Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

PubMed Central

Mohammadi, Erfan; Zhao, Chuankai; Meng, Yifei; Qu, Ge; Zhang, Fengjiao; Zhao, Xikang; Mei, Jianguo; Zuo, Jian-Min; Shukla, Diwakar; Diao, Ying

2017-01-01

Solution processable semiconducting polymers have been under intense investigations due to their diverse applications from printed electronics to biomedical devices. However, controlling the macromolecular assembly across length scales during solution coating remains a key challenge, largely due to the disparity in timescales of polymer assembly and high-throughput printing/coating. Herein we propose the concept of dynamic templating to expedite polymer nucleation and the ensuing assembly process, inspired by biomineralization templates capable of surface reconfiguration. Molecular dynamic simulations reveal that surface reconfigurability is key to promoting template–polymer interactions, thereby lowering polymer nucleation barrier. Employing ionic-liquid-based dynamic template during meniscus-guided coating results in highly aligned, highly crystalline donor–acceptor polymer thin films over large area (>1 cm2) and promoted charge transport along both the polymer backbone and the π–π stacking direction in field-effect transistors. We further demonstrate that the charge transport anisotropy can be reversed by tuning the degree of polymer backbone alignment. PMID:28703136

Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

DOE PAGES

Mohammadi, Erfan; Zhao, Chuankai; Meng, Yifei; ...

2017-07-13

Solution processable semiconducting polymers have been under intense investigations due to their diverse applications from printed electronics to biomedical devices. However, controlling the macromolecular assembly across length scales during solution coating remains a key challenge, largely due to the disparity in timescales of polymer assembly and high-throughput printing/coating. Herein we propose the concept of dynamic templating to expedite polymer nucleation and the ensuing assembly process, inspired by biomineralization templates capable of surface reconfiguration. Molecular dynamic simulations reveal that surface reconfigurability is key to promoting template–polymer interactions, thereby lowering polymer nucleation barrier. Employing ionic-liquid-based dynamic template during meniscus-guided coating results inmore » highly aligned, highly crystalline donor-acceptor polymer thin films over large area (41cm 2) and promoted charge transport along both the polymer backbone and the π-π stacking direction in field-effect transistors. We further demonstrate that the charge transport anisotropy can be reversed by tuning the degree of polymer backbone alignment.« less

GATA: A graphic alignment tool for comparative sequenceanalysis

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

Nix, David A.; Eisen, Michael B.

2005-01-01

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

Alignment of dynamic networks.

PubMed

Vijayan, V; Critchlow, D; Milenkovic, T

2017-07-15

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

Alignment of dynamic networks

PubMed Central

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

2017-01-01

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

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.

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.

Piezoelectric Response of Aligned Electrospun Polyvinylidene Fluoride/Carbon Nanotube Nanofibrous Membranes.

PubMed

Wu, Chang-Mou; Chou, Min-Hui; Zeng, Wun-Yuan

2018-06-10

Polyvinylidene fluoride (PVDF) shows piezoelectricity related to its β-phase content and mechanical and electrical properties influenced by its morphology and crystallinity. Electrospinning (ES) can produce ultrafine and well-aligned PVDF nanofibers. In this study, the effects of the presence of carbon nanotubes (CNT) and optimized ES parameters on the crystal structures and piezoelectric properties of aligned PVDF/CNT nanofibrous membranes were examined. The optimal β content and piezoelectric coefficient (d 33 ) of the aligned electrospun PVDF reached 88% and 27.4 pC/N; CNT addition increased the β-phase content to 89% and d 33 to 31.3 pC/N. The output voltages of piezoelectric units with aligned electrospun PVDF/CNT membranes increased linearly with applied loading and showed good stability during cyclic dynamic compression and tension. The sensitivities of the piezoelectric units with the membranes under dynamic compression and tension were 2.26 mV/N and 4.29 mV/%, respectively. In bending tests, the output voltage increased nonlinearly with bending angle because complicated forces were involved. The output of the aligned membrane-based piezoelectric unit with CNT was 1.89 V at the bending angle of 100°. The high electric outputs indicate that the aligned electrospun PVDF/CNT membranes are potentially effective for flexible wearable sensor application with high sensitivity.

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.

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

PubMed Central

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

2008-01-01

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

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

PubMed Central

2010-01-01

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size. PMID:20565983

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

Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding.

PubMed

Fuchs, Julian E; Waldner, Birgit J; Huber, Roland G; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-03-10

Conformational dynamics are central for understanding biomolecular structure and function, since biological macromolecules are inherently flexible at room temperature and in solution. Computational methods are nowadays capable of providing valuable information on the conformational ensembles of biomolecules. However, analysis tools and intuitive metrics that capture dynamic information from in silico generated structural ensembles are limited. In standard work-flows, flexibility in a conformational ensemble is represented through residue-wise root-mean-square fluctuations or B-factors following a global alignment. Consequently, these approaches relying on global alignments discard valuable information on local dynamics. Results inherently depend on global flexibility, residue size, and connectivity. In this study we present a novel approach for capturing positional fluctuations based on multiple local alignments instead of one single global alignment. The method captures local dynamics within a structural ensemble independent of residue type by splitting individual local and global degrees of freedom of protein backbone and side-chains. Dependence on residue type and size in the side-chains is removed via normalization with the B-factors of the isolated residue. As a test case, we demonstrate its application to a molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) on the millisecond time scale. This allows for illustrating different time scales of backbone and side-chain flexibility. Additionally, we demonstrate the effects of ligand binding on side-chain flexibility of three serine proteases. We expect our new methodology for quantifying local flexibility to be helpful in unraveling local changes in biomolecular dynamics.

Disparate ultrafast dynamics of itinerant and localized magnetic moments in gadolinium metal

PubMed Central

Frietsch, B.; Bowlan, J.; Carley, R.; Teichmann, M.; Wienholdt, S.; Hinzke, D.; Nowak, U.; Carva, K.; Oppeneer, P. M.; Weinelt, M.

