco; Antunes, Agostinho; Molina-Ruiz, Reinaldo; Agüero-Chapin, Guillermin

2018-05-03

The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were alignment-free features related to amino acid composition. The incorporation of alignment-free features in supervised big data models did not significantly improve ortholog detection in yeast proteomes regarding the classification qualities achieved with just alignment-based similarity measures. However, the similarity of their classification performance to that of traditional ortholog detection methods encourages the evaluation of other alignment-free protein pair descriptors in future research.

Quality of artemisinin-based combination formulations for malaria treatment: prevalence and risk factors for poor quality medicines in public facilities and private sector drug outlets in Enugu, Nigeria.

PubMed

Kaur, Harparkash; Allan, Elizabeth Louise; Mamadu, Ibrahim; Hall, Zoe; Ibe, Ogochukwu; El Sherbiny, Mohamed; van Wyk, Albert; Yeung, Shunmay; Swamidoss, Isabel; Green, Michael D; Dwivedi, Prabha; Culzoni, Maria Julia; Clarke, Siân; Schellenberg, David; Fernández, Facundo M; Onwujekwe, Obinna

2015-01-01

Artemisinin-based combination therapies are recommended by the World Health Organisation (WHO) as first-line treatment for Plasmodium falciparum malaria, yet medication must be of good quality for efficacious treatment. A recent meta-analysis reported 35% (796/2,296) of antimalarial drug samples from 21 Sub-Saharan African countries, purchased from outlets predominantly using convenience sampling, failed chemical content analysis. We used three sampling strategies to purchase artemisinin-containing antimalarials (ACAs) in Enugu metropolis, Nigeria, and compared the resulting quality estimates. ACAs were purchased using three sampling approaches--convenience, mystery clients and overt, within a defined area and sampling frame in Enugu metropolis. The active pharmaceutical ingredients were assessed using high-performance liquid chromatography and confirmed by mass spectrometry at three independent laboratories. Results were expressed as percentage of APIs stated on the packaging and used to categorise each sample as acceptable quality, substandard, degraded, or falsified. Content analysis of 3024 samples purchased from 421 outlets using convenience (n=200), mystery (n=1,919) and overt (n=905) approaches, showed overall 90.8% ACAs to be of acceptable quality, 6.8% substandard, 1.3% degraded and 1.2% falsified. Convenience sampling yielded a significantly higher prevalence of poor quality ACAs, but was not evident by the mystery and overt sampling strategies both of which yielded results that were comparable between each other. Artesunate (n=135; 4 falsified) and dihydroartemisinin (n=14) monotherapy tablets, not recommended by WHO, were also identified. Randomised sampling identified fewer falsified ACAs than previously reported by convenience approaches. Our findings emphasise the need for specific consideration to be given to sampling frame and sampling approach if representative information on drug quality is to be obtained.

Bottom-up photonic crystal approach with top-down defect and heterostructure fine-tuning.

PubMed

Ding, Tao; Song, Kai; Clays, Koen; Tung, Chen-Ho

2010-03-16

We combine the most efficient (chemical) approach toward three-dimensional photonic crystals with the most convenient (physical) technique for creating non-close-packed crystalline structures. Self-assembly of colloidal particles in artificial opals is followed by a carefully tuned plasma etching treatment. By covering the resulting top layer of more open structure with original dense opal, embedded defect layers and heterostructures can be conveniently designed for advanced photonic band gap and band edge engineering.

K2 and K2*: efficient alignment-free sequence similarity measurement based on Kendall statistics.

PubMed

Lin, Jie; Adjeroh, Donald A; Jiang, Bing-Hua; Jiang, Yue

2018-05-15

Alignment-free sequence comparison methods can compute the pairwise similarity between a huge number of sequences much faster than sequence-alignment based methods. We propose a new non-parametric alignment-free sequence comparison method, called K2, based on the Kendall statistics. Comparing to the other state-of-the-art alignment-free comparison methods, K2 demonstrates competitive performance in generating the phylogenetic tree, in evaluating functionally related regulatory sequences, and in computing the edit distance (similarity/dissimilarity) between sequences. Furthermore, the K2 approach is much faster than the other methods. An improved method, K2*, is also proposed, which is able to determine the appropriate algorithmic parameter (length) automatically, without first considering different values. Comparative analysis with the state-of-the-art alignment-free sequence similarity methods demonstrates the superiority of the proposed approaches, especially with increasing sequence length, or increasing dataset sizes. The K2 and K2* approaches are implemented in the R language as a package and is freely available for open access (http://community.wvu.edu/daadjeroh/projects/K2/K2_1.0.tar.gz). yueljiang@163.com. Supplementary data are available at Bioinformatics online.

Mango: multiple alignment with N gapped oligos.

PubMed

Zhang, Zefeng; Lin, Hao; Li, Ming

2008-06-01

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

DNA impedance biosensor for detection of cancer, TP53 gene mutation, based on gold nanoparticles/aligned carbon nanotubes modified electrode.

PubMed

Fayazfar, H; Afshar, A; Dolati, M; Dolati, A

2014-07-11

For the first time, a new platform based on electrochemical growth of Au nanoparticles on aligned multi-walled carbon nanotubes (A-MWCNT) was developed for sensitive lable-free DNA detection of the TP53 gene mutation, one of the most popular genes in cancer research. Electrochemical impedance spectroscopy (EIS) was used to monitor the sequence-specific DNA hybridization events related to TP53 gene. Compared to the bare Ta or MWCNT/Ta electrodes, the synergistic interactions of vertically aligned MWCNT array and gold nanoparticles at modified electrode could improve the density of the probe DNA attachment and resulting the sensitivity of the DNA sensor greatly. Using EIS, over the extended DNA concentration range, the change of charge transfer resistance was found to have a linear relationship in respect to the logarithm of the complementary oligonucleotides sequence concentrations in the wide range of 1.0×10(-15)-1.0×10(-7)M, with a detection limit of 1.0×10(-17)M (S/N=3). The prepared sensor also showed good stability (14 days), reproducibility (RSD=2.1%) and could be conveniently regenerated via dehybridization in hot water. The significant improvement in sensitivity illustrates that combining gold nanoparticles with the on-site fabricated aligned MWCNT array represents a promising platform for achieving sensitive biosensor for fast mutation screening related to most human cancer types. Copyright © 2014. Published by Elsevier B.V.

Lower limb alignment characteristics are not associated with running injuries in runners: Prospective cohort study.

PubMed

Hespanhol Junior, Luiz Carlos; de Carvalho, Aline Carla Araújo; Costa, Leonardo Oliveira Pena; Lopes, Alexandre Dias

2016-11-01

There is conflicting evidence on the association between lower limb alignment characteristics and the incidence of running-related injury (RRI). Therefore, the primary aim of this study was to investigate the association between lower limb alignment characteristics and the incidence proportion of RRI in a convenience sample of recreational runners. A total of 89 recreational runners were included in this prospective cohort study. These participants had been running for at least six months and were injury-free at baseline. Lower limb alignment measurements were conducted in order to calculate lower limb discrepancy, Q-angle, subtalar angle and plantar index. All participants also answered a baseline and biweekly online surveys about their running routine, history of RRI and newly developed RRI over a period of 12 weeks. The prevalence of previous RRI and the 12-week incidence proportion of new RRI were calculated. Logistic regression analysis was performed to estimate the association between lower limb length discrepancy, Q-angle, subtalar angle and plantar ach index with the incidence proportion of RRI. The prevalence of previous RRI was 55.1% (n = 49). The 12-week incidence proportion of new RRI was 27.0% (n = 24). Muscle injuries and tendinopathies were the main types of RRI identified. The lower leg and the knee were the main anatomical regions affected. We did not find significant associations between lower limb length discrepancy, Q-angle, subtalar angle and plantar arch index and injury occurrence.

Personologic alignment and the treatment of posttraumatic distress.

PubMed

Everly, G

2001-01-01

The therapeutic alliance is generally considered the sine qua non of successful psychotherapy. Yet, establishing the therapeutic alliance with patients suffering from syndromes of posttraumatic distress (including posttraumatic stress disorder) represents an unusual challenge. This paper describes the use of a personality-based approach to the establishment of the therapeutic alliance. This approach is referred to as personologic alignment and consists of alignment with preferential processes, as well as thematic belief systems. It represents an integration of the personology of Theodore Millon and the rhetoric of Aristotle.

Learning of Alignment Rules between Concept Hierarchies

NASA Astrophysics Data System (ADS)

Ichise, Ryutaro; Takeda, Hideaki; Honiden, Shinichi

With the rapid advances of information technology, we are acquiring much information than ever before. As a result, we need tools for organizing this data. Concept hierarchies such as ontologies and information categorizations are powerful and convenient methods for accomplishing this goal, which have gained wide spread acceptance. Although each concept hierarchy is useful, it is difficult to employ multiple concept hierarchies at the same time because it is hard to align their conceptual structures. This paper proposes a rule learning method that inputs information from a source concept hierarchy and finds suitable location for them in a target hierarchy. The key idea is to find the most similar categories in each hierarchy, where similarity is measured by the κ(kappa) statistic that counts instances belonging to both categories. In order to evaluate our method, we conducted experiments using two internet directories: Yahoo! and LYCOS. We map information instances from the source directory into the target directory, and show that our learned rules agree with a human-generated assignment 76% of the time.

The Map in Our Head Is Not Oriented North: Evidence from a Real-World Environment.

PubMed

Brunyé, Tad T; Burte, Heather; Houck, Lindsay A; Taylor, Holly A

2015-01-01

Like most physical maps, recent research has suggested that cognitive maps of familiar environments may have a north-up orientation. We demonstrate that north orientation is not a necessary feature of cognitive maps and instead may arise due to coincidental alignment between cardinal directions and the built and natural environment. Experiment 1 demonstrated that pedestrians have difficulty pointing north while navigating a familiar real-world environment with roads, buildings, and green spaces oriented oblique to cardinal axes. Instead, north estimates tended to be parallel or perpendicular to roads. In Experiment 2, participants did not demonstrate privileged memory access when oriented toward north while making relative direction judgments. Instead, retrieval was fastest and most accurate when orientations were aligned with roads. In sum, cognitive maps are not always oriented north. Rather, in some real-world environments they can be oriented with respect to environment-specific features, serving as convenient reference systems for organizing and using spatial memory.

Focusing on learning through constructive alignment with task-oriented portfolio assessment

NASA Astrophysics Data System (ADS)

Cain, A.; Grundy, J.; Woodward, C. J.

2018-07-01

Approaches to learning have been shown to have a significant impact on student success in technical units. This paper reports on an action research study that applied the principles of constructive alignment to improve student learning outcomes in programming units. The proposed model uses frequent formative feedback to engage students with unit material, and encourage them to adopt deep approaches to learning. Our results provide a set of guiding principles and a structured teaching approach that focuses students on meeting unit learning objectives, the goal of constructive alignment. The results are demonstrated via descriptions of the resulting teaching and learning environment, student results, and staff and student reflections.

Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.

PubMed

Oliver, Tim; Schmidt, Bertil; Nathan, Darran; Clemens, Ralf; Maskell, Douglas

2005-08-15

Aligning hundreds of sequences using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. We present a new approach to compute multiple sequence alignments in far shorter time using reconfigurable hardware. This results in an implementation of ClustalW with significant runtime savings on a standard off-the-shelf FPGA.

NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.

PubMed

Hu, Jialu; Kehr, Birte; Reinert, Knut

2014-02-15

Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing alignment tools encounter limitations in tackling this problem. Therefore, the demand for faster and more efficient alignment tools is growing. We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee. To assess its performance, NetCoffee was applied to four real datasets. Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful alignments. The source code and data are freely available for download under the GNU GPL v3 license at https://code.google.com/p/netcoffee/.

Direct-write 3D printing of composite materials with magnetically aligned discontinuous reinforcement

NASA Astrophysics Data System (ADS)

Martin, Joshua J.; Caunter, Andrew; Dendulk, Amy; Goodrich, Scott; Pembroke, Ryan; Shores, Dan; Erb, Randall M.

2017-05-01

Three-dimensional (3D) printing of fiber reinforced composites represents an enabling technology that may bring toughness and specific strength to complex parts. Recently, direct-write 3D printing has been offered as a promising route to manufacturing fiber reinforced composites that show high specific strength. These approaches primarily rely on the use of shear-alignment during the extrusion process to align fibers along the printing direction. Shear alignment prevents fibers from being oriented along principle stress directions of the final designed part. This paper describes a new direct-write style 3D printing system that incorporates magnetic fields to actively control the orientation of reinforcing fibers during the printing of fiber reinforced composites. Such a manufacturing system is fraught with complications from the high shear dominated alignment experienced by the fibers during extrusion to the slow magnetic alignment dynamics of fibers in viscous media. Here we characterize these issues and suggest effective operating windows in which magnetic alignment is a viable approach to orienting reinforcing particles during direct-write 3D printing.

Optical and x-ray alignment approaches for off-plane reflection gratings

NASA Astrophysics Data System (ADS)

Allured, Ryan; Donovan, Benjamin D.; DeRoo, Casey T.; Marlowe, Hannah R.; McEntaffer, Randall L.; Tutt, James H.; Cheimets, Peter N.; Hertz, Edward; Smith, Randall K.; Burwitz, Vadim; Hartner, Gisela; Menz, Benedikt

2015-09-01

Off-plane reflection gratings offer the potential for high-resolution, high-throughput X-ray spectroscopy on future missions. Typically, the gratings are placed in the path of a converging beam from an X-ray telescope. In the off-plane reflection grating case, these gratings must be co-aligned such that their diffracted spectra overlap at the focal plane. Misalignments degrade spectral resolution and effective area. In-situ X-ray alignment of a pair of off-plane reflection gratings in the path of a silicon pore optics module has been performed at the MPE PANTER beamline in Germany. However, in-situ X-ray alignment may not be feasible when assembling all of the gratings required for a satellite mission. In that event, optical methods must be developed to achieve spectral alignment. We have developed an alignment approach utilizing a Shack-Hartmann wavefront sensor and diffraction of an ultraviolet laser. We are fabricating the necessary hardware, and will be taking a prototype grating module to an X-ray beamline for performance testing following assembly and alignment.

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

NASA Astrophysics Data System (ADS)

Reid, Katharine L.

2018-03-01

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

Some Alignment Considerations for the Next Linear Collider

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

Ruland, R

Next Linear Collider type accelerators require a new level of alignment quality. The relative alignment of these machines is to be maintained in an error envelope dimensioned in micrometers and for certain parts in nanometers. In the nanometer domain our terra firma cannot be considered monolithic but compares closer to jelly. Since conventional optical alignment methods cannot deal with the dynamics and cannot approach the level of accuracy, special alignment and monitoring techniques must be pursued.

Fast and accurate phylogeny reconstruction using filtered spaced-word matches

PubMed Central

Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-01-01

Abstract Motivation: Word-based or ‘alignment-free’ algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. Results: We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don’t-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don’t-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don’t-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. Availability and Implementation: The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/ Contact: chris.leimeister@stud.uni-goettingen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28073754

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

PubMed

Leimeister, Chris-André; Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-04-01

Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. We propose Filtered Spaced Word Matches (FSWM) , a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don't-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don't-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don't-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/. chris.leimeister@stud.uni-goettingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

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

PubMed Central

2011-01-01

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

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

PubMed

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

2011-08-18

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

Relationship between postural alignment in sitting by photogrammetry and seated postural control in post-stroke subjects.

PubMed

Iyengar, Y R; Vijayakumar, K; Abraham, J M; Misri, Z K; Suresh, B V; Unnikrishnan, B

2014-01-01

This study was executed to find out correlation between postural alignment in sitting measured through photogrammetry and postural control in sitting following stroke. A cross-sectional study with convenient sampling consisting of 45 subjects with acute and sub-acute stroke. Postural alignment in sitting was measured through photogrammetry and relevant angles were obtained through software MB Ruler (version 5.0). Seated postural control was measured through Function in Sitting Test (FIST). Correlation was obtained using Spearman's Rank Correlation co-efficient in SPSS software (version 17.0). Moderate positive correlation (r = 0.385; p < 0.01) was found between angle of lordosis and angle between acromion, lateral epicondyle and point between radius and ulna. Strong negative correlation (r = -0.435; p < 0.01) was found between cranio-vertebral angle and kyphosis. FIST showed moderate positive correlation (r = 0.3446; p < 0.05) with cranio-vertebral angle and strong positive correlation (r = 0.4336; p < 0.01) with Brunnstrom's stage of recovery in upper extremity. Degree of forward head posture in sitting correlates directly with seated postural control and inversely with degree of kyphosis in sitting post-stroke. Postural control in sitting post-stroke is directly related with Brunnstrom's stage of recovery in affected upper extremity in sitting.

Sub-micron resolution selected area electron channeling patterns.

PubMed

Guyon, J; Mansour, H; Gey, N; Crimp, M A; Chalal, S; Maloufi, N

2015-02-01

Collection of selected area channeling patterns (SACPs) on a high resolution FEG-SEM is essential to carry out quantitative electron channeling contrast imaging (ECCI) studies, as it facilitates accurate determination of the crystal plane normal with respect to the incident beam direction and thus allows control the electron channeling conditions. Unfortunately commercial SACP modes developed in the past were limited in spatial resolution and are often no longer offered. In this contribution we present a novel approach for collecting high resolution SACPs (HR-SACPs) developed on a Gemini column. This HR-SACP technique combines the first demonstrated sub-micron spatial resolution with high angular accuracy of about 0.1°, at a convenient working distance of 10mm. This innovative approach integrates the use of aperture alignment coils to rock the beam with a digitally calibrated beam shift procedure to ensure the rocking beam is maintained on a point of interest. Moreover a new methodology to accurately measure SACP spatial resolution is proposed. While column considerations limit the rocking angle to 4°, this range is adequate to index the HR-SACP in conjunction with the pattern simulated from the approximate orientation deduced by EBSD. This new technique facilitates Accurate ECCI (A-ECCI) studies from very fine grained and/or highly strained materials. It offers also new insights for developing HR-SACP modes on new generation high-resolution electron columns. Copyright © 2014 Elsevier B.V. All rights reserved.

Self-aligned block technology: a step toward further scaling

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Relations between Student Perceptions of Assessment Authenticity, Study Approaches and Learning Outcome

ERIC Educational Resources Information Center

Gulikers, Judith T. M.; Bastiaens, Theo J.; Kirschner, Paul A.; Kester, Liesbeth

2006-01-01

This article examines the relationships between perceptions of authenticity and alignment on study approach and learning outcome. Senior students of a vocational training program performed an authentic assessment and filled in a questionnaire about the authenticity of various assessment characteristics and the alignment between the assessment and…

Aligning Accreditation and Academic Program Reviews: A Canadian Case Study

ERIC Educational Resources Information Center

Bowker, Lynne

2017-01-01

Purpose: This paper aims to investigate the potential benefits and limitations associated with aligning accreditation and academic program reviews in post-secondary institutions, using a descriptive case study approach. Design/methodology/approach: The paper describes two Canadian graduate programs that are subject to both external professional…

Holistic Approach to Learning and Teaching Introductory Object-Oriented Programming

ERIC Educational Resources Information Center

Thota, Neena; Whitfield, Richard

2010-01-01

This article describes a holistic approach to designing an introductory, object-oriented programming course. The design is grounded in constructivism and pedagogy of phenomenography. We use constructive alignment as the framework to align assessments, learning, and teaching with planned learning outcomes. We plan learning and teaching activities,…

Whole-body diffusion-weighted MR image stitching and alignment to anatomical MRI

NASA Astrophysics Data System (ADS)

Ceranka, Jakub; Polfliet, Mathias; Lecouvet, Frederic; Michoux, Nicolas; Vandemeulebroucke, Jef

2017-02-01

Whole-body diffusion-weighted (WB-DW) MRI in combination with anatomical MRI has shown a great poten- tial in bone and soft tissue tumour detection, evaluation of lymph nodes and treatment response assessment. Because of the vast body coverage, whole-body MRI is acquired in separate stations, which are subsequently combined into a whole-body image. However, inter-station and inter-modality image misalignments can occur due to image distortions and patient motion during acquisition, which may lead to inaccurate representations of patient anatomy and hinder visual assessment. Automated and accurate whole-body image formation and alignment of the multi-modal MRI images is therefore crucial. We investigated several registration approaches for the formation or stitching of the whole-body image stations, followed by a deformable alignment of the multi- modal whole-body images. We compared a pairwise approach, where diffusion-weighted (DW) image stations were sequentially aligned to a reference station (pelvis), to a groupwise approach, where all stations were simultaneously mapped to a common reference space while minimizing the overall transformation. For each, a choice of input images and corresponding metrics was investigated. Performance was evaluated by assessing the quality of the obtained whole-body images, and by verifying the accuracy of the alignment with whole-body anatomical sequences. The groupwise registration approach provided the best compromise between the formation of WB- DW images and multi-modal alignment. The fully automated method was found to be robust, making its use in the clinic feasible.

What to do When Scalar Invariance Fails: The Extended Alignment Method for Multi-Group Factor Analysis Comparison of Latent Means Across Many Groups.

PubMed

Marsh, Herbert W; Guo, Jiesi; Parker, Philip D; Nagengast, Benjamin; Asparouhov, Tihomir; Muthén, Bengt; Dicke, Theresa

2017-01-12

Scalar invariance is an unachievable ideal that in practice can only be approximated; often using potentially questionable approaches such as partial invariance based on a stepwise selection of parameter estimates with large modification indices. Study 1 demonstrates an extension of the power and flexibility of the alignment approach for comparing latent factor means in large-scale studies (30 OECD countries, 8 factors, 44 items, N = 249,840), for which scalar invariance is typically not supported in the traditional confirmatory factor analysis approach to measurement invariance (CFA-MI). Importantly, we introduce an alignment-within-CFA (AwC) approach, transforming alignment from a largely exploratory tool into a confirmatory tool, and enabling analyses that previously have not been possible with alignment (testing the invariance of uniquenesses and factor variances/covariances; multiple-group MIMIC models; contrasts on latent means) and structural equation models more generally. Specifically, it also allowed a comparison of gender differences in a 30-country MIMIC AwC (i.e., a SEM with gender as a covariate) and a 60-group AwC CFA (i.e., 30 countries × 2 genders) analysis. Study 2, a simulation study following up issues raised in Study 1, showed that latent means were more accurately estimated with alignment than with the scalar CFA-MI, and particularly with partial invariance scalar models based on the heavily criticized stepwise selection strategy. In summary, alignment augmented by AwC provides applied researchers from diverse disciplines considerable flexibility to address substantively important issues when the traditional CFA-MI scalar model does not fit the data. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments.

PubMed

Quinn, Terrance; Sinkala, Zachariah

2014-01-01

We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.

IMU-to-Segment Assignment and Orientation Alignment for the Lower Body Using Deep Learning

PubMed Central

2018-01-01

Human body motion analysis based on wearable inertial measurement units (IMUs) receives a lot of attention from both the research community and the and industrial community. This is due to the significant role in, for instance, mobile health systems, sports and human computer interaction. In sensor based activity recognition, one of the major issues for obtaining reliable results is the sensor placement/assignment on the body. For inertial motion capture (joint kinematics estimation) and analysis, the IMU-to-segment (I2S) assignment and alignment are central issues to obtain biomechanical joint angles. Existing approaches for I2S assignment usually rely on hand crafted features and shallow classification approaches (e.g., support vector machines), with no agreement regarding the most suitable features for the assignment task. Moreover, estimating the complete orientation alignment of an IMU relative to the segment it is attached to using a machine learning approach has not been shown in literature so far. This is likely due to the high amount of training data that have to be recorded to suitably represent possible IMU alignment variations. In this work, we propose online approaches for solving the assignment and alignment tasks for an arbitrary amount of IMUs with respect to a biomechanical lower body model using a deep learning architecture and windows of 128 gyroscope and accelerometer data samples. For this, we combine convolutional neural networks (CNNs) for local filter learning with long-short-term memory (LSTM) recurrent networks as well as generalized recurrent units (GRUs) for learning time dynamic features. The assignment task is casted as a classification problem, while the alignment task is casted as a regression problem. In this framework, we demonstrate the feasibility of augmenting a limited amount of real IMU training data with simulated alignment variations and IMU data for improving the recognition/estimation accuracies. With the proposed approaches and final models we achieved 98.57% average accuracy over all segments for the I2S assignment task (100% when excluding left/right switches) and an average median angle error over all segments and axes of 2.91° for the I2S alignment task. PMID:29351262

Alignment of Iron Nanoparticles in a Magnetic Field Due to Shape Anisotropy

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

Radhakrishnan, Balasubramaniam; Nicholson, Don M; Eisenbach, Markus

2015-07-09

During high magnetic field processing there is evidence for alignment of non-spherical metallic particles above the Curie temperature in alloys with negligible magneto-crystalline anisotropy. The main driving force for alignment is the magnetic shape anisotropy. Current understanding of the phenomenon is not adequate to quantify the effect of particle size, aspect ratio, temperature and the magnetic field on particle alignment. We demonstrate a Monte Carlo approach coupled with size scaling to show the conditions under which alignment is possible.

Raised crosswalks on entrance to the roundabout-a case study on effectiveness of treatment on pedestrian safety and convenience.

PubMed

Candappa, Nimmi; Stephan, Karen; Fotheringham, Nicola; Lenné, Michael G; Corben, Bruce

2014-01-01

A common concern in the use of a roundabout is providing adequately for the pedestrian. This unique roundabout layout, which introduces raised crosswalks directly at the roundabout entrance, as opposed to at a car length back, aims at improving safety and convenience for pedestrians at roundabouts. A preliminary evaluation of the layout was undertaken to establish its effectiveness in meeting study objectives. A quasi-experimental before-and-after study design was used to compare speeds on approach and immediately prior to the crossing to ascertain potential impact speed and implications for pedestrian safety. Compliance to crossing and crossing time were also compared in relation to safety and convenience outcomes. A questionnaire assessed pedestrian perception of the safety and convenience at the roundabout before and after treatment. Results from this case study indicate that mean approach speeds (free speeds 30 m from crossing) reduced from 32.7 to 30.7 km/h and immediately prior to crossing, mean speeds reduced from 19.1 to 16.3 km/h. There was also a marked reduction in proportions of vehicles traveling at speeds that could elevate risk to pedestrians. Total crossing time after treatment reduced by around 4 s, and crossing compliance increased from approximately half to approximately 90 percent. Survey of pedestrians indicated positive response to the perceived safety and convenience posttreatment. Preliminary results of the case study suggest positive safety and convenience outcomes. Implications for pedestrian safety include less exposure to traffic and lower risk of serious injury, particularly for elderly pedestrians; convenience outcomes include shorter waiting times to cross and greater compliance to the crossing. A larger study is required to substantiate the findings.

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

Alignment control study for the solar optical telescope

NASA Technical Reports Server (NTRS)

1976-01-01

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

Achieving Organisational Change through Values Alignment

ERIC Educational Resources Information Center

Branson, Christopher M.

2008-01-01

Purpose: The purpose of this paper is to, first, establish the interdependency between the successful achievement of organisational change and the attainment of values alignment within an organisation's culture and then, second, to describe an effective means for attaining such values alignment. Design/methodology/approach: Literature from the…

‘He's going to be a doctor in August’: a narrative interview study of medical students' and their educators' experiences of aligned and misaligned assistantships

PubMed Central

Jones, Owen Meurig; Okeke, Chiemeka; Bullock, Alison; Wells, Stephanie E; Monrouxe, Lynn V

2016-01-01

Objective To explore final-year students’ and clinical supervisors’ experiences of alignment and misalignment with future Foundation Year 1 (F1) posts in an assistantship programme in the UK. Setting Assistantships are clinical placements in which students assist junior doctors by undertaking similar duties under supervision. Models of assistantship programmes vary across curricula. Some actively seek to align with students’ initial postgraduate F1 post. To date, no research has examined the implications of this association for teaching and learning. Qualitative individual and group narrative interviews were conducted with students and supervisors of 2 Welsh medical schools to address: RQ1: How do students and supervisors understand the purpose of the longitudinal assistantship? RQ2: Does alignment/misalignment of the assistantship with students’ initial F1 post influence students’ and supervisors’ teaching and learning experiences? Audio-recordings of interviews were transcribed, participants anonymised and framework analysis was used. Participants A convenience sample of 4 participant groups comprised (1) final-year medical students whose assistantship and F1 post were aligned (n=27), (2) final-year medical students whose assistantship and F1 post were misaligned (n=18) and (3) supervisors (n=10, junior doctors; n=11, consultants). Results All participant groups highlighted increased student confidence in undertaking the duties of an F1 doctor arising from their assistantship period. Learning transferable skills was also highlighted. Many students considered themselves to be team members, ‘learning the trade’ as they shadowed their F1. Opportunities for caring for acutely unwell patients were scarce. The evidence shows enhanced engagement for students aligned to their first F1 post with greater opportunities for workplace acclimatisation. Those who were misaligned were perceived as being disadvantaged. Conclusions Our findings suggest that alignment with students’ first F1 post enhances the assistantship experience. Further longitudinal assessment is required to examine whether and how this translates into improvements in functioning and reductions in stress and anxiety during this transitional period. PMID:27288387

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.

Two means of sampling sexual minority women: how different are the samples of women?

PubMed

Boehmer, Ulrike; Clark, Melissa; Timm, Alison; Ozonoff, Al

2008-01-01

We compared 2 sampling approaches of sexual minority women in 1 limited geographic area to better understand the implications of these 2 sampling approaches. Sexual minority women identified through the Census did not differ on average age or the prevalence of raising children from those sampled using nonrandomized methods. Women in the convenience sample were better educated and lived in smaller households. Modeling the likelihood of disability in this population resulted in contradictory parameter estimates by sampling approach. The degree of variation observed both between sampling approaches and between different parameters suggests that the total population of sexual minority women is still unmeasured. Thoroughly constructed convenience samples will continue to be a useful sampling strategy to further research on this population.

Using Elephant's Toothpaste as an Engaging and Flexible Curriculum Alignment Project

ERIC Educational Resources Information Center

Eldridge, Daniel S.

2015-01-01

There is an increasing focus across all educational sectors to ensure that learning objectives are aligned with learning activities and assessments. An attractive approach previously published is that of curriculum alignment projects. This paper discusses the use of the fun and famous "Elephant's Toothpaste" experiment as a customizable…

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

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.

Biological intuition in alignment-free methods: response to Posada.

PubMed

Ragan, Mark A; Chan, Cheong Xin

2013-08-01

A recent editorial in Journal of Molecular Evolution highlights opportunities and challenges facing molecular evolution in the era of next-generation sequencing. Abundant sequence data should allow more-complex models to be fit at higher confidence, making phylogenetic inference more reliable and improving our understanding of evolution at the molecular level. However, concern that approaches based on multiple sequence alignment may be computationally infeasible for large datasets is driving the development of so-called alignment-free methods for sequence comparison and phylogenetic inference. The recent editorial characterized these approaches as model-free, not based on the concept of homology, and lacking in biological intuition. We argue here that alignment-free methods have not abandoned models or homology, and can be biologically intuitive.

12-GHz thin-film transistors on transferrable silicon nanomembranes for high-performance flexible electronics.

PubMed

Sun, Lei; Qin, Guoxuan; Seo, Jung-Hun; Celler, George K; Zhou, Weidong; Ma, Zhenqiang

2010-11-22

Multigigahertz flexible electronics are attractive and have broad applications. A gate-after-source/drain fabrication process using preselectively doped single-crystal silicon nanomembranes (SiNM) is an effective approach to realizing high device speed. However, further downscaling this approach has become difficult in lithography alignment. In this full paper, a local alignment scheme in combination with more accurate SiNM transfer measures for minimizing alignment errors is reported. By realizing 1 μm channel alignment for the SiNMs on a soft plastic substrate, thin-film transistors with a record speed of 12 GHz maximum oscillation frequency are demonstrated. These results indicate the great potential of properly processed SiNMs for high-performance flexible electronics.

Algorithms for Automatic Alignment of Arrays

NASA Technical Reports Server (NTRS)

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

1996-01-01

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

A Vision-Based Self-Calibration Method for Robotic Visual Inspection Systems

PubMed Central

Yin, Shibin; Ren, Yongjie; Zhu, Jigui; Yang, Shourui; Ye, Shenghua

2013-01-01

A vision-based robot self-calibration method is proposed in this paper to evaluate the kinematic parameter errors of a robot using a visual sensor mounted on its end-effector. This approach could be performed in the industrial field without external, expensive apparatus or an elaborate setup. A robot Tool Center Point (TCP) is defined in the structural model of a line-structured laser sensor, and aligned to a reference point fixed in the robot workspace. A mathematical model is established to formulate the misalignment errors with kinematic parameter errors and TCP position errors. Based on the fixed point constraints, the kinematic parameter errors and TCP position errors are identified with an iterative algorithm. Compared to the conventional methods, this proposed method eliminates the need for a robot-based-frame and hand-to-eye calibrations, shortens the error propagation chain, and makes the calibration process more accurate and convenient. A validation experiment is performed on an ABB IRB2400 robot. An optimal configuration on the number and distribution of fixed points in the robot workspace is obtained based on the experimental results. Comparative experiments reveal that there is a significant improvement of the measuring accuracy of the robotic visual inspection system. PMID:24300597

Improving phylogenetic analyses by incorporating additional information from genetic sequence databases.

PubMed

Liang, Li-Jung; Weiss, Robert E; Redelings, Benjamin; Suchard, Marc A

2009-10-01

Statistical analyses of phylogenetic data culminate in uncertain estimates of underlying model parameters. Lack of additional data hinders the ability to reduce this uncertainty, as the original phylogenetic dataset is often complete, containing the entire gene or genome information available for the given set of taxa. Informative priors in a Bayesian analysis can reduce posterior uncertainty; however, publicly available phylogenetic software specifies vague priors for model parameters by default. We build objective and informative priors using hierarchical random effect models that combine additional datasets whose parameters are not of direct interest but are similar to the analysis of interest. We propose principled statistical methods that permit more precise parameter estimates in phylogenetic analyses by creating informative priors for parameters of interest. Using additional sequence datasets from our lab or public databases, we construct a fully Bayesian semiparametric hierarchical model to combine datasets. A dynamic iteratively reweighted Markov chain Monte Carlo algorithm conveniently recycles posterior samples from the individual analyses. We demonstrate the value of our approach by examining the insertion-deletion (indel) process in the enolase gene across the Tree of Life using the phylogenetic software BALI-PHY; we incorporate prior information about indels from 82 curated alignments downloaded from the BAliBASE database.

Simple automatic strategy for background drift correction in chromatographic data analysis.

PubMed

Fu, Hai-Yan; Li, He-Dong; Yu, Yong-Jie; Wang, Bing; Lu, Peng; Cui, Hua-Peng; Liu, Ping-Ping; She, Yuan-Bin

2016-06-03

Chromatographic background drift correction, which influences peak detection and time shift alignment results, is a critical stage in chromatographic data analysis. In this study, an automatic background drift correction methodology was developed. Local minimum values in a chromatogram were initially detected and organized as a new baseline vector. Iterative optimization was then employed to recognize outliers, which belong to the chromatographic peaks, in this vector, and update the outliers in the baseline until convergence. The optimized baseline vector was finally expanded into the original chromatogram, and linear interpolation was employed to estimate background drift in the chromatogram. The principle underlying the proposed method was confirmed using a complex gas chromatographic dataset. Finally, the proposed approach was applied to eliminate background drift in liquid chromatography quadrupole time-of-flight samples used in the metabolic study of Escherichia coli samples. The proposed method was comparable with three classical techniques: morphological weighted penalized least squares, moving window minimum value strategy and background drift correction by orthogonal subspace projection. The proposed method allows almost automatic implementation of background drift correction, which is convenient for practical use. Copyright © 2016 Elsevier B.V. All rights reserved.

An efficient intensity-based ready-to-use X-ray image stitcher.

PubMed

Wang, Junchen; Zhang, Xiaohui; Sun, Zhen; Yuan, Fuzhen

2018-06-14

The limited field of view of the X-ray image intensifier makes it difficult to cover a large target area with a single X-ray image. X-ray image stitching techniques have been proposed to produce a panoramic X-ray image. This paper presents an efficient intensity-based X-ray image stitcher, which does not rely on accurate C-arm motion control or auxiliary devices and hence is ready to use in clinic. The stitcher consumes sequentially captured X-ray images with overlap areas and automatically produces a panoramic image. The gradient information for optimization of image alignment is obtained using a back-propagation scheme so that it is convenient to adopt various image warping models. The proposed stitcher has the following advantages over existing methods: (1) no additional hardware modification or auxiliary markers are needed; (2) it is robust against feature-based approaches; (3) arbitrary warping models and shapes of the region of interest are supported; (4) seamless stitching is achieved using multi-band blending. Experiments have been performed to confirm the effectiveness of the proposed method. The proposed X-ray image stitcher is efficient, accurate and ready to use in clinic. Copyright © 2018 John Wiley & Sons, Ltd.

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

PubMed

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

2017-04-20

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

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

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

PubMed Central

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

2017-01-01

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

Examining the concept of convenient collection: an application to extended producer responsibility and product stewardship frameworks.

PubMed

Wagner, Travis P

2013-03-01

Increasingly, Extended Producer Responsibility (EPR) and Product Stewardship (PS) frameworks are being adopted as a preferred policy approach to promote cost-effective diversion and recovery of post-consumer solid waste. Because the application of EPR/PS generally requires the creation of a separate and often parallel collection and/or management system, key to increasing the amount of waste recovered is to maximize the convenience of the collection system to maximize consumer participation. Convenient collection is often mandated in EPR/PS laws, however it is not defined. Convenience is a subjective construct rendering it extremely difficult to define. However, based on a dissection of post-consumer collection efforts under a generic EPR/PS system, this paper identifies and examines five categories of convenience - knowledge requirements, proximity to a collection site, opportunity to drop-off materials, the draw of the collection site, and the ease of the process-and the various factors of convenience within each of these categories. By using a simplified multiple criteria decision analysis, this paper proposes a performance matrix of criteria of convenience. Stakeholders can use this matrix to assist in the design, assessment, and/or implementation of a convenient post-consumer collection system under an EPR/PS framework. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

Quality of Artemisinin-Based Combination Formulations for Malaria Treatment: Prevalence and Risk Factors for Poor Quality Medicines in Public Facilities and Private Sector Drug Outlets in Enugu, Nigeria

PubMed Central

Kaur, Harparkash; Allan, Elizabeth Louise; Mamadu, Ibrahim; Hall, Zoe; Ibe, Ogochukwu; El Sherbiny, Mohamed; van Wyk, Albert; Yeung, Shunmay; Swamidoss, Isabel; Green, Michael D.; Dwivedi, Prabha; Culzoni, Maria Julia; Clarke, Siân; Schellenberg, David; Fernández, Facundo M.; Onwujekwe, Obinna

2015-01-01

Background Artemisinin-based combination therapies are recommended by the World Health Organisation (WHO) as first-line treatment for Plasmodium falciparum malaria, yet medication must be of good quality for efficacious treatment. A recent meta-analysis reported 35% (796/2,296) of antimalarial drug samples from 21 Sub-Saharan African countries, purchased from outlets predominantly using convenience sampling, failed chemical content analysis. We used three sampling strategies to purchase artemisinin-containing antimalarials (ACAs) in Enugu metropolis, Nigeria, and compared the resulting quality estimates. Methods ACAs were purchased using three sampling approaches - convenience, mystery clients and overt, within a defined area and sampling frame in Enugu metropolis. The active pharmaceutical ingredients were assessed using high-performance liquid chromatography and confirmed by mass spectrometry at three independent laboratories. Results were expressed as percentage of APIs stated on the packaging and used to categorise each sample as acceptable quality, substandard, degraded, or falsified. Results Content analysis of 3024 samples purchased from 421 outlets using convenience (n=200), mystery (n=1,919) and overt (n=905) approaches, showed overall 90.8% ACAs to be of acceptable quality, 6.8% substandard, 1.3% degraded and 1.2% falsified. Convenience sampling yielded a significantly higher prevalence of poor quality ACAs, but was not evident by the mystery and overt sampling strategies both of which yielded results that were comparable between each other. Artesunate (n=135; 4 falsified) and dihydroartemisinin (n=14) monotherapy tablets, not recommended by WHO, were also identified. Conclusion Randomised sampling identified fewer falsified ACAs than previously reported by convenience approaches. Our findings emphasise the need for specific consideration to be given to sampling frame and sampling approach if representative information on drug quality is to be obtained. PMID:26018221

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.

The Use of Conjugate Charts in Transfer Reactions: A Unified Approach

ERIC Educational Resources Information Center

Allnutt, Michael I.

2007-01-01

Redox reactions can be conveniently discussed in terms of the relative strengths of the oxidant, the reductant, and their conjugates; a conjugate chart is a most convenient and useful way of doing this. A similar chart for acids and bases is proposed, which can be applied in the same manner. (Contains 7 figures and 2 tables.)

Alignment in Teacher Education and Distribution of Leadership: An Example Concerning Learning Study

ERIC Educational Resources Information Center

Nilsson, Ingrid

2008-01-01

The critical aspects distribution of professional leadership, alignment in learning and research close to practices, were lifted forward in order to exemplify a research project with learning study as an approach for alignment between teacher education and practice, and as consequence an instrument for distribution of power. The results showed…

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

Creating Polymer Hydrogel Microfibres with Internal Alignment via Electrical and Mechanical Stretching

PubMed Central

Zhang, Shuming; Liu, Xi; Barreto-Ortiz, Sebastian F.; Yu, Yixuan; Ginn, Brian; DeSantis, Nicholas; Hutton, Daphne L; Grayson, Warren; Cui, Fu-Zhai; Korgel, Brian A.; Gerecht, Sharon; Mao, Hai-Quan

2014-01-01

Hydrogels have been widely used for 3-dimensional (3D) cell culture and tissue regeneration due to their tunable biochemical and physicochemical properties as well as their high water content, which resembles the aqueous microenvironment of the natural extracellular matrix. While many properties of natural hydrogel matrices are modifiable, their intrinsic isotropic structure limits the control over cellular organization, which is critical to restore tissue function. Here we report a generic approach to incorporate alignment topography inside the hydrogel matrix using a combination of electrical and mechanical stretching. Hydrogel fibres with uniaxial alignment were prepared from aqueous solutions of natural polymers such as alginate, fibrin, gelatin, and hyaluronic acid under ambient conditions. The unique internal alignment feature drastically enhances the mechanical properties of the hydrogel microfibres. Furthermore, the facile, organic solvent-free processing conditions are amenable to the incorporation of live cells within the hydrogel fibre or on the fibre surface; both approaches effectively induce cellular alignment. This work demonstrates a versatile and scalable strategy to create aligned hydrogel microfibres from various natural polymers. PMID:24439410

Facilitating Constructive Alignment in Power Systems Engineering Education Using Free and Open-Source Software

ERIC Educational Resources Information Center

Vanfretti, L.; Milano, F.

2012-01-01

This paper describes how the use of free and open-source software (FOSS) can facilitate the application of constructive alignment theory in power systems engineering education by enabling the deep learning approach in power system analysis courses. With this aim, this paper describes the authors' approach in using the Power System Analysis Toolbox…

COACH: profile-profile alignment of protein families using hidden Markov models.

PubMed

Edgar, Robert C; Sjölander, Kimmen

2004-05-22

Alignments of two multiple-sequence alignments, or statistical models of such alignments (profiles), have important applications in computational biology. The increased amount of information in a profile versus a single sequence can lead to more accurate alignments and more sensitive homolog detection in database searches. Several profile-profile alignment methods have been proposed and have been shown to improve sensitivity and alignment quality compared with sequence-sequence methods (such as BLAST) and profile-sequence methods (e.g. PSI-BLAST). Here we present a new approach to profile-profile alignment we call Comparison of Alignments by Constructing Hidden Markov Models (HMMs) (COACH). COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM. We compare the alignment accuracy of COACH with two recently published methods: Yona and Levitt's prof_sim and Sadreyev and Grishin's COMPASS. On two sets of reference alignments selected from the FSSP database, we find that COACH is able, on average, to produce alignments giving the best coverage or the fewest errors, depending on the chosen parameter settings. COACH is freely available from www.drive5.com/lobster

Near-Field Chipless Radio-Frequency Identification (RFID) Sensing and Identification System with Switching Reading.

PubMed

Paredes, Ferran; Herrojo, Cristian; Mata-Contreras, Javier; Moras, Miquel; Núñez, Alba; Ramon, Eloi; Martín, Ferran

2018-04-09

A chipless radio-frequency identification (chipless-RFID) and sensing system, where tags are read by proximity (near-field) through a switch, is presented. The tags consist of a set of identical resonant elements (split-ring resonators or SRRs), printed or etched at predefined and equidistant positions, forming a linear chain, each SRR providing a bit of information. The logic state ('1' or '0') associated with each resonator depends on whether it is present or not in the predefined position. The reader is an array of power splitters used to feed a set of SRR-loaded transmission lines (in equal number to the number of resonant elements, or bits, of the tag). The feeding (interrogation) signal is a harmonic (single-tone) signal tuned to a frequency in the vicinity of the fundamental resonance of the SRRs. The set of SRR-loaded lines must be designed so that the corresponding SRRs are in perfect alignment with the SRRs of the tag, provided the tag is positioned on top of the reader. Thus, in a reading operation, as long as the tag is very close to the reader, the SRRs of the tag modify (decrease) the transmission coefficient of the corresponding reader line (through electromagnetic coupling between both SRRs), and the amplitude of the output signal is severely reduced. Therefore, the identification (ID) code of the tag is contained in the amplitudes of the output signals of the SRR-loaded lines, which can be inferred sequentially by means of a switching system. Unlike previous chipless-RFID systems based on near-field and sequential bit reading, the tags in the proposed system can be merely positioned on top of the reader, conveniently aligned, without the need to mechanically place them across the reader. Since tag reading is only possible if the tag is very close to the reader, this system can be also used as a proximity sensor with applications such as target identification. The proposed chipless-RFID and sensing approach is validated by reading a designed 4-bit tag. For identification purposes, this system is of special interest in applications where a low number of bits suffice, and tag reading by proximity is acceptable (or even convenient). Applications mostly related to secure paper, particularly involving a limited number of items (e.g., exams, ballots, etc.), in order to provide authenticity and avoid counterfeiting, are envisaged. As a proximity sensor, the system may be of use in detecting and distinguishing different targets in applications such as smart packaging.

Near-Field Chipless Radio-Frequency Identification (RFID) Sensing and Identification System with Switching Reading

PubMed Central

Mata-Contreras, Javier; Moras, Miquel; Ramon, Eloi; Martín, Ferran

2018-01-01

A chipless radio-frequency identification (chipless-RFID) and sensing system, where tags are read by proximity (near-field) through a switch, is presented. The tags consist of a set of identical resonant elements (split-ring resonators or SRRs), printed or etched at predefined and equidistant positions, forming a linear chain, each SRR providing a bit of information. The logic state (‘1’ or ‘0’) associated with each resonator depends on whether it is present or not in the predefined position. The reader is an array of power splitters used to feed a set of SRR-loaded transmission lines (in equal number to the number of resonant elements, or bits, of the tag). The feeding (interrogation) signal is a harmonic (single-tone) signal tuned to a frequency in the vicinity of the fundamental resonance of the SRRs. The set of SRR-loaded lines must be designed so that the corresponding SRRs are in perfect alignment with the SRRs of the tag, provided the tag is positioned on top of the reader. Thus, in a reading operation, as long as the tag is very close to the reader, the SRRs of the tag modify (decrease) the transmission coefficient of the corresponding reader line (through electromagnetic coupling between both SRRs), and the amplitude of the output signal is severely reduced. Therefore, the identification (ID) code of the tag is contained in the amplitudes of the output signals of the SRR-loaded lines, which can be inferred sequentially by means of a switching system. Unlike previous chipless-RFID systems based on near-field and sequential bit reading, the tags in the proposed system can be merely positioned on top of the reader, conveniently aligned, without the need to mechanically place them across the reader. Since tag reading is only possible if the tag is very close to the reader, this system can be also used as a proximity sensor with applications such as target identification. The proposed chipless-RFID and sensing approach is validated by reading a designed 4-bit tag. For identification purposes, this system is of special interest in applications where a low number of bits suffice, and tag reading by proximity is acceptable (or even convenient). Applications mostly related to secure paper, particularly involving a limited number of items (e.g., exams, ballots, etc.), in order to provide authenticity and avoid counterfeiting, are envisaged. As a proximity sensor, the system may be of use in detecting and distinguishing different targets in applications such as smart packaging. PMID:29642560

Template-free magnesium oxide hollow sphere inclusion in organic-inorganic hybrid films via sol-gel reaction.

PubMed

Kang, Eun-Seok; Takahashi, Masahide; Tokuda, Yomei; Yoko, Toshinobu

2006-06-06

Magnesium oxide hollow spheres without a template core were conveniently prepared by stabilized bubble formation in a hybrid solution containing a magnesium acetate precursor, thus avoiding the complicated preparation process using a template. The hollow sphere could be aligned along the radial striation by spin coating, and its diameter from a micrometer to submicrometer dimension could be easily modified by the solution composition. It was also possible to control the open or closed hollow sphere by changing the solvent. Thus, the produced magnesium oxide hollow sphere is envisioned to have applications in many areas such as medicine, analysis, optics, and so on.

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

PubMed

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

2006-12-15

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

Perspective: Hospital support for anesthesiology departments: aligning incentives and improving productivity.

PubMed

Hill, Laureen L; Evers, Alex S

2012-03-01

Anesthesiology groups, particularly academic departments, are increasingly dependent on hospital support for financial viability. Economic stresses are driven by higher patient acuity, by multiple subspecialty service and call demands, by high-risk obstetric services, and by long case durations attributable to both case complexity and time for teaching. An unfavorable payer mix, university taxation, and other costs associated with academic education and research missions further compound these stresses. In addition, the current economic climate and the uncertainty surrounding health care reform measures will continue to increase performance pressures on hospitals and anesthesiology departments.Although many researchers have published on the mechanics of operating room (OR) productivity, their investigations do not usually address the motivational forces that drive individual and group behaviors. Institutional tradition, surgical convenience, and parochial interests continue to play predominant roles in OR governance and scheduling practices. Efforts to redefine traditional relationships, to coordinate operational decision-making processes, and to craft incentives that align individual performance goals with those of the institution are all essential for creating greater economic stability. Using the principles of shared costs, department autonomy, hospital flexibility and control over institutional issues, and alignment between individual and institutional goals, the authors developed a template to redefine the hospital-anesthesiology department relationship. Here, they describe both this contractual template and the results that followed implementation (2007-2009) at one institution.

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

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.

Two-Stream Transformer Networks for Video-based Face Alignment.

PubMed

Liu, Hao; Lu, Jiwen; Feng, Jianjiang; Zhou, Jie

2017-08-01

In this paper, we propose a two-stream transformer networks (TSTN) approach for video-based face alignment. Unlike conventional image-based face alignment approaches which cannot explicitly model the temporal dependency in videos and motivated by the fact that consistent movements of facial landmarks usually occur across consecutive frames, our TSTN aims to capture the complementary information of both the spatial appearance on still frames and the temporal consistency information across frames. To achieve this, we develop a two-stream architecture, which decomposes the video-based face alignment into spatial and temporal streams accordingly. Specifically, the spatial stream aims to transform the facial image to the landmark positions by preserving the holistic facial shape structure. Accordingly, the temporal stream encodes the video input as active appearance codes, where the temporal consistency information across frames is captured to help shape refinements. Experimental results on the benchmarking video-based face alignment datasets show very competitive performance of our method in comparisons to the state-of-the-arts.

Adaptive Local Realignment of Protein Sequences.

PubMed

DeBlasio, Dan; Kececioglu, John

2018-06-11

While mutation rates can vary markedly over the residues of a protein, multiple sequence alignment tools typically use the same values for their scoring-function parameters across a protein's entire length. We present a new approach, called adaptive local realignment, that in contrast automatically adapts to the diversity of mutation rates along protein sequences. This builds upon a recent technique known as parameter advising, which finds global parameter settings for an aligner, to now adaptively find local settings. Our approach in essence identifies local regions with low estimated accuracy, constructs a set of candidate realignments using a carefully-chosen collection of parameter settings, and replaces the region if a realignment has higher estimated accuracy. This new method of local parameter advising, when combined with prior methods for global advising, boosts alignment accuracy as much as 26% over the best default setting on hard-to-align protein benchmarks, and by 6.4% over global advising alone. Adaptive local realignment has been implemented within the Opal aligner using the Facet accuracy estimator.

An Approach to Object Recognition: Aligning Pictorial Descriptions.

DTIC Science & Technology

1986-12-01

PERFORMING 0RGANIZATION NAMIE ANDORS IS551. PROGRAM ELEMENT. PROJECT. TASK Artificial Inteligence Laboratory AREKA A WORK UNIT NUMBERS ( 545 Technology... ARTIFICIAL INTELLIGENCE LABORATORY A.I. Memo No. 931 December, 1986 AN APPROACH TO OBJECT RECOGNITION: ALIGNING PICTORIAL DESCRIPTIONS Shimon Ullman...within the Artificial Intelligence Laboratory at the Massachusetts Institute of Technology. Support for the A.I. Laboratory’s artificial intelligence

Camber Angle Inspection for Vehicle Wheel Alignments

PubMed Central

Young, Jieh-Shian; Hsu, Hong-Yi; Chuang, Chih-Yuan

2017-01-01

This paper introduces an alternative approach to the camber angle measurement for vehicle wheel alignment. Instead of current commercial approaches that apply computation vision techniques, this study aims at realizing a micro-control-unit (MCU)-based camber inspection system with a 3-axis accelerometer. We analyze the precision of the inspection system for the axis misalignments of the accelerometer. The results show that the axes of the accelerometer can be aligned to the axes of the camber inspection system imperfectly. The calibrations that can amend these axis misalignments between the camber inspection system and the accelerometer are also originally proposed since misalignments will usually happen in fabrications of the inspection systems. During camber angle measurements, the x-axis or z-axis of the camber inspection system and the wheel need not be perfectly aligned in the proposed approach. We accomplished two typical authentic camber angle measurements. The results show that the proposed approach is applicable with a precision of ±0.015∘ and therefore facilitates the camber measurement process without downgrading the precision by employing an appropriate 3-axis accelerometer. In addition, the measured results of camber angles can be transmitted via the medium such as RS232, Bluetooth, and Wi-Fi. PMID:28165365

Knowledge-Guided Docking of WW Domain Proteins and Flexible Ligands

NASA Astrophysics Data System (ADS)

Lu, Haiyun; Li, Hao; Banu Bte Sm Rashid, Shamima; Leow, Wee Kheng; Liou, Yih-Cherng

Studies of interactions between protein domains and ligands are important in many aspects such as cellular signaling. We present a knowledge-guided approach for docking protein domains and flexible ligands. The approach is applied to the WW domain, a small protein module mediating signaling complexes which have been implicated in diseases such as muscular dystrophy and Liddle’s syndrome. The first stage of the approach employs a substring search for two binding grooves of WW domains and possible binding motifs of peptide ligands based on known features. The second stage aligns the ligand’s peptide backbone to the two binding grooves using a quasi-Newton constrained optimization algorithm. The backbone-aligned ligands produced serve as good starting points to the third stage which uses any flexible docking algorithm to perform the docking. The experimental results demonstrate that the backbone alignment method in the second stage performs better than conventional rigid superposition given two binding constraints. It is also shown that using the backbone-aligned ligands as initial configurations improves the flexible docking in the third stage. The presented approach can also be applied to other protein domains that involve binding of flexible ligand to two or more binding sites.

A new approach to implant alignment and ligament balancing in total knee arthroplasty focussing on joint loads.

PubMed

Zimmermann, Frauke; Schwenninger, Christoph; Nolten, Ulrich; Firmbach, Franz Peter; Elfring, Robert; Radermacher, Klaus

2012-05-06

Preservation and recovery of the mechanical leg axis as well as good rotational alignment of the prosthesis components and well-balanced ligaments are essential for the longevity of total knee arthroplasty (TKA). In the framework of the OrthoMIT project, the genALIGN system, a new navigated implantation approach based on intra-operative force-torque measurements, has been developed. With this system, optical or magnetic position tracking as well as any fixation of invasive rigid bodies are no longer necessary. For the alignment of the femoral component along the mechanical axis, a sensor-integrated instrument measures the torques resulting from the deviation between the instrument's axis and the mechanical axis under manually applied axial compression load. When both axes are coaxial, the resulting torques equal zero, and the tool axis can be fixed with respect to the bone. For ligament balancing and rotational alignment of the femoral component, the genALIGN system comprises a sensor-integrated tibial trial inlay measuring the amplitude and application points of the forces transferred between femur and tibia. Hereby, the impact of ligament tensions on knee joint loads can be determined over the whole range of motion. First studies with the genALIGN system, including a comparison with an imageless navigation system, show the feasibility of the concept.

One-click scanning of large-size documents using mobile phone camera

NASA Astrophysics Data System (ADS)

Liu, Sijiang; Jiang, Bo; Yang, Yuanjie

2016-07-01

Currently mobile apps for document scanning do not provide convenient operations to tackle large-size documents. In this paper, we present a one-click scanning approach for large-size documents using mobile phone camera. After capturing a continuous video of documents, our approach automatically extracts several key frames by optical flow analysis. Then based on key frames, a mobile GPU based image stitching method is adopted to generate a completed document image with high details. There are no extra manual intervention in the process and experimental results show that our app performs well, showing convenience and practicability for daily life.

Rabi oscillations in the dissociative continuum: Rotation and alignment effects

NASA Astrophysics Data System (ADS)

Granucci, Giovanni; Magnier, Sylvie; Persico, Maurizio

2002-01-01

We have simulated a set of experiments in which Rabi oscillations are induced in bound-free and free-free transitions of a diatomic molecule. Dissociative vibrational states belonging to different electronic terms are involved. We show analytically and confirm computationally that a simple relationship exists between the one-dimensional dynamics of a molecule with fixed orientation with respect to the polarization of the radiation field and the three-dimensional dynamics of a rotating system. It is demonstrated that sufficiently short laser pulses can induce oscillations in the probabilities of two coupled electronic states, and in the yields of the respective dissociation products, as functions of the radiation intensity. As a result of molecular rotation the oscillations are damped but not washed out. The initial thermal distribution on several rotational levels has a negligible effect on the photodissociation yields and other experimentally relevant quantities. Since the molecule undergoes a strong alignment along the polarization axis of the laser field, the ejection of atoms and ions is anisotropic. We have chosen the well known diatomic ion Na2+ as a convenient example.

BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity.

PubMed

Wang, Lian; Pan, Danling; Hu, Xihao; Xiao, Jinyu; Gao, Yangyang; Zhang, Huifang; Zhang, Yan; Liu, Juan; Zhu, Shanfeng

2009-05-01

Effective identification of major histocompatibility complex (MHC) molecules restricted peptides is a critical step in discovering immune epitopes. Although many online servers have been built to predict class II MHC-peptide binding affinity, they have been trained on different datasets, and thus fail in providing a unified comparison of various methods. In this paper, we present our implementation of seven popular predictive methods, namely SMM-align, ARB, SVR-pairwise, Gibbs sampler, ProPred, LP-top2, and MHCPred, on a single web server named BiodMHC (http://biod.whu.edu.cn/BiodMHC/index.html, the software is available upon request). Using a standard measure of AUC (Area Under the receiver operating characteristic Curves), we compare these methods by means of not only cross validation but also prediction on independent test datasets. We find that SMM-align, ProPred, SVR-pairwise, ARB, and Gibbs sampler are the five best-performing methods. For the binding affinity prediction of class II MHC-peptide, BiodMHC provides a convenient online platform for researchers to obtain binding information simultaneously using various methods.

The number of reduced alignments between two DNA sequences

PubMed Central

2014-01-01

Background In this study we consider DNA sequences as mathematical strings. Total and reduced alignments between two DNA sequences have been considered in the literature to measure their similarity. Results for explicit representations of some alignments have been already obtained. Results We present exact, explicit and computable formulas for the number of different possible alignments between two DNA sequences and a new formula for a class of reduced alignments. Conclusions A unified approach for a wide class of alignments between two DNA sequences has been provided. The formula is computable and, if complemented by software development, will provide a deeper insight into the theory of sequence alignment and give rise to new comparison methods. AMS Subject Classification Primary 92B05, 33C20, secondary 39A14, 65Q30 PMID:24684679

Cryo-tomography Tilt-series Alignment with Consideration of the Beam-induced Sample Motion

PubMed Central

Fernandez, Jose-Jesus; Li, Sam; Bharat, Tanmay A. M.; Agard, David A.

2018-01-01

Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion. The model can be used during reconstruction to yield a motion-compensated tomogram. We evaluated our method on various datasets with different sample sizes. The results demonstrate that our method could be a useful tool to improve the quality of tomograms and the resolution in cryoET. PMID:29410148

Multilayer Microfluidic Devices Created From A Single Photomask

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

Kelly, Ryan T.; Sheen, Allison M.; Jambovane, Sachin R.

2013-08-28

The time and expense associated with high quality photomask production can discourage the creation of multilayer microfluidic devices, as each layer currently requires a separate photomask. Here we describe an approach in which multilayer microfabricated devices can be created from a single photomask. The separate layers and their corresponding alignment marks are arranged in separate halves of the mask for two layer devices or quadrants for four layer devices. Selective exposure of the photomask features and rotation of the device substrate between exposures result in multiple copies of the devices on each wafer. Subsequent layers are aligned to patterned featuresmore » on the substrate with the same alignment accuracy as when multiple photomasks are used. We demonstrate this approach for fabricating devices employing multilayer soft lithography (MSL) for pneumatic valving. MSL devices containing as many as 5 layers (4 aligned fluidic layers plus a manually aligned control layer) were successfully created using this approach. Device design is also modularized, enabling the presence or absence of features as well as channel heights to be selected independently from one another. The use of a single photomask to create multilayer devices results in a dramatic savings of time and/or money required to advance from device design to completed prototype.« less

Starting from the Classroom: How an Inter-Segmental Faculty Group Works toward Increased K-16 Alignment

ERIC Educational Resources Information Center

De Roy, Tessa Carmen

2011-01-01

There is a lack of alignment between K-12 and higher education about the expectations for student skill and content knowledge. Too often, students leave the K-12 system ill prepared for success in higher education. One approach to increasing alignment has been supported by the California Partnership for Achieving Student Success (Cal-PASS), which…

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

NASA Astrophysics Data System (ADS)

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

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

B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis

PubMed Central

Towfic, Fadi; Gupta, Shakti; Honavar, Vasant; Subramaniam, Shankar

2012-01-01

The initiation of B-cell ligand recognition is a critical step for the generation of an immune response against foreign bodies. We sought to identify the biochemical pathways involved in the B-cell ligand recognition cascade and sets of ligands that trigger similar immunological responses. We utilized several comparative approaches to analyze the gene coexpression networks generated from a set of microarray experiments spanning 33 different ligands. First, we compared the degree distributions of the generated networks. Second, we utilized a pairwise network alignment algorithm, BiNA, to align the networks based on the hubs in the networks. Third, we aligned the networks based on a set of KEGG pathways. We summarized our results by constructing a consensus hierarchy of pathways that are involved in B cell ligand recognition. The resulting pathways were further validated through literature for their common physiological responses. Collectively, the results based on our comparative analyses of degree distributions, alignment of hubs, and alignment based on KEGG pathways provide a basis for molecular characterization of the immune response states of B-cells and demonstrate the power of comparative approaches (e.g., gene coexpression network alignment algorithms) in elucidating biochemical pathways involved in complex signaling events in cells. PMID:22917187

Comparison of landmark-based and automatic methods for cortical surface registration

PubMed Central

Pantazis, Dimitrios; Joshi, Anand; Jiang, Jintao; Shattuck, David; Bernstein, Lynne E.; Damasio, Hanna; Leahy, Richard M.

2009-01-01

Group analysis of structure or function in cerebral cortex typically involves as a first step the alignment of the cortices. A surface based approach to this problem treats the cortex as a convoluted surface and coregisters across subjects so that cortical landmarks or features are aligned. This registration can be performed using curves representing sulcal fundi and gyral crowns to constrain the mapping. Alternatively, registration can be based on the alignment of curvature metrics computed over the entire cortical surface. The former approach typically involves some degree of user interaction in defining the sulcal and gyral landmarks while the latter methods can be completely automated. Here we introduce a cortical delineation protocol consisting of 26 consistent landmarks spanning the entire cortical surface. We then compare the performance of a landmark-based registration method that uses this protocol with that of two automatic methods implemented in the software packages FreeSurfer and BrainVoyager. We compare performance in terms of discrepancy maps between the different methods, the accuracy with which regions of interest are aligned, and the ability of the automated methods to correctly align standard cortical landmarks. Our results show similar performance for ROIs in the perisylvian region for the landmark based method and FreeSurfer. However, the discrepancy maps showed larger variability between methods in occipital and frontal cortex and also that automated methods often produce misalignment of standard cortical landmarks. Consequently, selection of the registration approach should consider the importance of accurate sulcal alignment for the specific task for which coregistration is being performed. When automatic methods are used, the users should ensure that sulci in regions of interest in their studies are adequately aligned before proceeding with subsequent analysis. PMID:19796696

Performance measures from the explorer platform berthing experiment

NASA Technical Reports Server (NTRS)

Leake, Stephen

1993-01-01

The Explorer Platform is a Modular Mission Spacecraft: it has several subunits that are designed to be replaced on orbit. The Goddard Space Flight Center Robotics Lab undertook an experiment to evaluate various robotic approaches to replacing one of the units; a large (approximately 1 meter by 1 meter by 0.5 meter) power box. The hardware consists of a Robotics Research Corporation K-1607 (RRC) manipulator mounted on a large gantry robot, a Kraft handcontroller for teleoperation of RRC, a Lightweight Servicing Tool (LST) mounted on the RRC, and an Explorer Platform mockup (EP) with a removable box (MMS) that has fixtures that mate with the LST. Sensors include a wrist wrench sensor on the RRC and Capaciflectors mounted on the LST and the MMS. There are also several cameras, but no machine vision is used. The control system for the RRC is entirely written by Goddard; it consists of Ada code on three Multibus I 386/387 CPU boards doing the real-time robot control, and C on a 386 PC processing Capaciflector data. The gantry is not moved during this experiment. The task is the exchange of the MMS; it is removed and replaced. This involves four basic steps: mating the LST to the MMS, demating the MMS from the EP, mating the MMS to the EP, and demating the LST form the MMS. Each of the mating steps must be preceeded by an alignment to bring the mechanical fixtures within their capture range. Two basic approaches to alignment are explored: teleoperation with the operator viewing thru cameras, and Capaciflector based autonomy. To evaluate the two alignment approaches, several runs were run with each approach and the final pose was recorded. Comparing this to the ideal alignment pose gives accuracy and repeatability data. In addition the wrenches exerted during the mating tasks were recorded; this gives information on how the alignment step affects the mating step. There are also two approaches to mating; teleoperation, and impedance based autonomy. The wrench data taken during mating using these two approaches is used to evaluate them. Section 2 describes the alignment results, section 3 describes the mating results, and finally Section 4 gives some conclusions.

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

PubMed

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

2015-08-01

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

Use artificial neural network to align biological ontologies.

PubMed

Huang, Jingshan; Dang, Jiangbo; Huhns, Michael N; Zheng, W Jim

2008-09-16

Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics. In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others. The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.

Chemometric Analysis of Gas Chromatography – Mass Spectrometry Data using Fast Retention Time Alignment via a Total Ion Current Shift Function

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

Nadeau, Jeremy S.; Wright, Bob W.; Synovec, Robert E.

2010-04-15

A critical comparison of methods for correcting severely retention time shifted gas chromatography-mass spectrometry (GC-MS) data is presented. The method reported herein is an adaptation to the Piecewise Alignment Algorithm to quickly align severely shifted one-dimensional (1D) total ion current (TIC) data, then applying these shifts to broadly align all mass channels throughout the separation, referred to as a TIC shift function (SF). The maximum shift varied from (-) 5 s in the beginning of the chromatographic separation to (+) 20 s toward the end of the separation, equivalent to a maximum shift of over 5 peak widths. Implementing themore » TIC shift function (TIC SF) prior to Fisher Ratio (F-Ratio) feature selection and then principal component analysis (PCA) was found to be a viable approach to classify complex chromatograms, that in this study were obtained from GC-MS separations of three gasoline samples serving as complex test mixtures, referred to as types C, M and S. The reported alignment algorithm via the TIC SF approach corrects for large dynamic shifting in the data as well as subtle peak-to-peak shifts. The benefits of the overall TIC SF alignment and feature selection approach were quantified using the degree-of-class separation (DCS) metric of the PCA scores plots using the type C and M samples, since they were the most similar, and thus the most challenging samples to properly classify. The DCS values showed an increase from an initial value of essentially zero for the unaligned GC-TIC data to a value of 7.9 following alignment; however, the DCS was unchanged by feature selection using F-Ratios for the GC-TIC data. The full mass spectral data provided an increase to a final DCS of 13.7 after alignment and two-dimensional (2D) F-Ratio feature selection.« less

Path querying system on mobile devices

NASA Astrophysics Data System (ADS)

Lin, Xing; Wang, Yifei; Tian, Yuan; Wu, Lun

2006-01-01

Traditional approaches to path querying problems are not efficient and convenient under most circumstances. A more convenient and reliable approach to this problem has to be found. This paper is devoted to a path querying solution on mobile devices. By using an improved Dijkstra's shortest path algorithm and a natural language translating module, this system can help people find the shortest path between two places through their cell phones or other mobile devices. The chosen path is prompted in text of natural language, as well as a map picture. This system would be useful in solving best path querying problems and have potential to be a profitable business system.

Processing and population genetic analysis of multigenic datasets with ProSeq3 software.

PubMed

Filatov, Dmitry A

2009-12-01

The current tendency in molecular population genetics is to use increasing numbers of genes in the analysis. Here I describe a program for handling and population genetic analysis of DNA polymorphism data collected from multiple genes. The program includes a sequence/alignment editor and an internal relational database that simplify the preparation and manipulation of multigenic DNA polymorphism datasets. The most commonly used DNA polymorphism analyses are implemented in ProSeq3, facilitating population genetic analysis of large multigenic datasets. Extensive input/output options make ProSeq3 a convenient hub for sequence data processing and analysis. The program is available free of charge from http://dps.plants.ox.ac.uk/sequencing/proseq.htm.

Convenient yet not a convenience sample: Jury pools as experimental subject pools.

PubMed

Murray, Gregg R; Rugeley, Cynthia R; Mitchell, Dona-Gene; Mondak, Jeffery J

2013-01-01

Scholars greatly benefit from access to convenient, inexpensive data sources. Many researchers rely on student subject pools, a practice that raises concern about the "college sophomore problem," or the possibility that findings from student subjects do not generalize beyond the campus. As an accessible, low cost, and heterogeneous data source, some researchers have used subjects recruited from jury pools, which are drawn from randomly-selected citizens required by law to appear for jury duty. In this paper, we discuss the strengths and weaknesses of this approach. First, we review pragmatic considerations involving access to jury pools, substantive content, the administration of survey-experiments, and the financial costs and benefits of this approach. Next, we present evidence regarding the quality of jury pool samples in terms of response rates, diversity, and representativeness. We conclude that jury pools, given proper attention to their limitations, offer an attractive addition to the viable sources of experimental data. Copyright © 2012 Elsevier Inc. All rights reserved.

Microscopic observation of magnetic bacteria in the magnetic field of a rotating permanent magnet.

PubMed

Smid, Pieter; Shcherbakov, Valeriy; Petersen, Nikolai

2015-09-01

Magnetotactic bacteria are ubiquitous and can be found in both freshwater and marine environments. Due to intracellular chains of magnetic single domain particles, they behave like swimming compass needles. In external magnetic fields like the Earth's magnetic field, a torque is acting on the chain. This will cause the bacterium to be rotated and aligned with the external field. The swimming direction of magnetotactic bacteria can be controlled with external magnetic fields, which makes it convenient to study them under a light microscope. Usually, a special set of coils arranged around a light microscope is used to control the swimming magnetotactic bacteria. Here, we present a simple mechanical system with a permanent magnet, which produces a rotating magnetic field of nearly constant amplitude in the focal plane of a light microscope. The device is placed beside the light microscope and easily adaptable to almost any microscope and thus convenient for field experiments. To describe the trajectories qualitatively, a theoretical model of the trajectories is presented. This device can be used to control the swimming direction of magnetotactic bacteria and also for studying their magnetic and hydrodynamic properties.

CsSNP: A Web-Based Tool for the Detecting of Comparative Segments SNPs.

PubMed

Wang, Yi; Wang, Shuangshuang; Zhou, Dongjie; Yang, Shuai; Xu, Yongchao; Yang, Chao; Yang, Long

2016-07-01

SNP (single nucleotide polymorphism) is a popular tool for the study of genetic diversity, evolution, and other areas. Therefore, it is necessary to develop a convenient, utility, robust, rapid, and open source detecting-SNP tool for all researchers. Since the detection of SNPs needs special software and series steps including alignment, detection, analysis and present, the study of SNPs is limited for nonprofessional users. CsSNP (Comparative segments SNP, http://biodb.sdau.edu.cn/cssnp/ ) is a freely available web tool based on the Blat, Blast, and Perl programs to detect comparative segments SNPs and to show the detail information of SNPs. The results are filtered and presented in the statistics figure and a Gbrowse map. This platform contains the reference genomic sequences and coding sequences of 60 plant species, and also provides new opportunities for the users to detect SNPs easily. CsSNP is provided a convenient tool for nonprofessional users to find comparative segments SNPs in their own sequences, and give the users the information and the analysis of SNPs, and display these data in a dynamic map. It provides a new method to detect SNPs and may accelerate related studies.

Probing the Energy Level Alignment and the Correlation with Open-Circuit Voltage in Solution-Processed Polymeric Bulk Heterojunction Photovoltaic Devices.

PubMed

Yang, Qing-Dan; Li, Ho-Wa; Cheng, Yuanhang; Guan, Zhiqiang; Liu, Taili; Ng, Tsz-Wai; Lee, Chun-Sing; Tsang, Sai-Wing

2016-03-23

Energy level alignment at the organic donor and acceptor interface is a key to determine the photovoltaic performance in organic solar cells, but direct probing of such energy alignment is still challenging especially for solution-processed bulk heterojunction (BHJ) thin films. Here we report a systematic investigation on probing the energy level alignment with different approaches in five commonly used polymer:[6,6]-phenyl-C71-butyric acid methyl ester (PCBM) BHJ systems. We find that by tuning the weight ratio of polymer to PCBM the electronic features from both polymer and PCBM can be obtained by photoemission spectroscopy. Using this approach, we find that some of the BHJ blends simply follow vacuum level alignment, but others show strong energy level shifting as a result of Fermi level pinning. Independently, by measuring the temperature-dependent open-circuit voltage (VOC), we find that the effective energy gap (Eeff), the energy difference between the highest occupied molecular orbital of the polymer donor (EHOMO-D) and lowest unoccupied molecular orbital of the PCBM acceptor (ELUMO-A), obtained by photoemission spectroscopy in all polymer:PCBM blends has an excellent agreement with the extrapolated VOC at 0 K. Consequently, the photovoltage loss of various organic BHJ photovoltaic devices at room temperature is in a range of 0.3-0.6 V. It is believed that the demonstrated direct measurement approach of the energy level alignment in solution-processed organic BHJ will bring deeper insight into the origin of the VOC and the corresponding photovoltage loss mechanism in organic photovoltaic cells.

New Zealand policy experts’ appraisal of interventions to reduce smoking in young adults: a qualitative investigation

PubMed Central

Hoek, Janet; Tautolo, El Shadan; Gifford, Heather

2017-01-01

Objectives Reducing smoking in young adults, particularly young Māori and Pacific, is vital for reducing tobacco harm and health inequalities in New Zealand (NZ). We investigated how NZ policy experts appraised the feasibility and likely effectiveness of interventions designed to reduce smoking prevalence among 18–24 year olds. Design We used a qualitative design, conducting semistructured interviews and applying thematic analysis. Participants We interviewed 15 key informants, including politicians, senior policy analysts and leading tobacco control advocates. Participant selection was based on seniority and expertise and ensuring diverse perspectives were represented. Interventions We examined nine interventions that could either promote greater mindfulness or introduce barriers impeding smoking uptake: smoke-free outdoor dining and bars; no tobacco sales where alcohol is sold; social marketing campaigns; real life stories (testimonials); life skills training; raise purchase age to 21; tobacco-free generation; smokers’ licence; make tobacco retail premises R18. Results The policies perceived as more effective denormalised tobacco; made it less convenient to access and use; highlighted immediate disadvantages (eg, impact on fitness); aligned with young people’s values; and addressed the underlying causes of smoking (eg, stress). Participants highlighted some political barriers and noted concerns that some interventions might widen ethnic disparities. Exceptions were social marketing campaigns and extending smoke-free regulations to include outdoor areas of cafes and bars, which participants saw as politically feasible and likely to be effective. Conclusions Our findings suggest the merit of an approach that combines social marketing with regulation that makes accessing and using tobacco less convenient for young adults; however, political barriers may limit the regulatory options available in the short term. Strategies to support self-determination and address the underlying causes of smoking in young people warrant further investigation. Determining policy acceptability to Māori and Pacific, and likely effectiveness for these populations, should be key priorities. PMID:29229655

SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.

PubMed

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.

SWPhylo – A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees

PubMed Central

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA. PMID:29511354

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

PubMed

Daily, Jeff

2016-02-10

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

Alignment-Based Prediction of Sites of Metabolism.

PubMed

de Bruyn Kops, Christina; Friedrich, Nils-Ole; Kirchmair, Johannes

2017-06-26

Prediction of metabolically labile atom positions in a molecule (sites of metabolism) is a key component of the simulation of xenobiotic metabolism as a whole, providing crucial information for the development of safe and effective drugs. In 2008, an exploratory study was published in which sites of metabolism were derived based on molecular shape- and chemical feature-based alignment to a molecule whose site of metabolism (SoM) had been determined by experiments. We present a detailed analysis of the breadth of applicability of alignment-based SoM prediction, including transfer of the approach from a structure- to ligand-based method and extension of the applicability of the models from cytochrome P450 2C9 to all cytochrome P450 isozymes involved in drug metabolism. We evaluate the effect of molecular similarity of the query and reference molecules on the ability of this approach to accurately predict SoMs. In addition, we combine the alignment-based method with a leading chemical reactivity model to take reactivity into account. The combined model yielded superior performance in comparison to the alignment-based approach and the reactivity models with an average area under the receiver operating characteristic curve of 0.85 in cross-validation experiments. In particular, early enrichment was improved, as evidenced by higher BEDROC scores (mean BEDROC = 0.59 for α = 20.0, mean BEDROC = 0.73 for α = 80.5).

Robustly Aligning a Shape Model and Its Application to Car Alignment of Unknown Pose.