2015-01-01

The Heisenberg–Dirac intra-atomic exchange coupling is responsible for the formation of the atomic spin moment and thus the strongest interaction in magnetism. Therefore, it is generally assumed that intra-atomic exchange leads to a quasi-instantaneous aligning process in the magnetic moment dynamics of spins in separate, on-site atomic orbitals. Following ultrashort optical excitation of gadolinium metal, we concurrently record in photoemission the 4f magnetic linear dichroism and 5d exchange splitting. Their dynamics differ by one order of magnitude, with decay constants of 14 versus 0.8 ps, respectively. Spin dynamics simulations based on an orbital-resolved Heisenberg Hamiltonian combined with first-principles calculations explain the particular dynamics of 5d and 4f spin moments well, and corroborate that the 5d exchange splitting traces closely the 5d spin-moment dynamics. Thus gadolinium shows disparate dynamics of the localized 4f and the itinerant 5d spin moments, demonstrating a breakdown of their intra-atomic exchange alignment on a picosecond timescale. PMID:26355196

LAMBADA and InflateGRO2: efficient membrane alignment and insertion of membrane proteins for molecular dynamics simulations.

PubMed

Schmidt, Thomas H; Kandt, Christian

2012-10-22

At the beginning of each molecular dynamics membrane simulation stands the generation of a suitable starting structure which includes the working steps of aligning membrane and protein and seamlessly accommodating the protein in the membrane. Here we introduce two efficient and complementary methods based on pre-equilibrated membrane patches, automating these steps. Using a voxel-based cast of the coarse-grained protein, LAMBADA computes a hydrophilicity profile-derived scoring function based on which the optimal rotation and translation operations are determined to align protein and membrane. Employing an entirely geometrical approach, LAMBADA is independent from any precalculated data and aligns even large membrane proteins within minutes on a regular workstation. LAMBADA is the first tool performing the entire alignment process automatically while providing the user with the explicit 3D coordinates of the aligned protein and membrane. The second tool is an extension of the InflateGRO method addressing the shortcomings of its predecessor in a fully automated workflow. Determining the exact number of overlapping lipids based on the area occupied by the protein and restricting expansion, compression and energy minimization steps to a subset of relevant lipids through automatically calculated and system-optimized operation parameters, InflateGRO2 yields optimal lipid packing and reduces lipid vacuum exposure to a minimum preserving as much of the equilibrated membrane structure as possible. Applicable to atomistic and coarse grain structures in MARTINI format, InflateGRO2 offers high accuracy, fast performance, and increased application flexibility permitting the easy preparation of systems exhibiting heterogeneous lipid composition as well as embedding proteins into multiple membranes. Both tools can be used separately, in combination with other methods, or in tandem permitting a fully automated workflow while retaining a maximum level of usage control and flexibility. To assess the performance of both methods, we carried out test runs using 22 membrane proteins of different size and transmembrane structure.

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.

Model-based estimation and control for off-axis parabolic mirror alignment

NASA Astrophysics Data System (ADS)

Fang, Joyce; Savransky, Dmitry

2018-02-01

This paper propose an model-based estimation and control method for an off-axis parabolic mirror (OAP) alignment. Current studies in automated optical alignment systems typically require additional wavefront sensors. We propose a self-aligning method using only focal plane images captured by the existing camera. Image processing methods and Karhunen-Loève (K-L) decomposition are used to extract measurements for the observer in closed-loop control system. Our system has linear dynamic in state transition, and a nonlinear mapping from the state to the measurement. An iterative extended Kalman filter (IEKF) is shown to accurately predict the unknown states, and nonlinear observability is discussed. Linear-quadratic regulator (LQR) is applied to correct the misalignments. The method is validated experimentally on the optical bench with a commercial OAP. We conduct 100 tests in the experiment to demonstrate the consistency in between runs.

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.

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.

Perception of socket alignment perturbations in amputees with transtibial prostheses.

PubMed

Boone, David A; Kobayashi, Toshiki; Chou, Teri G; Arabian, Adam K; Coleman, Kim L; Orendurff, Michael S; Zhang, Ming

2012-01-01

A person with amputation's subjective perception is the only tool available to describe fit and comfort to a prosthetist. However, few studies have investigated the effect of alignment on this perception. The aim of this article is to determine whether people with amputation could perceive the alignment perturbations of their prostheses and effectively communicate them. A randomized controlled perturbation of angular (3 and 6 degrees) and translational (5 and 10 mm) alignments in the sagittal (flexion, extension, and anterior and posterior translations) and coronal (abduction, adduction, and medial and lateral translations) planes were induced from an aligned condition in 11 subjects with transtibial prostheses. The perception was evaluated when standing (static) and immediately after walking (dynamic) using software that used a visual analog scale under each alignment condition. In the coronal plane, Friedman test demonstrated general statistical differences in static (p < 0.001) and dynamic (p < 0.001) measures of perceptions with angular perturbations. In the sagittal plane, it also demonstrated general statistical differences in late-stance dynamic measures of perceptions (p < 0.001) with angular perturbations, as well as in early-stance dynamic measures of perceptions (p < 0.05) with translational perturbations. Fisher exact test suggested that people with amputation's perceptions were good indicators for coronal angle malalignments but less reliable when defining other alignment conditions.

Optical mounts for harsh environments

NASA Astrophysics Data System (ADS)

Mimovich, Mark E.; Griffee, Jonathan C.; Goodding, James C.