PubMed

Li, Yan; Gu, Leon; Kanade, Takeo

2011-09-01

Precisely localizing in an image a set of feature points that form a shape of an object, such as car or face, is called alignment. Previous shape alignment methods attempted to fit a whole shape model to the observed data, based on the assumption of Gaussian observation noise and the associated regularization process. However, such an approach, though able to deal with Gaussian noise in feature detection, turns out not to be robust or precise because it is vulnerable to gross feature detection errors or outliers resulting from partial occlusions or spurious features from the background or neighboring objects. We address this problem by adopting a randomized hypothesis-and-test approach. First, a Bayesian inference algorithm is developed to generate a shape-and-pose hypothesis of the object from a partial shape or a subset of feature points. For alignment, a large number of hypotheses are generated by randomly sampling subsets of feature points, and then evaluated to find the one that minimizes the shape prediction error. This method of randomized subset-based matching can effectively handle outliers and recover the correct object shape. We apply this approach on a challenging data set of over 5,000 different-posed car images, spanning a wide variety of car types, lighting, background scenes, and partial occlusions. Experimental results demonstrate favorable improvements over previous methods on both accuracy and robustness.

Development of a group work assessment pedagogy using constructive alignment theory.

PubMed

Croy, Suzanne R

2018-02-01

The purpose of this paper is to explore group work assessment underpinned by constructive alignment theory to develop a new assessment pedagogy. A review was undertaken of an existing module 'Mental Health Nursing 1', with student nurses participating in the BSc (Hons) Nursing Programme. Constructive alignment theory requires teachers to adopt a deep approach to learning where module learning outcomes are aligned with the teaching environment and modes of assessment. As the module progressed, reviewing the Mental Health Nursing 1 module became an excellent opportunity to begin to understand how constructive alignment theory can inform a group work assessment pedagogy. Working using a constructively aligned assessment process became a valuable learning experience for the module leader whilst at the same time revealed a gap in the research around the impact of constructively aligned teaching and group work assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparative study of different approaches for multivariate image analysis in HPTLC fingerprinting of natural products such as plant resin.

PubMed

Ristivojević, Petar; Trifković, Jelena; Vovk, Irena; Milojković-Opsenica, Dušanka

2017-01-01

Considering the introduction of phytochemical fingerprint analysis, as a method of screening the complex natural products for the presence of most bioactive compounds, use of chemometric classification methods, application of powerful scanning and image capturing and processing devices and algorithms, advancement in development of novel stationary phases as well as various separation modalities, high-performance thin-layer chromatography (HPTLC) fingerprinting is becoming attractive and fruitful field of separation science. Multivariate image analysis is crucial in the light of proper data acquisition. In a current study, different image processing procedures were studied and compared in detail on the example of HPTLC chromatograms of plant resins. In that sense, obtained variables such as gray intensities of pixels along the solvent front, peak area and mean values of peak were used as input data and compared to obtained best classification models. Important steps in image analysis, baseline removal, denoising, target peak alignment and normalization were pointed out. Numerical data set based on mean value of selected bands and intensities of pixels along the solvent front proved to be the most convenient for planar-chromatographic profiling, although required at least the basic knowledge on image processing methodology, and could be proposed for further investigation in HPLTC fingerprinting. Copyright © 2016 Elsevier B.V. All rights reserved.

Inflight alignment of payload inertial reference from Shuttle navigation system

NASA Astrophysics Data System (ADS)

Treder, A. J.; Norris, R. E.; Ruprecht, R.

Two methods for payload attitude initialization from the STS Orbiter have been proposed: body axis maneuvers (BAM) and star line maneuvers (SLM). The first achieves alignment directly through the Shuttle star tracker, while the second, indirectly through the stellar-updated Shuttle inertial platform. The Inertial Upper Stage (IUS) with its strapdown navigation system is used to demonstrate in-flight alignment techniques. Significant accuracy can be obtained with minimal impact on Orbiter operations, with payload inertial reference potentially approaching the accuracy of the Shuttle star tracker. STS-6 flight performance parameters, including alignment stability, are discussed and compared with operational complexity. Results indicate overall alignment stability of .06 deg, 3 sigma per axis.

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

PubMed Central

2013-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2009-02-01

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

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.

BatMis: a fast algorithm for k-mismatch mapping.

PubMed

Tennakoon, Chandana; Purbojati, Rikky W; Sung, Wing-Kin

2012-08-15

Second-generation sequencing (SGS) generates millions of reads that need to be aligned to a reference genome allowing errors. Although current aligners can efficiently map reads allowing a small number of mismatches, they are not well suited for handling a large number of mismatches. The efficiency of aligners can be improved using various heuristics, but the sensitivity and accuracy of the alignments are sacrificed. In this article, we introduce Basic Alignment tool for Mismatches (BatMis)--an efficient method to align short reads to a reference allowing k mismatches. BatMis is a Burrows-Wheeler transformation based aligner that uses a seed and extend approach, and it is an exact method. Benchmark tests show that BatMis performs better than competing aligners in solving the k-mismatch problem. Furthermore, it can compete favorably even when compared with the heuristic modes of the other aligners. BatMis is a useful alternative for applications where fast k-mismatch mappings, unique mappings or multiple mappings of SGS data are required. BatMis is written in C/C++ and is freely available from http://code.google.com/p/batmis/

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

Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

PubMed

Soares, Inês; Goios, Ana; Amorim, António

2012-01-01

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

PubMed

Verzotto, Davide; M Teo, Audrey S; Hillmer, Axel M; Nagarajan, Niranjan

2016-01-01

Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences. We introduce a novel seed-and-extend glocal (short for global-local) alignment method, OPTIMA (and a sliding-window extension for overlap alignment, OPTIMA-Overlap), which is the first to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic with respect to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests. We show that OPTIMA and OPTIMA-Overlap outperform other state-of-the-art approaches (1.6-2 times more sensitive) and are more efficient (170-200 %) and precise in their alignments (nearly 99 % precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust, provide improved sensitivity and guarantee high precision.

Organizational Alignment Supporting Distance Education in Post-Secondary Institutions.

ERIC Educational Resources Information Center

Prestera, Gustavo E.; Moller, Leslie A.

2001-01-01

Applies an established model of organizational alignment to distance education in postsecondary institutions and recommends performance-oriented approaches to support growth by analyzing goals, structure, and management practices across the organization. Presents performance improvement strategies such as benchmarking and documenting workflows,…

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

PubMed

Lin, Hsien-Cheng

2017-02-01

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

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

Entangled time in flocking: Multi-time-scale interaction reveals emergence of inherent noise

PubMed Central

Murakami, Hisashi

2018-01-01

Collective behaviors that seem highly ordered and result in collective alignment, such as schooling by fish and flocking by birds, arise from seamless shuffling (such as super-diffusion) and bustling inside groups (such as Lévy walks). However, such noisy behavior inside groups appears to preclude the collective behavior: intuitively, we expect that noisy behavior would lead to the group being destabilized and broken into small sub groups, and high alignment seems to preclude shuffling of neighbors. Although statistical modeling approaches with extrinsic noise, such as the maximum entropy approach, have provided some reasonable descriptions, they ignore the cognitive perspective of the individuals. In this paper, we try to explain how the group tendency, that is, high alignment, and highly noisy individual behavior can coexist in a single framework. The key aspect of our approach is multi-time-scale interaction emerging from the existence of an interaction radius that reflects short-term and long-term predictions. This multi-time-scale interaction is a natural extension of the attraction and alignment concept in many flocking models. When we apply this method in a two-dimensional model, various flocking behaviors, such as swarming, milling, and schooling, emerge. The approach also explains the appearance of super-diffusion, the Lévy walk in groups, and local equilibria. At the end of this paper, we discuss future developments, including extending our model to three dimensions. PMID:29689074

MO-FG-CAMPUS-JeP3-02: A Novel Setup Approach to Improve C-Spine Curvature Reproducibility for Head and Neck Radiotherapy Using Optical Surface Imaging with Two Regions of Interest

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

Ryan, K; Gil, M; Li, G

Purpose: To develop a novel approach to improve cervical spine (c-spine) curvature reproducibility for head and neck (HN) patients using optical surface imaging (OSI) with two regions of interests (ROIs). Methods: The OSI-guided, two-step setup procedure requires two ROIs: ROI-1 of the shoulders and ROI-2 of the face. The neck can be stretched or squeezed in superior-inferior (SI) direction using a specially-designed sliding head support. We hypothesize that when these two ROIs are aligned, the c-spine should fall into a naturally reproducible position under same setup conditions. An anthropomorphous phantom test was performed to examine neck pitch angles comparing withmore » the calculated angles. Three volunteers participated in the experiments, which start with conventional HN setup using skin markers and room lasers. An OSI image and lateral photo-picture were acquired as the references. In each of the three replicate tests, conventional setup was first applied after volunteers got on the couch. ROI-1 was aligned by moving the body, followed by ROI-2 alignment via adjusting head position and orientation under real-time OSI guidance. A final static OSI image and lateral picture were taken to evaluate both anterior and posterior surface alignments. Three degrees of freedom can be adjusted if an open-face mask was applied, including head SI shift using the sliding head support and pitch-and-roll rotations using a commercial couch extension. Surface alignment was analyzed comparing with conventional setup. Results: The neck pitch angle measured by OSI is consistent with the calculated (0.2±0.6°). Volunteer study illustrated improved c-spine setup reproducibility using OSI comparing with conventional setup. ROI alignments with 2mm/1° tolerance are achieved within 3 minutes. Identical knee support is important to achieve ROI-1 pitch alignment. Conclusion: The feasibility of this novel approach has been demonstrated for c-spine curvature setup reproducibility. Further evaluation is necessary with bony alignment variation in patient studies. This study is in part supported by the NIH (U54CA137788).« less

High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network.

PubMed

Maleki, Ehsan; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra

2017-07-01

This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the basic local alignment search tool.

Mobile and replicated alignment of arrays in data-parallel programs

NASA Technical Reports Server (NTRS)

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

1993-01-01

When a data-parallel language like FORTRAN 90 is compiled for a distributed-memory machine, aggregate data objects (such as arrays) are distributed across the processor memories. The mapping determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: first, an alignment that maps all the objects to an abstract template, and then a distribution that maps the template to the processors. We solve two facets of the problem of finding alignments that reduce residual communication: we determine alignments that vary in loops, and objects that should have replicated alignments. We show that loop-dependent mobile alignment is sometimes necessary for optimum performance, and we provide algorithms with which a compiler can determine good mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself (via spread operations) or can be used to improve performance. We propose an algorithm based on network flow that determines which objects to replicate so as to minimize the total amount of broadcast communication in replication. This work on mobile and replicated alignment extends our earlier work on determining static alignment.

An optically passive method that doubles the rate of 2-Ghz timing fiducials

NASA Astrophysics Data System (ADS)

Boni, R.; Kendrick, J.; Sorce, C.

2017-08-01

Solid-state optical comb-pulse generators provide a convenient and accurate method to include timing fiducials in a streak camera image for time base correction. Commercially available vertical-cavity surface-emitting lasers (VCSEL's) emitting in the visible currently in use can be modulated up to 2 GHz. An optically passive method is presented to interleave a time-delayed path of the 2-GHz comb with itself, producing a 4-GHz comb. This technique can be applied to VCSEL's with higher modulation rates. A fiber-delivered, randomly polarized 2-GHz VCSEL comb is polarization split into s-polarization and p-polarization paths. One path is time delayed relative to the other by twice the 2-GHz rate with +/-1-ps accuracy; the two paths then recombine at the fiber-coupled output. High throughput (>=90%) is achieved by carefully using polarization beam-splitting cubes, a total internal reflection beam-path-steering prism, and antireflection coatings. The glass path-length delay block and turning prism are optically contacted together. The beam polarizer cubes that split and recombine the paths are precision aligned and permanently cemented into place. We expect the palm-sized, inline fiber-coupled, comb-rate-doubling device to maintain its internal alignment indefinitely.

Defocus and magnification dependent variation of TEM image astigmatism.

PubMed

Yan, Rui; Li, Kunpeng; Jiang, Wen

2018-01-10

Daily alignment of the microscope is a prerequisite to reaching optimal lens conditions for high resolution imaging in cryo-EM. In this study, we have investigated how image astigmatism varies with the imaging conditions (e.g. defocus, magnification). We have found that the large change of defocus/magnification between visual correction of astigmatism and subsequent data collection tasks, or during data collection, will inevitably result in undesirable astigmatism in the final images. The dependence of astigmatism on the imaging conditions varies significantly from time to time, so that it cannot be reliably compensated by pre-calibration of the microscope. Based on these findings, we recommend that the same magnification and the median defocus of the intended defocus range for final data collection are used in the objective lens astigmatism correction task during microscope alignment and in the focus mode of the iterative low-dose imaging. It is also desirable to develop a fast, accurate method that can perform dynamic correction of the astigmatism for different intended defocuses during automated imaging. Our findings also suggest that the slope of astigmatism changes caused by varying defocuses can be used as a convenient measurement of objective lens rotation symmetry and potentially an acceptance test of new electron microscopes.

Deformation and electrical properties of magnetic and vertically conductive composites with a chain-of-spheres structure

NASA Astrophysics Data System (ADS)

Choi, Chulmin; Hong, Soonkook; Chen, Li-Han; Liu, Chin-Hung; Choi, Duyoung; Kuru, Cihan; Jin, Sungho

2014-05-01

Vertically anisotropically conductive composites with aligned chain-of-spheres of 20-75 mm Ni particles in an elastomer matrix have been prepared by curing the mixture at 100°C-150°C under an applied magnetic field of ˜300-1000 Oe. The particles are coated with a ˜120 nm thick Au layer for enhanced electrical conductivity. The resultant vertically aligned but laterally isolated columns of conductive particles extend through the whole composite thickness and the end of the Ni columns protrude from the surface, contributing to enhanced electrical contact on the composite surface. The stress-strain curve on compressive deformation exhibits a nonlinear behavior with a rapidly increasing Young's modulus with stress (or pressure). The electrical contact resistance Rc decreases rapidly when the applied pressure is small and then more gradually after the applied pressure reaches 500 psi (˜3.4 MPa), corresponding to a 30% deformation. The directionally conductive elastomer composite material with metal pads and conductive electrodes on the substrate surface can be used as a convenient tactile shear sensor for applications involving artificial limbs, robotic devices, and other visual communication devices such as touch sensitive screens.

Centroid stabilization in alignment of FOA corner cube: designing of a matched filter

NASA Astrophysics Data System (ADS)

Awwal, Abdul; Wilhelmsen, Karl; Roberts, Randy; Leach, Richard; Miller Kamm, Victoria; Ngo, Tony; Lowe-Webb, Roger

2015-02-01

The current automation of image-based alignment of NIF high energy laser beams is providing the capability of executing multiple target shots per day. An important aspect of performing multiple shots in a day is to reduce additional time spent aligning specific beams due to perturbations in those beam images. One such alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retro-reflecting corner cubes to represent the beam center. The FOA houses the frequency conversion crystals for third harmonic generation as the beams enters the target chamber. Beam-to-beam variations and systematic beam changes over time in the FOA corner-cube images can lead to a reduction in accuracy as well as increased convergence durations for the template based centroid detector. This work presents a systematic approach of maintaining FOA corner cube centroid templates so that stable position estimation is applied thereby leading to fast convergence of alignment control loops. In the matched filtering approach, a template is designed based on most recent images taken in the last 60 days. The results show that new filter reduces the divergence of the position estimation of FOA images.

A framework for the identification of reusable processes

NASA Astrophysics Data System (ADS)

de Vries, Marné; Gerber, Aurona; van der Merwe, Alta

2013-11-01

A significant challenge that faces IT management is that of aligning the IT infrastructure of an enterprise with its business goals and practices, also called business-IT alignment. A particular business-IT alignment approach, the foundation for execution approach, was well-accepted by practitioners due to a novel construct, called the operating model (OM). The OM supports business-IT alignment by directing the coherent and consistent design of business and IT components. Even though the OM is a popular construct, our previous research detected the need to enhance the OM, since the OM does not specify methods to identify opportunities for data sharing and process reuse in an enterprise. In this article, we address one of the identified deficiencies in the OM. We present a process reuse identification framework (PRIF) that could be used to enhance the OM in identifying process reuse opportunities in an enterprise. We applied design research to develop PRIF as an artefact, where the development process of PRIF was facilitated by means of the business-IT alignment model (BIAM). We demonstrate the use of the PRIF as well as report on the results of evaluating PRIF in terms of its usefulness and ease-of-use, using experimentation and a questionnaire.

Divergent synthetic approach to 6”-modified α-GalCer analogues

PubMed Central

Pauwels, Nora; Aspeslagh, Sandrine; Vanhoenacker, Gerd; Sandra, Koen; Yu, Esther D.; Zajonc, Dirk M.; Elewaut, Dirk; Linclau, Bruno; Van Calenbergh, Serge

2011-01-01

A synthetic approach is presented for the synthesis of galacturonic acid and d-fucosyl modified KRN7000. The approach allows for late-stage functionalisation of both the sugar 6”-OH and the sphingosine amino groups, which enables convenient synthesis of promising 6”-modified KRN7000 analogues. PMID:22042483

An efficient multi-resolution GA approach to dental image alignment

NASA Astrophysics Data System (ADS)

Nassar, Diaa Eldin; Ogirala, Mythili; Adjeroh, Donald; Ammar, Hany

2006-02-01

Automating the process of postmortem identification of individuals using dental records is receiving an increased attention in forensic science, especially with the large volume of victims encountered in mass disasters. Dental radiograph alignment is a key step required for automating the dental identification process. In this paper, we address the problem of dental radiograph alignment using a Multi-Resolution Genetic Algorithm (MR-GA) approach. We use location and orientation information of edge points as features; we assume that affine transformations suffice to restore geometric discrepancies between two images of a tooth, we efficiently search the 6D space of affine parameters using GA progressively across multi-resolution image versions, and we use a Hausdorff distance measure to compute the similarity between a reference tooth and a query tooth subject to a possible alignment transform. Testing results based on 52 teeth-pair images suggest that our algorithm converges to reasonable solutions in more than 85% of the test cases, with most of the error in the remaining cases due to excessive misalignments.

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

PubMed

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

2016-07-08

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

A flexible and cost-effective compensation method for leveling using large-scale coordinate measuring machines and its application in aircraft digital assembly

NASA Astrophysics Data System (ADS)

Deng, Zhengping; Li, Shuanggao; Huang, Xiang

2018-06-01

In the assembly process of large-size aerospace products, the leveling and horizontal alignment of large components are essential prior to the installation of an inertial navigation system (INS) and the final quality inspection. In general, the inherent coordinate systems of large-scale coordinate measuring devices are not coincident with the geodetic horizontal system, and a dual-axis compensation system is commonly required for the measurement of difference in heights. These compensation systems are expensive and dedicated designs for different devices at present. Considering that a large-size assembly site usually needs more than one measuring device, a compensation approach which is versatile for different devices would be a more convenient and economic choice for manufacturers. In this paper, a flexible and cost-effective compensation method is proposed. Firstly, an auxiliary measuring device called a versatile compensation fixture (VCF) is designed, which mainly comprises reference points for coordinate transformation and a dual-axis inclinometer, and a kind of network tighten points (NTPs) are introduced and temporarily deployed in the large measuring space to further reduce transformation error. Secondly, the measuring principle of height difference is studied, based on coordinate transformation theory and trigonometry while considering the effects of earth curvature, and the coordinate transformation parameters are derived by least squares adjustment. Thirdly, the analytical solution of leveling uncertainty is analyzed, based on which the key parameters of the VCF and the proper deployment of NTPs are determined according to the leveling accuracy requirement. Furthermore, the proposed method is practically applied to the assembly of a large helicopter by developing an automatic leveling and alignment system. By measuring four NTPs, the leveling uncertainty (2σ) is reduced by 29.4% to about 0.12 mm, compared with that without NTPs.

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

PubMed

Lack, Justin B; Cardeno, Charis M; Crepeau, Marc W; Taylor, William; Corbett-Detig, Russell B; Stevens, Kristian A; Langley, Charles H; Pool, John E

2015-04-01

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets. Copyright © 2015 by the Genetics Society of America.

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

PubMed

Franz, Nico M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2015-01-01

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.

Reliable energy level alignment at physisorbed molecule-metal interfaces from density functional theory.

PubMed

Egger, David A; Liu, Zhen-Fei; Neaton, Jeffrey B; Kronik, Leeor

2015-04-08

A key quantity for molecule-metal interfaces is the energy level alignment of molecular electronic states with the metallic Fermi level. We develop and apply an efficient theoretical method, based on density functional theory (DFT) that can yield quantitatively accurate energy level alignment information for physisorbed metal-molecule interfaces. The method builds on the "DFT+Σ" approach, grounded in many-body perturbation theory, which introduces an approximate electron self-energy that corrects the level alignment obtained from conventional DFT for missing exchange and correlation effects associated with the gas-phase molecule and substrate polarization. Here, we extend the DFT+Σ approach in two important ways: first, we employ optimally tuned range-separated hybrid functionals to compute the gas-phase term, rather than rely on GW or total energy differences as in prior work; second, we use a nonclassical DFT-determined image-charge plane of the metallic surface to compute the substrate polarization term, rather than the classical DFT-derived image plane used previously. We validate this new approach by a detailed comparison with experimental and theoretical reference data for several prototypical molecule-metal interfaces, where excellent agreement with experiment is achieved: benzene on graphite (0001), and 1,4-benzenediamine, Cu-phthalocyanine, and 3,4,9,10-perylene-tetracarboxylic-dianhydride on Au(111). In particular, we show that the method correctly captures level alignment trends across chemical systems and that it retains its accuracy even for molecules for which conventional DFT suffers from severe self-interaction errors.

Reliable Energy Level Alignment at Physisorbed Molecule–Metal Interfaces from Density Functional Theory

PubMed Central

2015-01-01

A key quantity for molecule–metal interfaces is the energy level alignment of molecular electronic states with the metallic Fermi level. We develop and apply an efficient theoretical method, based on density functional theory (DFT) that can yield quantitatively accurate energy level alignment information for physisorbed metal–molecule interfaces. The method builds on the “DFT+Σ” approach, grounded in many-body perturbation theory, which introduces an approximate electron self-energy that corrects the level alignment obtained from conventional DFT for missing exchange and correlation effects associated with the gas-phase molecule and substrate polarization. Here, we extend the DFT+Σ approach in two important ways: first, we employ optimally tuned range-separated hybrid functionals to compute the gas-phase term, rather than rely on GW or total energy differences as in prior work; second, we use a nonclassical DFT-determined image-charge plane of the metallic surface to compute the substrate polarization term, rather than the classical DFT-derived image plane used previously. We validate this new approach by a detailed comparison with experimental and theoretical reference data for several prototypical molecule–metal interfaces, where excellent agreement with experiment is achieved: benzene on graphite (0001), and 1,4-benzenediamine, Cu-phthalocyanine, and 3,4,9,10-perylene-tetracarboxylic-dianhydride on Au(111). In particular, we show that the method correctly captures level alignment trends across chemical systems and that it retains its accuracy even for molecules for which conventional DFT suffers from severe self-interaction errors. PMID:25741626

Customisation of the exome data analysis pipeline using a combinatorial approach.

PubMed

Pattnaik, Swetansu; Vaidyanathan, Srividya; Pooja, Durgad G; Deepak, Sa; Panda, Binay

2012-01-01

The advent of next generation sequencing (NGS) technologies have revolutionised the way biologists produce, analyse and interpret data. Although NGS platforms provide a cost-effective way to discover genome-wide variants from a single experiment, variants discovered by NGS need follow up validation due to the high error rates associated with various sequencing chemistries. Recently, whole exome sequencing has been proposed as an affordable option compared to whole genome runs but it still requires follow up validation of all the novel exomic variants. Customarily, a consensus approach is used to overcome the systematic errors inherent to the sequencing technology, alignment and post alignment variant detection algorithms. However, the aforementioned approach warrants the use of multiple sequencing chemistry, multiple alignment tools, multiple variant callers which may not be viable in terms of time and money for individual investigators with limited informatics know-how. Biologists often lack the requisite training to deal with the huge amount of data produced by NGS runs and face difficulty in choosing from the list of freely available analytical tools for NGS data analysis. Hence, there is a need to customise the NGS data analysis pipeline to preferentially retain true variants by minimising the incidence of false positives and make the choice of right analytical tools easier. To this end, we have sampled different freely available tools used at the alignment and post alignment stage suggesting the use of the most suitable combination determined by a simple framework of pre-existing metrics to create significant datasets.

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

PubMed Central

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

2015-01-01

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

Electrode alignment of transverse tripoles using a percutaneous triple-lead approach in spinal cord stimulation

NASA Astrophysics Data System (ADS)

Sankarasubramanian, V.; Buitenweg, J. R.; Holsheimer, J.; Veltink, P.

2011-02-01

The aim of this modeling study is to determine the influence of electrode alignment of transverse tripoles on the paresthesia coverage of the pain area in spinal cord stimulation, using a percutaneous triple-lead approach. Transverse tripoles, comprising a central cathode and two lateral anodes, were modeled on the low-thoracic vertebral region (T10-T12) using percutaneous triple-lead configurations, with the center lead on the spinal cord midline. The triple leads were oriented both aligned and staggered. In the staggered configuration, the anodes were offset either caudally (caudally staggered) or rostrally (rostrally staggered) with respect to the midline cathode. The transverse tripolar field steering with the aligned and staggered configurations enabled the estimation of dorsal column fiber thresholds (IDC) and dorsal root fiber thresholds (IDR) at various anodal current ratios. IDC and IDR were considerably higher for the aligned transverse tripoles as compared to the staggered transverse tripoles. The aligned transverse tripoles facilitated deeper penetration into the medial dorsal columns (DCs). The staggered transverse tripoles always enabled broad and bilateral DC activation, at the expense of mediolateral steerability. The largest DC recruited area was obtained with the rostrally staggered transverse tripole. Transverse tripolar geometries, using percutaneous leads, allow for selective targeting of either medial or lateral DC fibers, if and only if the transverse tripole is aligned. Steering of anodal currents between the lateral leads of the staggered transverse tripoles cannot target medially confined populations of DC fibers in the spinal cord. An aligned transverse tripolar configuration is strongly recommended, because of its ability to provide more post-operative flexibility than other configurations.

Robust video copy detection approach based on local tangent space alignment

NASA Astrophysics Data System (ADS)

Nie, Xiushan; Qiao, Qianping

2012-04-01

We propose a robust content-based video copy detection approach based on local tangent space alignment (LTSA), which is an efficient dimensionality reduction algorithm. The idea is motivated by the fact that the content of video becomes richer and the dimension of content becomes higher. It does not give natural tools for video analysis and understanding because of the high dimensionality. The proposed approach reduces the dimensionality of video content using LTSA, and then generates video fingerprints in low dimensional space for video copy detection. Furthermore, a dynamic sliding window is applied to fingerprint matching. Experimental results show that the video copy detection approach has good robustness and discrimination.

New Approaches to Novel Organosilanes

DTIC Science & Technology

1987-12-01

Dean Seidler Mr. Sean Ouyang PUBLICATIONS resulting from support through AFOSR 88-0060 56. "A Convenient, Naphthalene-Catalyzed Synthesis of Alkali...and P. Boudjouk, Synthesi , (1989) 306. 91 8 0 6 2 03 Approve 6 ~or p,.o r aleese; dis5t r Ibut 0. u" 61. "Inorganic and Organometallic Synthesis with...34Dehydration of Metal Hydrates with Trimethylchlorosilane. A Simple and Convenient Route to Anhydrous Complexes ." P. Boudjouk and J.-H. So, Inorg. Chem

Compliance to two city convenience store ordinance requirements

PubMed Central

Menéndez, Cammie K Chaumont; Amandus, Harlan E; Wu, Nan; Hendricks, Scott A

2015-01-01

Background Robbery-related homicides and assaults are the leading cause of death in retail businesses. Robbery reduction approaches focus on compliance to Crime Prevention Through Environmental Design (CPTED) guidelines. Purpose We evaluated the level of compliance to CPTED guidelines specified by convenience store safety ordinances effective in 2010 in Dallas and Houston, Texas, USA. Methods Convenience stores were defined as businesses less than 10 000 square feet that sell grocery items. Store managers were interviewed for store ordinance requirements from August to November 2011, in a random sample of 594 (289 in Dallas, 305 in Houston) convenience stores that were open before and after the effective dates of their city’s ordinance. Data were collected in 2011 and analysed in 2012–2014. Results Overall, 9% of stores were in full compliance, although 79% reported being registered with the police departments as compliant. Compliance was consistently significantly higher in Dallas than in Houston for many requirements and by store type. Compliance was lower among single owner-operator stores compared with corporate/franchise stores. Compliance to individual requirements was lowest for signage and visibility. Conclusions Full compliance to the required safety measures is consistent with industry ‘best practices’ and evidence-based workplace violence prevention research findings. In Houston and Dallas compliance was higher for some CPTED requirements but not the less costly approaches that are also the more straightforward to adopt. PMID:26337569

Self-optimizing approach for automated laser resonator alignment

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

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

PubMed

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

2016-07-01

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

Local alignment vectors reveal cancer cell-induced ECM fiber remodeling dynamics

PubMed Central

Lee, Byoungkoo; Konen, Jessica; Wilkinson, Scott; Marcus, Adam I.; Jiang, Yi

2017-01-01

Invasive cancer cells interact with the surrounding extracellular matrix (ECM), remodeling ECM fiber network structure by condensing, degrading, and aligning these fibers. We developed a novel local alignment vector analysis method to quantitatively measure collagen fiber alignment as a vector field using Circular Statistics. This method was applied to human non-small cell lung carcinoma (NSCLC) cell lines, embedded as spheroids in a collagen gel. Collagen remodeling was monitored using second harmonic generation imaging under normal conditions and when the LKB1-MARK1 pathway was disrupted through RNAi-based approaches. The results showed that inhibiting LKB1 or MARK1 in NSCLC increases the collagen fiber alignment and captures outward alignment vectors from the tumor spheroid, corresponding to high invasiveness of LKB1 mutant cancer cells. With time-lapse imaging of ECM micro-fiber morphology, the local alignment vector can measure the dynamic signature of invasive cancer cell activity and cell-migration-induced ECM and collagen remodeling and realigning dynamics. PMID:28045069

Macroscopic Ensembles of Aligned Carbon Nanotubes in Bubble Imprints Studied by Polarized Raman Microscopy

DOE PAGES

Ushiba, Shota; Hoyt, Jordan; Masui, Kyoko; ...

2014-01-01

We study the alignment of single-wall carbon nanotubes (SWCNTs) in bubble imprints through polarized Raman microscopy. A hemispherical bubble containing SWCNTs is pressed against a glass substrate, resulting in an imprint of the bubble membrane with a coffee ring on the substrate. We find that macroscopic ensembles of aligned SWCNTs are obtained in the imprints, in which there are three patterns of orientations: (i) azimuthal alignment on the coffee ring, (ii) radial alignment at the edge of the membrane, and (iii) random orientation at the center of the membrane. We also find that the alignment of SWCNTs in the imprintsmore » can be manipulated by spinning bubbles. The orientation of SWCNTs on the coffee ring is directed radially, which is orthogonal to the case of unspun bubbles. This approach enables one to align SWCNTs in large quantities and in a short time, potentially opening up a wide range of CNT-based electronic and optical applications.« less

Development and evaluation of an airplane electronic display format aligned with the inertial velocity vector

NASA Technical Reports Server (NTRS)

Steinmetz, G. G.

1986-01-01

The development of an electronic primary flight display format aligned with the aircraft velocity vector, a simulation evaluation comparing this format with an electronic attitude-aligned primary flight display format, and a flight evaluation of the velocity-vector-aligned display format are described. Earlier tests in turbulent conditions with the electronic attitude-aligned display format had exhibited unsteadiness. A primary objective of aligning the display format with the velocity vector was to take advantage of a velocity-vector control-wheel steering system to provide steadiness of display during turbulent conditions. Better situational awareness under crosswind conditions was also achieved. The evaluation task was a curved, descending approach with turbulent and crosswind conditions. Primary flight display formats contained computer-drawn perspective runway images and flight-path angle information. The flight tests were conducted aboard the NASA Transport Systems Research Vehicle (TSRV). Comparative results of the simulation and flight tests were principally obtained from subjective commentary. Overall, the pilots preferred the display format aligned with the velocity vector.

A global CT to US registration of the lumbar spine

NASA Astrophysics Data System (ADS)

Nagpal, Simrin; Hacihaliloglu, Ilker; Ungi, Tamas; Rasoulian, Abtin; Osborn, Jill; Lessoway, Victoria A.; Rohling, Robert N.; Borschneck, Daniel P.; Abolmaesumi, Purang; Mousavi, Parvin

2014-03-01

During percutaneous lumbar spine needle interventions, alignment of the preoperative computed tomography (CT) with intraoperative ultrasound (US) can augment anatomical visualization for the clinician. We propose an approach to rigidly align CT and US data of the lumbar spine. The approach involves an intensity-based volume registration step, followed by a surface segmentation and a point-based registration of the entire lumbar spine volume. A clinical feasibility study resulted in mean registration error of approximately 3 mm between CT and US data.

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

PubMed

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

2004-09-09

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

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

PubMed

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

2017-12-15

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

Enhancing Teaching through Constructive Alignment.

ERIC Educational Resources Information Center

Biggs, John

1996-01-01

An approach to college-level instructional design that incorporates the principles of constructivism, termed "constructive alignment," is described. The process is then illustrated with reference to a professional development unit in educational psychology for teachers, but the model is viewed as generalizable to most units or programs in higher…

X-Ray Testing Constellation-X Optics at MSFC's 100-m Facility

NASA Technical Reports Server (NTRS)

O'Dell, Stephen; Baker, Markus; Content, David; Freeman, Mark; Glenn, Paul; Gubarev, Mikhail; Hair, Jason; Jones, William; Joy, Marshall

2003-01-01

In addition to the 530-m-long X-Ray Calibration Facility (XRCF), NASA's Marshall Space Flight Center (MSFC) operates a 104-m-long (source-to-detector) X-ray-test facility. Originally developed and still occasionally used for stray-light testing of visible-fight optical systems, the so-called "Stray-Light Facility" now serves primarily as a convenient and inexpensive facility for performance evaluation and calibration of X-ray optics and detectors. The facility can accommodate X-ray optics up to about 1-m diameter and 12-m focal length. Currently available electron-impact sources at the facility span the approximate energy range 0.2 to 100 keV, thus supporting testing of soft- and hard-X-ray optics and detectors. Available MSFC detectors are a front-illuminated CCD (charge-coupled device) and a scanning CZT (cadmium--zinc--telluride) detector, with low-energy cut-offs of about 0.8 and 3 keV, respectively. In order to test developmental optics for the Constellation-X Project, led by NASA's Goddard Space Flight Center (GSFC), MSFC undertook several enhancements to the facility. Foremost among these was development and fabrication of a five-degree-of-freedom (5-DoF) optics mount and control system, which translates and tilts the user-provided mirror assembly suspended from its interface plate. Initial Constellation-X tests characterize the performance of the Optical Alignment Pathfinder Two (OAP2) for the large Spectroscopy X-ray Telescope (SXT) and of demonstration mirror assemblies for the Hard X-ray Telescope (HXT). With the Centroid Detector Assembly (CDA), used for precision alignment of the Chandra (nee AXAF) mirrors, the Constellation-X SXT Team optically aligned the individual mirrors of the OAPZ at GSFC. The team then developed set-up and alignment procedures, including transfer of the alignment from the optical alignment facility at GSFC to the X-ray test facility at MSFC, using a reference flat and fiducials. The OAPZ incorporates additional ancillary features --- fixed aperture mask and movable sub-aperture mask --- to facilitate X-ray characterization of the optics. Although the OAPZ was designed to- have low sensitivity to temperature offsets and gradients, analyses showed the necessity of active temperature control for the X-ray performance testing. Thus, the Smithsonian Astrophysical Observatory (SAO) implemented a thermal control and monitoring system, designed to hold the OAP2 close to its assembly.

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

PubMed Central

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

2015-01-01

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

AllergenFP: allergenicity prediction by descriptor fingerprints.

PubMed

Dimitrov, Ivan; Naneva, Lyudmila; Doytchinova, Irini; Bangov, Ivan

2014-03-15

Allergenicity, like antigenicity and immunogenicity, is a property encoded linearly and non-linearly, and therefore the alignment-based approaches are not able to identify this property unambiguously. A novel alignment-free descriptor-based fingerprint approach is presented here and applied to identify allergens and non-allergens. The approach was implemented into a four step algorithm. Initially, the protein sequences are described by amino acid principal properties as hydrophobicity, size, relative abundance, helix and β-strand forming propensities. Then, the generated strings of different length are converted into vectors with equal length by auto- and cross-covariance (ACC). The vectors were transformed into binary fingerprints and compared in terms of Tanimoto coefficient. The approach was applied to a set of 2427 known allergens and 2427 non-allergens and identified correctly 88% of them with Matthews correlation coefficient of 0.759. The descriptor fingerprint approach presented here is universal. It could be applied for any classification problem in computational biology. The set of E-descriptors is able to capture the main structural and physicochemical properties of amino acids building the proteins. The ACC transformation overcomes the main problem in the alignment-based comparative studies arising from the different length of the aligned protein sequences. The conversion of protein ACC values into binary descriptor fingerprints allows similarity search and classification. The algorithm described in the present study was implemented in a specially designed Web site, named AllergenFP (FP stands for FingerPrint). AllergenFP is written in Python, with GIU in HTML. It is freely accessible at http://ddg-pharmfac.net/Allergen FP. idoytchinova@pharmfac.net or ivanbangov@shu-bg.net.

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

PubMed

Ranwez, Vincent

2016-01-01

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

Relative properties of smooth terminating bands

NASA Astrophysics Data System (ADS)

Afanasjev, A. V.; Ragnarsson, I.

1998-01-01

The relative properties of smooth terminating bands observed in the A ∼ 110 mass region are studied within the effective alignment approach. Theoretical values of ietf are calculated using the configuration-dependent shell-correction model with the cranked Nilsson potential. Reasonable agreement with experiment shows that previous interpretations of these bands are consistent with the present study. Contrary to the case of superdeformed bands, the effective alignments of these bands deviate significantly from the pure single-particle alignments of the corresponding orbitals. This indicates that in the case of smooth terminating bands, the effects associated with changes in equilibrium deformations contribute significantly to the effective alignment.

Parallel alignment of bacteria using near-field optical force array for cell sorting

NASA Astrophysics Data System (ADS)

Zhao, H. T.; Zhang, Y.; Chin, L. K.; Yap, P. H.; Wang, K.; Ser, W.; Liu, A. Q.

2017-08-01

This paper presents a near-field approach to align multiple rod-shaped bacteria based on the interference pattern in silicon nano-waveguide arrays. The bacteria in the optical field will be first trapped by the gradient force and then rotated by the scattering force to the equilibrium position. In the experiment, the Shigella bacteria is rotated 90 deg and aligned to horizontal direction in 9.4 s. Meanwhile, 150 Shigella is trapped on the surface in 5 min and 86% is aligned with angle < 5 deg. This method is a promising toolbox for the research of parallel single-cell biophysical characterization, cell-cell interaction, etc.

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

MUSE optical alignment procedure

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

The design of electronic map displays

NASA Technical Reports Server (NTRS)

Aretz, Anthony J.

1991-01-01

This paper presents a cognitive analysis of a pilot's navigation task and describes an experiment comparing a new map display that employs the principle of visual momentum with the two traditional approaches, track-up and north-up. The data show that the advantage of a track-up alignment is its congruence with the egocentered forward view; however, the inconsistency of the rotating display hinders development of a cognitive map. The stability of a north-up alignment aids the acquisition of a cognitive map, but there is a cost associated with the mental rotation of the display to a track-up alignment for tasks involving the ego-centered forward view. The data also show that the visual momentum design captures the benefits and reduces the costs associated with the two traditional approaches.