2009-08-01

Development and testing of a lightweight-kinematic optical mount with integrated passive vibration-and-shock mitigation technologies and simple / robust optical alignment functionality is presented. Traditionally, optical mounts are designed for use in laboratory environments where the thermal-mechanical environments are carefully controlled to preserve beam path conditions and background disturbances are minimized to facilitate precise optically based measurements. Today's weapon and surveillance systems, however, have optical sensor suites where static and dynamic alignment performance in the presence of harsh operating environments is required to nearly the same precision and where the system cannot afford the mass of laboratory-grade stabilized mounting systems. Jitter and alignment stability is particularly challenging for larger optics operating within moving vehicles and aircraft where high shock and significant temperature excursions occur. The design intent is to have the mount be suitable for integration into existing defense and security optical systems while also targeting new commercial and military components for improved structural dynamic and thermal distortion performance. A mount suitable for moderate-sized optics and an integrated disturbance-optical metrology system are described. The mount design has performance enhancements derived from the integration of proven aerospace mechanical vibration and shock mitigation technologies (i.e. multi-axis passive isolation and integral damping), precision alignment adjustment and lock-out functionality, high dimensional stability materials and design practices which provide benign optical surface figure errors under harsh thermal-mechanical loading. Optical jitter, alignment, and wave-front performance testing of an eight-inch-aperture optical mount based on this design approach are presented to validate predicted performance improvements over an existing commercial off-the-shelf (COTS) design.

High dynamic range image acquisition based on multiplex cameras

NASA Astrophysics Data System (ADS)

Zeng, Hairui; Sun, Huayan; Zhang, Tinghua

2018-03-01

High dynamic image is an important technology of photoelectric information acquisition, providing higher dynamic range and more image details, and it can better reflect the real environment, light and color information. Currently, the method of high dynamic range image synthesis based on different exposure image sequences cannot adapt to the dynamic scene. It fails to overcome the effects of moving targets, resulting in the phenomenon of ghost. Therefore, a new high dynamic range image acquisition method based on multiplex cameras system was proposed. Firstly, different exposure images sequences were captured with the camera array, using the method of derivative optical flow based on color gradient to get the deviation between images, and aligned the images. Then, the high dynamic range image fusion weighting function was established by combination of inverse camera response function and deviation between images, and was applied to generated a high dynamic range image. The experiments show that the proposed method can effectively obtain high dynamic images in dynamic scene, and achieves good results.

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

PubMed

Cao, Hu; Lu, Yonggang

2017-01-01

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

Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines.

PubMed

Oliveira, Francisco P M; Tavares, João Manuel R S

2013-03-01

This article presents an enhanced methodology to align plantar pressure image sequences simultaneously in time and space. The temporal alignment of the sequences is accomplished using B-splines in the time modeling, and the spatial alignment can be attained using several geometric transformation models. The methodology was tested on a dataset of 156 real plantar pressure image sequences (3 sequences for each foot of the 26 subjects) that was acquired using a common commercial plate during barefoot walking. In the alignment of image sequences that were synthetically deformed both in time and space, an outstanding accuracy was achieved with the cubic B-splines. This accuracy was significantly better (p < 0.001) than the one obtained using the best solution proposed in our previous work. When applied to align real image sequences with unknown transformation involved, the alignment based on cubic B-splines also achieved superior results than our previous methodology (p < 0.001). The consequences of the temporal alignment on the dynamic center of pressure (COP) displacement was also assessed by computing the intraclass correlation coefficients (ICC) before and after the temporal alignment of the three image sequence trials of each foot of the associated subject at six time instants. The results showed that, generally, the ICCs related to the medio-lateral COP displacement were greater when the sequences were temporally aligned than the ICCs of the original sequences. Based on the experimental findings, one can conclude that the cubic B-splines are a remarkable solution for the temporal alignment of plantar pressure image sequences. These findings also show that the temporal alignment can increase the consistency of the COP displacement on related acquired plantar pressure image sequences.

Note: A simple image processing based fiducial auto-alignment method for sample registration.

PubMed

Robertson, Wesley D; Porto, Lucas R; Ip, Candice J X; Nantel, Megan K T; Tellkamp, Friedjof; Lu, Yinfei; Miller, R J Dwayne

2015-08-01

A simple method for the location and auto-alignment of sample fiducials for sample registration using widely available MATLAB/LabVIEW software is demonstrated. The method is robust, easily implemented, and applicable to a wide variety of experiment types for improved reproducibility and increased setup speed. The software uses image processing to locate and measure the diameter and center point of circular fiducials for distance self-calibration and iterative alignment and can be used with most imaging systems. The method is demonstrated to be fast and reliable in locating and aligning sample fiducials, provided here by a nanofabricated array, with accuracy within the optical resolution of the imaging system. The software was further demonstrated to register, load, and sample the dynamically wetted array.

Effects of geometry and cell-matrix interactions on the mechanics of 3D engineered microtissues

NASA Astrophysics Data System (ADS)

Bose, Prasenjit; Eyckmans, Jeroen; Chen, Christopher; Reich, Daniel

Approaches to measure and control cell-extracellular matrix (ECM) interactions in a dynamic mechanical environment are important both for studies of mechanobiology and for tissue design for bioengineering applications. We have developed a microtissue-based platform capable of controlling the ECM alignment of 3D engineered microtissues while simultaneously permitting measurement of cellular contractile forces and the tissues' mechanical properties. The tissues self-assemble from cell-laden collagen gels placed in micro-fabricated wells containing sets of flexible elastic pillars. Tissue geometry and ECM alignment are controlled by the pillars' number, shape and location. Optical tracking of the pillars provides readout of the tissues' contractile forces. Magnetic materials bound to selected pillars allow quasi-static or dynamic stretching of the tissue, and together with simultaneous measurements of the tissues' local dynamic strain field, enable characterization of the mechanical properties of the system, including their degree of anisotropy. Results on the effects of symmetry and degree of ECM alignment and organization on the role of cell-ECM interactions in determining tissue mechanical properties will be discussed. This work is supported by NSF CMMI-1463011 and CMMI-1462710.