Attitude sensor alignment calibration for the solar maximum mission

NASA Technical Reports Server (NTRS)

Pitone, Daniel S.; Shuster, Malcolm D.

1990-01-01

An earlier heuristic study of the fine attitude sensors for the Solar Maximum Mission (SMM) revealed a temperature dependence of the alignment about the yaw axis of the pair of fixed-head star trackers relative to the fine pointing Sun sensor. Here, new sensor alignment algorithms which better quantify the dependence of the alignments on the temperature are developed and applied to the SMM data. Comparison with the results from the previous study reveals the limitations of the heuristic approach. In addition, some of the basic assumptions made in the prelaunch analysis of the alignments of the SMM are examined. The results of this work have important consequences for future missions with stringent attitude requirements and where misalignment variations due to variations in the temperature will be significant.

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

PubMed

Treangen, Todd J; Ondov, Brian D; Koren, Sergey; Phillippy, Adam M

2014-01-01

Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.

Dynamic interferometer alignment and its utility in UV Fourier transform spectrometer systems

NASA Technical Reports Server (NTRS)

Dorval, Rick K.; Engel, James R.; Wyntjes, Geert J.

1993-01-01

Dynamic alignment has been demonstrated as a practical approach to alignment maintenance for systems in the infrared region of the spectrum. On the basis of work done by OPTRA, this technique was introduced in commercial Fourier transform spectrometer systems in 1982 and in various forms is now available from a number of manufacturers. This paper reports on work by OPTRA to extend the basic technique to systems operating in the ultraviolet. In addition, this paper reports the preliminary results of the development of an alignment system using a laser diode in place of a gas laser normally found in dynamic alignment systems. A unique optical system and spatial heterodyne technique allows for achievement of a metrology system with characteristics that fully satisfy the requirements of an ultraviolet spectrometer system.

The Alignment of Global Management Strategies, International Communication Approaches, and Individual Rhetorical Choices.

ERIC Educational Resources Information Center

Leininger, Carol

1997-01-01

Suggests that thinking about international communication within a framework that aligns an organization's global management strategies with international communication practices enhances not only consulting practice but teaching as well. Describes the framework, and argues it introduces ways of thinking about global management strategies and their…

Expanding Evidence Approaches for Learning in a Digital World

ERIC Educational Resources Information Center

Means, Barbara; Anderson, Kea

2013-01-01

This report describes how big data and an evidence framework can align across five contexts of educational improvement. It explains that before working with big data, there is an important prerequisite: the proposed innovation should align with deeper learning objectives and should incorporate sound learning sciences principles. New curriculum…

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…

Investigating How to Align Schools' Marketing Environments with Federal Standards for Competitive Foods

ERIC Educational Resources Information Center

Polacsek, Michele; O'Brien, Liam M.; Pratt, Elizabeth; Whatley-Blum, Janet; Adler, Sabrina

2017-01-01

Background: Limiting food and beverage marketing to children is a promising approach to influence children's nutrition behavior. School-based marketing influences nutrition behavior and studies have consistently found marketing for nonnutritious foods and beverages in schools. No studies have examined the resources necessary to align school…

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

Profile-Based LC-MS Data Alignment—A Bayesian Approach

PubMed Central

Tsai, Tsung-Heng; Tadesse, Mahlet G.; Wang, Yue; Ressom, Habtom W.

2014-01-01

A Bayesian alignment model (BAM) is proposed for alignment of liquid chromatography-mass spectrometry (LC-MS) data. BAM belongs to the category of profile-based approaches, which are composed of two major components: a prototype function and a set of mapping functions. Appropriate estimation of these functions is crucial for good alignment results. BAM uses Markov chain Monte Carlo (MCMC) methods to draw inference on the model parameters and improves on existing MCMC-based alignment methods through 1) the implementation of an efficient MCMC sampler and 2) an adaptive selection of knots. A block Metropolis-Hastings algorithm that mitigates the problem of the MCMC sampler getting stuck at local modes of the posterior distribution is used for the update of the mapping function coefficients. In addition, a stochastic search variable selection (SSVS) methodology is used to determine the number and positions of knots. We applied BAM to a simulated data set, an LC-MS proteomic data set, and two LC-MS metabolomic data sets, and compared its performance with the Bayesian hierarchical curve registration (BHCR) model, the dynamic time-warping (DTW) model, and the continuous profile model (CPM). The advantage of applying appropriate profile-based retention time correction prior to performing a feature-based approach is also demonstrated through the metabolomic data sets. PMID:23929872

Stepwise detection of recombination breakpoints in sequence alignments.

PubMed

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

2005-03-01

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

Prediction of biochar yield from cattle manure pyrolysis via least squares support vector machine intelligent approach.

PubMed

Cao, Hongliang; Xin, Ya; Yuan, Qiaoxia

2016-02-01

To predict conveniently the biochar yield from cattle manure pyrolysis, intelligent modeling approach was introduced in this research. A traditional artificial neural networks (ANN) model and a novel least squares support vector machine (LS-SVM) model were developed. For the identification and prediction evaluation of the models, a data set with 33 experimental data was used, which were obtained using a laboratory-scale fixed bed reaction system. The results demonstrated that the intelligent modeling approach is greatly convenient and effective for the prediction of the biochar yield. In particular, the novel LS-SVM model has a more satisfying predicting performance and its robustness is better than the traditional ANN model. The introduction and application of the LS-SVM modeling method gives a successful example, which is a good reference for the modeling study of cattle manure pyrolysis process, even other similar processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

ARYANA: Aligning Reads by Yet Another Approach

PubMed Central

2014-01-01

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

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

PubMed

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

2011-03-15

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

ARYANA: Aligning Reads by Yet Another Approach.

PubMed

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

2014-01-01

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

AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

PubMed Central

Aniba, Mohamed Radhouene; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

2010-01-01

Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. This has led to the development of a number of ‘meta-methods’ that systematically run several aligners and merge the output into one single solution. Although these methods generally produce more accurate alignments, they are inefficient because all the aligners need to be run first and the choice of the best solution is made a posteriori. Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences. AlexSys incorporates an intelligent inference engine to automatically select an appropriate aligner a priori, depending only on the nature of the input sequences. The inference engine was trained on a large set of reference multiple alignments, using a novel machine learning approach. Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects. AlexSys is freely available from http://alnitak.u-strasbg.fr/∼aniba/alexsys. PMID:20530533

A day in the life of third-year medical students: using an ethnographic method to understand information seeking and use.

PubMed

Twiss-Brooks, Andrea B; Andrade, Ricardo; Bass, Michelle B; Kern, Barbara; Peterson, Jonna; Werner, Debra A

2017-01-01

The authors undertook this project to learn how third-year medical students seek and use information in the course of daily activities, especially activities conducted in clinical settings in a variety of institutions. We recruited sixty-eight third-year undergraduate medical school students to create a mapping diary of a day that included clinical activities. We conducted semi-structured interviews based on the mapping diaries. Using content and thematic analyses of the resulting interview transcripts, we developed an ethnographic case study for each participant. In the studied sample, we identified a broad range of information resources used for personal, clinical, and educational use. Participants relied heavily on technology throughout their day, including desktop computers, smart phones, handheld tablets, and laptops. Time management was a pervasive theme in the interviews, with participants squeezing in time to study for exams wherever and whenever they could. Selection of a particular information resource or technology to use was governed largely by the convenience of using that resource or technology. When obstacles were encountered, workarounds might be sought, but in many cases, the resource or technology would be abandoned in favor of a more convenient solution. Convenience was also a consideration in choosing spaces to use for clinical duties or for study, with specific considerations of available technology, proximity to clinical areas, and security for belongings contributing to choices made. Some of our results align with those of other recent studies of information use among medical students, residents, and practicing physicians. In particular, the fast-paced clinical setting favors use of information resources that are fast and easy to use. We demonstrated that the methods used are suitable to better understand clinicians' discovery and use of information.

A day in the life of third-year medical students: using an ethnographic method to understand information seeking and use*

PubMed Central

Twiss-Brooks, Andrea B.; Andrade, Ricardo; Bass, Michelle B.; Kern, Barbara; Peterson, Jonna; Werner, Debra A.

2017-01-01

Objective The authors undertook this project to learn how third-year medical students seek and use information in the course of daily activities, especially activities conducted in clinical settings in a variety of institutions. Methods We recruited sixty-eight third-year undergraduate medical school students to create a mapping diary of a day that included clinical activities. We conducted semi-structured interviews based on the mapping diaries. Using content and thematic analyses of the resulting interview transcripts, we developed an ethnographic case study for each participant. Results In the studied sample, we identified a broad range of information resources used for personal, clinical, and educational use. Participants relied heavily on technology throughout their day, including desktop computers, smart phones, handheld tablets, and laptops. Time management was a pervasive theme in the interviews, with participants squeezing in time to study for exams wherever and whenever they could. Selection of a particular information resource or technology to use was governed largely by the convenience of using that resource or technology. When obstacles were encountered, workarounds might be sought, but in many cases, the resource or technology would be abandoned in favor of a more convenient solution. Convenience was also a consideration in choosing spaces to use for clinical duties or for study, with specific considerations of available technology, proximity to clinical areas, and security for belongings contributing to choices made. Conclusions Some of our results align with those of other recent studies of information use among medical students, residents, and practicing physicians. In particular, the fast-paced clinical setting favors use of information resources that are fast and easy to use. We demonstrated that the methods used are suitable to better understand clinicians’ discovery and use of information. PMID:28096741

Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers.

PubMed

Mote, Kaustubh R; Gopinath, T; Traaseth, Nathaniel J; Kitchen, Jason; Gor'kov, Peter L; Brey, William W; Veglia, Gianluigi

2011-11-01

Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring (1)H-(15)N dipolar couplings (DC) and (15)N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles' heel of this approach is the lack of suitable experiments for sequential assignment of the amide resonances. In this Article, we present a new pulse sequence that integrates proton driven spin diffusion (PDSD) with sensitivity-enhanced PISEMA in a 3D experiment ([(1)H,(15)N]-SE-PISEMA-PDSD). The incorporation of 2D (15)N/(15)N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the (15)N resonances. The feasibility of this approach is demonstrated for the membrane protein sarcolipin reconstituted in magnetically aligned lipid bicelles. Taken with low electric field probe technology, this approach will propel the determination of sequential assignment as well as structure and topology of larger integral membrane proteins in aligned lipid bilayers. © Springer Science+Business Media B.V. 2011

Electrochemical polishing of notches

DOEpatents

Kephart, A.R.; Alberts, A.H.

1989-02-21

An apparatus and method are disclosed for the selective electrochemical polishing of a lateral tip of a deep longitudinal notch in a work piece used to test crack initiation properties of materials. A DC power source is connected to the work piece and to an electrode disposed laterally along the distal end of an insulated body which is inserted in the longitudinal notch. The electrode and distal end of the body are disposed along the tip of the notch, but are spaced from the notch so as to provide a lateral passage for an electrolyte. The electrolyte is circulated through the passage so that the electrolyte only contacts the work piece adjacent the passage. Conveniently, the electrolyte is circulated by use of an inlet tube and an outlet tube provided at opposite ends of the passage. These tubes are preferably detachably located adjacent the ends of the passage and suitable seals are provided. A holding device including arms to which the tubes are attached is conveniently used to rapidly and easily locate the test specimen with the passage aligned with the tubes. The electrode is preferably a wire which is located in grooves along the distal end of the insulated body and up one side of the body or a plastic sheath insulated thin metal strip. 4 figs.

Electrochemical polishing of notches

DOEpatents

Kephart, Alan R.; Alberts, Alfred H.

1989-01-01

An apparatus and method are disclosed for the selective electrochemical polishing of a lateral tip of a deep longitudinal notch in a work piece used to test crack initiation properties of materials. A DC power source is connected to the work piece and to an electrode disposed laterally along the distal end of an insulated body which is inserted in the longitudinal notch. The electrode and distal end of the body are disposed along the tip of the notch, but are spaced from the notch so as to provide a lateral passage for an electrolyte. The electrolyte is circulated through the passage so that the electrolyte only contacts the work piece adjacent the passage. Conveniently, the electrolyte is circulated by use of an inlet tube and an outlet tube provided at opposite ends of the passage. These tubes are preferably detachably located adjacent the ends of the passage and suitable seals are provided. A holding device including arms to which the tubes are attached is conveniently used to rapidly and easily locate the test specimen with the passage aligned with the tubes. The electrode is preferably a wire which is located in grooves along the distal end of the insulated body and up one side of the body or a plastic sheath insulated thin metal strip.

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).

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

NASA Technical Reports Server (NTRS)

Wheeler, Ward C.

2003-01-01

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

Composite Nature of Layered Hybrid Perovskites: Assessment on Quantum and Dielectric Confinements and Band Alignment.

PubMed

Traore, Boubacar; Pedesseau, Laurent; Assam, Linda; Che, Xiaoyang; Blancon, Jean-Christophe; Tsai, Hsinhan; Nie, Wanyi; Stoumpos, Constantinos C; Kanatzidis, Mercouri G; Tretiak, Sergei; Mohite, Aditya D; Even, Jacky; Kepenekian, Mikaël; Katan, Claudine

2018-04-24

Layered hybrid organic-inorganic perovskites (HOPs) have re-emerged as potential technological solutions for next-generation photovoltaic and optoelectronic applications. Their two-dimensional (2D) nature confers them a significant flexibility and results in the appearance of quantum and dielectric confinements. Such confinements are at the origin of their fascinating properties, and understanding them from a fundamental level is of paramount importance for optimization. Here, we provide an in-depth investigation of band alignments of 2D HOP allowing access to carriers' confinement potentials. 2D HOPs are conceptualized as composite materials in which pseudoinorganic and -organic components are defined. In this way, computational modeling of band alignments becomes affordable using first-principles methods. First, we show that the composite approach is suitable to study the position-dependent dielectric profiles and enables clear differentiation of the respective contributions of inorganic and organic components. Then we apply the composite approach to a variety of 2D HOPs, assessing the impact on the confinement potentials of well and barrier thickness, of the nature of the inorganic well, and of structural transitions. Using the deduced potentials, we further discuss the limitations of the effective mass approximation, scrutinizing the electronic properties of this family of composite materials. Our simulations demonstrate type-I dominant band alignment in 2D HOPs. Finally, we outline design principles on band alignment toward achieving specific optoelectronic properties. Thus, we present alternative theoretical methods to inspect the properties of 2D hybrid perovskites and expect that the composite approach will be applicable to other classes of layered materials.

Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

PubMed Central

Franz, Nico M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2015-01-01

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations. PMID:25700173

Reliable Energy Level Alignment at Physisorbed Molecule–Metal Interfaces from Density Functional Theory

DOE PAGES

Egger, David A.; Liu, Zhen-Fei; Neaton, Jeffrey B.; ...

2015-03-05

We report a key quantity for molecule–metal interfaces is the energy level alignment of molecular electronic states with the metallic Fermi level. We develop and apply an efficient theoretical method, based on density functional theory (DFT) that can yield quantitatively accurate energy level alignment information for physisorbed metal–molecule interfaces. The method builds on the “DFT+Σ” approach, grounded in many-body perturbation theory, which introduces an approximate electron self-energy that corrects the level alignment obtained from conventional DFT for missing exchange and correlation effects associated with the gas-phase molecule and substrate polarization. Here, we extend the DFT+Σ approach in two important ways:more » first, we employ optimally tuned range-separated hybrid functionals to compute the gas-phase term, rather than rely on GW or total energy differences as in prior work; second, we use a nonclassical DFT-determined image-charge plane of the metallic surface to compute the substrate polarization term, rather than the classical DFT-derived image plane used previously. We validate this new approach by a detailed comparison with experimental and theoretical reference data for several prototypical molecule–metal interfaces, where excellent agreement with experiment is achieved: benzene on graphite (0001), and 1,4-benzenediamine, Cu-phthalocyanine, and 3,4,9,10-perylene-tetracarboxylic-dianhydride on Au(111). In particular, we show that the method correctly captures level alignment trends across chemical systems and that it retains its accuracy even for molecules for which conventional DFT suffers from severe self-interaction errors.« less

Orientational control of block copolymer microdomains by sub-tesla magnetic fields

NASA Astrophysics Data System (ADS)

Gopinadhan, Manesh; Choo, Youngwoo; Feng, Xunda; Kawabata, Kohsuke; di, Xiaojun; Osuji, Chinedum

Magnetic fields offer a versatile approach to controlling the orientation of block copolymer (BCP) microdomains during self-assembly. To date however, such control has required the imposition of large magnetic fields (>3T), necessitating the use of complex magnet systems - either superconducting or very large conventional resistive magnets. Here we demonstrate the ability to direct BCP self-assembly using considerably smaller fields (<1T) which are accessible using simple rare-earth permanent magnets. The low field alignment is enabled by the presence of small quantities of mesogenic species that are blended into, and co-assemble with the liquid crystalline (LC) mesophase of the side-chain LC BCP under study. In situ SAXS experiments reveal a pronounced dependence of the critical alignment field strength on the stoichiometry of the blend, and the ability to generate aligned microdomains with orientational distribution coefficients exceeding 0.95 at sub-1 T fields for appropriate stoichiometries. The alignment response overall can be rationalized in terms of increased mobility and grain size due to the presence of the mesogenic additive. We use a permanent magnet to fabricate films with aligned nanopores, and the utility of this approach to generate complex BCP microdomain patterns in thin films by local field screening are highlighted. NSF DMR-1410568 and DMR-0847534.

Toward a view-oriented approach for aligning RDF-based biomedical repositories.

PubMed

Anguita, A; García-Remesal, M; de la Iglesia, D; Graf, N; Maojo, V

2015-01-01

This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". The need for complementary access to multiple RDF databases has fostered new lines of research, but also entailed new challenges due to data representation disparities. While several approaches for RDF-based database integration have been proposed, those focused on schema alignment have become the most widely adopted. All state-of-the-art solutions for aligning RDF-based sources resort to a simple technique inherited from legacy relational database integration methods. This technique - known as element-to-element (e2e) mappings - is based on establishing 1:1 mappings between single primitive elements - e.g. concepts, attributes, relationships, etc. - belonging to the source and target schemas. However, due to the intrinsic nature of RDF - a representation language based on defining tuples < subject, predicate, object > -, one may find RDF elements whose semantics vary dramatically when combined into a view involving other RDF elements - i.e. they depend on their context. The latter cannot be adequately represented in the target schema by resorting to the traditional e2e approach. These approaches fail to properly address this issue without explicitly modifying the target ontology, thus lacking the required expressiveness for properly reflecting the intended semantics in the alignment information. To enhance existing RDF schema alignment techniques by providing a mechanism to properly represent elements with context-dependent semantics, thus enabling users to perform more expressive alignments, including scenarios that cannot be adequately addressed by the existing approaches. Instead of establishing 1:1 correspondences between single primitive elements of the schemas, we propose adopting a view-based approach. The latter is targeted at establishing mapping relationships between RDF subgraphs - that can be regarded as the equivalent of views in traditional databases -, rather than between single schema elements. This approach enables users to represent scenarios defined by context-dependent RDF elements that cannot be properly represented when adopting the currently existing approaches. We developed a software tool implementing our view-based strategy. Our tool is currently being used in the context of the European Commission funded p-medicine project, targeted at creating a technological framework to integrate clinical and genomic data to facilitate the development of personalized drugs and therapies for cancer, based on the genetic profile of the patient. We used our tool to integrate different RDF-based databases - including different repositories of clinical trials and DICOM images - using the Health Data Ontology Trunk (HDOT) ontology as the target schema. The importance of database integration methods and tools in the context of biomedical research has been widely recognized. Modern research in this area - e.g. identification of disease biomarkers, or design of personalized therapies - heavily relies on the availability of a technical framework to enable researchers to uniformly access disparate repositories. We present a method and a tool that implement a novel alignment method specifically designed to support and enhance the integration of RDF-based data sources at schema (metadata) level. This approach provides an increased level of expressiveness compared to other existing solutions, and allows solving heterogeneity scenarios that cannot be properly represented using other state-of-the-art techniques.

Dry contact transfer printing of aligned carbon nanotube patterns and characterization of their optical properties for diameter distribution and alignment.

PubMed

Pint, Cary L; Xu, Ya-Qiong; Moghazy, Sharief; Cherukuri, Tonya; Alvarez, Noe T; Haroz, Erik H; Mahzooni, Salma; Doorn, Stephen K; Kono, Junichiro; Pasquali, Matteo; Hauge, Robert H

2010-02-23

A scalable and facile approach is demonstrated where as-grown patterns of well-aligned structures composed of single-walled carbon nanotubes (SWNT) synthesized via water-assisted chemical vapor deposition (CVD) can be transferred, or printed, to any host surface in a single dry, room-temperature step using the growth substrate as a stamp. We demonstrate compatibility of this process with multiple transfers for large-scale device and specifically tailored pattern fabrication. Utilizing this transfer approach, anisotropic optical properties of the SWNT films are probed via polarized absorption, Raman, and photoluminescence spectroscopies. Using a simple model to describe optical transitions in the large SWNT species present in the aligned samples, polarized absorption data are demonstrated as an effective tool for accurate assignment of the diameter distribution from broad absorption features located in the infrared. This can be performed on either well-aligned samples or unaligned doped samples, allowing simple and rapid feedback of the SWNT diameter distribution that can be challenging and time-consuming to obtain in other optical methods. Furthermore, we discuss challenges in accurately characterizing alignment in structures of long versus short carbon nanotubes through optical techniques, where SWNT length makes a difference in the information obtained in such measurements. This work provides new insight to the efficient transfer and optical properties of an emerging class of long, large diameter SWNT species typically produced in the CVD process.

SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments.

PubMed

Hayes, Wayne B; Mamano, Nil

2018-04-15

Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure GO similarity between proteins in isolation, but proteins in a network alignment are not isolated: each pairing is dependent on every other via the alignment itself. Existing measures fail to take into account the frequency of GO terms across networks, instead imposing arbitrary rules on when to allow GO terms. Here we develop NetGO, a new measure that naturally weighs infrequent, informative GO terms more heavily than frequent, less informative GO terms, without arbitrary cutoffs, instead downweighting GO terms according to their frequency in the networks being aligned. This is a global measure applicable only to alignments, independent of pairwise GO measures, in the same sense that the edge-based EC or S3 scores are global measures of topological similarity independent of pairwise topological similarities. We demonstrate the superiority of NetGO in alignments of predetermined quality and show that NetGO correlates with alignment quality better than any existing GO-based alignment measures. We also demonstrate that NetGO provides a measure of taxonomic similarity between species, consistent with existing taxonomic measuresa feature not shared with existing GObased network alignment measures. Finally, we re-score alignments produced by almost a dozen aligners from a previous study and show that NetGO does a better job at separating good alignments from bad ones. Available as part of SANA. whayes@uci.edu. Supplementary data are available at Bioinformatics online.

A Framework for Evaluating and Enhancing Alignment in Self-Regulated Learning Research

ERIC Educational Resources Information Center

Dent, Amy L.; Hoyle, Rick H.

2015-01-01

We discuss the articles of this special issue with reference to an important yet previously only implicit dimension of study quality: alignment across the theoretical and methodological decisions that collectively define an approach to self-regulated learning. Integrating and extending work by leaders in the field, we propose a framework for…

Alignment 2.0: Strategic Use of New Internet Technologies in Government

ERIC Educational Resources Information Center

Meijer, Albert; Thaens, Marcel

2010-01-01

This paper challenges the view that strategies for using Web 2.0 should primarily be based upon technological characteristics. The value of the organizational strategic alignment approach for developing specific operational Web 2.0 strategies for government organizations is explored both theoretically and empirically. On the basis of a review of…

Early Learning Foundations. Indiana's Early Learning Development Framework Aligned to the Indiana Academic Standards, 2014

ERIC Educational Resources Information Center

Indiana Department of Education, 2015

2015-01-01

The "Foundations" (English/language arts, mathematics, social emotional skills, approaches to play and learning, science, social studies, creative arts, and physical health and growth) are Indiana's early learning development framework and are aligned to the 2014 Indiana Academic Standards. This framework provides core elements that…

Constructive Alignment in Economics Teaching: A Reflection on Effective Implementation

ERIC Educational Resources Information Center

McCann, Michael

2017-01-01

The typical approach to student-centred learning in Economics has focused on innovation within the classroom, with little thought given to how this complements teaching and learning and, crucially, assessment. This paper reflects on the implementation of constructive alignment in a final year managerial economics course. It demonstrates how it is…

Unifying Experiences: Learner and Instructor Approaches and Reactions to ePortfolio Usage in Higher Education

ERIC Educational Resources Information Center

Scholz, Kyle; Tse, Crystal; Lithgow, Katherine

2017-01-01

This paper explores the alignment of student and instructor experiences when employing ePortfolio activities in a Canadian higher education context. Successful ePortfolio activities are operationalized as exhibiting alignment of expectations between students and instructors, whereas misalignment of expectations is characteristic of a poorer…

Chinese Business Students' Changes in Beliefs and Strategy Use in a Constructively Aligned PBL Course

ERIC Educational Resources Information Center

Zhao, Ke; Zhang, Jie; Du, Xiangyun

2017-01-01

This study adopted a longitudinal retrospective case study approach to investigate Chinese business students' transitional learning experience in a problem-based learning (PBL) course with innovative assessment practices. The study focused on students' beliefs and strategy use in a constructively aligned PBL course for business communication.…

Understanding the Value of Enterprise Architecture for Organizations: A Grounded Theory Approach

ERIC Educational Resources Information Center

Nassiff, Edwin

2012-01-01

There is a high rate of information system implementation failures attributed to the lack of alignment between business and information technology strategy. Although enterprise architecture (EA) is a means to correct alignment problems and executives highly rate the importance of EA, it is still not used in most organizations today. Current…

Challenges of Adopting Constructive Alignment in Action Learning Education

ERIC Educational Resources Information Center

Remneland Wikhamn, Björn

2017-01-01

This paper will critically examine how the two influential pedagogical approaches of action-based learning and constructive alignment relate to each other, and how they may differ in focus and basic assumptions. From the outset, they are based on similar underpinnings, with the student and the learning outcomes in the center. Drawing from…

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

The kinetic regime of the Vicsek model

NASA Astrophysics Data System (ADS)

Chepizhko, A. A.; Kulinskii, V. L.

2009-12-01

We consider the dynamics of the system of self-propelling particles modeled via the Vicsek algorithm in continuum time limit. It is shown that the alignment process for the velocities can be subdivided into two regimes: "fast" kinetic and "slow" hydrodynamic ones. In fast kinetic regime the alignment of the particle velocity to the local neighborhood takes place with characteristic relaxation time. So, that the bigger regions arise with the velocity alignment. These regions align their velocities thus giving rise to hydrodynamic regime of the dynamics. We propose the mean-field-like approach in which we take into account the correlations between density and velocity. The comparison of the theoretical predictions with the numerical simulations is given. The relation between Vicsek model in the zero velocity limit and the Kuramoto model is stated. The mean-field approach accounting for the dynamic change of the neighborhood is proposed. The nature of the discontinuity of the dependence of the order parameter in case of vectorial noise revealed in Gregorie and Chaite, Phys. Rev. Lett., 92, 025702 (2004) is discussed and the explanation of it is proposed.

Compliance to two city convenience store ordinance requirements.

PubMed

Chaumont Menéndez, Cammie K; Amandus, Harlan E; Wu, Nan; Hendricks, Scott A

2016-04-01

Robbery-related homicides and assaults are the leading cause of death in retail businesses. Robbery reduction approaches focus on compliance to Crime Prevention Through Environmental Design (CPTED) guidelines. We evaluated the level of compliance to CPTED guidelines specified by convenience store safety ordinances effective in 2010 in Dallas and Houston, Texas, USA. Convenience stores were defined as businesses less than 10 000 square feet that sell grocery items. Store managers were interviewed for store ordinance requirements from August to November 2011, in a random sample of 594 (289 in Dallas, 305 in Houston) convenience stores that were open before and after the effective dates of their city's ordinance. Data were collected in 2011 and analysed in 2012-2014. Overall, 9% of stores were in full compliance, although 79% reported being registered with the police departments as compliant. Compliance was consistently significantly higher in Dallas than in Houston for many requirements and by store type. Compliance was lower among single owner-operator stores compared with corporate/franchise stores. Compliance to individual requirements was lowest for signage and visibility. Full compliance to the required safety measures is consistent with industry 'best practices' and evidence-based workplace violence prevention research findings. In Houston and Dallas compliance was higher for some CPTED requirements but not the less costly approaches that are also the more straightforward to adopt. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

A mean-field theory for self-propelled particles interacting by velocity alignment mechanisms

NASA Astrophysics Data System (ADS)

Peruani, F.; Deutsch, A.; Bär, M.

2008-04-01

A mean-field approach (MFA) is proposed for the analysis of orientational order in a two-dimensional system of stochastic self-propelled particles interacting by local velocity alignment mechanism. The treatment is applied to the cases of ferromagnetic (F) and liquid-crystal (LC) alignment. In both cases, MFA yields a second order phase transition for a critical noise strength and a scaling exponent of 1/2 for the respective order parameters. We find that the critical noise amplitude ηc at which orientational order emerges in the LC case is smaller than in the F-alignment case, i.e. ηLC C<ηF C. A comparison with simulations of individual-based models with F- resp. LC-alignment shows that the predictions about the critical behavior and the qualitative relation between the respective critical noise amplitudes are correct.

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

Current distribution and ac susceptibility response of a thin superconducting disc in an axial field: a theoretical approach

NASA Astrophysics Data System (ADS)

Aruna, S. A.; Zhang, P.; Lin, F. Y.; Ding, S. Y.; Yao, X. X.

2000-04-01

Within the framework of the thermally activated process of the flux line or flux line bundles, and by time integration of the 1D equation of motion of the circulating current density icons/Journals/Common/vecJ" ALT="vecJ" ALIGN="TOP"/> (icons/Journals/Common/rho" ALT="rho" ALIGN="TOP"/> ,t ), which is suitable for thin superconducting films (R >>d ,icons/Journals/Common/le" ALT="le" ALIGN="TOP"/> icons/Journals/Common/lambda" ALT="lambda" ALIGN="TOP"/> ), we present numerical calculations of the current profiles, magnetization hysteresis loops and ac susceptibility icons/Journals/Common/chi" ALT="chi" ALIGN="TOP"/> n = icons/Journals/Common/chi" ALT="chi" ALIGN="TOP"/> ´n +iicons/Journals/Common/chi" ALT="chi" ALIGN="TOP"/> ´´n for n = 1, 3 and 5 of a thin disc immersed in an axial time-dependent external magnetic field Ba (t ) = Bdc +Bac cos(2icons/Journals/Common/pi" ALT="pi" ALIGN="TOP"/> icons/Journals/Common/nu" ALT="nu" ALIGN="TOP"/> t ). Our calculated results are compared with those of the critical state model (CSM) and found to prove the approximate validity of the CSM below the irreversibility field. The differences between our computed results and those of the CSM are also discussed.

Spatiotemporal alignment of in utero BOLD-MRI series.

PubMed

Turk, Esra Abaci; Luo, Jie; Gagoski, Borjan; Pascau, Javier; Bibbo, Carolina; Robinson, Julian N; Grant, P Ellen; Adalsteinsson, Elfar; Golland, Polina; Malpica, Norberto

2017-08-01

To present a method for spatiotemporal alignment of in-utero magnetic resonance imaging (MRI) time series acquired during maternal hyperoxia for enabling improved quantitative tracking of blood oxygen level-dependent (BOLD) signal changes that characterize oxygen transport through the placenta to fetal organs. The proposed pipeline for spatiotemporal alignment of images acquired with a single-shot gradient echo echo-planar imaging includes 1) signal nonuniformity correction, 2) intravolume motion correction based on nonrigid registration, 3) correction of motion and nonrigid deformations across volumes, and 4) detection of the outlier volumes to be discarded from subsequent analysis. BOLD MRI time series collected from 10 pregnant women during 3T scans were analyzed using this pipeline. To assess pipeline performance, signal fluctuations between consecutive timepoints were examined. In addition, volume overlap and distance between manual region of interest (ROI) delineations in a subset of frames and the delineations obtained through propagation of the ROIs from the reference frame were used to quantify alignment accuracy. A previously demonstrated rigid registration approach was used for comparison. The proposed pipeline improved anatomical alignment of placenta and fetal organs over the state-of-the-art rigid motion correction methods. In particular, unexpected temporal signal fluctuations during the first normoxia period were significantly decreased (P < 0.01) and volume overlap and distance between region boundaries measures were significantly improved (P < 0.01). The proposed approach to align MRI time series enables more accurate quantitative studies of placental function by improving spatiotemporal alignment across placenta and fetal organs. 1 Technical Efficacy: Stage 1 J. MAGN. RESON. IMAGING 2017;46:403-412. © 2017 International Society for Magnetic Resonance in Medicine.

Pairwise Sequence Alignment Library

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

Jeff Daily, PNNL

2015-05-20

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

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.

TIM Barrel Protein Structure Classification Using Alignment Approach and Best Hit Strategy

NASA Astrophysics Data System (ADS)

Chu, Jia-Han; Lin, Chun Yuan; Chang, Cheng-Wen; Lee, Chihan; Yang, Yuh-Shyong; Tang, Chuan Yi

2007-11-01

The classification of protein structures is essential for their function determination in bioinformatics. It has been estimated that around 10% of all known enzymes have TIM barrel domains from the Structural Classification of Proteins (SCOP) database. With its high sequence variation and diverse functionalities, TIM barrel protein becomes to be an attractive target for protein engineering and for the evolution study. Hence, in this paper, an alignment approach with the best hit strategy is proposed to classify the TIM barrel protein structure in terms of superfamily and family levels in the SCOP. This work is also used to do the classification for class level in the Enzyme nomenclature (ENZYME) database. Two testing data sets, TIM40D and TIM95D, both are used to evaluate this approach. The resulting classification has an overall prediction accuracy rate of 90.3% for the superfamily level in the SCOP, 89.5% for the family level in the SCOP and 70.1% for the class level in the ENZYME. These results demonstrate that the alignment approach with the best hit strategy is a simple and viable method for the TIM barrel protein structure classification, even only has the amino acid sequences information.

Template-Based Modeling of Protein-RNA Interactions.

PubMed

Zheng, Jinfang; Kundrotas, Petras J; Vakser, Ilya A; Liu, Shiyong

2016-09-01

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.

Retention time alignment of LC/MS data by a divide-and-conquer algorithm.

PubMed

Zhang, Zhongqi

2012-04-01

Liquid chromatography-mass spectrometry (LC/MS) has become the method of choice for characterizing complex mixtures. These analyses often involve quantitative comparison of components in multiple samples. To achieve automated sample comparison, the components of interest must be detected and identified, and their retention times aligned and peak areas calculated. This article describes a simple pairwise iterative retention time alignment algorithm, based on the divide-and-conquer approach, for alignment of ion features detected in LC/MS experiments. In this iterative algorithm, ion features in the sample run are first aligned with features in the reference run by applying a single constant shift of retention time. The sample chromatogram is then divided into two shorter chromatograms, which are aligned to the reference chromatogram the same way. Each shorter chromatogram is further divided into even shorter chromatograms. This process continues until each chromatogram is sufficiently narrow so that ion features within it have a similar retention time shift. In six pairwise LC/MS alignment examples containing a total of 6507 confirmed true corresponding feature pairs with retention time shifts up to five peak widths, the algorithm successfully aligned these features with an error rate of 0.2%. The alignment algorithm is demonstrated to be fast, robust, fully automatic, and superior to other algorithms. After alignment and gap-filling of detected ion features, their abundances can be tabulated for direct comparison between samples.

An Event-Triggered Machine Learning Approach for Accelerometer-Based Fall Detection.

PubMed

Putra, I Putu Edy Suardiyana; Brusey, James; Gaura, Elena; Vesilo, Rein

2017-12-22

The fixed-size non-overlapping sliding window (FNSW) and fixed-size overlapping sliding window (FOSW) approaches are the most commonly used data-segmentation techniques in machine learning-based fall detection using accelerometer sensors. However, these techniques do not segment by fall stages (pre-impact, impact, and post-impact) and thus useful information is lost, which may reduce the detection rate of the classifier. Aligning the segment with the fall stage is difficult, as the segment size varies. We propose an event-triggered machine learning (EvenT-ML) approach that aligns each fall stage so that the characteristic features of the fall stages are more easily recognized. To evaluate our approach, two publicly accessible datasets were used. Classification and regression tree (CART), k -nearest neighbor ( k -NN), logistic regression (LR), and the support vector machine (SVM) were used to train the classifiers. EvenT-ML gives classifier F-scores of 98% for a chest-worn sensor and 92% for a waist-worn sensor, and significantly reduces the computational cost compared with the FNSW- and FOSW-based approaches, with reductions of up to 8-fold and 78-fold, respectively. EvenT-ML achieves a significantly better F-score than existing fall detection approaches. These results indicate that aligning feature segments with fall stages significantly increases the detection rate and reduces the computational cost.

Generation of Ground Truth Datasets for the Analysis of 3d Point Clouds in Urban Scenes Acquired via Different Sensors

NASA Astrophysics Data System (ADS)

Xu, Y.; Sun, Z.; Boerner, R.; Koch, T.; Hoegner, L.; Stilla, U.

2018-04-01

In this work, we report a novel way of generating ground truth dataset for analyzing point cloud from different sensors and the validation of algorithms. Instead of directly labeling large amount of 3D points requiring time consuming manual work, a multi-resolution 3D voxel grid for the testing site is generated. Then, with the help of a set of basic labeled points from the reference dataset, we can generate a 3D labeled space of the entire testing site with different resolutions. Specifically, an octree-based voxel structure is applied to voxelize the annotated reference point cloud, by which all the points are organized by 3D grids of multi-resolutions. When automatically annotating the new testing point clouds, a voting based approach is adopted to the labeled points within multiple resolution voxels, in order to assign a semantic label to the 3D space represented by the voxel. Lastly, robust line- and plane-based fast registration methods are developed for aligning point clouds obtained via various sensors. Benefiting from the labeled 3D spatial information, we can easily create new annotated 3D point clouds of different sensors of the same scene directly by considering the corresponding labels of 3D space the points located, which would be convenient for the validation and evaluation of algorithms related to point cloud interpretation and semantic segmentation.

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.

Aligning for Innovation - Alignment Strategy to Drive Innovation

NASA Technical Reports Server (NTRS)

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

2010-01-01

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

Exploring Dance Movement Data Using Sequence Alignment Methods

PubMed Central

Chavoshi, Seyed Hossein; De Baets, Bernard; Neutens, Tijs; De Tré, Guy; Van de Weghe, Nico

2015-01-01

Despite the abundance of research on knowledge discovery from moving object databases, only a limited number of studies have examined the interaction between moving point objects in space over time. This paper describes a novel approach for measuring similarity in the interaction between moving objects. The proposed approach consists of three steps. First, we transform movement data into sequences of successive qualitative relations based on the Qualitative Trajectory Calculus (QTC). Second, sequence alignment methods are applied to measure the similarity between movement sequences. Finally, movement sequences are grouped based on similarity by means of an agglomerative hierarchical clustering method. The applicability of this approach is tested using movement data from samba and tango dancers. PMID:26181435

Patient Safety Incident Reporting: Current Trends and Gaps Within the Canadian Health System.