Theory of the deformation of aligned polyethylene.

PubMed

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

2015-08-08

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

Flexible Semitransparent Energy Harvester with High Pressure Sensitivity and Power Density Based on Laterally Aligned PZT Single-Crystal Nanowires.

PubMed

Zhao, Quan-Liang; He, Guang-Ping; Di, Jie-Jian; Song, Wei-Li; Hou, Zhi-Ling; Tan, Pei-Pei; Wang, Da-Wei; Cao, Mao-Sheng

2017-07-26

A flexible semitransparent energy harvester is assembled based on laterally aligned Pb(Zr 0.52 Ti 0.48 )O 3 (PZT) single-crystal nanowires (NWs). Such a harvester presents the highest open-circuit voltage and a stable area power density of up to 10 V and 0.27 μW/cm 2 , respectively. A high pressure sensitivity of 0.14 V/kPa is obtained in the dynamic pressure sensing, much larger than the values reported in other energy harvesters based on piezoelectric single-crystal NWs. Furthermore, theoretical and finite element analyses also confirm that the piezoelectric voltage constant g 33 of PZT NWs is competitive to the lead-based bulk single crystals and ceramics, and the enhanced pressure sensitivity and power density are substantially linked to the flexible structure with laterally aligned PZT NWs. The energy harvester in this work holds great potential in flexible and transparent sensing and self-powered systems.

A polarized view on DNA under tension

NASA Astrophysics Data System (ADS)

van Mameren, Joost; Vermeulen, Karen; Wuite, Gijs J. L.; Peterman, Erwin J. G.

2018-03-01

In the past decades, sensitive fluorescence microscopy techniques have contributed significantly to our understanding of the dynamics of DNA. The specific labeling of DNA using intercalating dyes has allowed for quantitative measurement of the thermal fluctuations the polymers undergo. On the other hand, recent advances in single-molecule manipulation techniques have unraveled the mechanical and elastic properties of this intricate polymer. Here, we have combined these two approaches to study the conformational dynamics of DNA under a wide range of tensions. Using polarized fluorescence microscopy in conjunction with optical-tweezers-based manipulation of YOYO-intercalated DNA, we controllably align the YOYO dyes using DNA tension, enabling us to disentangle the rapid dynamics of the dyes from that of the DNA itself. With unprecedented control of the DNA alignment, we resolve an inconsistency in reports about the tilted orientation of intercalated dyes. We find that intercalated dyes are on average oriented perpendicular to the long axis of the DNA, yet undergo fast dynamics on the time scale of absorption and fluorescence emission. In the overstretching transition of double-stranded DNA, we do not observe changes in orientation or orientational dynamics of the dyes. Only beyond the overstretching transition, a considerable depolarization is observed, presumably caused by an average tilting of the DNA base pairs. Our combined approach thus contributes to the elucidation of unique features of the molecular dynamics of DNA.

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.

The dynamic nature of alignment and variations in normal knees.

PubMed

Deep, K; Eachempati, K K; Apsingi, S

2015-04-01

The restoration of knee alignment is an important goal during total knee arthroplasty (TKA). In the past surgeons aimed to restore neutral limb alignment during surgery. However, previous studies have demonstrated alignment to be dynamic, varying depending on the position of the limb and the degree of weight-bearing, and between patients. We used a validated computer navigation system to measure the femorotibial mechanical angle (FTMA) in 264 knees in 77 male and 55 female healthy volunteers aged 18 to 35 years (mean 26.2). We found the mean supine alignment to be a varus angle of 1.2° (standard deviation (sd) 4), with few patients having neutral alignment. FTMA differs significantly between males and females (with a mean varus of 1.7° (sd 4) and 0.4° (sd 3.9), respectively; p = 0.008). It changes significantly with posture, the knee hyperextending by a mean of 5.6°, and coronal plane alignment becoming more varus by 2.2° (sd 3.6) on standing compared with supine. Knee alignment is different in different individuals and is dynamic in nature, changing with different postures. This may have implications for the assessment of alignment in TKA, which is achieved in non-weight-bearing conditions and which may not represent the situation observed during weight-bearing. ©2015 The British Editorial Society of Bone & Joint Surgery.

A hybrid short read mapping accelerator

PubMed Central

2013-01-01

Background The rapid growth of short read datasets poses a new challenge to the short read mapping problem in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing the alignments to improve speed, whereas more flexible error models are generally too slow for large-scale applications. A number of short read mapping software tools have been proposed. However, designs based on hardware are relatively rare. Field programmable gate arrays (FPGAs) have been successfully used in a number of specific application areas, such as the DSP and communications domains due to their outstanding parallel data processing capabilities, making them a competitive platform to solve problems that are “inherently parallel”. Results We present a hybrid system for short read mapping utilizing both FPGA-based hardware and CPU-based software. The computation intensive alignment and the seed generation operations are mapped onto an FPGA. We present a computationally efficient, parallel block-wise alignment structure (Align Core) to approximate the conventional dynamic programming algorithm. The performance is compared to the multi-threaded CPU-based GASSST and BWA software implementations. For single-end alignment, our hybrid system achieves faster processing speed than GASSST (with a similar sensitivity) and BWA (with a higher sensitivity); for pair-end alignment, our design achieves a slightly worse sensitivity than that of BWA but has a higher processing speed. Conclusions This paper shows that our hybrid system can effectively accelerate the mapping of short reads to a reference genome based on the seed-and-extend approach. The performance comparison to the GASSST and BWA software implementations under different conditions shows that our hybrid design achieves a high degree of sensitivity and requires less overall execution time with only modest FPGA resource utilization. Our hybrid system design also shows that the performance bottleneck for the short read mapping problem can be changed from the alignment stage to the seed generation stage, which provides an additional requirement for the future development of short read aligners. PMID:23441908

Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria

PubMed Central

Balagam, Rajesh; Igoshin, Oleg A.

2015-01-01

Myxococcus xanthus cells self-organize into aligned groups, clusters, at various stages of their lifecycle. Formation of these clusters is crucial for the complex dynamic multi-cellular behavior of these bacteria. However, the mechanism underlying the cell alignment and clustering is not fully understood. Motivated by studies of clustering in self-propelled rods, we hypothesized that M. xanthus cells can align and form clusters through pure mechanical interactions among cells and between cells and substrate. We test this hypothesis using an agent-based simulation framework in which each agent is based on the biophysical model of an individual M. xanthus cell. We show that model agents, under realistic cell flexibility values, can align and form cell clusters but only when periodic reversals of cell directions are suppressed. However, by extending our model to introduce the observed ability of cells to deposit and follow slime trails, we show that effective trail-following leads to clusters in reversing cells. Furthermore, we conclude that mechanical cell alignment combined with slime-trail-following is sufficient to explain the distinct clustering behaviors observed for wild-type and non-reversing M. xanthus mutants in recent experiments. Our results are robust to variation in model parameters, match the experimentally observed trends and can be applied to understand surface motility patterns of other bacterial species. PMID:26308508

Analytical structure, dynamics, and coarse graining of a kinetic model of an active fluid

NASA Astrophysics Data System (ADS)

Gao, Tong; Betterton, Meredith D.; Jhang, An-Sheng; Shelley, Michael J.

2017-09-01

We analyze one of the simplest active suspensions with complex dynamics: a suspension of immotile "extensor" particles that exert active extensile dipolar stresses on the fluid in which they are immersed. This is relevant to several experimental systems, such as recently studied tripartite rods that create extensile flows by consuming a chemical fuel. We first describe the system through a Doi-Onsager kinetic theory based on microscopic modeling. This theory captures the active stresses produced by the particles that can drive hydrodynamic instabilities, as well as the steric interactions of rodlike particles that lead to nematic alignment. This active nematic system yields complex flows and disclination defect dynamics very similar to phenomenological Landau-deGennes Q -tensor theories for active nematic fluids, as well as by more complex Doi-Onsager theories for polar microtubule-motor-protein systems. We apply the quasiequilibrium Bingham closure, used to study suspensions of passive microscopic rods, to develop a nonstandard Q -tensor theory. We demonstrate through simulation that this B Q -tensor theory gives an excellent analytical and statistical accounting of the suspension's complex dynamics, at a far reduced computational cost. Finally, we apply the B Q -tensor model to study the dynamics of extensor suspensions in circular and biconcave domains. In circular domains, we reproduce previous results for systems with weak nematic alignment, but for strong alignment we find unusual dynamics with activity-controlled defect production and absorption at the boundaries of the domain. In biconcave domains, a Fredericks-like transition occurs as the width of the neck connecting the two disks is varied.

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/

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

In-flight alignment using H ∞ filter for strapdown INS on aircraft.

PubMed

Pei, Fu-Jun; Liu, Xuan; Zhu, Li

2014-01-01

In-flight alignment is an effective way to improve the accuracy and speed of initial alignment for strapdown inertial navigation system (INS). During the aircraft flight, strapdown INS alignment was disturbed by lineal and angular movements of the aircraft. To deal with the disturbances in dynamic initial alignment, a novel alignment method for SINS is investigated in this paper. In this method, an initial alignment error model of SINS in the inertial frame is established. The observability of the system is discussed by piece-wise constant system (PWCS) theory and observable degree is computed by the singular value decomposition (SVD) theory. It is demonstrated that the system is completely observable, and all the system state parameters can be estimated by optimal filter. Then a H ∞ filter was designed to resolve the uncertainty of measurement noise. The simulation results demonstrate that the proposed algorithm can reach a better accuracy under the dynamic disturbance condition.

Molecular alignment and orientation with a hybrid Raman scattering technique

NASA Astrophysics Data System (ADS)

Bustard, Philip J.; Lausten, R.; Sussman, Benjamin J.

2012-11-01

We demonstrate a scheme for the preparation of molecular alignment and angular momentum orientation using a hybrid combination of two limits of Raman scattering. First a weak, impulsive pump pulse initializes the system via the nonresonant dynamic Stark effect. Then, having overcome the influence of the vacuum fluctuations, an amplification pulse selectively enhances the initial coherences by transient stimulated Raman scattering, generating alignment and angular momentum orientation of molecular hydrogen. The amplitude and phase of the resulting coherent dynamics are experimentally probed, indicating an amplification factor of 4.5. An analytic theory is developed to model the dynamics.

Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.

PubMed

Salmon, Loïc; Giambaşu, George M; Nikolova, Evgenia N; Petzold, Katja; Bhattacharya, Akash; Case, David A; Al-Hashimi, Hashim M

2015-10-14

Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution.

Quadrupole Alignment and Trajectory Correction for Future Linear Colliders: SLC Tests of a Dispersion-Free Steering Algorithm