PubMed

Boucaud, Sarah; Dorschner, Danielle

2016-01-01

Patient safety incidents are a national-level phenomenon, requiring a pan-Canadian approach to ensure that incidents are reported and lessons are learned and broadly disseminated. This work explores the variation in current provincial and local approaches to reporting through a literature review. Trends are consolidated and recommendations are offered to foster better alignment of existing systems. These include adopting a common terminology, defining the patient role in reporting, increasing system users' perception of safety and further investigating the areas of home and community care in ensuring standard approaches at the local level. These steps can promote alignment, reducing barriers to a future pan-Canadian reporting and learning system.

Alignment of the measurement scale mark during immersion hydrometer calibration using an image processing system.

PubMed

Peña-Perez, Luis Manuel; Pedraza-Ortega, Jesus Carlos; Ramos-Arreguin, Juan Manuel; Arriaga, Saul Tovar; Fernandez, Marco Antonio Aceves; Becerra, Luis Omar; Hurtado, Efren Gorrostieta; Vargas-Soto, Jose Emilio

2013-10-24

The present work presents an improved method to align the measurement scale mark in an immersion hydrometer calibration system of CENAM, the National Metrology Institute (NMI) of Mexico, The proposed method uses a vision system to align the scale mark of the hydrometer to the surface of the liquid where it is immersed by implementing image processing algorithms. This approach reduces the variability in the apparent mass determination during the hydrostatic weighing in the calibration process, therefore decreasing the relative uncertainty of calibration.

Alignment of the Measurement Scale Mark during Immersion Hydrometer Calibration Using an Image Processing System

PubMed Central

Peña-Perez, Luis Manuel; Pedraza-Ortega, Jesus Carlos; Ramos-Arreguin, Juan Manuel; Arriaga, Saul Tovar; Fernandez, Marco Antonio Aceves; Becerra, Luis Omar; Hurtado, Efren Gorrostieta; Vargas-Soto, Jose Emilio

2013-01-01

The present work presents an improved method to align the measurement scale mark in an immersion hydrometer calibration system of CENAM, the National Metrology Institute (NMI) of Mexico, The proposed method uses a vision system to align the scale mark of the hydrometer to the surface of the liquid where it is immersed by implementing image processing algorithms. This approach reduces the variability in the apparent mass determination during the hydrostatic weighing in the calibration process, therefore decreasing the relative uncertainty of calibration. PMID:24284770

On aggregation in CA models in biology

NASA Astrophysics Data System (ADS)

Alber, Mark S.; Kiskowski, Audi

2001-12-01

Aggregation of randomly distributed particles into clusters of aligned particles is modeled using a cellular automata (CA) approach. The CA model accounts for interactions between more than one type of particle, in which pressures for angular alignment with neighbors compete with pressures for grouping by cell type. In the case of only one particle type clusters tend to unite into one big cluster. In the case of several types of particles the dynamics of clusters is more complicated and for specific choices of parameters particle sorting occurs simultaneously with the formation of clusters of aligned particles.

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

Three Dimensional Microfabrication On Thick Film Photoresist Mandrels

NASA Astrophysics Data System (ADS)

Salmre, William

1984-05-01

Small, three-dimensional structures are fabricated by the use of thick film photoresist mandrels as substrates for electoforming or other deposition techniques. Novel methods have been developed for the sculpting of the resist to desired shapes. These techniques rely heavily on the use of glass or other substrates coated with layers of metal. The metal serves both as a photomask and as a conductor of electricity. Commercially available chrome-on-glass photomasks are convenient for this purpose although other substrates have also been used. By controlling the thickness and light transmission of the metal layer, the amount of exposure of the resist can also be controlled to produce the desired shapes in the resist. For even more complex mandrels the resist can be exposed from both sides using self-aligned photomasks.

Millimeter-Wave Localizers for Aircraft-to-Aircraft Approach Navigation

NASA Technical Reports Server (NTRS)

Tang, Adrian J.

2013-01-01

Aerial refueling technology for both manned and unmanned aircraft is critical for operations where extended aircraft flight time is required. Existing refueling assets are typically manned aircraft, which couple to a second aircraft through the use of a refueling boom. Alignment and mating of the two aircraft continues to rely on human control with use of high-resolution cameras. With the recent advances in unmanned aircraft, it would be highly advantageous to remove/reduce human control from the refueling process, simplifying the amount of remote mission management and enabling new operational scenarios. Existing aerial refueling uses a camera, making it non-autonomous and prone to human error. Existing commercial localizer technology has proven robust and reliable, but not suited for aircraft-to-aircraft approaches like in aerial refueling scenarios since the resolution is too coarse (approximately one meter). A localizer approach system for aircraft-to-aircraft docking can be constructed using the same modulation with a millimeterwave carrier to provide high resolution. One technology used to remotely align commercial aircraft on approach to a runway are ILS (instrument landing systems). ILS have been in service within the U.S. for almost 50 years. In a commercial ILS, two partially overlapping beams of UHF (109 to 126 MHz) are broadcast from an antenna array so that their overlapping region defines the centerline of the runway. This is called a localizer system and is responsible for horizontal alignment of the approach. One beam is modulated with a 150-Hz tone, while the other with a 90-Hz tone. Through comparison of the modulation depths of both tones, an autopilot system aligns the approaching aircraft with the runway centerline. A similar system called a glide-slope (GS) exists in the 320-to-330MHz band for vertical alignment of the approach. While this technology has been proven reliable for millions of commercial flights annually, its UHF nature limits its ability to operate beyond the 1-to-2-meter precisions associated with commercial runway width. A prototype ILS-type system operates at millimeter-wave frequencies to provide automatic and robust approach control for aerial refueling. The system allows for the coupling process to remain completely autonomous, as a boom operator is no longer required. Operating beyond 100 GHz provides enough resolution and a narrow enough beamwidth that an approach corridor of centimeter scales can be maintained. Two modules were used to accomplish this task. The first module is a localizer/glide-slope module that can be fitted on a refueling aircraft. This module provides the navigation beams for aligning the approaching aircraft. The second module is navigational receiver fitted onto the approaching aircraft to be re fueled that can detect the approach beams. Since unmanned aircraft have a limited payload size and limited electrical power, the receiver portion was implemented in CMOS (complementary metal oxide semiconductor) technology based on a super-regenerative receiver (SRR) architecture. The SRR achieves mW-level power consumption and chip sizes less than l mm2. While super-regenerative techniques have small bandwidths that limit use in communication systems, their advantages of high sensitivity, low complexity, and low power make them ideal in this situation where modulating tones of less than 1 kHz are used.

A correlative microscopy approach relates microtubule behaviour, local organ geometry, and cell growth at the Arabidopsis shoot apical meristem

PubMed Central

Burian, Agata; Uyttewaal, Magalie

2013-01-01

Cortical microtubules (CMTs) are often aligned in a particular direction in individual cells or even in groups of cells and play a central role in the definition of growth anisotropy. How the CMTs themselves are aligned is not well known, but two hypotheses have been proposed. According to the first hypothesis, CMTs align perpendicular to the maximal growth direction, and, according to the second, CMTs align parallel to the maximal stress direction. Since both hypotheses were formulated on the basis of mainly qualitative assessments, the link between CMT organization, organ geometry, and cell growth is revisited using a quantitative approach. For this purpose, CMT orientation, local curvature, and growth parameters for each cell were measured in the growing shoot apical meristem (SAM) of Arabidopsis thaliana. Using this approach, it has been shown that stable CMTs tend to be perpendicular to the direction of maximal growth in cells at the SAM periphery, but parallel in the cells at the boundary domain. When examining the local curvature of the SAM surface, no strict correlation between curvature and CMT arrangement was found, which implies that SAM geometry, and presumed geometry-derived stress distribution, is not sufficient to prescribe the CMT orientation. However, a better match between stress and CMTs was found when mechanical stress derived from differential growth was also considered. PMID:24153420

Aligning Ag Nanowires by a Facile Bioinspired Directional Liquid Transfer: Toward Anisotropic Flexible Conductive Electrodes.

PubMed

Meng, Lili; Bian, Ruixin; Guo, Cheng; Xu, Bojie; Liu, Huan; Jiang, Lei

2018-06-01

Recent years have witnessed the booming development of transparent flexible electrodes (TFEs) for their applications in electronics and optoelectronic devices. Various strategies have thus been developed for preparing TFEs with higher flexibility and conductivity. However, little work has focused on TFEs with anisotropic conductivity. Here, a facile strategy of directional liquid transfer is proposed, guided by a conical fibers array (CFA), based on which silver nanowires (AgNWs) are aligned on a soft poly(ethylene terephthalate) substrate in large scale. After further coating a second thin layer of the conductive polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate), a TFE with notable anisotropic conductivity and excellent optical transmittance of 95.2% is prepared. It is proposed that the CFA enables fine control over the receding of the three-phase contact line during the dewetting process, where AgNWs are guided and aligned by the as-generated directional stress. Moreover, anisotropic electrochemical deposition is enabled where the Cu nanoparticles deposit only on the oriented AgNWs, leading to a surface with anisotropic wetting behavior. Importantly, the approach enables alignment of AgNWs via multiple directions at one step. It is envisioned that the as-developed approach will provide an optional approach for simple and low-cost preparation of TFE with various functions. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A correlative microscopy approach relates microtubule behaviour, local organ geometry, and cell growth at the Arabidopsis shoot apical meristem.

PubMed

Burian, Agata; Ludynia, Michal; Uyttewaal, Magalie; Traas, Jan; Boudaoud, Arezki; Hamant, Olivier; Kwiatkowska, Dorota

2013-12-01

Cortical microtubules (CMTs) are often aligned in a particular direction in individual cells or even in groups of cells and play a central role in the definition of growth anisotropy. How the CMTs themselves are aligned is not well known, but two hypotheses have been proposed. According to the first hypothesis, CMTs align perpendicular to the maximal growth direction, and, according to the second, CMTs align parallel to the maximal stress direction. Since both hypotheses were formulated on the basis of mainly qualitative assessments, the link between CMT organization, organ geometry, and cell growth is revisited using a quantitative approach. For this purpose, CMT orientation, local curvature, and growth parameters for each cell were measured in the growing shoot apical meristem (SAM) of Arabidopsis thaliana. Using this approach, it has been shown that stable CMTs tend to be perpendicular to the direction of maximal growth in cells at the SAM periphery, but parallel in the cells at the boundary domain. When examining the local curvature of the SAM surface, no strict correlation between curvature and CMT arrangement was found, which implies that SAM geometry, and presumed geometry-derived stress distribution, is not sufficient to prescribe the CMT orientation. However, a better match between stress and CMTs was found when mechanical stress derived from differential growth was also considered.

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

NASA Technical Reports Server (NTRS)

1979-01-01

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

Bending Behavior of Plain-Woven Fabric Air Beams: Fluid-Structure Interaction Approach

DTIC Science & Technology

2006-09-01

hoses . The warp yarns were aligned in the longitudinal direction of the fire hose and the weft yams, orthogonal to the warp yams, were aligned in the...both terms. Plain-woven air beams typically operate at low-pressure levels (less than those for triaxial-woven or braided air beams) because of safety

Teaching a Sense of Initiative and Entrepreneurship with Constructive Alignment in Tertiary Non-Business Contexts

ERIC Educational Resources Information Center

Morselli, Daniele

2018-01-01

Purpose: The purpose of this paper is to focus on a course in entrepreneurship education for students studying for a Masters in Educational Sciences at a Finnish university. The course was structured around the principles of constructive alignment and aimed to move beyond reflection on entrepreneurship towards action Design/methodology/approach:…

TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.

PubMed

Menges, Fabian; Narzisi, Giuseppe; Mishra, Bud

2011-09-01

Currently, re-sequencing approaches use multiple modules serially to interpret raw sequencing data from next-generation sequencing platforms, while remaining oblivious to the genomic information until the final alignment step. Such approaches fail to exploit the full information from both raw sequencing data and the reference genome that can yield better quality sequence reads, SNP-calls, variant detection, as well as an alignment at the best possible location in the reference genome. Thus, there is a need for novel reference-guided bioinformatics algorithms for interpreting analog signals representing sequences of the bases ({A, C, G, T}), while simultaneously aligning possible sequence reads to a source reference genome whenever available. Here, we propose a new base-calling algorithm, TotalReCaller, to achieve improved performance. A linear error model for the raw intensity data and Burrows-Wheeler transform (BWT) based alignment are combined utilizing a Bayesian score function, which is then globally optimized over all possible genomic locations using an efficient branch-and-bound approach. The algorithm has been implemented in soft- and hardware [field-programmable gate array (FPGA)] to achieve real-time performance. Empirical results on real high-throughput Illumina data were used to evaluate TotalReCaller's performance relative to its peers-Bustard, BayesCall, Ibis and Rolexa-based on several criteria, particularly those important in clinical and scientific applications. Namely, it was evaluated for (i) its base-calling speed and throughput, (ii) its read accuracy and (iii) its specificity and sensitivity in variant calling. A software implementation of TotalReCaller as well as additional information, is available at: http://bioinformatics.nyu.edu/wordpress/projects/totalrecaller/ fabian.menges@nyu.edu.

Fabrication of cross-shaped Cu-nanowire resistive memory devices using a rapid, scalable, and designable inorganic-nanowire-digital-alignment technique (Conference Presentation)

NASA Astrophysics Data System (ADS)

Xu, Wentao; Lee, Yeongjun; Min, Sung-Yong; Park, Cheolmin; Lee, Tae-Woo

2016-09-01

Resistive random-access memory (RRAM) is a candidate next generation nonvolatile memory due to its high access speed, high density and ease of fabrication. Especially, cross-point-access allows cross-bar arrays that lead to high-density cells in a two-dimensional planar structure. Use of such designs could be compatible with the aggressive scaling down of memory devices, but existing methods such as optical or e-beam lithographic approaches are too complicated. One-dimensional inorganic nanowires (i-NWs) are regarded as ideal components of nanoelectronics to circumvent the limitations of conventional lithographic approaches. However, post-growth alignment of these i-NWs precisely on a large area with individual control is still a difficult challenge. Here, we report a simple, inexpensive, and rapid method to fabricate two-dimensional arrays of perpendicularly-aligned, individually-conductive Cu-NWs with a nanometer-scale CuxO layer sandwiched at each cross point, by using an inorganic-nanowire-digital-alignment technique (INDAT) and a one-step reduction process. In this approach, the oxide layer is self-formed and patterned, so conventional deposition and lithography are not necessary. INDAT eliminates the difficulties of alignment and scalable fabrication that are encountered when using currently-available techniques that use inorganic nanowires. This simple process facilitates fabrication of cross-point nonvolatile memristor arrays. Fabricated arrays had reproducible resistive switching behavior, high on/off current ratio (Ion/Ioff) 10 6 and extensive cycling endurance. This is the first report of memristors with the resistive switching oxide layer self-formed, self-patterned and self-positioned; we envision that the new features of the technique will provide great opportunities for future nano-electronic circuits.

First-Principles Approach to Energy Level Alignment at Aqueous Semiconductor Interfaces

NASA Astrophysics Data System (ADS)

Hybertsen, Mark

2015-03-01

We have developed a first principles method to calculate the energy level alignment between semiconductor band edges and reference energy levels at aqueous interfaces. This alignment is fundamental to understand the electrochemical characteristics of any semiconductor electrode in general and the potential for photocatalytic activity in particular. For example, in the search for new photo-catalytic materials, viable candidates must demonstrate both efficient absorption of the solar spectrum and an appropriate alignment of the band edge levels in the semiconductor to the redox levels for the target reactions. In our approach, the interface-specific contribution to the electrostatic step across the interface is evaluated using density functional theory (DFT) based molecular dynamics to sample the physical interface structure and the corresponding change in the electrostatic potential at the interface. The reference electronic levels in the semiconductor and in the water are calculated using the GW approach, which naturally corrects for errors inherent in the use of Kohn-Sham energy eigenvalues to approximate the electronic excitation energies in each material. Taken together, our calculations provide the alignment of the semiconductor valence band edge to the centroid of the highest occupied 1b1 level in water. The known relationship of the 1b1 level to the normal hydrogen electrode completes the connection to electrochemical levels. We discuss specific results for GaN, ZnO, and TiO2. The effect of interface structural motifs, such as different degrees of water dissociation, and of dynamical characteristics, will be presented together with available experimental data. Work supported by the US Department of Energy, Office of Basic Energy Sciences under Contract No. DE-AC02-98CH10886.

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.

MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment.

PubMed

Nguyen, Minh Anh Thi; Klaere, Steffen; von Haeseler, Arndt

2011-01-01

As models of sequence evolution become more and more complicated, many criteria for model selection have been proposed, and tools are available to select the best model for an alignment under a particular criterion. However, in many instances the selected model fails to explain the data adequately as reflected by large deviations between observed pattern frequencies and the corresponding expectation. We present MISFITS, an approach to evaluate the goodness of fit (http://www.cibiv.at/software/misfits). MISFITS introduces a minimum number of "extra substitutions" on the inferred tree to provide a biologically motivated explanation why the alignment may deviate from expectation. These extra substitutions plus the evolutionary model then fully explain the alignment. We illustrate the method on several examples and then give a survey about the goodness of fit of the selected models to the alignments in the PANDIT database.

Thermal Conductivity of Polyimide/Carbon Nanofiller Blends

NASA Technical Reports Server (NTRS)

Delozier, D. M.; Watson, K. A.; Ghose, S.; Working, D. C.; Connell, J. W.; Smith, J. G.; Sun, Y. P.; Lin, Y.

2006-01-01

Ultem(TM) was mixed with three different carbon-based nanofillers in efforts to increase the thermal conductivity of the polymer. After initial mixing, the nanocomposites were extruded or processed via the Laboratory Mixing Molder (LMM) process. High resolution scanning electron microscopy (HRSEM) revealed significant alignment of the nanofillers in the extruded samples. Thermal conductivity measurements were made both in the direction and perpendicular to the direction of alignment of nanofillers as well as for unaligned samples. It was found that the largest improvement in thermal conductivity was achieved in the case of aligned samples when the measurement was performed in the direction of alignment. Unaligned samples also showed a significant improvement in thermal conductivity and may be useful in applications when it is not possible to align the nanofiller. However the improvements in thermal conductivity did not approach those expected based on a rule of mixtures. This is likely due to poor phonon transfer through the matrix.

Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism.

PubMed

Yu, Jia; Blom, Jochen; Sczyrba, Alexander; Goesmann, Alexander

2017-09-10

The introduction of next generation sequencing has caused a steady increase in the amounts of data that have to be processed in modern life science. Sequence alignment plays a key role in the analysis of sequencing data e.g. within whole genome sequencing or metagenome projects. BLAST is a commonly used alignment tool that was the standard approach for more than two decades, but in the last years faster alternatives have been proposed including RapSearch, GHOSTX, and DIAMOND. Here we introduce HAMOND, an application that uses Apache Hadoop to parallelize DIAMOND computation in order to scale-out the calculation of alignments. HAMOND is fault tolerant and scalable by utilizing large cloud computing infrastructures like Amazon Web Services. HAMOND has been tested in comparative genomics analyses and showed promising results both in efficiency and accuracy. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

AmpliVar: mutation detection in high-throughput sequence from amplicon-based libraries.

PubMed

Hsu, Arthur L; Kondrashova, Olga; Lunke, Sebastian; Love, Clare J; Meldrum, Cliff; Marquis-Nicholson, Renate; Corboy, Greg; Pham, Kym; Wakefield, Matthew; Waring, Paul M; Taylor, Graham R

2015-04-01

Conventional means of identifying variants in high-throughput sequencing align each read against a reference sequence, and then call variants at each position. Here, we demonstrate an orthogonal means of identifying sequence variation by grouping the reads as amplicons prior to any alignment. We used AmpliVar to make key-value hashes of sequence reads and group reads as individual amplicons using a table of flanking sequences. Low-abundance reads were removed according to a selectable threshold, and reads above this threshold were aligned as groups, rather than as individual reads, permitting the use of sensitive alignment tools. We show that this approach is more sensitive, more specific, and more computationally efficient than comparable methods for the analysis of amplicon-based high-throughput sequencing data. The method can be extended to enable alignment-free confirmation of variants seen in hybridization capture target-enrichment data. © 2015 WILEY PERIODICALS, INC.

Prediction of Antimicrobial Peptides Based on Sequence Alignment and Feature Selection Methods

PubMed Central

Wang, Ping; Hu, Lele; Liu, Guiyou; Jiang, Nan; Chen, Xiaoyun; Xu, Jianyong; Zheng, Wen; Li, Li; Tan, Ming; Chen, Zugen; Song, Hui; Cai, Yu-Dong; Chou, Kuo-Chen

2011-01-01

Antimicrobial peptides (AMPs) represent a class of natural peptides that form a part of the innate immune system, and this kind of ‘nature's antibiotics’ is quite promising for solving the problem of increasing antibiotic resistance. In view of this, it is highly desired to develop an effective computational method for accurately predicting novel AMPs because it can provide us with more candidates and useful insights for drug design. In this study, a new method for predicting AMPs was implemented by integrating the sequence alignment method and the feature selection method. It was observed that, the overall jackknife success rate by the new predictor on a newly constructed benchmark dataset was over 80.23%, and the Mathews correlation coefficient is 0.73, indicating a good prediction. Moreover, it is indicated by an in-depth feature analysis that the results are quite consistent with the previously known knowledge that some amino acids are preferential in AMPs and that these amino acids do play an important role for the antimicrobial activity. For the convenience of most experimental scientists who want to use the prediction method without the interest to follow the mathematical details, a user-friendly web-server is provided at http://amp.biosino.org/. PMID:21533231

(125)I-Tetrazines and Inverse-Electron-Demand Diels-Alder Chemistry: A Convenient Radioiodination Strategy for Biomolecule Labeling, Screening, and Biodistribution Studies.

PubMed

Albu, Silvia A; Al-Karmi, Salma A; Vito, Alyssa; Dzandzi, James P K; Zlitni, Aimen; Beckford-Vera, Denis; Blacker, Megan; Janzen, Nancy; Patel, Ramesh M; Capretta, Alfredo; Valliant, John F

2016-01-20

A convenient method to prepare radioiodinated tetrazines was developed, such that a bioorthogonal inverse electron demand Diels-Alder reaction can be used to label biomolecules with iodine-125 for in vitro screening and in vivo biodistribution studies. The tetrazine was prepared by employing a high-yielding oxidative halo destannylation reaction that concomitantly oxidized the dihydrotetrazine precursor. The product reacts quickly and efficiently with trans-cyclooctene derivatives. Utility was demonstrated through antibody and hormone labeling experiments and by evaluating products using standard analytical methods, in vitro assays, and quantitative biodistribution studies where the latter was performed in direct comparison to Bolton-Hunter and direct iodination methods. The approach described provides a convenient and advantageous alternative to conventional protein iodination methods that can expedite preclinical development and evaluation of biotherapeutics.

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

Teens in the Twenty-First Century Still Prefer People over Machines: Importance of Intervention Delivery Style in Adolescent HIV/STD Prevention

ERIC Educational Resources Information Center

Pendleton, Sara M.; Stanton, Bonita; Cottrell, Lesley A.; Marshall, Sharon; Pack, Robert; Burns, James; Gibson, Catherine; Wu, Ying; Li, Xiaoming; Cole, Matthew

2007-01-01

Purpose: To assess and compare youth satisfaction with two delivery approaches to a HIV/STD risk reduction intervention targeting adolescents: an on-site, face-to-face (FTF) approach versus a long distance interactive televised (DIT) approach. Methods: A convenience sample of 571 rural adolescents ages 12-16 years who participated in an HIV/STD…

Validating Coherence Measurements Using Aligned and Unaligned Coherence Functions

NASA Technical Reports Server (NTRS)

Miles, Jeffrey Hilton

2006-01-01

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

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.

Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene.

PubMed

Seuring, Carolin; Ayyer, Kartik; Filippaki, Eleftheria; Barthelmess, Miriam; Longchamp, Jean-Nicolas; Ringler, Philippe; Pardini, Tommaso; Wojtas, David H; Coleman, Matthew A; Dörner, Katerina; Fuglerud, Silje; Hammarin, Greger; Habenstein, Birgit; Langkilde, Annette E; Loquet, Antoine; Meents, Alke; Riek, Roland; Stahlberg, Henning; Boutet, Sébastien; Hunter, Mark S; Koglin, Jason; Liang, Mengning; Ginn, Helen M; Millane, Rick P; Frank, Matthias; Barty, Anton; Chapman, Henry N

2018-05-09

Here we present a new approach to diffraction imaging of amyloid fibrils, combining a free-standing graphene support and single nanofocused X-ray pulses of femtosecond duration from an X-ray free-electron laser. Due to the very low background scattering from the graphene support and mutual alignment of filaments, diffraction from tobacco mosaic virus (TMV) filaments and amyloid protofibrils is obtained to 2.7 Å and 2.4 Å resolution in single diffraction patterns, respectively. Some TMV diffraction patterns exhibit asymmetry that indicates the presence of a limited number of axial rotations in the XFEL focus. Signal-to-noise levels from individual diffraction patterns are enhanced using computational alignment and merging, giving patterns that are superior to those obtainable from synchrotron radiation sources. We anticipate that our approach will be a starting point for further investigations into unsolved structures of filaments and other weakly scattering objects.

Encouraging Creativity in the Face of Administrative Convenience: How Our Schools Discourage Divergent Thinking

ERIC Educational Resources Information Center

Geist, Eugene; Hohn, Jennifer

2009-01-01

This article reports observations of 2 classrooms in which arts based creative activities were integrated with curricular subject areas. One successfully incorporated a positive approach to supporting creativity. The other classroom used a more traditional approach to creative activities in the classroom. Suggestions for and possible outcomes of…

Scrutinizing the alignment limit in two-Higgs-doublet models. II. mH=125 GeV

NASA Astrophysics Data System (ADS)

Bernon, Jérémy; Gunion, John F.; Haber, Howard E.; Jiang, Yun; Kraml, Sabine

2016-02-01

In the alignment limit of a multidoublet Higgs sector, one of the Higgs mass eigenstates aligns in field space with the direction of the scalar field vacuum expectation values, and its couplings approach those of the Standard Model (SM) Higgs boson. We consider C P -conserving two-Higgs-doublet models (2HDMs) of type I and type II near the alignment limit in which the heavier of the two C P -even Higgs bosons, H , is the SM-like state observed with a mass of 125 GeV, and the couplings of H to gauge bosons approach those of the SM. We review the theoretical structure and analyze the phenomenological implications of this particular realization of the alignment limit, where decoupling of the extra states cannot occur given that the lighter C P -even state h must, by definition, have a mass below 125 GeV. For the numerical analysis, we perform scans of the 2HDM parameter space employing the software packages 2hdmc and lilith, taking into account all relevant pre-LHC constraints, constraints from the measurements of the 125 GeV Higgs signal at the LHC, as well as the most recent limits coming from searches for other Higgs-like states. Implications for Run 2 at the LHC, including expectations for observing the other scalar states, are also discussed.

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.

DNAAlignEditor: DNA alignment editor tool

PubMed Central

Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

2008-01-01

Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism. PMID:18366684

New Zealand policy experts' appraisal of interventions to reduce smoking in young adults: a qualitative investigation.

PubMed

Ball, Jude; Hoek, Janet; Tautolo, El Shadan; Gifford, Heather

2017-12-10

Reducing smoking in young adults, particularly young Māori and Pacific, is vital for reducing tobacco harm and health inequalities in New Zealand (NZ). We investigated how NZ policy experts appraised the feasibility and likely effectiveness of interventions designed to reduce smoking prevalence among 18-24 year olds. We used a qualitative design, conducting semistructured interviews and applying thematic analysis. We interviewed 15 key informants, including politicians, senior policy analysts and leading tobacco control advocates. Participant selection was based on seniority and expertise and ensuring diverse perspectives were represented. We examined nine interventions that could either promote greater mindfulness or introduce barriers impeding smoking uptake: smoke-free outdoor dining and bars; no tobacco sales where alcohol is sold; social marketing campaigns; real life stories (testimonials); life skills training; raise purchase age to 21; tobacco-free generation; smokers' licence; make tobacco retail premises R18. The policies perceived as more effective denormalised tobacco; made it less convenient to access and use; highlighted immediate disadvantages (eg, impact on fitness); aligned with young people's values; and addressed the underlying causes of smoking (eg, stress). Participants highlighted some political barriers and noted concerns that some interventions might widen ethnic disparities. Exceptions were social marketing campaigns and extending smoke-free regulations to include outdoor areas of cafes and bars, which participants saw as politically feasible and likely to be effective. Our findings suggest the merit of an approach that combines social marketing with regulation that makes accessing and using tobacco less convenient for young adults; however, political barriers may limit the regulatory options available in the short term. Strategies to support self-determination and address the underlying causes of smoking in young people warrant further investigation. Determining policy acceptability to Māori and Pacific, and likely effectiveness for these populations, should be key priorities. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Prevalence of substandard and falsified artemisinin-based combination antimalarial medicines on Bioko Island, Equatorial Guinea.

PubMed

Kaur, Harparkash; Allan, Elizabeth Louise; Mamadu, Ibrahim; Hall, Zoe; Green, Michael D; Swamidos, Isabel; Dwivedi, Prabha; Culzoni, Maria Julia; Fernandez, Facundo M; Garcia, Guillermo; Hergott, Dianna; Monti, Feliciano

2017-01-01

Poor-quality artemisinin-containing antimalarials (ACAs), including falsified and substandard formulations, pose serious health concerns in malaria endemic countries. They can harm patients, contribute to the rise in drug resistance and increase the public's mistrust of health systems. Systematic assessment of drug quality is needed to gain knowledge on the prevalence of the problem, to provide Ministries of Health with evidence on which local regulators can take action. We used three sampling approaches to purchase 677 ACAs from 278 outlets on Bioko Island, Equatorial Guinea as follows: convenience survey using mystery client (n=16 outlets, 31 samples), full island-wide survey using mystery client (n=174 outlets, 368 samples) and randomised survey using an overt sampling approach (n=88 outlets, 278 samples). The stated active pharmaceutical ingredients (SAPIs) were assessed using high-performance liquid chromatography and confirmed by mass spectrometry at three independent laboratories. Content analysis showed 91.0% of ACAs were of acceptable quality, 1.6% were substandard and 7.4% falsified. No degraded medicines were detected. The prevalence of medicines without the SAPIs was higher for ACAs purchased in the convenience survey compared with the estimates obtained using the full island-wide survey-mystery client and randomised-overt sampling approaches. Comparable results were obtained for full island survey-mystery client and randomised overt. However, the availability of purchased artesunate monotherapies differed substantially according to the sampling approach used (convenience, 45.2%; full island-wide survey-mystery client, 32.6%; random-overt sampling approach, 21.9%). Of concern is that 37.1% (n=62) of these were falsified. Falsified ACAs were found on Bioko Island, with the prevalence ranging between 6.1% and 16.1%, depending on the sampling method used. These findings underscore the vital need for national authorities to track the scale of ineffective medicines that jeopardise treatment of life-threatening diseases and value of a representative sampling approach to obtain/measure the true prevalence of poor-quality medicines.

Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.

PubMed

Rahn, René; Budach, Stefan; Costanza, Pascal; Ehrhardt, Marcel; Hancox, Jonny; Reinert, Knut

2018-05-03

Pairwise sequence alignment is undoubtedly a central tool in many bioinformatics analyses. In this paper, we present a generically accelerated module for pairwise sequence alignments applicable for a broad range of applications. In our module, we unified the standard dynamic programming kernel used for pairwise sequence alignments and extended it with a generalized inter-sequence vectorization layout, such that many alignments can be computed simultaneously by exploiting SIMD (Single Instruction Multiple Data) instructions of modern processors. We then extended the module by adding two layers of thread-level parallelization, where we a) distribute many independent alignments on multiple threads and b) inherently parallelize a single alignment computation using a work stealing approach producing a dynamic wavefront progressing along the minor diagonal. We evaluated our alignment vectorization and parallelization on different processors, including the newest Intel® Xeon® (Skylake) and Intel® Xeon Phi™ (KNL) processors, and use cases. The instruction set AVX512-BW (Byte and Word), available on Skylake processors, can genuinely improve the performance of vectorized alignments. We could run single alignments 1600 times faster on the Xeon Phi™ and 1400 times faster on the Xeon® than executing them with our previous sequential alignment module. The module is programmed in C++ using the SeqAn (Reinert et al., 2017) library and distributed with version 2.4. under the BSD license. We support SSE4, AVX2, AVX512 instructions and included UME::SIMD, a SIMD-instruction wrapper library, to extend our module for further instruction sets. We thoroughly test all alignment components with all major C++ compilers on various platforms. rene.rahn@fu-berlin.de.

Aligning Biomolecular Networks Using Modular Graph Kernels

NASA Astrophysics Data System (ADS)

Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

Constructively Aligned Teaching and Learning in Higher Education in Engineering: What Do Students Perceive as Contributing to the Learning of Interdisciplinary Thinking?

ERIC Educational Resources Information Center

Spelt, E. J. H.; Luning, P. A.; van Boekel, M. A. J. S.; Mulder, M.

2015-01-01

Increased attention to the need for constructively aligned teaching and learning in interdisciplinary higher education in engineering is observed. By contrast, little research has been conducted on the implementation of the outcome-based pedagogical approach to interdisciplinary higher education in engineering. Therefore, the present design-based…

Career Pathways: Aligning Public Resources to Support Individual and Regional Economic Advancement in the Knowledge Economy

ERIC Educational Resources Information Center

Jenkins, Davis

2006-01-01

This paper describes career pathways, a framework or approach by which regions can better align publicly supported systems and programs to build a knowledge-economy workforce customized to the needs of local labor markets. A career pathway is a series of connected education and training programs and support services that enable individuals to…

Aligning Game Activity with Educational Goals: Following a Constrained Design Approach to Instructional Computer Games

ERIC Educational Resources Information Center

Shelton, Brett E.; Scoresby, Jon

2011-01-01

We discuss the design, creation and implementation of an instructional game for use in a high school poetry class following a commitment to an educational game design principle of "alignment". We studied groups of instructional designers and an interactive fiction computer game they built. The game was implemented in a 9th grade English classroom…

System Alignment and Consensus Discourses in Reforms: "School Effectiveness Frameworks and Instructional Rounds." Philosophical Responses with Oakeshott, Mouffe and Rancière

ERIC Educational Resources Information Center

Stickney, Jeff

2015-01-01

In this commentary 26-year Ontario district teacher, Jeff Stickney, begins by surveying balanced approaches to large- and small-scale education reforms: contrasting linear alignment with more complex ecological models, drawing on recent work by Andy Hargreaves (2008; Hargreaves & Shirley, 2012). Next, through a brief case study of School…

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

NASA Astrophysics Data System (ADS)

Gonzalez, M.

2018-04-01

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

Alignment and the States: Three Approaches to Aligning the National Assessment of Educational Progress with State Assessments, Other Assessments, and Standards

ERIC Educational Resources Information Center

Vockley, Martha; Lang, Vockley

2009-01-01

Since 1969, the National Assessment of Educational Progress (NAEP) has been the common yardstick for measuring the progress of students' education over time across the country. Teachers, principals, parents, policymakers, and researchers all use NAEP results to assess progress and develop ways to improve education in America. To make the…

"No Child Left Behind," the "Individuals with Disabilities Education Act" and Functional Curricula: A Conflict of Interest?

ERIC Educational Resources Information Center

Bouck, Emily C.

2009-01-01

Is a functional curriculum aligned with the federal education policies of No Child Left Behind (2002) and the Individuals with Disabilities Education Act (IDEA, 2004)? This article analyzes the alignment, or lack thereof, between this approach to educating secondary students with mild mental impairment and the two main federal education laws…

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

PubMed Central

Steele, Joe; Bastola, Dhundy

2014-01-01

Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base–base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel–Ziv techniques from data compression. PMID:23904502

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures.

PubMed

Stamatakis, Alexandros; Ott, Michael

2008-12-27

The continuous accumulation of sequence data, for example, due to novel wet-laboratory techniques such as pyrosequencing, coupled with the increasing popularity of multi-gene phylogenies and emerging multi-core processor architectures that face problems of cache congestion, poses new challenges with respect to the efficient computation of the phylogenetic maximum-likelihood (ML) function. Here, we propose two approaches that can significantly speed up likelihood computations that typically represent over 95 per cent of the computational effort conducted by current ML or Bayesian inference programs. Initially, we present a method and an appropriate data structure to efficiently compute the likelihood score on 'gappy' multi-gene alignments. By 'gappy' we denote sampling-induced gaps owing to missing sequences in individual genes (partitions), i.e. not real alignment gaps. A first proof-of-concept implementation in RAXML indicates that this approach can accelerate inferences on large and gappy alignments by approximately one order of magnitude. Moreover, we present insights and initial performance results on multi-core architectures obtained during the transition from an OpenMP-based to a Pthreads-based fine-grained parallelization of the ML function.

Electrohydrodynamic assisted droplet alignment for lens fabrication by droplet evaporation

NASA Astrophysics Data System (ADS)

Wang, Guangxu; Deng, Jia; Guo, Xing

2018-04-01

Lens fabrication by droplet evaporation has attracted a lot of attention since the fabrication approach is simple and moldless. Droplet position accuracy is a critical parameter in this approach, and thus it is of great importance to use accurate methods to realize the droplet position alignment. In this paper, we propose an electrohydrodynamic (EHD) assisted droplet alignment method. An electrostatic force was induced at the interface between materials to overcome the surface tension and gravity. The deviation of droplet position from the center region was eliminated and alignment was successfully realized. We demonstrated the capability of the proposed method theoretically and experimentally. First, we built a simulation model coupled with the three-phase flow formulations and the EHD equations to study the three-phase flowing process in an electric field. Results show that it is the uneven electric field distribution that leads to the relative movement of the droplet. Then, we conducted experiments to verify the method. Experimental results are consistent with the numerical simulation results. Moreover, we successfully fabricated a crater lens after applying the proposed method. A light emitting diode module packaging with the fabricated crater lens shows a significant light intensity distribution adjustment compared with a spherical cap lens.

A Framework for Evaluating and Enhancing Alignment in Self-Regulated Learning Research

PubMed Central

Dent, Amy L.; Hoyle, Rick H.

2015-01-01

We discuss the articles of this special issue with reference to an important yet previously only implicit dimension of study quality: alignment across the theoretical and methodological decisions that collectively define an approach to self-regulated learning. Integrating and extending work by leaders in the field, we propose a framework for evaluating alignment in the way self-regulated learning research is both conducted and reported. Within this framework, the special issue articles provide a springboard for discussing methodological promises and pitfalls of increasingly sophisticated research on the dynamic, contingent, and contextualized features of self-regulated learning. PMID:25825589

The energy level alignment at metal–molecule interfaces using Wannier–Koopmans method

DOE PAGES

Ma, Jie; Liu, Zhen-Fei; Neaton, Jeffrey B.; ...

2016-06-30

We apply a recently developed Wannier-Koopmans method (WKM), based on density functional theory (DFT), to calculate the electronic energy level alignment at an interface between a molecule and metal substrate. We consider two systems: benzenediamine on Au (111), and a bipyridine-Au molecular junction. The WKM calculated level alignment agrees well with the experimental measurements where available, as well as previous GW and DFT + Σ results. These results suggest that the WKM is a general approach that can be used to correct DFT eigenvalue errors, not only in bulk semiconductors and isolated molecules, but also in hybrid interfaces.

Template-Based Modeling of Protein-RNA Interactions

PubMed Central

Zheng, Jinfang; Kundrotas, Petras J.; Vakser, Ilya A.

2016-01-01

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes. PMID:27662342

Convenience experimentation.

PubMed

Krohs, Ulrich

2012-03-01

Systems biology aims at explaining life processes by means of detailed models of molecular networks, mainly on the whole-cell scale. The whole cell perspective distinguishes the new field of systems biology from earlier approaches within molecular cell biology. The shift was made possible by the high throughput methods that were developed for gathering 'omic' (genomic, proteomic, etc.) data. These new techniques are made commercially available as semi-automatic analytic equipment, ready-made analytic kits and probe arrays. There is a whole industry of supplies for what may be called convenience experimentation. My paper inquires some epistemic consequences of strong reliance on convenience experimentation in systems biology. In times when experimentation was automated to a lesser degree, modeling and in part even experimentation could be understood fairly well as either being driven by hypotheses, and thus proceed by the testing of hypothesis, or as being performed in an exploratory mode, intended to sharpen concepts or initially vague phenomena. In systems biology, the situation is dramatically different. Data collection became so easy (though not cheap) that experimentation is, to a high degree, driven by convenience equipment, and model building is driven by the vast amount of data that is produced by convenience experimentation. This results in a shift in the mode of science. The paper shows that convenience driven science is not primarily hypothesis-testing, nor is it in an exploratory mode. It rather proceeds in a gathering mode. This shift demands another shift in the mode of evaluation, which now becomes an exploratory endeavor, in response to the superabundance of gathered data. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

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

PubMed

Margelevicius, Mindaugas

2018-06-15

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

Transcription Factor Map Alignment of Promoter Regions

PubMed Central

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

2006-01-01

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

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.

Theoferometer for the Construction of Precision Optomechanical Assemblies

NASA Technical Reports Server (NTRS)

Korzun, Ashley M.

2006-01-01

The increasing difficulty of metrology requirements on projects involving optics and the alignment of instrumentation on spacecraft has reached a turning point. Requirements as low as 0.1 arcseconds for the static, rotational alignment of components within a coordinate system cannot be met with a theodolite, the alignment tool currently in use. A "theoferometer" is an interferometer mounted on a rotation stage with degrees of freedom in azimuth and elevation for metrology and alignment applications. The success of a prototype theoferometer in approaching these metrology requirements led to a redesign stressing mechanical, optical, and software changes to increase the sensitivity and portability of the unit. This paper covers the improvements made to the first prototype theoferometer, characteristic testing, and demonstration of the redesigned theoferometer s capabilities as a "theodolite replacement" and low-uncertainty metrology tool.

Cascaded face alignment via intimacy definition feature

NASA Astrophysics Data System (ADS)

Li, Hailiang; Lam, Kin-Man; Chiu, Man-Yau; Wu, Kangheng; Lei, Zhibin

2017-09-01

Recent years have witnessed the emerging popularity of regression-based face aligners, which directly learn mappings between facial appearance and shape-increment manifolds. We propose a random-forest based, cascaded regression model for face alignment by using a locally lightweight feature, namely intimacy definition feature. This feature is more discriminative than the pose-indexed feature, more efficient than the histogram of oriented gradients feature and the scale-invariant feature transform feature, and more compact than the local binary feature (LBF). Experimental validation of our algorithm shows that our approach achieves state-of-the-art performance when testing on some challenging datasets. Compared with the LBF-based algorithm, our method achieves about twice the speed, 20% improvement in terms of alignment accuracy and saves an order of magnitude on memory requirement.

Microfluidic Analysis with Front-Face Fluorometric Detection for the Determination of Total Inorganic Iodine in Drinking Water.

PubMed

Inpota, Prawpan; Strzelak, Kamil; Koncki, Robert; Sripumkhai, Wisaroot; Jeamsaksiri, Wutthinan; Ratanawimarnwong, Nuanlaor; Wilairat, Prapin; Choengchan, Nathawut; Chantiwas, Rattikan; Nacapricha, Duangjai

2018-01-01

A microfluidic method with front-face fluorometric detection was developed for the determination of total inorganic iodine in drinking water. A polydimethylsiloxane (PDMS) microfluidic device was employed in conjunction with the Sandell-Kolthoff reaction, in which iodide catalyzed the redox reaction between Ce(IV) and As(III). Direct alignment of an optical fiber attached to a spectrofluorometer was used as a convenient detector for remote front-face fluorometric detection. Trace inorganic iodine (IO 3 - and I - ) present naturally in drinking water was measured by on-line conversion of iodate to iodide for determination of total inorganic iodine. On-line conversion efficiency of iodate to iodide using the microfluidic device was investigated. Excellent conversion efficiency of 93 - 103% (%RSD = 1.6 - 11%) was obtained. Inorganic iodine concentrations in drinking water samples were measured, and the results obtained were in good agreement with those obtained by an ICP-MS method. Spiked sample recoveries were in the range of 86%(±5) - 128%(±8) (n = 12). Interference of various anions and cations were investigated with tolerance limit concentrations ranging from 10 -6 to 2.5 M depending on the type of ions. The developed method is simple and convenient, and it is a green method for iodine analysis, as it greatly reduces the amount of toxic reagent consumed with reagent volumes in the microfluidic scale.

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.

PubMed

Hahn, Lars; Leimeister, Chris-André; Ounit, Rachid; Lonardi, Stefano; Morgenstern, Burkhard

2016-10-01

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de/.

Direct synthesis of alkenyl iodides via indium-catalyzed iodoalkylation of alkynes with alcohols and aqueous HI.

PubMed

Wu, Chao; Wang, Zheng; Hu, Zhan; Zeng, Fei; Zhang, Xing-Yu; Cao, Zhong; Tang, Zilong; He, Wei-Min; Xu, Xin-Hua

2018-05-02

A convenient and efficient indium-catalyzed approach to synthesize alkenyl iodides has been developed through direct iodoalkylation of alkynes with alcohols and aqueous HI under mild conditions. This catalytic protocol offers an attractive approach for the synthesis of a diverse range of alkenyl iodides in good to excellent yields.

LPV Modeling of a Flexible Wing Aircraft Using Modal Alignment and Adaptive Gridding Methods

NASA Technical Reports Server (NTRS)

Al-Jiboory, Ali Khudhair; Zhu, Guoming; Swei, Sean Shan-Min; Su, Weihua; Nguyen, Nhan T.

2017-01-01

One of the earliest approaches in gain-scheduling control is the gridding based approach, in which a set of local linear time-invariant models are obtained at various gridded points corresponding to the varying parameters within the flight envelop. In order to ensure smooth and effective Linear Parameter-Varying control, aligning all the flexible modes within each local model and maintaining small number of representative local models over the gridded parameter space are crucial. In addition, since the flexible structural models tend to have large dimensions, a tractable model reduction process is necessary. In this paper, the notion of s-shifted H2- and H Infinity-norm are introduced and used as a metric to measure the model mismatch. A new modal alignment algorithm is developed which utilizes the defined metric for aligning all the local models over the entire gridded parameter space. Furthermore, an Adaptive Grid Step Size Determination algorithm is developed to minimize the number of local models required to represent the gridded parameter space. For model reduction, we propose to utilize the concept of Composite Modal Cost Analysis, through which the collective contribution of each flexible mode is computed and ranked. Therefore, a reduced-order model is constructed by retaining only those modes with significant contribution. The NASA Generic Transport Model operating at various flight speeds is studied for verification purpose, and the analysis and simulation results demonstrate the effectiveness of the proposed modeling approach.

Enhancing facial features by using clear facial features

NASA Astrophysics Data System (ADS)

Rofoo, Fanar Fareed Hanna

2017-09-01

The similarity of features between individuals of same ethnicity motivated the idea of this project. The idea of this project is to extract features of clear facial image and impose them on blurred facial image of same ethnic origin as an approach to enhance a blurred facial image. A database of clear images containing 30 individuals equally divided to five different ethnicities which were Arab, African, Chines, European and Indian. Software was built to perform pre-processing on images in order to align the features of clear and blurred images. And the idea was to extract features of clear facial image or template built from clear facial images using wavelet transformation to impose them on blurred image by using reverse wavelet. The results of this approach did not come well as all the features did not align together as in most cases the eyes were aligned but the nose or mouth were not aligned. Then we decided in the next approach to deal with features separately but in the result in some cases a blocky effect was present on features due to not having close matching features. In general the available small database did not help to achieve the goal results, because of the number of available individuals. The color information and features similarity could be more investigated to achieve better results by having larger database as well as improving the process of enhancement by the availability of closer matches in each ethnicity.

Obstetric "conveniences": elective induction of labor, cesarean birth on demand, and other potentially unnecessary interventions.

PubMed

Simpson, Kathleen Rice; Thorman, Kathleen E

2005-01-01

Common obstetric interventions are often for "convenience" rather than for clinical indications. Before proceeding, it should be clear who is the beneficiary of the convenience. The primary healthcare provider must make sure that women and their partners have a full understanding of what is known about the associated risks, benefits, and alternative approaches of the proposed intervention. Thorough and accurate information allows women to choose what is best for them and their infant on the basis of the individual clinical situation. Ideally, this discussion takes place during the prenatal period when there is ample opportunity to ask questions, reflect on the potential implications, and confer with partners and family members. A review of common obstetric interventions is provided. While these interventions often are medically indicated for the well-being of mothers and infants, the evidence supporting their benefits when used electively is controversial.

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

PubMed Central

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

2010-01-01

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

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

NASA Astrophysics Data System (ADS)

Krappig, Reik; Schmitt, Robert

2017-02-01

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

ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.

PubMed

Bonizzoni, Paola; Rizzi, Raffaella; Pesole, Graziano

2005-10-05

Currently available methods to predict splice sites are mainly based on the independent and progressive alignment of transcript data (mostly ESTs) to the genomic sequence. Apart from often being computationally expensive, this approach is vulnerable to several problems--hence the need to develop novel strategies. We propose a method, based on a novel multiple genome-EST alignment algorithm, for the detection of splice sites. To avoid limitations of splice sites prediction (mainly, over-predictions) due to independent single EST alignments to the genomic sequence our approach performs a multiple alignment of transcript data to the genomic sequence based on the combined analysis of all available data. We recast the problem of predicting constitutive and alternative splicing as an optimization problem, where the optimal multiple transcript alignment minimizes the number of exons and hence of splice site observations. We have implemented a splice site predictor based on this algorithm in the software tool ASPIC (Alternative Splicing PredICtion). It is distinguished from other methods based on BLAST-like tools by the incorporation of entirely new ad hoc procedures for accurate and computationally efficient transcript alignment and adopts dynamic programming for the refinement of intron boundaries. ASPIC also provides the minimal set of non-mergeable transcript isoforms compatible with the detected splicing events. The ASPIC web resource is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility. Extensive bench marking shows that ASPIC outperforms other existing methods in the detection of novel splicing isoforms and in the minimization of over-predictions. ASPIC also requires a lower computation time for processing a single gene and an EST cluster. The ASPIC web resource is available at http://aspic.algo.disco.unimib.it/aspic-devel/.

EPE analysis of sub-N10 BEoL flow with and without fully self-aligned via using Coventor SEMulator3D

NASA Astrophysics Data System (ADS)

Franke, Joern-Holger; Gallagher, Matt; Murdoch, Gayle; Halder, Sandip; Juncker, Aurelie; Clark, William

2017-03-01

During the last few decades, the semiconductor industry has been able to scale device performance up while driving costs down. What started off as simple geometrical scaling, driven mostly by advances in lithography, has recently been accompanied by advances in processing techniques and in device architectures. The trend to combine efforts using process technology and lithography is expected to intensify, as further scaling becomes ever more difficult. One promising component of future nodes are "scaling boosters", i.e. processing techniques that enable further scaling. An indispensable component in developing these ever more complex processing techniques is semiconductor process modeling software. Visualization of complex 3D structures in SEMulator3D, along with budget analysis on film thicknesses, CD and etch budgets, allow process integrators to compare flows before any physical wafers are run. Hundreds of "virtual" wafers allow comparison of different processing approaches, along with EUV or DUV patterning options for defined layers and different overlay schemes. This "virtual fabrication" technology produces massively parallel process variation studies that would be highly time-consuming or expensive in experiment. Here, we focus on one particular scaling booster, the fully self-aligned via (FSAV). We compare metal-via-metal (mevia-me) chains with self-aligned and fully-self-aligned via's using a calibrated model for imec's N7 BEoL flow. To model overall variability, 3D Monte Carlo modeling of as many variability sources as possible is critical. We use Coventor SEMulator3D to extract minimum me-me distances and contact areas and show how fully self-aligned vias allow a better me-via distance control and tighter via-me contact area variability compared with the standard self-aligned via (SAV) approach.

Two Influential Primate Classifications Logically Aligned

PubMed Central

Franz, Nico M.; Pier, Naomi M.; Reeder, Deeann M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2016-01-01

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2–317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3–483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments—in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms. PMID:27009895

Computational design and engineering of polymeric orthodontic aligners.

PubMed

Barone, S; Paoli, A; Razionale, A V; Savignano, R

2016-10-05

Transparent and removable aligners represent an effective solution to correct various orthodontic malocclusions through minimally invasive procedures. An aligner-based treatment requires patients to sequentially wear dentition-mating shells obtained by thermoforming polymeric disks on reference dental models. An aligner is shaped introducing a geometrical mismatch with respect to the actual tooth positions to induce a loading system, which moves the target teeth toward the correct positions. The common practice is based on selecting the aligner features (material, thickness, and auxiliary elements) by only considering clinician's subjective assessments. In this article, a computational design and engineering methodology has been developed to reconstruct anatomical tissues, to model parametric aligner shapes, to simulate orthodontic movements, and to enhance the aligner design. The proposed approach integrates computer-aided technologies, from tomographic imaging to optical scanning, from parametric modeling to finite element analyses, within a 3-dimensional digital framework. The anatomical modeling provides anatomies, including teeth (roots and crowns), jaw bones, and periodontal ligaments, which are the references for the down streaming parametric aligner shaping. The biomechanical interactions between anatomical models and aligner geometries are virtually reproduced using a finite element analysis software. The methodology allows numerical simulations of patient-specific conditions and the comparative analyses of different aligner configurations. In this article, the digital framework has been used to study the influence of various auxiliary elements on the loading system delivered to a maxillary and a mandibular central incisor during an orthodontic tipping movement. Numerical simulations have shown a high dependency of the orthodontic tooth movement on the auxiliary element configuration, which should then be accurately selected to maximize the aligner's effectiveness. Copyright © 2016 John Wiley & Sons, Ltd.

Effects of alignment on the roll-over shapes of prosthetic feet.

PubMed

Hansen, Andrew

2008-12-01

Recent work suggests that a prosthetic ankle-foot component's roll-over shape - the effective rocker it conforms to between initial contact and opposite initial contact (the 'roll-over' interval of walking) - is closely linked to its final alignment in the prosthesis (as determined by a skilled prosthetist using heuristic techniques). If true, this information may help to determine the appropriate alignment for a lower limb prosthesis before it is built, or a priori. Knowledge is needed for future models that will incorporate the roll-over shape including the relative effect of alignment on the roll-over shape's radius of curvature and arc length. The purpose of this study was to evaluate the hypotheses that: (i) Changes in prosthesis alignment alter the position and orientation of a foot's roll-over shape in prosthesis-based coordinates, and (ii) these changes occur without changing the radius of curvature or arc length of the roll-over shape. To examine the hypotheses, this study examined the effects of nine alignment settings on the roll-over shapes of two prosthetic feet. The idea that alignment changes move and rotate roll-over shapes of prosthetic feet in prosthesis coordinates is supported by this work, but the hypothesis that the radius of curvature and arc length do not change for different alignments is not strongly supported by the data. A revised approach is presented that explains some of the changes to the roll-over shape parameters due to changes in rotational alignment.

Sub-cell turning to accomplish micron-level alignment of precision assemblies

NASA Astrophysics Data System (ADS)

Kumler, James J.; Buss, Christian

2017-08-01

Higher performance expectations for complex optical systems demand tighter alignment requirements for lens assembly alignment. In order to meet diffraction limited imaging performance over wide spectral bands across the UV and visible wavebands, new manufacturing approaches and tools must be developed if the optical systems will be produced consistently in volume production. This is especially applicable in the field of precision microscope objectives for life science, semiconductor inspection and laser material processing systems. We observe a rising need for the improvement in the optical imaging performance of objective lenses. The key challenge lies in the micron-level decentration and tilt of each lens element. One solution for the production of high quality lens systems is sub-cell assembly with alignment turning. This process relies on an automatic alignment chuck to align the optical axis of a mounted lens to the spindle axis of the machine. Subsequently, the mount is cut with diamond tools on a lathe with respect to the optical axis of the mount. Software controlled integrated measurement technology ensures highest precision. In addition to traditional production processes, further dimensions can be controlled in a very precise manner, e.g. the air gaps between the lenses. Using alignment turning simplifies further alignment steps and reduces the risk of errors. This paper describes new challenges in microscope objective design and manufacturing, and addresses difficulties with standard production processes. A new measurement and alignment technique is described, and strengths and limitations are outlined.

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

PubMed

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

2013-04-19

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

Hadoop-BAM: directly manipulating next generation sequencing data in the cloud.

PubMed

Niemenmaa, Matti; Kallio, Aleksi; Schumacher, André; Klemelä, Petri; Korpelainen, Eija; Heljanko, Keijo

2012-03-15

Hadoop-BAM is a novel library for the scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM files that are processed using Hadoop. Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for implementing map and reduce functions that can directly operate on BAM records. It builds on top of the Picard SAM JDK, so tools that rely on the Picard API are expected to be easily convertible to support large-scale distributed processing. In this article we demonstrate the use of Hadoop-BAM by building a coverage summarizing tool for the Chipster genome browser. Our results show that Hadoop offers good scalability, and one should avoid moving data in and out of Hadoop between analysis steps.

Plexciton Dirac points and topological modes

DOE PAGES

Yuen-Zhou, Joel; Saikin, Semion K.; Zhu, Tony; ...

2016-06-09

Plexcitons are polaritonic modes that result from the strong coupling between excitons and plasmons. Here, we consider plexcitons emerging from the interaction of excitons in an organic molecular layer with surface plasmons in a metallic film. We predict the emergence of Dirac cones in the two-dimensional band-structure of plexcitons due to the inherent alignment of the excitonic transitions in the organic layer. An external magnetic field opens a gap between the Dirac cones if the plexciton system is interfaced with a magneto-optical layer. The resulting energy gap becomes populated with topologically protected one-way modes, which travel at the interface ofmore » this plexcitonic system. Furthermore, our theoretical proposal suggests that plexcitons are a convenient and simple platform for the exploration of exotic phases of matter and for the control of energy flow at the nanoscale.« less

High-density carbon nanotube buckypapers with superior transport and mechanical properties.

PubMed

Zhang, Ling; Zhang, Guang; Liu, Changhong; Fan, Shoushan

2012-09-12

High-density buckypapers were obtained by using well-aligned carbon nanotube arrays. The density of the buckypapers was as high as 1.39 g cm(-3), which is close to the ultimate density of ideal buckypapers. Then we measured the transport and mechanical properties of the buckypapers. Our results demonstrated that its electrical and thermal conductivities could be almost linearly improved by increasing its density. In particular, its superior thermal conductivity is nearly twice that of common metals, which enables it a lightweight and more efficient heat-transfer materials. The Young's modulus of the buckypapers could reach a magnitude over 2 GPa, which is greatly improved compared with previous reported results. In view of this, our work provided a simple and convenient method to prepare high-density buckypapers with excellent transport and mechanical properties.

Entrepreneurship in the academic radiology environment.

PubMed

Itri, Jason N; Ballard, David H; Kantartzis, Stamatis; Sullivan, Joseph C; Weisman, Jeffery A; Durand, Daniel J; Ali, Sayed; Kansagra, Akash P

2015-01-01

Innovation and entrepreneurship in health care can help solve the current health care crisis by creating products and services that improve quality and convenience while reducing costs. To effectively drive innovation and entrepreneurship within the current health care delivery environment, academic institutions will need to provide education, promote networking across disciplines, align incentives, and adapt institutional cultures. This article provides a general review of entrepreneurship and commercialization from the perspective of academic radiology departments, drawing on information sources in several disciplines including radiology, medicine, law, and business. Our review will discuss the role of universities in supporting academic entrepreneurship, identify drivers of entrepreneurship, detail opportunities for academic radiologists, and outline key strategies that foster greater involvement of radiologists in entrepreneurial efforts and encourage leadership to embrace and support entrepreneurship. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

Investigation of RF excited CW CO2 waveguide lasers local oscillator - RF excitation

NASA Technical Reports Server (NTRS)

Hochuli, U.

1988-01-01

A new local oscillator housing was built which seems to have improved laser life. Laser cooling was changed from internal water cooling to the more convenient thermal contact cooling. At the present time, a conclusion can not be made if the 20 percent reduction in power output is the result of poorer cooling or poorer grating alignment. The coupling-starting network was improved from 55 to about 90 percent. It can be adjusted by varying trimmers C sub 1 and C sub 2 to match RF power levels between 10 and 30 W. If the laser admittance changes greatly with laser life rematching will have to be achieved by remote control for space applications. The same holds true if the RF power level has to be changed with a maximum efficiency constraint.

Mounting and Alignment of IXO Mirror Segments

NASA Technical Reports Server (NTRS)

Chan, Kai-Wing; Zhang, William; Evans, Tyler; McClelland, Ryan; Hong, Melinda; Mazzarella, James; Saha, Timo; Jalota, Lalit; Olsen, Lawrence; Byron, Glenn

2010-01-01

A suspension-mounting scheme is developed for the IXO (International X-ray Observatory) mirror segments in which the figure of the mirror segment is preserved in each stage of mounting. The mirror, first fixed on a thermally compatible strongback, is subsequently transported, aligned and transferred onto its mirror housing. In this paper, we shall outline the requirement, approaches, and recent progress of the suspension mount processes.

Pharmacy patronage: identifying key factors in the decision making process using the determinant attribute approach.

PubMed

Franic, Duska M; Haddock, Sarah M; Tucker, Leslie Tootle; Wooten, Nathan

2008-01-01

To use the determinant attribute approach, a research method commonly used in marketing to identify the wants of various consumer groups, to evaluate consumer pharmacy choice when having a prescription order filled in different pharmacy settings. Cross sectional. Community independent, grocery store, community chain, and discount store pharmacies in Georgia between April 2005 and April 2006. Convenience sample of adult pharmacy consumers (n = 175). Survey measuring consumer preferences on 26 attributes encompassing general pharmacy site features (16 items), pharmacist characteristics (5 items), and pharmacy staff characteristics (5 items). 26 potential determinant attributes for pharmacy selection. 175 consumers were surveyed at community independent (n = 81), grocery store (n = 44), community chain (n = 27), or discount store (n = 23) pharmacy settings. The attributes of pharmacists and staff at all four pharmacy settings were shown to affect pharmacy patronage motives, although consumers frequenting non-community independent pharmacies were also motivated by secondary convenience factors, e.g., hours of operation, and prescription coverage. Most consumers do not perceive pharmacies as merely prescription-distribution centers that vary only by convenience. Prescriptions are not just another economic good. Pharmacy personnel influence pharmacy selection; therefore, optimal staff selection and training is likely the greatest asset and most important investment for ensuring pharmacy success.

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

Markov random field based automatic image alignment for electron tomography.

PubMed

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

2008-03-01

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

Strongly aligned gas-phase molecules at free-electron lasers

DOE PAGES

Kierspel, Thomas; Wiese, Joss; Mullins, Terry; ...

2015-09-16

Here, we demonstrate a novel experimental implementation to strongly align molecules at full repetition rates of free-electron lasers. We utilized the available in-house laser system at the coherent x-ray imaging beamline at the linac coherent light source. Chirped laser pulses, i.e., the direct output from the regenerative amplifier of the Ti:Sa chirped pulse amplification laser system, were used to strongly align 2, 5-diiodothiophene molecules in a molecular beam. The alignment laser pulses had pulse energies of a few mJ and a pulse duration of 94 ps. A degree of alignment ofmore » $$\\langle {\\mathrm{cos}}^{2}{\\theta }_{2{\\rm{D}}}\\rangle =0.85$$ was measured, limited by the intrinsic temperature of the molecular beam rather than by the available laser system. With the general availability of synchronized chirped-pulse-amplified near-infrared laser systems at short-wavelength laser facilities, our approach allows for the universal preparation of molecules tightly fixed in space for experiments with x-ray pulses.« less

Transcript mapping for handwritten English documents

NASA Astrophysics Data System (ADS)

Jose, Damien; Bharadwaj, Anurag; Govindaraju, Venu

2008-01-01

Transcript mapping or text alignment with handwritten documents is the automatic alignment of words in a text file with word images in a handwritten document. Such a mapping has several applications in fields ranging from machine learning where large quantities of truth data are required for evaluating handwriting recognition algorithms, to data mining where word image indexes are used in ranked retrieval of scanned documents in a digital library. The alignment also aids "writer identity" verification algorithms. Interfaces which display scanned handwritten documents may use this alignment to highlight manuscript tokens when a person examines the corresponding transcript word. We propose an adaptation of the True DTW dynamic programming algorithm for English handwritten documents. The integration of the dissimilarity scores from a word-model word recognizer and Levenshtein distance between the recognized word and lexicon word, as a cost metric in the DTW algorithm leading to a fast and accurate alignment, is our primary contribution. Results provided, confirm the effectiveness of our approach.

A Lossy Compression Technique Enabling Duplication-Aware Sequence Alignment

PubMed Central

Freschi, Valerio; Bogliolo, Alessandro

2012-01-01

In spite of the recognized importance of tandem duplications in genome evolution, commonly adopted sequence comparison algorithms do not take into account complex mutation events involving more than one residue at the time, since they are not compliant with the underlying assumption of statistical independence of adjacent residues. As a consequence, the presence of tandem repeats in sequences under comparison may impair the biological significance of the resulting alignment. Although solutions have been proposed, repeat-aware sequence alignment is still considered to be an open problem and new efficient and effective methods have been advocated. The present paper describes an alternative lossy compression scheme for genomic sequences which iteratively collapses repeats of increasing length. The resulting approximate representations do not contain tandem duplications, while retaining enough information for making their comparison even more significant than the edit distance between the original sequences. This allows us to exploit traditional alignment algorithms directly on the compressed sequences. Results confirm the validity of the proposed approach for the problem of duplication-aware sequence alignment. PMID:22518086

Tweaked residual convolutional network for face alignment

NASA Astrophysics Data System (ADS)

Du, Wenchao; Li, Ke; Zhao, Qijun; Zhang, Yi; Chen, Hu

2017-08-01

We propose a novel Tweaked Residual Convolutional Network approach for face alignment with two-level convolutional networks architecture. Specifically, the first-level Tweaked Convolutional Network (TCN) module predicts the landmark quickly but accurately enough as a preliminary, by taking low-resolution version of the detected face holistically as the input. The following Residual Convolutional Networks (RCN) module progressively refines the landmark by taking as input the local patch extracted around the predicted landmark, particularly, which allows the Convolutional Neural Network (CNN) to extract local shape-indexed features to fine tune landmark position. Extensive evaluations show that the proposed Tweaked Residual Convolutional Network approach outperforms existing methods.

Telescope Multi-Field Wavefront Control with a Kalman Filter

NASA Technical Reports Server (NTRS)

Lou, John Z.; Redding, David; Sigrist, Norbert; Basinger, Scott

2008-01-01

An effective multi-field wavefront control (WFC) approach is demonstrated for an actuated, segmented space telescope using wavefront measurements at the exit pupil, and the optical and computational implications of this approach are discussed. The integration of a Kalman Filter as an optical state estimator into the wavefront control process to further improve the robustness of the optical alignment of the telescope will also be discussed. Through a comparison of WFC performances between on-orbit and ground-test optical system configurations, the connection (and a possible disconnection) between WFC and optical system alignment under these circumstances are analyzed. Our MACOS-based computer simulation results will be presented and discussed.

Hidden Markov models of biological primary sequence information.

PubMed Central

Baldi, P; Chauvin, Y; Hunkapiller, T; McClure, M A

1994-01-01

Hidden Markov model (HMM) techniques are used to model families of biological sequences. A smooth and convergent algorithm is introduced to iteratively adapt the transition and emission parameters of the models from the examples in a given family. The HMM approach is applied to three protein families: globins, immunoglobulins, and kinases. In all cases, the models derived capture the important statistical characteristics of the family and can be used for a number of tasks, including multiple alignments, motif detection, and classification. For K sequences of average length N, this approach yields an effective multiple-alignment algorithm which requires O(KN2) operations, linear in the number of sequences. PMID:8302831

The component alignment model: a new approach to health care information technology strategic planning.

PubMed

Martin, J B; Wilkins, A S; Stawski, S K

1998-08-01

The evolving health care environment demands that health care organizations fully utilize information technologies (ITs). The effective deployment of IT requires the development and implementation of a comprehensive IT strategic plan. A number of approaches to health care IT strategic planning exist, but they are outdated or incomplete. The component alignment model (CAM) introduced here recognizes the complexity of today's health care environment, emphasizing continuous assessment and realignment of seven basic components: external environment, emerging ITs, organizational infrastructure, mission, IT infrastructure, business strategy, and IT strategy. The article provides a framework by which health care organizations can develop an effective IT strategic planning process.

First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces.

PubMed

Kharche, Neerav; Muckerman, James T; Hybertsen, Mark S

2014-10-24

A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The  GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b1 energy level in water. The application to the specific cases of nonpolar (101¯0) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. These effects contribute up to 0.5 eV.

Representativeness of two sampling procedures for an internet intervention targeting cancer-related distress: a comparison of convenience and registry samples.

PubMed

Owen, Jason E; Bantum, Erin O'Carroll; Criswell, Kevin; Bazzo, Julie; Gorlick, Amanda; Stanton, Annette L

2014-08-01

Internet interventions often rely on convenience sampling, yet convenience samples may differ in important ways from systematic recruitment approaches. The purpose of this study was to evaluate potential demographic, medical, and psychosocial differences between Internet-recruited and registry-recruited cancer survivors in an Internet-based intervention. Participants were recruited from a cancer registry (n = 80) and via broad Internet outreach efforts (n = 160). Participants completed a set of self-report questionnaires, and both samples were compared to a population-based sample of cancer survivors (n = 5,150). The Internet sample was younger, better educated, more likely to be female, had longer time since diagnosis, and had more advanced stage of disease (p's < .001), and the registry-sample was over-represented by men and those with prostate or other cancer types (p's < .001). The Internet sample also exhibited lower quality of life and social support and greater mood disturbance (p's < .001). Understanding how convenience and systematic samples differ has important implications for external validity and potential for dissemination of Internet-based interventions.

Understanding factors that influence the integration of acute malnutrition interventions into the national health system in Niger.

PubMed

Deconinck, Hedwig; Hallarou, Mahaman Elh; Pesonen, Anais; Gérard, Jean Christophe; Criel, Bart; Donnen, Philippe; Macq, Jean

2016-12-01

Since 2007 to address a high burden, integration of acute malnutrition has been promoted in Niger. This paper studies factors that influenced the integration process of acute malnutrition into the Niger national health system.We used qualitative methods of observation, key informant interviews and focus group discussions at national level, two districts and nine communities selected through convenience sampling, as well as document review. A framework approach constructed around the problem, intervention, adoption system, health system characteristics and broad context guided the analysis. Data were recorded on paper, transcribed in a descriptive record, coded by themes deduced by building on the framework and triangulated for comprehensiveness.Key facilitating factors identified were knowledge and recognition of the problem helped by accurate information; effectiveness of decentralized continuity of care; compatibility with goals, support and involvement of health actors; and leadership for aligning policies and partnerships and mobilizing resources within a favourable political context driven by multisectoral development goals. Key hindering factors identified were not fully understanding severity, causes and consequences of the problem; limited utilization and trust in health interventions; high workload, and health worker turnover and attrition; and high dependence on financial and technical support based on short-term emergency funding within a context of high demographic pressure.The study uncovered influencing factors of integrating acute malnutrition into the national health system and their complex dynamics and relationships. It elicited the need for goal-oriented strategies and alignment of health actors to achieve sustainability, and systems thinking to understand pathways that foster integration. We recommend that context-specific learning of integrating acute malnutrition may expand to include causal modelling and scenario testing to inform strategy designs. The method may also be applied to monitor progress of integrating nutrition by the multisectoral nutrition plan to guide change. © The Author 2016. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evolutionary distances in the twilight zone--a rational kernel approach.

PubMed

Schwarz, Roland F; Fletcher, William; Förster, Frank; Merget, Benjamin; Wolf, Matthias; Schultz, Jörg; Markowetz, Florian

2010-12-31

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes use of indel information and known substitution models without the need for a multiple alignment. Here we propose a new evolutionary distance metric to close this gap. It uses finite-state transducers to create a biologically motivated similarity score which models substitutions and indels, and does not depend on a multiple sequence alignment. The sequence similarity score is defined in analogy to pairwise alignments and additionally has the positive semi-definite property. We describe its derivation and show in simulation studies and real-world examples that it is more accurate in reconstructing phylogenies than competing methods. The result is a new and accurate way of determining evolutionary distances in and beyond the twilight zone of sequence alignments that is suitable for large datasets.

On decomposing stimulus and response waveforms in event-related potentials recordings.

PubMed

Yin, Gang; Zhang, Jun

2011-06-01

Event-related potentials (ERPs) reflect the brain activities related to specific behavioral events, and are obtained by averaging across many trial repetitions with individual trials aligned to the onset of a specific event, e.g., the onset of stimulus (s-aligned) or the onset of the behavioral response (r-aligned). However, the s-aligned and r-aligned ERP waveforms do not purely reflect, respectively, underlying stimulus (S-) or response (R-) component waveform, due to their cross-contaminations in the recorded ERP waveforms. Zhang [J. Neurosci. Methods, 80, pp. 49-63, 1998] proposed an algorithm to recover the pure S-component waveform and the pure R-component waveform from the s-aligned and r-aligned ERP average waveforms-however, due to the nature of this inverse problem, a direct solution is sensitive to noise that disproportionally affects low-frequency components, hindering the practical implementation of this algorithm. Here, we apply the Wiener deconvolution technique to deal with noise in input data, and investigate a Tikhonov regularization approach to obtain a stable solution that is robust against variances in the sampling of reaction-time distribution (when number of trials is low). Our method is demonstrated using data from a Go/NoGo experiment about image classification and recognition.

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

NASA Technical Reports Server (NTRS)

Decker, Arthur J.; Krasowski, Michael J.; Weiland, Kenneth E.

1993-01-01

This report describes an effort at NASA Lewis Research Center to use artificial neural networks to automate the alignment and control of optical measurement systems. Specifically, it addresses the use of commercially available neural network software and hardware to direct alignments of the common laser-beam-smoothing spatial filter. The report presents a general approach for designing alignment records and combining these into training sets to teach optical alignment functions to neural networks and discusses the use of these training sets to train several types of neural networks. Neural network configurations used include the adaptive resonance network, the back-propagation-trained network, and the counter-propagation network. This work shows that neural networks can be used to produce robust sequencers. These sequencers can learn by example to execute the step-by-step procedures of optical alignment and also can learn adaptively to correct for environmentally induced misalignment. The long-range objective is to use neural networks to automate the alignment and operation of optical measurement systems in remote, harsh, or dangerous aerospace environments. This work also shows that when neural networks are trained by a human operator, training sets should be recorded, training should be executed, and testing should be done in a manner that does not depend on intellectual judgments of the human operator.

Self-Aligned van der Waals Heterojunction Diodes and Transistors.

PubMed

Sangwan, Vinod K; Beck, Megan E; Henning, Alex; Luo, Jiajia; Bergeron, Hadallia; Kang, Junmo; Balla, Itamar; Inbar, Hadass; Lauhon, Lincoln J; Hersam, Mark C

2018-02-14

A general self-aligned fabrication scheme is reported here for a diverse class of electronic devices based on van der Waals materials and heterojunctions. In particular, self-alignment enables the fabrication of source-gated transistors in monolayer MoS 2 with near-ideal current saturation characteristics and channel lengths down to 135 nm. Furthermore, self-alignment of van der Waals p-n heterojunction diodes achieves complete electrostatic control of both the p-type and n-type constituent semiconductors in a dual-gated geometry, resulting in gate-tunable mean and variance of antiambipolar Gaussian characteristics. Through finite-element device simulations, the operating principles of source-gated transistors and dual-gated antiambipolar devices are elucidated, thus providing design rules for additional devices that employ self-aligned geometries. For example, the versatility of this scheme is demonstrated via contact-doped MoS 2 homojunction diodes and mixed-dimensional heterojunctions based on organic semiconductors. The scalability of this approach is also shown by fabricating self-aligned short-channel transistors with subdiffraction channel lengths in the range of 150-800 nm using photolithography on large-area MoS 2 films grown by chemical vapor deposition. Overall, this self-aligned fabrication method represents an important step toward the scalable integration of van der Waals heterojunction devices into more sophisticated circuits and systems.

The energy level alignment at metal–molecule interfaces using Wannier–Koopmans method

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

Ma, Jie; Wang, Lin-Wang, E-mail: lwwang@lbl.gov; Liu, Zhen-Fei

2016-06-27

We apply a recently developed Wannier–Koopmans method (WKM), based on density functional theory (DFT), to calculate the electronic energy level alignment at an interface between a molecule and metal substrate. We consider two systems: benzenediamine on Au (111), and a bipyridine-Au molecular junction. The WKM calculated level alignment agrees well with the experimental measurements where available, as well as previous GW and DFT + Σ results. Our results suggest that the WKM is a general approach that can be used to correct DFT eigenvalue errors, not only in bulk semiconductors and isolated molecules, but also in hybrid interfaces.

Pairwise alignment of chromatograms using an extended Fisher-Rao metric.

PubMed

Wallace, W E; Srivastava, A; Telu, K H; Simón-Manso, Y

2014-09-02

A conceptually new approach for aligning chromatograms is introduced and applied to examples of metabolite identification in human blood plasma by liquid chromatography-mass spectrometry (LC-MS). A square-root representation of the chromatogram's derivative coupled with an extended Fisher-Rao metric enables the computation of relative differences between chromatograms. Minimization of these differences using a common dynamic programming algorithm brings the chromatograms into alignment. Application to a complex sample, National Institute of Standards and Technology (NIST) Standard Reference Material 1950, Metabolites in Human Plasma, analyzed by two different LC-MS methods having significantly different ranges of elution time is described. Published by Elsevier B.V.

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

NASA Astrophysics Data System (ADS)

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

2016-10-01

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

Ferroelectric switching of band alignments in LSMO/PZT/Co multiferroic tunnel junctions: an ab initio study.

PubMed

Imam, M; Stojić, N; Binggeli, N

2017-08-04

Band alignments in ferroelectric tunnel junctions (FTJs) are expected to play a critical role in determining the charge transport across the tunneling barrier. In general, however, the interface band discontinuities and their polarization dependence are not well known in these systems. Using a first-principles density-functional-theory approach, we explore the ferroelectric (FE) polarization dependence of the band alignments in [Formula: see text] (LSMO/PZT/Co) multiferroic tunnel junctions, for which recent experiments indicated an ON/OFF conductivity behavior upon switching the PZT FE polarization. Our results on the pseudomorphic defect-free LSMO/PZT/Co FTJs evidence a major FE switching effect on the band discontinuities at both interfaces. Based on the changes in the band alignments, we provide a possible explanation for the observed trends in the resistive switching.

Boresight alignment method for mobile laser scanning systems

NASA Astrophysics Data System (ADS)

Rieger, P.; Studnicka, N.; Pfennigbauer, M.; Zach, G.