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

Assmann, R

2004-06-08

The feasibility of future linear colliders depends on achieving very tight alignment and steering tolerances. All proposals (NLC, JLC, CLIC, TESLA and S-BAND) currently require a total emittance growth in the main linac of less than 30-100% [1]. This should be compared with a 100% emittance growth in the much smaller SLC linac [2]. Major advances in alignment and beam steering techniques beyond those used in the SLC are necessary for the next generation of linear colliders. In this paper, we present an experimental study of quadrupole alignment with a dispersion-free steering algorithm. A closely related method (wakefield-free steering) takesmore » into account wakefield effects [3]. However, this method can not be studied at the SLC. The requirements for future linear colliders lead to new and unconventional ideas about alignment and beam steering. For example, no dipole correctors are foreseen for the standard trajectory correction in the NLC [4]; beam steering will be done by moving the quadrupole positions with magnet movers. This illustrates the close symbiosis between alignment, beam steering and beam dynamics that will emerge. It is no longer possible to consider the accelerator alignment as static with only a few surveys and realignments per year. The alignment in future linear colliders will be a dynamic process in which the whole linac, with thousands of beam-line elements, is aligned in a few hours or minutes, while the required accuracy of about 5 pm for the NLC quadrupole alignment [4] is a factor of 20 higher than in existing accelerators. The major task in alignment and steering is the accurate determination of the optimum beam-line position. Ideally one would like all elements to be aligned along a straight line. However, this is not practical. Instead a ''smooth curve'' is acceptable as long as its wavelength is much longer than the betatron wavelength of the accelerated beam. Conventional alignment methods are limited in accuracy by errors in the survey and the fiducials. Beam-based alignment methods ideally only depend upon the BPM resolution and generally provide much better precision. Many of those techniques are described in other contributions to this workshop. In this paper we describe our experiences with a dispersion-free steering algorithm for linacs. This algorithm was first suggested by Raubenheimer and Ruth in 1990 [5]. It h as been studied in simulations for NLC [5], TESLA [6], the S-BAND proposal [7] and CLIC [8]. The dispersion-free steering technique can be applied to the whole linac at once and returns the alignment (or trajectory) that minimizes the dispersive emittance growth of the beam. Thus it allows an extremely fast alignment of the beam-line. As we will show dispersion-free steering is only sensitive to quadrupole misalignments. Wakefield-free steering [3] as mentioned before is a closely related technique that minimizes the emittance growth caused by both dispersion and wakefields. Due to hardware limitations (i.e. insufficient relative range of power supplies) we could not study this method experimentally in the SLC. However, its systematics are very similar to those of dispersion-free steering. The studies of dispersion-free steering which are presented made extensive use of the unique potential of the SLC as the only operating linear collider. We used it to study the performance and problems of advanced beam-based optimization tools in a real beam-line environment and on a large scale. We should mention that the SLC has utilized beam-based alignment for years [9], using the difference of electron and positron trajectories. This method, however, cannot be used in future linear colliders. The goal of our work is to demonstrate the performance of advanced beam-based alignment techniques in linear colliders and to anticipate possible reality-related problems. Those can then be solved in the design state for the next generation of linear colliders.« less

Probing topology and dynamics of the second transmembrane domain (M2δ) of the acetyl choline receptor using magnetically aligned lipid bilayers (bicelles) and EPR spectroscopy.

PubMed

Sahu, Indra D; Mayo, Daniel J; Subbaraman, Nidhi; Inbaraj, Johnson J; McCarrick, Robert M; Lorigan, Gary A

2017-08-01

Characterizing membrane protein structure and dynamics in the lipid bilayer membrane is very important but experimentally challenging. EPR spectroscopy offers a unique set of techniques to investigate a membrane protein structure, dynamics, topology, and distance constraints in lipid bilayers. Previously our lab demonstrated the use of magnetically aligned phospholipid bilayers (bicelles) for probing topology and dynamics of the membrane peptide M2δ of the acetyl choline receptor (AchR) as a proof of concept. In this study, magnetically aligned phospholipid bilayers and rigid spin labels were further utilized to provide improved dynamic information and topology of M2δ peptide. Seven TOAC-labeled AchR M2δ peptides were synthesized to demonstrate the utility of a multi-labeling amino acid substitution alignment strategy. Our data revealed the helical tilts to be 11°, 17°, 9°, 17°, 16°, 11°, 9°±4° for residues I7TOAC, Q13TOAC, A14TOAC, V15TOAC, C16TOAC, L17TOAC, and L18TOAC, respectively. The average helical tilt of the M2δ peptide was determined to be ∼13°. This study also revealed that the TOAC labels were attached to the M2δ peptide with different dynamics suggesting that the sites towards the C-terminal end are more rigid when compared to the sites towards the N-terminus. The dynamics of the TOAC labeled sites were more resolved in the aligned samples when compared to the randomly disordered samples. This study highlights the use of magnetically aligned lipid bilayer EPR technique to determine a more accurate helical tilt and more resolved local dynamics of AchR M2δ peptide. Copyright © 2017 Elsevier B.V. All rights reserved.

Dissipation dynamics of field-free molecular alignment for symmetric-top molecules: Ethane (C2H6)

NASA Astrophysics Data System (ADS)

Zhang, H.; Billard, F.; Yu, X.; Faucher, O.; Lavorel, B.

2018-03-01

The field-free molecular alignment of symmetric-top molecules, ethane, induced by intense non-resonant linearly polarized femtosecond laser pulses is investigated experimentally in the presence of collisional relaxation. The dissipation dynamics of field-free molecular alignment are measured by the balanced detection of ultrafast molecular birefringence of ethane gas samples at high pressures. By separating the molecular alignment into the permanent alignment and the transient alignment, the decay time-constants of both components are quantified at the same pressure. It is observed that the permanent alignment always decays slower compared to the transient alignment within the measured pressure range. This demonstrates that the propensity of molecules to conserve the orientation of angular momentum during collisions, previously observed for linear species, is also applicable to symmetric-top molecules. The results of this work provide valuable information for further theoretical understanding of collisional relaxation within nonlinear polyatomic molecules, which are expected to present interesting and nontrivial features due to an extra rotational degree of freedom.

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.

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.

libgapmis: extending short-read alignments

PubMed Central

2013-01-01

Background A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. Results In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. Conclusions We present libgapmis, a library for extending pairwise short-read alignments. We show that libgapmis is better-suited and more efficient than existing algorithms for this task. The importance of our contribution is underlined by the fact that the provided functions may be seamlessly integrated into any short-read alignment pipeline. The open-source code of libgapmis is available at http://www.exelixis-lab.org/gapmis. PMID:24564250

European Scientific Notes. Volume 37, Number 1.