2010-06-01

Mobile laser scanning (MLS) is the latest approach towards fast and cost-efficient acquisition of 3-dimensional spatial data. Accurately evaluating the boresight alignment in MLS systems is an obvious necessity. However, recent systems available on the market may lack of suitable and efficient practical workflows on how to perform this calibration. This paper discusses an innovative method for accurately determining the boresight alignment of MLS systems by employing 3D laser scanners. Scanning objects using a 3D laser scanner operating in a 2D line-scan mode from various different runs and scan directions provides valuable scan data for determining the angular alignment between inertial measurement unit and laser scanner. Field data is presented demonstrating the final accuracy of the calibration and the high quality of the point cloud acquired during an MLS campaign.

A novel surface registration algorithm with biomedical modeling applications.

PubMed

Huang, Heng; Shen, Li; Zhang, Rong; Makedon, Fillia; Saykin, Andrew; Pearlman, Justin

2007-07-01

In this paper, we propose a novel surface matching algorithm for arbitrarily shaped but simply connected 3-D objects. The spherical harmonic (SPHARM) method is used to describe these 3-D objects, and a novel surface registration approach is presented. The proposed technique is applied to various applications of medical image analysis. The results are compared with those using the traditional method, in which the first-order ellipsoid is used for establishing surface correspondence and aligning objects. In these applications, our surface alignment method is demonstrated to be more accurate and flexible than the traditional approach. This is due in large part to the fact that a new surface parameterization is generated by a shortcut that employs a useful rotational property of spherical harmonic basis functions for a fast implementation. In order to achieve a suitable computational speed for practical applications, we propose a fast alignment algorithm that improves computational complexity of the new surface registration method from O(n3) to O(n2).

Initial Navigation Alignment of Optical Instruments on GOES-R

NASA Technical Reports Server (NTRS)

Isaacson, Peter J.; DeLuccia, Frank J.; Reth, Alan D.; Igli, David A.; Carter, Delano R.

2016-01-01

Post-launch alignment errors for the Advanced Baseline Imager (ABI) and Geospatial Lightning Mapper (GLM) on GOES-R may be too large for the image navigation and registration (INR) processing algorithms to function without an initial adjustment to calibration parameters. We present an approach that leverages a combination of user-selected image-to-image tie points and image correlation algorithms to estimate this initial launch-induced offset and calculate adjustments to the Line of Sight Motion Compensation (LMC) parameters. We also present an approach to generate synthetic test images, to which shifts and rotations of known magnitude are applied. Results of applying the initial alignment tools to a subset of these synthetic test images are presented. The results for both ABI and GLM are within the specifications established for these tools, and indicate that application of these tools during the post-launch test (PLT) phase of GOES-R operations will enable the automated INR algorithms for both instruments to function as intended.

Registration of 3D fetal neurosonography and MRI☆

PubMed Central

Kuklisova-Murgasova, Maria; Cifor, Amalia; Napolitano, Raffaele; Papageorghiou, Aris; Quaghebeur, Gerardine; Rutherford, Mary A.; Hajnal, Joseph V.; Noble, J. Alison; Schnabel, Julia A.

2013-01-01

We propose a method for registration of 3D fetal brain ultrasound with a reconstructed magnetic resonance fetal brain volume. This method, for the first time, allows the alignment of models of the fetal brain built from magnetic resonance images with 3D fetal brain ultrasound, opening possibilities to develop new, prior information based image analysis methods for 3D fetal neurosonography. The reconstructed magnetic resonance volume is first segmented using a probabilistic atlas and a pseudo ultrasound image volume is simulated from the segmentation. This pseudo ultrasound image is then affinely aligned with clinical ultrasound fetal brain volumes using a robust block-matching approach that can deal with intensity artefacts and missing features in the ultrasound images. A qualitative and quantitative evaluation demonstrates good performance of the method for our application, in comparison with other tested approaches. The intensity average of 27 ultrasound images co-aligned with the pseudo ultrasound template shows good correlation with anatomy of the fetal brain as seen in the reconstructed magnetic resonance image. PMID:23969169

Aligning vocabulary for interoperability of ISR assets using authoritative sources

NASA Astrophysics Data System (ADS)

Hookway, Steve; Patten, Terry; Gorman, Joe

2017-05-01

The growing arsenal of network-centric sensor platforms shows great potential to enhance situational awareness capabilities. Non-traditional sensors collect a diverse range of data that can provide a more accurate and comprehensive common operational picture when combined with conventional intelligence, surveillance, and reconnaissance (ISR) products. One of the integration challenges is mediating differences in terminology that different data providers use to describe the data they have extracted. A data consumer should be able to reference information using the vocabulary that they are familiar with and rely on the framework to handle the mediation; for example, it should be up to the framework to identify that two different terms are synonyms for the same concept. In this paper we present an approach for automatically performing this alignment using authoritative sources such as Wikipedia (a stand-in for the Intellipedia wiki), and present experimental results that demonstrate that this approach is able to align a large number of concepts between different terminologies.

Towards automation of user interface design

NASA Technical Reports Server (NTRS)

Gastner, Rainer; Kraetzschmar, Gerhard K.; Lutz, Ernst

1992-01-01

This paper suggests an approach to automatic software design in the domain of graphical user interfaces. There are still some drawbacks in existing user interface management systems (UIMS's) which basically offer only quantitative layout specifications via direct manipulation. Our approach suggests a convenient way to get a default graphical user interface which may be customized and redesigned easily in further prototyping cycles.

Metabarcoding of marine nematodes – evaluation of reference datasets used in tree-based taxonomy assignment approach

PubMed Central

2016-01-01

Abstract Background Metabarcoding is becoming a common tool used to assess and compare diversity of organisms in environmental samples. Identification of OTUs is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task. This publication evaluates the quality of reference datasets, alongside with several alignment and phylogeny inference methods used in one of the taxonomy assignment methods, called tree-based approach. This approach assigns anonymous OTUs to taxonomic categories based on relative placements of OTUs and reference sequences on the cladogram and support that these placements receive. New information In tree-based taxonomy assignment approach, reliable identification of anonymous OTUs is based on their placement in monophyletic and highly supported clades together with identified reference taxa. Therefore, it requires high quality reference dataset to be used. Resolution of phylogenetic trees is strongly affected by the presence of erroneous sequences as well as alignment and phylogeny inference methods used in the process. Two preparation steps are essential for the successful application of tree-based taxonomy assignment approach. Curated collections of genetic information do include erroneous sequences. These sequences have detrimental effect on the resolution of cladograms used in tree-based approach. They must be identified and excluded from the reference dataset beforehand. Various combinations of multiple sequence alignment and phylogeny inference methods provide cladograms with different topology and bootstrap support. These combinations of methods need to be tested in order to determine the one that gives highest resolution for the particular reference dataset. Completing the above mentioned preparation steps is expected to decrease the number of unassigned OTUs and thus improve the results of the tree-based taxonomy assignment approach. PMID:27932919

Metabarcoding of marine nematodes - evaluation of reference datasets used in tree-based taxonomy assignment approach.

PubMed

Holovachov, Oleksandr

2016-01-01

Metabarcoding is becoming a common tool used to assess and compare diversity of organisms in environmental samples. Identification of OTUs is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task. This publication evaluates the quality of reference datasets, alongside with several alignment and phylogeny inference methods used in one of the taxonomy assignment methods, called tree-based approach. This approach assigns anonymous OTUs to taxonomic categories based on relative placements of OTUs and reference sequences on the cladogram and support that these placements receive. In tree-based taxonomy assignment approach, reliable identification of anonymous OTUs is based on their placement in monophyletic and highly supported clades together with identified reference taxa. Therefore, it requires high quality reference dataset to be used. Resolution of phylogenetic trees is strongly affected by the presence of erroneous sequences as well as alignment and phylogeny inference methods used in the process. Two preparation steps are essential for the successful application of tree-based taxonomy assignment approach. Curated collections of genetic information do include erroneous sequences. These sequences have detrimental effect on the resolution of cladograms used in tree-based approach. They must be identified and excluded from the reference dataset beforehand.Various combinations of multiple sequence alignment and phylogeny inference methods provide cladograms with different topology and bootstrap support. These combinations of methods need to be tested in order to determine the one that gives highest resolution for the particular reference dataset.Completing the above mentioned preparation steps is expected to decrease the number of unassigned OTUs and thus improve the results of the tree-based taxonomy assignment approach.

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice[C][W][OA

PubMed Central

Ficklin, Stephen P.; Feltus, F. Alex

2011-01-01

One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species. PMID:21606319

Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice.

PubMed

Ficklin, Stephen P; Feltus, F Alex

2011-07-01

One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species.

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis.

PubMed

Bonham-Carter, Oliver; Steele, Joe; Bastola, Dhundy

2014-11-01

Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base-base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel-Ziv techniques from data compression. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Efficient visual grasping alignment for cylinders

NASA Technical Reports Server (NTRS)

Nicewarner, Keith E.; Kelley, Robert B.

1992-01-01

Monocular information from a gripper-mounted camera is used to servo the robot gripper to grasp a cylinder. The fundamental concept for rapid pose estimation is to reduce the amount of information that needs to be processed during each vision update interval. The grasping procedure is divided into four phases: learn, recognition, alignment, and approach. In the learn phase, a cylinder is placed in the gripper and the pose estimate is stored and later used as the servo target. This is performed once as a calibration step. The recognition phase verifies the presence of a cylinder in the camera field of view. An initial pose estimate is computed and uncluttered scan regions are selected. The radius of the cylinder is estimated by moving the robot a fixed distance toward the cylinder and observing the change in the image. The alignment phase processes only the scan regions obtained previously. Rapid pose estimates are used to align the robot with the cylinder at a fixed distance from it. The relative motion of the cylinder is used to generate an extrapolated pose-based trajectory for the robot controller. The approach phase guides the robot gripper to a grasping position. The cylinder can be grasped with a minimal reaction force and torque when only rough global pose information is initially available.

Efficient visual grasping alignment for cylinders

NASA Technical Reports Server (NTRS)

Nicewarner, Keith E.; Kelley, Robert B.

1991-01-01

Monocular information from a gripper-mounted camera is used to servo the robot gripper to grasp a cylinder. The fundamental concept for rapid pose estimation is to reduce the amount of information that needs to be processed during each vision update interval. The grasping procedure is divided into four phases: learn, recognition, alignment, and approach. In the learn phase, a cylinder is placed in the gripper and the pose estimate is stored and later used as the servo target. This is performed once as a calibration step. The recognition phase verifies the presence of a cylinder in the camera field of view. An initial pose estimate is computed and uncluttered scan regions are selected. The radius of the cylinder is estimated by moving the robot a fixed distance toward the cylinder and observing the change in the image. The alignment phase processes only the scan regions obtained previously. Rapid pose estimates are used to align the robot with the cylinder at a fixed distance from it. The relative motion of the cylinder is used to generate an extrapolated pose-based trajectory for the robot controller. The approach phase guides the robot gripper to a grasping position. The cylinder can be grasped with a minimal reaction force and torque when only rough global pose information is initially available.

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification.

PubMed

Beirnaert, Charlie; Meysman, Pieter; Vu, Trung Nghia; Hermans, Nina; Apers, Sandra; Pieters, Luc; Covaci, Adrian; Laukens, Kris

2018-03-01

Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. Meanwhile its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction. The tool offers a fast and easy workflow that starts with the common approach of peak-picking, followed by grouping, thus avoiding the binning step. This yields a matrix consisting of features, samples and peak values that can be conveniently processed either by using included multivariate statistical functions or by using many other recently developed methods for NMR data analysis. speaq 2.0 facilitates robust and high-throughput metabolomics based on 1D NMR but is also compatible with other NMR frameworks or complementary LC-MS workflows. The methods are benchmarked using a simulated dataset and two publicly available datasets. speaq 2.0 is distributed through the existing speaq R package to provide a complete solution for NMR data processing. The package and the code for the presented case studies are freely available on CRAN (https://cran.r-project.org/package=speaq) and GitHub (https://github.com/beirnaert/speaq).

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification

PubMed Central

Pieters, Luc; Covaci, Adrian

2018-01-01

Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. Meanwhile its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction. The tool offers a fast and easy workflow that starts with the common approach of peak-picking, followed by grouping, thus avoiding the binning step. This yields a matrix consisting of features, samples and peak values that can be conveniently processed either by using included multivariate statistical functions or by using many other recently developed methods for NMR data analysis. speaq 2.0 facilitates robust and high-throughput metabolomics based on 1D NMR but is also compatible with other NMR frameworks or complementary LC-MS workflows. The methods are benchmarked using a simulated dataset and two publicly available datasets. speaq 2.0 is distributed through the existing speaq R package to provide a complete solution for NMR data processing. The package and the code for the presented case studies are freely available on CRAN (https://cran.r-project.org/package=speaq) and GitHub (https://github.com/beirnaert/speaq). PMID:29494588

A Toolkit for ARB to Integrate Custom Databases and Externally Built Phylogenies

DOE PAGES

Essinger, Steven D.; Reichenberger, Erin; Morrison, Calvin; ...

2015-01-21

Researchers are perpetually amassing biological sequence data. The computational approaches employed by ecologists for organizing this data (e.g. alignment, phylogeny, etc.) typically scale nonlinearly in execution time with the size of the dataset. This often serves as a bottleneck for processing experimental data since many molecular studies are characterized by massive datasets. To keep up with experimental data demands, ecologists are forced to choose between continually upgrading expensive in-house computer hardware or outsourcing the most demanding computations to the cloud. Outsourcing is attractive since it is the least expensive option, but does not necessarily allow direct user interaction with themore » data for exploratory analysis. Desktop analytical tools such as ARB are indispensable for this purpose, but they do not necessarily offer a convenient solution for the coordination and integration of datasets between local and outsourced destinations. Therefore, researchers are currently left with an undesirable tradeoff between computational throughput and analytical capability. To mitigate this tradeoff we introduce a software package to leverage the utility of the interactive exploratory tools offered by ARB with the computational throughput of cloud-based resources. Our pipeline serves as middleware between the desktop and the cloud allowing researchers to form local custom databases containing sequences and metadata from multiple resources and a method for linking data outsourced for computation back to the local database. Furthermore, a tutorial implementation of the toolkit is provided in the supporting information, S1 Tutorial.« less

Impaired limb position sense after stroke: a quantitative test for clinical use.

PubMed

Carey, L M; Oke, L E; Matyas, T A

1996-12-01

A quantitative measure of wrist position sense was developed to advance clinical measurement of proprioceptive limb sensibility after stroke. Test-retest reliability, normative standards, and ability to discriminate impaired and unimpaired performance were investigated. Retest reliability was assessed over three sessions, and a matched-pairs study compared stroke and unimpaired subjects. Both wrists were tested, in counterbalanced order. Patients were tested in hospital-based rehabilitation units. Reliability was investigated on a consecutive sample of 35 adult stroke patients with a range of proprioceptive discrimination abilities and no evidence of neglect. A consecutive sample of 50 stroke patients and convenience sample of 50 healthy volunteers, matched for age, sex, and hand dominance, were tested in the normative-discriminative study. Age and sex were representative of the adult stroke population. The test required matching of imposed wrist positions using a pointer aligned with the axis of movement and a protractor scale. The test was reliable (r = .88 and .92) and observed changes of 8 degrees can be interpreted, with 95% confidence, as genuine. Scores of healthy volunteers ranged from 3.1 degrees to 10.9 degrees average error. The criterion of impairment was conservatively defined as 11 degrees (+/-4.8 degrees) average error. Impaired and unimpaired performance were well differentiated. Clinicians can confidently and quantitatively sample one aspect of proprioceptive sensibility in stroke patients using the wrist position sense test. Development of tests on other joints using the present approach is supported by our findings.

A Toolkit for ARB to Integrate Custom Databases and Externally Built Phylogenies

PubMed Central

Essinger, Steven D.; Reichenberger, Erin; Morrison, Calvin; Blackwood, Christopher B.; Rosen, Gail L.

2015-01-01

Researchers are perpetually amassing biological sequence data. The computational approaches employed by ecologists for organizing this data (e.g. alignment, phylogeny, etc.) typically scale nonlinearly in execution time with the size of the dataset. This often serves as a bottleneck for processing experimental data since many molecular studies are characterized by massive datasets. To keep up with experimental data demands, ecologists are forced to choose between continually upgrading expensive in-house computer hardware or outsourcing the most demanding computations to the cloud. Outsourcing is attractive since it is the least expensive option, but does not necessarily allow direct user interaction with the data for exploratory analysis. Desktop analytical tools such as ARB are indispensable for this purpose, but they do not necessarily offer a convenient solution for the coordination and integration of datasets between local and outsourced destinations. Therefore, researchers are currently left with an undesirable tradeoff between computational throughput and analytical capability. To mitigate this tradeoff we introduce a software package to leverage the utility of the interactive exploratory tools offered by ARB with the computational throughput of cloud-based resources. Our pipeline serves as middleware between the desktop and the cloud allowing researchers to form local custom databases containing sequences and metadata from multiple resources and a method for linking data outsourced for computation back to the local database. A tutorial implementation of the toolkit is provided in the supporting information, S1 Tutorial. Availability: http://www.ece.drexel.edu/gailr/EESI/tutorial.php. PMID:25607539

Multiview echocardiography fusion using an electromagnetic tracking system.

PubMed

Punithakumar, Kumaradevan; Hareendranathan, Abhilash R; Paakkanen, Riitta; Khan, Nehan; Noga, Michelle; Boulanger, Pierre; Becher, Harald

2016-08-01

Three-dimensional ultrasound is an emerging modality for the assessment of complex cardiac anatomy and function. The advantages of this modality include lack of ionizing radiation, portability, low cost, and high temporal resolution. Major limitations include limited field-of-view, reliance on frequently limited acoustic windows, and poor signal to noise ratio. This study proposes a novel approach to combine multiple views into a single image using an electromagnetic tracking system in order to improve the field-of-view. The novel method has several advantages: 1) it does not rely on image information for alignment, and therefore, the method does not require image overlap; 2) the alignment accuracy of the proposed approach is not affected by any poor image quality as in the case of image registration based approaches; 3) in contrast to previous optical tracking based system, the proposed approach does not suffer from line-of-sight limitation; and 4) it does not require any initial calibration. In this pilot project, we were able to show that using a heart phantom, our method can fuse multiple echocardiographic images and improve the field-of view. Quantitative evaluations showed that the proposed method yielded a nearly optimal alignment of image data sets in three-dimensional space. The proposed method demonstrates the electromagnetic system can be used for the fusion of multiple echocardiography images with a seamless integration of sensors to the transducer.

MC64-ClustalWP2: A Highly-Parallel Hybrid Strategy to Align Multiple Sequences in Many-Core Architectures

PubMed Central

Díaz, David; Esteban, Francisco J.; Hernández, Pilar; Caballero, Juan Antonio; Guevara, Antonio

2014-01-01

We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance to reveal key points to exploit and optimize the full potential of parallelism in many-core CPU systems. The new parallelization approach has focused into the most time-consuming stages of this algorithm. In particular, the so-called progressive alignment has drastically improved the performance, due to a fine-grained approach where the forward and backward loops were unrolled and parallelized. Another key approach has been the implementation of the new algorithm in a hybrid-computing system, integrating both an Intel Xeon multi-core CPU and a Tilera Tile64 many-core card. A comparison with other Clustal W implementations reveals the high-performance of the new algorithm and strategy in many-core CPU architectures, in a scenario where the sequences to align are relatively long (more than 10 kb) and, hence, a many-core GPU hardware cannot be used. Thus, the MC64-ClustalWP2 runs multiple alignments more than 18x than the original Clustal W algorithm, and more than 7x than the best x86 parallel implementation to date, being publicly available through a web service. Besides, these developments have been deployed in cost-effective personal computers and should be useful for life-science researchers, including the identification of identities and differences for mutation/polymorphism analyses, biodiversity and evolutionary studies and for the development of molecular markers for paternity testing, germplasm management and protection, to assist breeding, illegal traffic control, fraud prevention and for the protection of the intellectual property (identification/traceability), including the protected designation of origin, among other applications. PMID:24710354

Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment

PubMed Central

Kam, Alfred; Kwak, Daniel; Leung, Clarence; Wu, Chu; Zarour, Eleyine; Sarmenta, Luis; Blanchette, Mathieu; Waldispühl, Jérôme

2012-01-01

Background Comparative genomics, or the study of the relationships of genome structure and function across different species, offers a powerful tool for studying evolution, annotating genomes, and understanding the causes of various genetic disorders. However, aligning multiple sequences of DNA, an essential intermediate step for most types of analyses, is a difficult computational task. In parallel, citizen science, an approach that takes advantage of the fact that the human brain is exquisitely tuned to solving specific types of problems, is becoming increasingly popular. There, instances of hard computational problems are dispatched to a crowd of non-expert human game players and solutions are sent back to a central server. Methodology/Principal Findings We introduce Phylo, a human-based computing framework applying “crowd sourcing” techniques to solve the Multiple Sequence Alignment (MSA) problem. The key idea of Phylo is to convert the MSA problem into a casual game that can be played by ordinary web users with a minimal prior knowledge of the biological context. We applied this strategy to improve the alignment of the promoters of disease-related genes from up to 44 vertebrate species. Since the launch in November 2010, we received more than 350,000 solutions submitted from more than 12,000 registered users. Our results show that solutions submitted contributed to improving the accuracy of up to 70% of the alignment blocks considered. Conclusions/Significance We demonstrate that, combined with classical algorithms, crowd computing techniques can be successfully used to help improving the accuracy of MSA. More importantly, we show that an NP-hard computational problem can be embedded in casual game that can be easily played by people without significant scientific training. This suggests that citizen science approaches can be used to exploit the billions of “human-brain peta-flops” of computation that are spent every day playing games. Phylo is available at: http://phylo.cs.mcgill.ca. PMID:22412834

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.

Reliability of lower limb alignment measures using an established landmark-based method with a customized computer software program

PubMed Central

Sled, Elizabeth A.; Sheehy, Lisa M.; Felson, David T.; Costigan, Patrick A.; Lam, Miu; Cooke, T. Derek V.

2010-01-01

The objective of the study was to evaluate the reliability of frontal plane lower limb alignment measures using a landmark-based method by (1) comparing inter- and intra-reader reliability between measurements of alignment obtained manually with those using a computer program, and (2) determining inter- and intra-reader reliability of computer-assisted alignment measures from full-limb radiographs. An established method for measuring alignment was used, involving selection of 10 femoral and tibial bone landmarks. 1) To compare manual and computer methods, we used digital images and matching paper copies of five alignment patterns simulating healthy and malaligned limbs drawn using AutoCAD. Seven readers were trained in each system. Paper copies were measured manually and repeat measurements were performed daily for 3 days, followed by a similar routine with the digital images using the computer. 2) To examine the reliability of computer-assisted measures from full-limb radiographs, 100 images (200 limbs) were selected as a random sample from 1,500 full-limb digital radiographs which were part of the Multicenter Osteoarthritis (MOST) Study. Three trained readers used the software program to measure alignment twice from the batch of 100 images, with two or more weeks between batch handling. Manual and computer measures of alignment showed excellent agreement (intraclass correlations [ICCs] 0.977 – 0.999 for computer analysis; 0.820 – 0.995 for manual measures). The computer program applied to full-limb radiographs produced alignment measurements with high inter- and intra-reader reliability (ICCs 0.839 – 0.998). In conclusion, alignment measures using a bone landmark-based approach and a computer program were highly reliable between multiple readers. PMID:19882339

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.

Fast and accurate reference-free alignment of subtomograms.

PubMed

Chen, Yuxiang; Pfeffer, Stefan; Hrabe, Thomas; Schuller, Jan Michael; Förster, Friedrich

2013-06-01

In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20Å and 16Å, respectively. The software is ready-to-use and made public to the community. Copyright © 2013 Elsevier Inc. All rights reserved.

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

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

Taylor, R.C.

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

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

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

Taylor, Ronald C.

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

Robust through-the-wall radar image classification using a target-model alignment procedure.

PubMed

Smith, Graeme E; Mobasseri, Bijan G

2012-02-01

A through-the-wall radar image (TWRI) bears little resemblance to the equivalent optical image, making it difficult to interpret. To maximize the intelligence that may be obtained, it is desirable to automate the classification of targets in the image to support human operators. This paper presents a technique for classifying stationary targets based on the high-range resolution profile (HRRP) extracted from 3-D TWRIs. The dependence of the image on the target location is discussed using a system point spread function (PSF) approach. It is shown that the position dependence will cause a classifier to fail, unless the image to be classified is aligned to a classifier-training location. A target image alignment technique based on deconvolution of the image with the system PSF is proposed. Comparison of the aligned target images with measured images shows the alignment process introducing normalized mean squared error (NMSE) ≤ 9%. The HRRP extracted from aligned target images are classified using a naive Bayesian classifier supported by principal component analysis. The classifier is tested using a real TWRI of canonical targets behind a concrete wall and shown to obtain correct classification rates ≥ 97%. © 2011 IEEE

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

PubMed

Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin

2017-09-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

Composite Nature of Layered Hybrid Perovskites: Assessment on Quantum and Dielectric Confinements and Band Alignment

DOE PAGES

Traore, Boubacar; Pedesseau, Laurent; Assam, Linda; ...

2018-02-26

Layered hybrid organic–inorganic perovskites (HOPs) have re-emerged as potential technological solutions for next-generation photovoltaic and optoelectronic applications. Their two-dimensional (2D) nature confers them a significant flexibility and results in the appearance of quantum and dielectric confinements. Such confinements are at the origin of their fascinating properties, and understanding them from a fundamental level is of paramount importance for optimization. Here, we provide an in-depth investigation of band alignments of 2D HOP allowing access to carriers’ confinement potentials. 2D HOPs are conceptualized as composite materials in which pseudoinorganic and -organic components are defined. In this way, computational modeling of band alignmentsmore » becomes affordable using first-principles methods. First, we show that the composite approach is suitable to study the position-dependent dielectric profiles and enables clear differentiation of the respective contributions of inorganic and organic components. Then we apply the composite approach to a variety of 2D HOPs, assessing the impact on the confinement potentials of well and barrier thickness, of the nature of the inorganic well, and of structural transitions. Using the deduced potentials, we further discuss the limitations of the effective mass approximation, scrutinizing the electronic properties of this family of composite materials. Our simulations demonstrate type-I dominant band alignment in 2D HOPs. Finally, we outline design principles on band alignment toward achieving specific optoelectronic properties. Furthermore, we present alternative theoretical methods to inspect the properties of 2D hybrid perovskites and expect that the composite approach will be applicable to other classes of layered materials.« less

Composite Nature of Layered Hybrid Perovskites: Assessment on Quantum and Dielectric Confinements and Band Alignment

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

Traore, Boubacar; Pedesseau, Laurent; Assam, Linda

Layered hybrid organic–inorganic perovskites (HOPs) have re-emerged as potential technological solutions for next-generation photovoltaic and optoelectronic applications. Their two-dimensional (2D) nature confers them a significant flexibility and results in the appearance of quantum and dielectric confinements. Such confinements are at the origin of their fascinating properties, and understanding them from a fundamental level is of paramount importance for optimization. Here, we provide an in-depth investigation of band alignments of 2D HOP allowing access to carriers’ confinement potentials. 2D HOPs are conceptualized as composite materials in which pseudoinorganic and -organic components are defined. In this way, computational modeling of band alignmentsmore » becomes affordable using first-principles methods. First, we show that the composite approach is suitable to study the position-dependent dielectric profiles and enables clear differentiation of the respective contributions of inorganic and organic components. Then we apply the composite approach to a variety of 2D HOPs, assessing the impact on the confinement potentials of well and barrier thickness, of the nature of the inorganic well, and of structural transitions. Using the deduced potentials, we further discuss the limitations of the effective mass approximation, scrutinizing the electronic properties of this family of composite materials. Our simulations demonstrate type-I dominant band alignment in 2D HOPs. Finally, we outline design principles on band alignment toward achieving specific optoelectronic properties. Furthermore, we present alternative theoretical methods to inspect the properties of 2D hybrid perovskites and expect that the composite approach will be applicable to other classes of layered materials.« less

Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps.

PubMed

Aires-de-Sousa, João; Aires-de-Sousa, Luisa

2003-01-01

We propose representing individual positions in DNA sequences by virtual potentials generated by other bases of the same sequence. This is a compact representation of the neighbourhood of a base. The distribution of the virtual potentials over the whole sequence can be used as a representation of the entire sequence (SEQREP code). It is a flexible code, with a length independent of the sequence size, does not require previous alignment, and is convenient for processing by neural networks or statistical techniques. To evaluate its biological significance, the SEQREP code was used for training Kohonen self-organizing maps (SOMs) in two applications: (a) detection of Alu sequences, and (b) classification of sequences encoding for HIV-1 envelope glycoprotein (env) into subtypes A-G. It was demonstrated that SOMs clustered sequences belonging to different classes into distinct regions. For independent test sets, very high rates of correct predictions were obtained (97% in the first application, 91% in the second). Possible areas of application of SEQREP codes include functional genomics, phylogenetic analysis, detection of repetitions, database retrieval, and automatic alignment. Software for representing sequences by SEQREP code, and for training Kohonen SOMs is made freely available from http://www.dq.fct.unl.pt/qoa/jas/seqrep. Supplementary material is available at http://www.dq.fct.unl.pt/qoa/jas/seqrep/bioinf2002

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.

PubMed

Cornwell, MacIntosh; Vangala, Mahesh; Taing, Len; Herbert, Zachary; Köster, Johannes; Li, Bo; Sun, Hanfei; Li, Taiwen; Zhang, Jian; Qiu, Xintao; Pun, Matthew; Jeselsohn, Rinath; Brown, Myles; Liu, X Shirley; Long, Henry W

2018-04-12

RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion.

Underwater Multi-Vehicle Trajectory Alignment and Mapping Using Acoustic and Optical Constraints

PubMed Central

Campos, Ricard; Gracias, Nuno; Ridao, Pere

2016-01-01

Multi-robot formations are an important advance in recent robotic developments, as they allow a group of robots to merge their capacities and perform surveys in a more convenient way. With the aim of keeping the costs and acoustic communications to a minimum, cooperative navigation of multiple underwater vehicles is usually performed at the control level. In order to maintain the desired formation, individual robots just react to simple control directives extracted from range measurements or ultra-short baseline (USBL) systems. Thus, the robots are unaware of their global positioning, which presents a problem for the further processing of the collected data. The aim of this paper is two-fold. First, we present a global alignment method to correct the dead reckoning trajectories of multiple vehicles to resemble the paths followed during the mission using the acoustic messages passed between vehicles. Second, we focus on the optical mapping application of these types of formations and extend the optimization framework to allow for multi-vehicle geo-referenced optical 3D mapping using monocular cameras. The inclusion of optical constraints is not performed using the common bundle adjustment techniques, but in a form improving the computational efficiency of the resulting optimization problem and presenting a generic process to fuse optical reconstructions with navigation data. We show the performance of the proposed method on real datasets collected within the Morph EU-FP7 project. PMID:26999144

BowMapCL: Burrows-Wheeler Mapping on Multiple Heterogeneous Accelerators.

PubMed

Nogueira, David; Tomas, Pedro; Roma, Nuno

2016-01-01

The computational demand of exact-search procedures has pressed the exploitation of parallel processing accelerators to reduce the execution time of many applications. However, this often imposes strict restrictions in terms of the problem size and implementation efforts, mainly due to their possibly distinct architectures. To circumvent this limitation, a new exact-search alignment tool (BowMapCL) based on the Burrows-Wheeler Transform and FM-Index is presented. Contrasting to other alternatives, BowMapCL is based on a unified implementation using OpenCL, allowing the exploitation of multiple and possibly different devices (e.g., NVIDIA, AMD/ATI, and Intel GPUs/APUs). Furthermore, to efficiently exploit such heterogeneous architectures, BowMapCL incorporates several techniques to promote its performance and scalability, including multiple buffering, work-queue task-distribution, and dynamic load-balancing, together with index partitioning, bit-encoding, and sampling. When compared with state-of-the-art tools, the attained results showed that BowMapCL (using a single GPU) is 2 × to 7.5 × faster than mainstream multi-threaded CPU BWT-based aligners, like Bowtie, BWA, and SOAP2; and up to 4 × faster than the best performing state-of-the-art GPU implementations (namely, SOAP3 and HPG-BWT). When multiple and completely distinct devices are considered, BowMapCL efficiently scales the offered throughput, ensuring a convenient load-balance of the involved processing in the several distinct devices.

Salt as a public health challenge in continental European convenience and ready meals.

PubMed

Kanzler, Sonja; Hartmann, Christina; Gruber, Anita; Lammer, Guido; Wagner, Karl-Heinz

2014-11-01

To assess the salt content of continental European convenience and ready meals. A multistage study in which, after laboratory analysis of the products' salt contents (n 32), new salt-reduced meals were developed through food reformulation. Additionally, a comprehensive survey of convenience meals from the Austrian market (n 572) was conducted to evaluate the salt contents of a wider product range. Six continental European countries participated. No subjects enrolled. The salt contents of continental European convenience and ready meals mostly exceeded 1·8 g/100 g, which is 30 % of the targeted daily intake level; some contained even more than the recommended daily intake of 6 g. The highest salt contents were found in pizzas and pasta dishes, the lowest ones in sweet meals. Large variations in salt levels were found not only between and within meal type categories, but also between similar meals from different producers. In addition, our approach to develop new salt-reduced meals showed that a stepwise reduction of the ready meals' salt contents is possible without compromising the sensory quality. To address the problem of hypertension and increased risk for CVD through high salt intake, a reduction of the salt levels in continental European convenience and ready meals is urgently needed, since they are providing a major part of the daily salt intake. Successful national-wide salt reduction strategies in the UK or Finland have already demonstrated the public health impact of this setting.

An intervention to reduce the number of convenience stores selling tobacco: feasibility study.

PubMed

Paynter, Janine; Glover, Marewa; Bullen, Chris; Sonia, Deepika

2016-05-01

Reduction of the availability of tobacco has been proposed as a means of reducing and denormalising tobacco use. Some retailers have stopped selling tobacco. Therefore, we investigated how willing New Zealand convenience store owners were to stop selling tobacco or sell nicotine replacement therapy. Promotion of their stores was offered as an incentive to stop selling tobacco. We asked convenience store owners in the Auckland metropolitan region of New Zealand to choose one of three actions. The first was to stop selling tobacco for a short period of time; the second was to restrict the hours that they sold tobacco; the third was to display and sell nicotine replacement therapy. All participating retailers completed a short interview about selling tobacco. We also surveyed customers about nicotine replacement and cessation. One-third of eligible retailers agreed to participate. Most who participated (93%) were unwilling to stop or restrict tobacco sales and 2 (7%) had already stopped selling tobacco. Tobacco was perceived as a key product for their businesses. Very few customers who purchased cigarettes noticed nicotine replacement therapy or obtained it from convenience stores. Substantially reducing the availability of tobacco in communities is likely to require legislative approaches, underpinned by sustained community pressure and support for convenience store owners who are willing to change their business model. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Aligning Collaborative and Culturally Responsive Evaluation Approaches

ERIC Educational Resources Information Center

Askew, Karyl; Beverly, Monifa Green; Jay, Michelle L.

2012-01-01

The authors, three African-American women trained as collaborative evaluators, offer a comparative analysis of collaborative evaluation (O'Sullivan, 2004) and culturally responsive evaluation approaches (Frierson, Hood, & Hughes, 2002; Kirkhart & Hopson, 2010). Collaborative evaluation techniques immerse evaluators in the cultural milieu…

Music Confucius Institute: Evaluating Its Approach as an Agent for International Chinese Music Dissemination

ERIC Educational Resources Information Center

Guo, Wei; Li, Sheng Bing

2016-01-01

The paper identifies the educational and presentational functions of the Confucius Institute (MCI) at the Royal Danish Academy of Music (RDAM) as its core approaches which mostly influence Chinese cultural dissemination in its host country. The MCI's utilization of the two dissemination approaches aligns with the "receiver-centered"…

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

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

Daily, Jeffrey A.

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

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

DOE PAGES

Daily, Jeffrey A.

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards

PubMed Central

Tsai, Tsung-Heng; Tadesse, Mahlet G.; Di Poto, Cristina; Pannell, Lewis K.; Mechref, Yehia; Wang, Yue; Ressom, Habtom W.

2013-01-01

Motivation: Liquid chromatography-mass spectrometry (LC-MS) has been widely used for profiling expression levels of biomolecules in various ‘-omic’ studies including proteomics, metabolomics and glycomics. Appropriate LC-MS data preprocessing steps are needed to detect true differences between biological groups. Retention time (RT) alignment, which is required to ensure that ion intensity measurements among multiple LC-MS runs are comparable, is one of the most important yet challenging preprocessing steps. Current alignment approaches estimate RT variability using either single chromatograms or detected peaks, but do not simultaneously take into account the complementary information embedded in the entire LC-MS data. Results: We propose a Bayesian alignment model for LC-MS data analysis. The alignment model provides estimates of the RT variability along with uncertainty measures. The model enables integration of multiple sources of information including internal standards and clustered chromatograms in a mathematically rigorous framework. We apply the model to LC-MS metabolomic, proteomic and glycomic data. The performance of the model is evaluated based on ground-truth data, by measuring correlation of variation, RT difference across runs and peak-matching performance. We demonstrate that Bayesian alignment model improves significantly the RT alignment performance through appropriate integration of relevant information. Availability and implementation: MATLAB code, raw and preprocessed LC-MS data are available at http://omics.georgetown.edu/alignLCMS.html Contact: hwr@georgetown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24013927

First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces

DOE PAGES

Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.

2014-10-21

A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1 b₁ energy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation andmore » the dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.« less

Towards a Unified Framework for Pose, Expression, and Occlusion Tolerant Automatic Facial Alignment.

PubMed

Seshadri, Keshav; Savvides, Marios

2016-10-01

We propose a facial alignment algorithm that is able to jointly deal with the presence of facial pose variation, partial occlusion of the face, and varying illumination and expressions. Our approach proceeds from sparse to dense landmarking steps using a set of specific models trained to best account for the shape and texture variation manifested by facial landmarks and facial shapes across pose and various expressions. We also propose the use of a novel l1-regularized least squares approach that we incorporate into our shape model, which is an improvement over the shape model used by several prior Active Shape Model (ASM) based facial landmark localization algorithms. Our approach is compared against several state-of-the-art methods on many challenging test datasets and exhibits a higher fitting accuracy on all of them.

Conservation success as a function of good alignment of social and ecological structures and processes.

PubMed

Bodin, Orjan; Crona, Beatrice; Thyresson, Matilda; Golz, Anna-Lea; Tengö, Maria

2014-10-01

How to create and adjust governing institutions so that they align (fit) with complex ecosystem processes and structures across scales is an issue of increasing concern in conservation. It is argued that lack of such social-ecological fit makes governance and conservation difficult, yet progress in explicitly defining and rigorously testing what constitutes a good fit has been limited. We used a novel modeling approach and data from case studies of fishery and forest conservation to empirically test presumed relationships between conservation outcomes and certain patterns of alignment of social-ecological interdependences. Our approach made it possible to analyze conservation outcome on a systems level while also providing information on how individual actors are positioned in the complex web of social-ecological interdependencies. We found that when actors who shared resources were also socially linked, conservation at the level of the whole social-ecological system was positively affected. When the scales at which individual actors used resources and the scale at which ecological resources were interconnected to other ecological resources were aligned through tightened feedback loops, conservation outcome was better than when they were not aligned. The analysis of individual actors' positions in the web of social-ecological interdependencies was helpful in understanding why a system has a certain level of social-ecological fit. Results of analysis of positions showed that different actors contributed in very different ways to achieve a certain fit and revealed some underlying difference between the actors, for example in terms of actors' varying rights to access and use different ecological resources. © 2014 Society for Conservation Biology.

Physician clinical alignment and integration: a community-academic hospital approach.

PubMed

Salas-Lopez, Debbie; Weiss, Sandra Jarva; Nester, Brian; Whalen, Thomas

2014-01-01

An overwhelming need for change in the U.S. healthcare delivery system, coupled with the need to improve clinical and financial outcomes, has prompted hospitals to direct renewed efforts toward achieving high quality and cost-effectiveness. Additionally, with the dawn of accountable care organizations and increasing focus on patient expectations, hospitals have begun to seek physician partners through clinical alignment. Contrary to the unsuccessful alignment strategies of the 1990s, today's efforts are more mutually beneficial, driven by the need to achieve better care coordination, increased access to infrastructure, improved quality, and lower costs. In this article, we describe a large, academic, tertiary care hospital's approach to developing and implementing alignment and integration models with its collaboration-ready physicians and physician groups. We developed four models--short of physicians' employment with the organization--tailored to meet the needs of both the physician group and the hospital: (1) medical directorship (group physicians are appointed to serve as medical directors of a clinical area), (2) professional services agreement (specific clinical services, such as overnight admissions help, are contracted), (3) co-management services agreement (one specialty group co-manages all services within the specialty service lines), and (4) lease arrangement (closest in scope to employment, in which the hospital pays all expenses and receives all revenue). Successful hospital-physician alignment requires careful planning and the early engagement of legal counsel to ensure compliance with federal statutes. Establishing an integrated system with mutually identified goals better positions hospitals to deliver cost-effective and high-quality care under the new paradigm of healthcare reform.

Modeling of the coupled magnetospheric and neutral wind dynamos

NASA Technical Reports Server (NTRS)

Thayer, Jeffrey P.

1994-01-01

This report summarizes the progress made in the first year of NASA Grant No. NAGW-3508 entitled 'Modeling of the Coupled Magnetospheric and Neutral Wind Dynamos.' The approach taken has been to impose magnetospheric boundary conditions with either pure voltage or current characteristics and solve the neutral wind dynamo equation under these conditions. The imposed boundary conditions determine whether the neutral wind dynamo will contribute to the high-latitude current system or the electric potential. The semi-annual technical report, dated December 15, 1993, provides further detail describing the scientific and numerical approach of the project. The numerical development has progressed and the dynamo solution for the case when the magnetosphere acts as a voltage source has been evaluated completely using spectral techniques. The simulation provides the field-aligned current distribution at high latitudes due to the neutral wind dynamo. A number of geophysical conditions can be simulated to evaluate the importance of the neutral wind dynamo contribution to the field-aligned current system. On average, field-aligned currents generated by the neutral wind dynamo contributed as much as 30 percent to the large-scale field-aligned current system driven by the magnetosphere. A term analysis of the high-latitude neutral wind dynamo equation describing the field aligned current distribution has also been developed to illustrate the important contributing factors involved in the process. The case describing the neutral dynamo response for a magnetosphere acting as a pure current generator requires the existing spectral code to be extended to a pseudo-spectral method and is currently under development.

Fourier transform power spectrum is a potential measure of tissue alignment in standard MRI: A multiple sclerosis study.

PubMed

Sharma, Shrushrita; Zhang, Yunyan

2017-01-01

Loss of tissue coherency in brain white matter is found in many neurological diseases such as multiple sclerosis (MS). While several approaches have been proposed to evaluate white matter coherency including fractional anisotropy and fiber tracking in diffusion-weighted imaging, few are available for standard magnetic resonance imaging (MRI). Here we present an image post-processing method for this purpose based on Fourier transform (FT) power spectrum. T2-weighted images were collected from 19 patients (10 relapsing-remitting and 9 secondary progressive MS) and 19 age- and gender-matched controls. Image processing steps included: computation, normalization, and thresholding of FT power spectrum; determination of tissue alignment profile and dominant alignment direction; and calculation of alignment complexity using a new measure named angular entropy. To test the validity of this method, we used a highly organized brain white matter structure, corpus callosum. Six regions of interest were examined from the left, central and right aspects of both genu and splenium. We found that the dominant orientation of each ROI derived from our method was significantly correlated with the predicted directions based on anatomy. There was greater angular entropy in patients than controls, and a trend to be greater in secondary progressive MS patients. These findings suggest that it is possible to detect tissue alignment and anisotropy using traditional MRI, which are routinely acquired in clinical practice. Analysis of FT power spectrum may become a new approach for advancing the evaluation and management of patients with MS and similar disorders. Further confirmation is warranted.

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.

Functionalization of vertically aligned carbon nanotubes.

PubMed

Van Hooijdonk, Eloise; Bittencourt, Carla; Snyders, Rony; Colomer, Jean-François

2013-01-01

This review focuses and summarizes recent studies on the functionalization of carbon nanotubes oriented perpendicularly to their substrate, so-called vertically aligned carbon nanotubes (VA-CNTs). The intrinsic properties of individual nanotubes make the VA-CNTs ideal candidates for integration in a wide range of devices, and many potential applications have been envisaged. These applications can benefit from the unidirectional alignment of the nanotubes, the large surface area, the high carbon purity, the outstanding electrical conductivity, and the uniformly long length. However, practical uses of VA-CNTs are limited by their surface characteristics, which must be often modified in order to meet the specificity of each particular application. The proposed approaches are based on the chemical modifications of the surface by functionalization (grafting of functional chemical groups, decoration with metal particles or wrapping of polymers) to bring new properties or to improve the interactions between the VA-CNTs and their environment while maintaining the alignment of CNTs.

Functionalization of vertically aligned carbon nanotubes

PubMed Central

Snyders, Rony; Colomer, Jean-François

2013-01-01

Summary This review focuses and summarizes recent studies on the functionalization of carbon nanotubes oriented perpendicularly to their substrate, so-called vertically aligned carbon nanotubes (VA-CNTs). The intrinsic properties of individual nanotubes make the VA-CNTs ideal candidates for integration in a wide range of devices, and many potential applications have been envisaged. These applications can benefit from the unidirectional alignment of the nanotubes, the large surface area, the high carbon purity, the outstanding electrical conductivity, and the uniformly long length. However, practical uses of VA-CNTs are limited by their surface characteristics, which must be often modified in order to meet the specificity of each particular application. The proposed approaches are based on the chemical modifications of the surface by functionalization (grafting of functional chemical groups, decoration with metal particles or wrapping of polymers) to bring new properties or to improve the interactions between the VA-CNTs and their environment while maintaining the alignment of CNTs. PMID:23504581

A novel mechanism important for the alignment of microtubules.

PubMed

Wightman, Raymond; Turner, Simon R

2008-04-01

Using a live-cell imaging approach to study individual micro-tubules, we have compared microtubule behavior between net-like and aligned cortical arrays. In contrast to previous studies, a steep angled collision between the growing end of a microtubule and a preexisting microtubule was found to favor crossover. Frequencies of microtubule crossovers, bundling and catastrophes are similar regardless of whether the cell exhibited a net-like or aligned microtubule array. In the predominantly aligned array of petiole cells, severing occurs at the sites of microtubule crossovers and serves to remove unaligned microtubules and to increase microtubule density. Severing was observed to be rare in net-like arrays. Microtubule severing is carried out by the katanin enzyme. In this addendum, we present new insights into the possible mechanism of crossing over and preliminary data looking at organization of the array in a katanin mutant.

Prevalence of substandard and falsified artemisinin-based combination antimalarial medicines on Bioko Island, Equatorial Guinea

PubMed Central

Kaur, Harparkash; Allan, Elizabeth Louise; Mamadu, Ibrahim; Hall, Zoe; Green, Michael D; Swamidos, Isabel; Dwivedi, Prabha; Culzoni, Maria Julia; Fernandez, Facundo M; Garcia, Guillermo; Hergott, Dianna; Monti, Feliciano

2017-01-01

Introduction Poor-quality artemisinin-containing antimalarials (ACAs), including falsified and substandard formulations, pose serious health concerns in malaria endemic countries. They can harm patients, contribute to the rise in drug resistance and increase the public’s mistrust of health systems. Systematic assessment of drug quality is needed to gain knowledge on the prevalence of the problem, to provide Ministries of Health with evidence on which local regulators can take action. Methods We used three sampling approaches to purchase 677 ACAs from 278 outlets on Bioko Island, Equatorial Guinea as follows: convenience survey using mystery client (n=16 outlets, 31 samples), full island-wide survey using mystery client (n=174 outlets, 368 samples) and randomised survey using an overt sampling approach (n=88 outlets, 278 samples). The stated active pharmaceutical ingredients (SAPIs) were assessed using high-performance liquid chromatography and confirmed by mass spectrometry at three independent laboratories. Results Content analysis showed 91.0% of ACAs were of acceptable quality, 1.6% were substandard and 7.4% falsified. No degraded medicines were detected. The prevalence of medicines without the SAPIs was higher for ACAs purchased in the convenience survey compared with the estimates obtained using the full island-wide survey-mystery client and randomised-overt sampling approaches. Comparable results were obtained for full island survey-mystery client and randomised overt. However, the availability of purchased artesunate monotherapies differed substantially according to the sampling approach used (convenience, 45.2%; full island-wide survey-mystery client, 32.6%; random-overt sampling approach, 21.9%). Of concern is that 37.1% (n=62) of these were falsified. Conclusion Falsified ACAs were found on Bioko Island, with the prevalence ranging between 6.1% and 16.1%, depending on the sampling method used. These findings underscore the vital need for national authorities to track the scale of ineffective medicines that jeopardise treatment of life-threatening diseases and value of a representative sampling approach to obtain/measure the true prevalence of poor-quality medicines. PMID:29082025

Methods used to identify seafloor spreading magnetic anomalies and to establish their relationship with the top of the basement topography in the Argentine continental margin between 35° S and 48° S

NASA Astrophysics Data System (ADS)

Abraham, D. A.; Ghidella, M. E.; Tassone, A.; Paterlini, M.; Ancarola, M.

2013-05-01

This paper discusses some methods for better identification of the spreading seafloor magnetic anomalies in the region between 35° S and 48° S at the outer edge of the continental margin of Argentina. In the area of Rio de la Plata craton and Patagonia Argentina, there is an extensional volcanic passive margin. This segment of the Atlantic continental margin is characterized by the existence of seismic reflectors sequences that lean toward the sea (seaward dipping reflectors - SDRs). These sequences of seismic reflectors, located in the transitional-continental basement wedge, are portrayed in seismic profiles as an interference pattern interpreted as basalt flows intercalated with sedimentary layers, and its origin is ascribed to volcanism occurred during the Early Cretaceous. The magnetic response of SDRs is in the area of the magnetic anomaly G (Rabinowitz and LaBrecque, 1979). Magnetic alignments are highlighted on a map by superimposing total field anomaly semitransparent layer of calculated numerical curvature. This method allows a regional identification of the most prominent alignments. It is convenient to calculate the curvature in the direction perpendicular to the magnetic alignments. The identification of seafloor spreading magnetic anomalies located in the eastern margin helps in the knowledge of the history of the Atlantic Ocean opening. M series magnetic alignments: M5n, M3n M0r (between 132 and 120 Ma) were identified in the analyzed area. The roughness of the top of the oceanic basement presents a contrast of amplitudes, in a wavelength range between about 4 km and 6 km, with the corresponding amplitudes in the area of the transitional crust. This contrast of amplitudes can be detected using spectral methods, especially short Fourier transform. The quantitative evaluation of the spectral energy density allowed the identification of wave numbers characterizing oceanic basement area and thus perform subsequent filtering of the signal with wavelengths found with the spectral method. The top of basement roughness was quantified using the root mean square (RMS), in sections of about 2 km, of residues between the depth of the basement top and first-degree polynomial that best fitted the sections. The spreading seafloor magnetic alignments are on oceanic crust area identified by the point of view of the roughness analysis. The combined use of the methods that we have developed on the magnetic surveys in the study area, allowed us to improve the layout of the magnetic alignments and identify the transition between oceanic and continental crust.

Alignment and Calibration of Optical and Inertial Sensors Using Stellar Observations

DTIC Science & Technology

2007-01-01

Force, Department of Defense, or the U.S Government. References [1] R. G. Brown and P. Y. Hwang . Introduction to Ran- dom Signals and Applied Kalman ...and stellar observations using an extended Kalman filter algorithm. The approach is verified using simulation and experimental data, and con- clusions...an extended Kalman filter (EKF) algorithm (see [10], [11]) to recur- sively estimate camera alignment and calibration param- eters by measuring the

Centroid stabilization for laser alignment to corner cubes: designing a matched filter

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

Awwal, Abdul A. S.; Bliss, Erlan; Brunton, Gordon

2016-11-08

Automation of image-based alignment of National Ignition Facility high energy laser beams is providing the capability of executing multiple target shots per day. One important alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retroreflecting corner cubes as centering references for each beam. Beam-to-beam variations and systematic beam changes over time in the FOA corner cube images can lead to a reduction in accuracy as well as increased convergence durations for the template-based position detector. A systematic approach is described that maintains FOA corner cube templates and guaranteesmore » stable position estimation.« less

Centroid stabilization for laser alignment to corner cubes: designing a matched filter

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

Awwal, Abdul A. S.; Bliss, Erlan; Brunton, Gordon

2016-11-08

Automation of image-based alignment of NIF high energy laser beams is providing the capability of executing multiple target shots per day. One important alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retro-reflecting corner cubes as centering references for each beam. Beam-to-beam variations and systematic beam changes over time in the FOA corner cube images can lead to a reduction in accuracy as well as increased convergence durations for the template-based position detector. A systematic approach is described that maintains FOA corner cube templates and guarantees stable positionmore » estimation.« less

Beauty and the beast: Aligning national curriculum standards with state (high school) graduation requirements

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

Linder-Scholer, B.

1994-12-31

An overview of SCI/MATH/MN - Minnesota`s standards-based, systemic approach to the reform and improvement of the K-12 science and mathematics education delivery system - is offered as an illustration of the challenges of aligning state educational practices with the national curriculum standards, and as a model for business involvement in state educational policy issues that will enable fundamental, across-the-system reform. SCI/MATH/MN illustrates the major challenges involved in developing a statewide vision for math and science education reform, articulating frameworks aligned with the national standards, building capacity for system-oriented change at the local level, and involving business in systemic reform.

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

PubMed

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

2014-12-01

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

Agent-Customized Training for Human Learning Performance Enhancement

ERIC Educational Resources Information Center

Blake, M. Brian; Butcher-Green, Jerome D.

2009-01-01

Training individuals from diverse backgrounds and in changing environments requires customized training approaches that align with the individual learning styles and ever-evolving organizational needs. Scaffolding is a well-established instructional approach that facilitates learning by incrementally removing training aids as the learner…

Poly(hydroxybutyrate)/chitosan Aligned Electrospun Scaffold as a Novel Substrate for Nerve Tissue Engineering.

PubMed

Karimi, Afarin; Karbasi, Saeed; Razavi, Shahnaz; Zargar, Elham Naghash

2018-01-01

Reconstruction of nervous system is a great challenge in the therapeutic medical field. Nerve tissue engineering is a novel method to regenerate nervous system in human health care. Tissue engineering has introduced novel approaches to promote and guide peripheral nerve regeneration using submicron and nanoscale fibrous scaffolds. In this study, 9 wt% poly(3-hydroxybutyrate) (PHB) solutions with two different ratios of chitosan (CTS) (15%, and 20%) were mixed in trifluoroacetic acid as a cosolvent. Thereafter, random and aligned PHB/CTS scaffolds were fabricated by electrospinning method in an appropriate condition. Average diameters for aligned PHB, PHB/CTS 85:15 and PHB/CTS 80:20 were obtained as 675 nm, 740.3 nm, and 870.74 nm, which was lesser than random fibers. The solution components entity authenticity was approved by Fourier transform infrared. The addition of CTS decreased both water droplet contact angle from 124.79° to 43.14° in random and 110.87° to 33.49° in aligned PHB/CTS fibrous scaffold. Moreover, alignment of fibers causes tremendous increase in hydrophilicity of fibrous PHB/CTS substrate. Tensile strength increased from 6.41 MPa for random to 8.73 MPa for aligned PHB/CTS 85:15. Our results indicated that aligned PHB/CTS 85:15 nanofibers are the desired scaffold than the random PHB/CTS nanofibers for application in nerve tissue regeneration.

Perceptually aligning apical frequency regions leads to more binaural fusion of speech in a cochlear implant simulation.

PubMed

Staisloff, Hannah E; Lee, Daniel H; Aronoff, Justin M

2016-07-01

For bilateral cochlear implant users, the left and right arrays are typically not physically aligned, resulting in a degradation of binaural fusion, which can be detrimental to binaural abilities. Perceptually aligning the two arrays can be accomplished by disabling electrodes in one ear that do not have a perceptually corresponding electrode in the other side. However, disabling electrodes at the edges of the array will cause compression of the input frequency range into a smaller cochlear extent, which may result in reduced spectral resolution. An alternative approach to overcome this mismatch would be to only align one edge of the array. By aligning either only the apical or basal end of the arrays, fewer electrodes would be disabled, potentially causing less reduction in spectral resolution. The goal of this study was to determine the relative effect of aligning either the basal or apical end of the electrode with regards to binaural fusion. A vocoder was used to simulate cochlear implant listening conditions in normal hearing listeners. Speech signals were vocoded such that the two ears were either predominantly aligned at only the basal or apical end of the simulated arrays. The experiment was then repeated with a spectrally inverted vocoder to determine whether the detrimental effects on fusion were related to the spectral-temporal characteristics of the stimuli or the location in the cochlea where the misalignment occurred. In Experiment 1, aligning the basal portion of the simulated arrays led to significantly less binaural fusion than aligning the apical portions of the simulated array. However, when the input was spectrally inverted, aligning the apical portion of the simulated array led to significantly less binaural fusion than aligning the basal portions of the simulated arrays. These results suggest that, for speech, with its predominantly low frequency spectral-temporal modulations, it is more important to perceptually align the apical portion of the array to better preserve binaural fusion. By partially aligning these arrays, cochlear implant users could potentially increase their ability to fuse speech sounds presented to the two ears while maximizing spectral resolution. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparing the Pre- and Posttest Scores in Relations to the Emporium and the Hands-on Instructional Approaches of Teaching Science in Prekindergarten

NASA Astrophysics Data System (ADS)

Headen, Patricia Ann

This quantitative, quasi-experimental research investigated if two instructional approaches, the Emporium Computer-Based (Group 2) versus the hands-on approach (Group 1), resulted any difference in student achievement in science for four-year-old prekindergarten students at a private childcare facility in North Carolina. Three research questions hypothesized these relationships: (a) Group 2 versus Group 1 assessed student achievement as theoretically based on Piaget and Vygotsky's perspectives of child development, (b) the instructional approaches related to gender, and (c) the instructional approaches interrelated to ethnicity. Using a two-factor ANOVA and ANCOVA techniques, involved a convenience sample of 126 four-year-old prekindergarten students of which a convenience sample of 126 participated. The Assessment of Measurements for Pre-K (AMP-K), pretest and posttest scores of each group of 63 students measured student achievement. The t tests determined if a significant difference in student achievement existed (dependent variable) with the Emporium Computer-Based versus hands-on instructional approaches (independent variables). The posttest scores of Group 2 (p = 0.00), indicated a significant difference in student achievement. However, gender and ethnicity variables had no effect on student achievement, male (M = 36.14, SD = 19.61) and female (M = 42.91, SD = 18.99) with (p = 0.49), and ethnicity resulted, F (1,125) = 1.65, (p = 0.20). These results suggested that further research on the Emporium Computer-Based instructional approach could improve students' intellectual abilities through more innovative practices.

AVIRIS foreoptics, fiber optics and on-board calibrator

NASA Technical Reports Server (NTRS)

Chrisp, Michael P.; Chrien, Thomas G.; Steimle, L.

1987-01-01

The foreoptics, fiber optic system and calibration source of the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) are described. The foreoptics, based on a modified Kennedy scanner, is coupled by optical fibers to the four spectrometers. The optical fibers allow convenient positioning of the spectrometers in the limited space and enable simple compensation of the scanner's thermal defocus (at the -23 C operating temp) by active control of the fiber focal plane position. A challenging requirement for the fiber optic system was the transmission to the spectral range 1.85 to 2.45 microns at .45 numerical aperture. This was solved with custom fluoride glass fibers from Verre Fluore. The onboard calibration source is also coupled to the spectrometers by the fibers and provides two radiometric levels and a reference spectrum to check the spectrometers' alignment. Results of the performance of the assembled subsystems are presented.

Modulation of spin transfer torque amplitude in double barrier magnetic tunnel junctions

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

Clément, P.-Y.; Baraduc, C., E-mail: claire.baraduc@cea.fr; Chshiev, M.

2015-09-07

Magnetization switching induced by spin transfer torque is used to write magnetic memories (Magnetic Random Access Memory, MRAM) but can be detrimental to the reading process. It would be quite convenient therefore to modulate the efficiency of spin transfer torque. A solution is adding an extra degree of freedom by using double barrier magnetic tunnel junctions with two spin-polarizers, with controllable relative magnetic alignment. We demonstrate, for these structures, that the amplitude of in-plane spin transfer torque on the middle free layer can be efficiently tuned via the magnetic configuration of the electrodes. Using the proposed design could thus pavemore » the way towards more reliable read/write schemes for MRAM. Moreover, our results suggest an intriguing effect associated with the out-of-plane (field-like) spin transfer torque, which has to be further investigated.« less

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

NASA Astrophysics Data System (ADS)

Lizotte, Todd E.

2011-10-01

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

A machine-learning approach reveals that alignment properties alone can accurately predict inference of lateral gene transfer from discordant phylogenies.

PubMed

Roettger, Mayo; Martin, William; Dagan, Tal

2009-09-01

Among the methods currently used in phylogenomic practice to detect the presence of lateral gene transfer (LGT), one of the most frequently employed is the comparison of gene tree topologies for different genes. In cases where the phylogenies for different genes are incompatible, or discordant, for well-supported branches there are three simple interpretations for the result: 1) gene duplications (paralogy) followed by many independent gene losses have occurred, 2) LGT has occurred, or 3) the phylogeny is well supported but for reasons unknown is nonetheless incorrect. Here, we focus on the third possibility by examining the properties of 22,437 published multiple sequence alignments, the Bayesian maximum likelihood trees for which either do or do not suggest the occurrence of LGT by the criterion of discordant branches. The alignments that produce discordant phylogenies differ significantly in several salient alignment properties from those that do not. Using a support vector machine, we were able to predict the inference of discordant tree topologies with up to 80% accuracy from alignment properties alone.

QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families

PubMed Central

Gudyś, Adam; Deorowicz, Sebastian

2017-01-01

The ever-increasing size of sequence databases caused by the development of high throughput sequencing, poses to multiple alignment algorithms one of the greatest challenges yet. As we show, well-established techniques employed for increasing alignment quality, i.e., refinement and consistency, are ineffective when large protein families are investigated. We present QuickProbs 2, an algorithm for multiple sequence alignment. Based on probabilistic models, equipped with novel column-oriented refinement and selective consistency, it offers outstanding accuracy. When analysing hundreds of sequences, Quick-Probs 2 is noticeably better than ClustalΩ and MAFFT, the previous leaders for processing numerous protein families. In the case of smaller sets, for which consistency-based methods are the best performing, QuickProbs 2 is also superior to the competitors. Due to low computational requirements of selective consistency and utilization of massively parallel architectures, presented algorithm has similar execution times to ClustalΩ, and is orders of magnitude faster than full consistency approaches, like MSAProbs or PicXAA. All these make QuickProbs 2 an excellent tool for aligning families ranging from few, to hundreds of proteins. PMID:28139687

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.

Mechanical design implementation and mathematical considerations for ultra precise diamond turning of multiple freeform mirrors on a common substrate

NASA Astrophysics Data System (ADS)

Hartung, Johannes; Beier, Matthias; Peschel, Thomas; Gebhardt, Andreas; Risse, Stefan

2015-09-01

For optical systems consisting of metal (in general freeform) mirrors there exist several diamond turning fabrication approaches. These are distuingished by the effort in manufacturing and integration of the later system. The more work one puts into the manufacturing stage the less complicated is the alignment and integration afterwards. For example the most degrees of freedom have to be aligned in integration phase if every mirror of the system is fabricated as a single optical component. For a three mirror anastigmat with three freeform mirrors the degrees of freedom sum up to 18. Therefore the mirror fabrication itself is more or less easy, but the integration is very difficult. There are three major parts in the design and manufacturing process chain to be considered for tackling this integration problem. At the first position in the process chain there is the optical design occuring. At this stage a negotiation between manufacturing and design could improve manufacturability because of more possible integration approaches. The second stage is the mechanical design. Here the appropriate manufacturing approach is already chosen, but may be revisited due to incompatiblities with, e.g., stress specifications. The third level is the manufacturing stage. Here are different clamping approaches and fabrication methods possible. The current article will focus on an approach ("snap-together") where two mirrors are fabricated on one substrate and therefore a reduction of the number of degrees of freedom to be aligned are reduced to six. This improves the amount of time needed for the system integration significantly in contrast to a single mirror fabrication.

Safety Culture and Senior Leadership Behavior: Using Negative Safety Ratings to Align Clinical Staff and Senior Leadership.

PubMed

O'Connor, Shawn; Carlson, Elizabeth

2016-04-01

This report describes how staff-designed behavior changes among senior leaders can have a positive impact on clinical nursing staff and enhance the culture of safety in a community hospital. A positive culture of safety in a hospital improves outcomes for patients and staff. Senior leaders are accountable for developing an environment that supports a culture of safety. At 1 community hospital, surveys demonstrated that staff members did not view senior leaders as supportive of or competent in creating a culture of safety. After approval from the hospital's institutional review board was obtained, clinical nurses generated and selected ideas for senior leader behavior change. The new behaviors were assessed by a convenience sample survey of clinical nurses. In addition, culture of safety survey results were compared. Risk reports and harm events were also measured before and after behavior changes. The volume of risk and near-miss reports increased, showing that clinical staff were more inclined to report events after senior leader communication, access, and visibility increased. Harm events went down. The culture of safety survey demonstrated an improvement in the senior leadership domain in 4 of 6 units. The anonymous convenience survey demonstrated that staff members recognized changes that senior leaders had made and felt that these changes positively impacted the culture of safety. By developing skills in communication, advocacy, visibility, and access, senior leaders can enhance a hospital's culture of safety and create stronger ties with clinical staff.

Two Influential Primate Classifications Logically Aligned.

PubMed

Franz, Nico M; Pier, Naomi M; Reeder, Deeann M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2016-07-01

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments-in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

Total knee arthroplasty with a computer-navigated saw: a pilot study.

PubMed

Garvin, Kevin L; Barrera, Andres; Mahoney, Craig R; Hartman, Curtis W; Haider, Hani

2013-01-01

Computer-aided surgery aims to improve implant alignment in TKA but has only been adopted by a minority for routine use. A novel approach, navigated freehand bone cutting (NFC), is intended to achieve wider acceptance by eliminating the need for cumbersome, implant-specific mechanical jigs and avoiding the expense of navigation. We determined cutting time, surface quality, implant fit, and implant alignment after NFC of synthetic femoral specimens and the feasibility and alignment of a complete TKA performed with NFC technology in cadaveric specimens. Seven surgeons prepared six synthetic femoral specimens each, using our custom NFC system. Cutting times, quality of bone cuts, and implant fit and alignment were assessed quantitatively by CT surface scanning and computational measurements. Additionally, a single surgeon performed a complete TKA on two cadaveric specimens using the NFC system, with cutting time and implant alignment analyzed through plain radiographs and CT. For the synthetic specimens, femoral coronal alignment was within ± 2° of neutral in 94% of the specimens. Sagittal alignment was within 0° to 5° of flexion in all specimens. Rotation was within ± 1° of the epicondylar axis in 97% of the specimens. The mean time to make cuts improved from 13 minutes for the first specimen to 9 minutes for the fourth specimen. TKA was performed in two cadaveric specimens without complications and implants were well aligned. TKA is feasible with NFC, which eliminates the need for implant-specific instruments. We observed a fast learning curve. NFC has the potential to improve TKA alignment, reduce operative time, and reduce the number of instruments in surgery. Fewer instruments and less sterilization could reduce costs associated with TKA.

The Relationship between First-Year Achievement and the Pedagogical-Didactical Fit between Secondary School and University

ERIC Educational Resources Information Center

Torenbeek, Marjolein; Jansen, Ellen; Hofman, Adriaan

2011-01-01

Central in this study is the degree to which the pedagogical-didactical approach in undergraduate programmes aligns with the pedagogical-didactical approach in secondary schools, and how this is related to first-year achievement. Approaches to teaching at secondary schools and in first-year university programmes were examined by interviewing…

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

NASA Astrophysics Data System (ADS)

Kacenjar, Steve; Zook, Matthew; Balint, Michael

2011-03-01

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

Rationale for Research on Including Sustainable Agriculture in the High School Agricultural Education Curriculum.

ERIC Educational Resources Information Center

Williams, David L.; Dollisso, Awoke D.

1998-01-01

Sustainable agriculture is a multidisciplinary approach to food and fiber problems. Its inclusion in the secondary curriculum would enrich and align it with social concerns. Research is needed in the scholarship functions of discovery, integrative approaches, and teaching. (SK)

Personalizing Distance Learning

ERIC Educational Resources Information Center

Coombs-Richardson, Rita

2007-01-01

This article discusses how a personal approach to online learning can yield a successful experience for adults earning advanced degrees or certification in teaching. Distance learning has become increasingly popular among learners with family and work obligations. Degree-seeking adult learners appreciate the flexibility and convenience of learning…

STATISTICS-BASED APPROACH TO WASTEWATER TREATMENT PLANT OPERATIONS

EPA Science Inventory

This paper describes work toward development of a convenient decision support system to improve everyday operation and control of the wastewater treatment process. The goal is to help the operator detect problems in the process and select appropriate control actions. The system...

Preparation of Tyrian purple (6,6'-dibromoindigo): past and present.

PubMed

Wolk, Joel L; Frimer, Aryeh A

2010-08-10

Over the past century, various synthetic approaches have been suggested to the most famous dye of antiquity, Tyrian purple (6,6'-dibromoindigo). These synthetic routes have been exhaustively surveyed and critically evaluated from the perspective of convenience, cost, safety and yield.

RAMTaB: Robust Alignment of Multi-Tag Bioimages

PubMed Central

Raza, Shan-e-Ahmed; Humayun, Ahmad; Abouna, Sylvie; Nattkemper, Tim W.; Epstein, David B. A.; Khan, Michael; Rajpoot, Nasir M.

2012-01-01

Background In recent years, new microscopic imaging techniques have evolved to allow us to visualize several different proteins (or other biomolecules) in a visual field. Analysis of protein co-localization becomes viable because molecules can interact only when they are located close to each other. We present a novel approach to align images in a multi-tag fluorescence image stack. The proposed approach is applicable to multi-tag bioimaging systems which (a) acquire fluorescence images by sequential staining and (b) simultaneously capture a phase contrast image corresponding to each of the fluorescence images. To the best of our knowledge, there is no existing method in the literature, which addresses simultaneous registration of multi-tag bioimages and selection of the reference image in order to maximize the overall overlap between the images. Methodology/Principal Findings We employ a block-based method for registration, which yields a confidence measure to indicate the accuracy of our registration results. We derive a shift metric in order to select the Reference Image with Maximal Overlap (RIMO), in turn minimizing the total amount of non-overlapping signal for a given number of tags. Experimental results show that the Robust Alignment of Multi-Tag Bioimages (RAMTaB) framework is robust to variations in contrast and illumination, yields sub-pixel accuracy, and successfully selects the reference image resulting in maximum overlap. The registration results are also shown to significantly improve any follow-up protein co-localization studies. Conclusions For the discovery of protein complexes and of functional protein networks within a cell, alignment of the tag images in a multi-tag fluorescence image stack is a key pre-processing step. The proposed framework is shown to produce accurate alignment results on both real and synthetic data. Our future work will use the aligned multi-channel fluorescence image data for normal and diseased tissue specimens to analyze molecular co-expression patterns and functional protein networks. PMID:22363510

Fabrication of aligned magnetic nanoparticles using tobamoviruses.

PubMed

Kobayashi, Mime; Seki, Munetoshi; Tabata, Hitoshi; Watanabe, Yuichiro; Yamashita, Ichiro

2010-03-10

We used genetically modified tube-shaped tobamoviruses to produce 3 nm aligned magnetic nanoparticles. Amino acid residues facing the central channel of the virus were modified to increase the number of nucleation sites. Energy dispersive X-ray spectroscopy and superconducting quantum interference device analysis suggest that the particles consisted of Co-Pt alloy. The use of tobamovirus mutants is a promising approach to making a variety of components that can be applied to fabricate nanometer-scaled electronic devices.

Single-molecule tracking studies of flow-induced microdomain alignment in cylinder-forming polystyrene-poly(ethylene oxide) diblock copolymer films.

PubMed

Tran-Ba, Khanh-Hoa; Higgins, Daniel A; Ito, Takashi

2014-09-25

Flow-based approaches are promising routes to preparation of aligned block copolymer microdomains within confined spaces. An in-depth characterization of such nanoscale morphologies within macroscopically nonuniform materials under ambient conditions is, however, often challenging. In this study, single-molecule tracking (SMT) methods were employed to probe the flow-induced alignment of cylindrical microdomains (ca. 22 nm in diameter) in polystyrene-poly(ethylene oxide) diblock copolymer (PS-b-PEO) films. Films of micrometer-scale thicknesses were prepared by overlaying a benzene solution droplet on a glass coverslip with a rectangular glass plate, followed by solvent evaporation under a nitrogen atmosphere. The microdomain alignment was quantitatively assessed from SMT data exhibiting the diffusional motions of individual sulforhodamine B fluorescent probes that preferentially partitioned into cylindrical PEO microdomains. Better overall microdomain orientation along the flow direction was observed near the substrate interface in films prepared at a higher flow rate, suggesting that the microdomain alignment was primarily induced by shear flow. The SMT data also revealed the presence of micrometer-scale grains consisting of highly ordered microdomains with coherent orientation. The results of this study provide insights into shear-based preparation of aligned cylindrical microdomains in block copolymer films from solutions within confined spaces.

Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods.

PubMed

Wan, Xiaohua; Katchalski, Tsvi; Churas, Christopher; Ghosh, Sreya; Phan, Sebastien; Lawrence, Albert; Hao, Yu; Zhou, Ziying; Chen, Ruijuan; Chen, Yu; Zhang, Fa; Ellisman, Mark H

2017-05-01

Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless, verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment. This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise. We report an electron tomography (ET) simulator with accurate ray optics modeling of image formation that includes curvilinear trajectories through the sample, warping of the sample and noise. As a demonstration of the utility of our approach, we have concentrated on providing verification of the class of reconstruction methods applicable to wide field images of stained plastic-embedded samples. Accordingly, we have also constructed digital phantoms derived from serial block face scanning electron microscope images. These phantoms are also easily modified to include alignment features to test alignment algorithms. The combination of more realistic phantoms with more faithful simulations facilitates objective comparison of acquisition parameters, alignment and reconstruction algorithms and their range of applicability. With proper phantoms, this approach can also be modified to include more complex optical models, including distance-dependent blurring and phase contrast functions, such as may occur in cryotomography. Copyright © 2017 Elsevier Inc. All rights reserved.

Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters.

PubMed

Lan, Haidong; Chan, Yuandong; Xu, Kai; Schmidt, Bertil; Peng, Shaoliang; Liu, Weiguo

2016-07-19

Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data parallelism, thread-level coarse-grained parallelism, and vector-level fine-grained parallelism. Furthermore, we re-organize the sequence datasets and use Xeon Phi shuffle operations to improve I/O efficiency. Evaluations show that our method achieves a peak overall performance up to 220 GCUPS for scanning real protein sequence databanks on a single node consisting of two Intel E5-2620 CPUs and two Intel Xeon Phi 7110P cards. It also exhibits good scalability in terms of sequence length and size, and number of compute nodes for both database scanning and multiple sequence alignment. Furthermore, the achieved performance is highly competitive in comparison to optimized Xeon Phi and GPU implementations. Our implementation is available at https://github.com/turbo0628/LSDBS-mpi .

A Molecular Phylogeny of the Chalcidoidea (Hymenoptera)

PubMed Central

Munro, James B.; Heraty, John M.; Burks, Roger A.; Hawks, David; Mottern, Jason; Cruaud, Astrid; Rasplus, Jean-Yves; Jansta, Petr

2011-01-01

Chalcidoidea (Hymenoptera) are extremely diverse with more than 23,000 species described and over 500,000 species estimated to exist. This is the first comprehensive phylogenetic analysis of the superfamily based on a molecular analysis of 18S and 28S ribosomal gene regions for 19 families, 72 subfamilies, 343 genera and 649 species. The 56 outgroups are comprised of Ceraphronoidea and most proctotrupomorph families, including Mymarommatidae. Data alignment and the impact of ambiguous regions are explored using a secondary structure analysis and automated (MAFFT) alignments of the core and pairing regions and regions of ambiguous alignment. Both likelihood and parsimony approaches are used to analyze the data. Overall there is no impact of alignment method, and few but substantial differences between likelihood and parsimony approaches. Monophyly of Chalcidoidea and a sister group relationship between Mymaridae and the remaining Chalcidoidea is strongly supported in all analyses. Either Mymarommatoidea or Diaprioidea are the sister group of Chalcidoidea depending on the analysis. Likelihood analyses place Rotoitidae as the sister group of the remaining Chalcidoidea after Mymaridae, whereas parsimony nests them within Chalcidoidea. Some traditional family groups are supported as monophyletic (Agaonidae, Eucharitidae, Encyrtidae, Eulophidae, Leucospidae, Mymaridae, Ormyridae, Signiphoridae, Tanaostigmatidae and Trichogrammatidae). Several other families are paraphyletic (Perilampidae) or polyphyletic (Aphelinidae, Chalcididae, Eupelmidae, Eurytomidae, Pteromalidae, Tetracampidae and Torymidae). Evolutionary scenarios discussed for Chalcidoidea include the evolution of phytophagy, egg parasitism, sternorrhynchan parasitism, hypermetamorphic development and heteronomy. PMID:22087244

From Wood to Textiles: Top-Down Assembly of Aligned Cellulose Nanofibers.

PubMed

Jia, Chao; Chen, Chaoji; Kuang, Yudi; Fu, Kun; Wang, Yilin; Yao, Yonggang; Kronthal, Spencer; Hitz, Emily; Song, Jianwei; Xu, Fujun; Liu, Boyang; Hu, Liangbing

2018-06-07

Advanced textiles made of macroscopic fibers are usually prepared from synthetic fibers, which have changed lives over the past century. The shortage of petrochemical resources, however, greatly limits the development of the textile industry. Here, a facile top-down approach for fabricating macroscopic wood fibers for textile applications (wood-textile fibers) comprising aligned cellulose nanofibers directly from natural wood via delignification and subsequent twisting is demonstrated. Inherently aligned cellulose nanofibers are well retained, while the microchannels in the delignified wood are squeezed and totally removed by twisting, resulting in a dense structure with approximately two times higher mechanical strength (106.5 vs 54.9 MPa) and ≈20 times higher toughness (7.70 vs 0.36 MJ m -3 ) than natural wood. Dramatically different from natural wood, which is brittle in nature, the resultant wood-textile fibers are highly flexible and bendable, likely due to the twisted structures. The wood-textile fibers also exhibit excellent knitting properties and dyeability, which are critical for textile applications. Furthermore, functional wood-textile fibers can be achieved by preinfiltrating functional materials in the delignified wood film before twisting. This top-down approach of fabricating aligned macrofibers is simple, scalable, and cost-effective, representing a promising direction for the development of smart textiles and wearable electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.