DTIC Science & Technology

1983-01-31

instantoneous sea-state condition can be tions vary widely in their realism , with computed from a special data base coded some producing dynamic color pictures...between the variables of accuracy, approach channels, the alignment of practicality, realism , and expense. jetties, and the establishment of Because the...tidal current variables The system certainly seems to be valid, have been played into some of the and the smooth dynamics, realism , and simulator runs

Mirroring and beyond: coupled dynamics as a generalized framework for modelling social interactions

PubMed Central

Hasson, Uri; Frith, Chris D.

2016-01-01

When people observe one another, behavioural alignment can be detected at many levels, from the physical to the mental. Likewise, when people process the same highly complex stimulus sequences, such as films and stories, alignment is detected in the elicited brain activity. In early sensory areas, shared neural patterns are coupled to the low-level properties of the stimulus (shape, motion, volume, etc.), while in high-order brain areas, shared neural patterns are coupled to high-levels aspects of the stimulus, such as meaning. Successful social interactions require such alignments (both behavioural and neural), as communication cannot occur without shared understanding. However, we need to go beyond simple, symmetric (mirror) alignment once we start interacting. Interactions are dynamic processes, which involve continuous mutual adaptation, development of complementary behaviour and division of labour such as leader–follower roles. Here, we argue that interacting individuals are dynamically coupled rather than simply aligned. This broader framework for understanding interactions can encompass both processes by which behaviour and brain activity mirror each other (neural alignment), and situations in which behaviour and brain activity in one participant are coupled (but not mirrored) to the dynamics in the other participant. To apply these more sophisticated accounts of social interactions to the study of the underlying neural processes we need to develop new experimental paradigms and novel methods of data analysis PMID:27069044

Grasping Beer Mugs: On the Dynamics of Alignment Effects Induced by Handled Objects

ERIC Educational Resources Information Center

Bub, Daniel N.; Masson, Michael E. J.

2010-01-01

We examined automatic spatial alignment effects evoked by handled objects. Using color as the relevant cue carried by an irrelevant handled object aligned or misaligned with the response hand, responses to color were faster when the handle aligned with the response hand. Alignment effects were observed only when the task was to make a reach and…

Stability limits and dynamics of nonaxisymmetric liquid bridges

NASA Technical Reports Server (NTRS)

Alexander, J. Iwan D.; Resnik, Andy; Kaukler, William F.

1993-01-01

This program of theoretical and experimental ground-based and low gravity research is focussed on the understanding of the dynamics and stability limits of nonaxisymmetric liquid bridges. There are three basic objectives to the proposed work: (1) to determine the stability limits of nonaxisymmetric liquid bridges held between non-coaxially aligned disks; (2) to examine the dynamics of nonaxisymmetric bridges and nonaxisymmetric oscillations of initially axisymmetric bridges (some of these experiments require a low gravity environment and the ground-based research will culminate in a definitive flight experiment); and (3) to experimentally investigate the vibration sensitivity of liquid bridges under terrestrial and low gravity conditions.

Liquid crystal dynamic flow control by bidirectional alignment surface

NASA Astrophysics Data System (ADS)

Li, Y. W.; Lee, C. Y.; Kwok, H. S.

2009-02-01

We investigate the behavior of liquid crystal dynamic flow in a cell with a bidirectional alignment (BDA) surface. Numerical simulations show that with a BDA surface having a pitch comparable to the cell gap d, the liquid crystal dynamic flow direction can be controlled by the driving voltage. Such an effect can be applied to bistable twisted nematic displays without the need for anchoring breaking.

Enhancing the Motor Skills of Children with Autism Spectrum Disorders: A Pool-Based Approach

ERIC Educational Resources Information Center

Lee, Jihyun; Porretta, David L.

2013-01-01

Children with autism spectrum disorders (ASDs) often experience difficulties with motor skill learning and performance. The pool is a unique learning environment that can help children with ASDs learn or improve aquatic skills, fitness, and social skills. A pool-based approach is also aligned with the elements of dynamic systems theory, which…

Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations.

PubMed

Linke, Max; Köfinger, Jürgen; Hummer, Gerhard

2018-05-31

We present a method to calculate the fully anisotropic rotational diffusion tensor from molecular dynamics simulations. Our approach is based on fitting the time-dependent covariance matrix of the quaternions that describe the rigid-body rotational dynamics. Explicit analytical expressions have been derived for the covariances by Favro, which are valid irrespective of the degree of anisotropy. We use these expressions to determine an optimal rotational diffusion tensor from trajectory data. The molecular structures are aligned against a reference by optimal rigid-body superposition. The quaternion covariances can then be obtained directly from the rotation matrices used in the alignment. The rotational diffusion tensor is determined by a fit to the time-dependent quaternion covariances, or directly by Laplace transformation and matrix diagonalization. To quantify uncertainties in the fit, we derive analytical expressions and compare them with the results of Brownian dynamics simulations of anisotropic rotational diffusion. We apply the method to microsecond long trajectories of the Dickerson-Drew B-DNA dodecamer and of horse heart myoglobin. The anisotropic rotational diffusion tensors calculated from simulations agree well with predictions from hydrodynamics.

In-Flight Alignment Using H ∞ Filter for Strapdown INS on Aircraft

PubMed Central

Pei, Fu-Jun; Liu, Xuan; Zhu, Li

2014-01-01

In-flight alignment is an effective way to improve the accuracy and speed of initial alignment for strapdown inertial navigation system (INS). During the aircraft flight, strapdown INS alignment was disturbed by lineal and angular movements of the aircraft. To deal with the disturbances in dynamic initial alignment, a novel alignment method for SINS is investigated in this paper. In this method, an initial alignment error model of SINS in the inertial frame is established. The observability of the system is discussed by piece-wise constant system (PWCS) theory and observable degree is computed by the singular value decomposition (SVD) theory. It is demonstrated that the system is completely observable, and all the system state parameters can be estimated by optimal filter. Then a H ∞ filter was designed to resolve the uncertainty of measurement noise. The simulation results demonstrate that the proposed algorithm can reach a better accuracy under the dynamic disturbance condition. PMID:24511300

Living nanofiber yarn-based woven biotextiles for tendon tissue engineering using cell tri-culture and mechanical stimulation.

PubMed

Wu, Shaohua; Wang, Ying; Streubel, Philipp N; Duan, Bin

2017-10-15

Non-woven nanofibrous scaffolds have been developed for tendon graft application by using electrospinning strategies. However, electrospun nanofibrous scaffolds face some obstacles and limitations, including suboptimal scaffold structure, weak tensile and suture-retention strengths, and compact structure for cell infiltration. In this work, a novel nanofibrous, woven biotextile, fabricated based on electrospun nanofiber yarns, was implemented as a tissue engineered tendon scaffold. Based on our modified electrospinning setup, polycaprolactone (PCL) nanofiber yarns were fabricated with reproducible quality, and were further processed into plain-weaving fabrics interlaced with polylactic acid (PLA) multifilaments. Nonwoven nanofibrous PCL meshes with random or aligned fiber structures were generated using typical electrospinning as comparative counterparts. The woven fabrics contained 3D aligned microstructures with significantly larger pore size and obviously enhanced tensile mechanical properties than their nonwoven counterparts. The biological results revealed that cell proliferation and infiltration, along with the expression of tendon-specific genes by human adipose derived mesenchymal stem cells (HADMSC) and human tenocytes (HT), were significantly enhanced on the woven fabrics compared with those on randomly-oriented or aligned nanofiber meshes. Co-cultures of HADMSC with HT or human umbilical vein endothelial cells (HUVEC) on woven fabrics significantly upregulated the functional expression of most tenogenic markers. HADMSC/HT/HUVEC tri-culture on woven fabrics showed the highest upregulation of most tendon-associated markers than all the other mono- and co-culture groups. Furthermore, we conditioned the tri-cultured constructs with dynamic conditioning and demonstrated that dynamic stretch promoted total collagen secretion and tenogenic differentiation. Our nanofiber yarn-based biotextiles have significant potential to be used as engineered scaffolds to synergize the multiple cell interaction and mechanical stimulation for promoting tendon regeneration. Tendon grafts are essential for the treatment of various tendon-related conditions due to the inherently poor healing capacity of native tendon tissues. In this study, we combined electrospun nanofiber yarns with textile manufacturing strategies to fabricate nanofibrous woven biotextiles with hierarchical features, aligned fibrous topography, and sufficient mechanical properties as tendon tissue engineered scaffolds. Comparing to traditional electrospun random or aligned meshes, our novel nanofibrous woven fabrics possess strong tensile and suture-retention strengths and larger pore size. We also demonstrated that the incorporation of tendon cells and vascular cells promoted the tenogenic differentiation of the engineered tendon constructs, especially under dynamic stretch. This study not only presents a novel tissue engineered tendon scaffold fabrication technique but also provides a useful strategy to promote tendon differentiation and regeneration. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

TLM-PSD model for optimization of energy and power density of vertically aligned carbon nanotube supercapacitor

PubMed Central

Ghosh, Arunabha; Le, Viet Thong; Bae, Jung Jun; Lee, Young Hee

2013-01-01

Electrochemical capacitors with fast charging-discharging rates are very promising for hybrid electric vehicle industries including portable electronics. Complicated pore structures have been implemented in active materials to increase energy storage capacity, which often leads to degrade dynamic response of ions. In order to understand this trade-off phenomenon, we report a theoretical model based on transmission line model which is further combined with pore size distribution function. The model successfully explained how pores length, and pore radius of active materials and electrolyte conductivity can affect capacitance and dynamic performance of different capacitors. The powerfulness of the model was confirmed by comparing with experimental results of a micro-supercapacitor consisted of vertically aligned multiwalled carbon nanotubes (v-MWCNTs), which revealed a linear current increase up to 600 Vs−1 scan rate demonstrating an ultrafast dynamic behavior, superior to randomly entangled singlewalled carbon nanotube device, which is clearly explained by the theoretical model. PMID:24145831

Robust temporal alignment of multimodal cardiac sequences

NASA Astrophysics Data System (ADS)

Perissinotto, Andrea; Queirós, Sandro; Morais, Pedro; Baptista, Maria J.; Monaghan, Mark; Rodrigues, Nuno F.; D'hooge, Jan; Vilaça, João. L.; Barbosa, Daniel

2015-03-01

Given the dynamic nature of cardiac function, correct temporal alignment of pre-operative models and intraoperative images is crucial for augmented reality in cardiac image-guided interventions. As such, the current study focuses on the development of an image-based strategy for temporal alignment of multimodal cardiac imaging sequences, such as cine Magnetic Resonance Imaging (MRI) or 3D Ultrasound (US). First, we derive a robust, modality-independent signal from the image sequences, estimated by computing the normalized cross-correlation between each frame in the temporal sequence and the end-diastolic frame. This signal is a resembler for the left-ventricle (LV) volume curve over time, whose variation indicates different temporal landmarks of the cardiac cycle. We then perform the temporal alignment of these surrogate signals derived from MRI and US sequences of the same patient through Dynamic Time Warping (DTW), allowing to synchronize both sequences. The proposed framework was evaluated in 98 patients, which have undergone both 3D+t MRI and US scans. The end-systolic frame could be accurately estimated as the minimum of the image-derived surrogate signal, presenting a relative error of 1.6 +/- 1.9% and 4.0 +/- 4.2% for the MRI and US sequences, respectively, thus supporting its association with key temporal instants of the cardiac cycle. The use of DTW reduces the desynchronization of the cardiac events in MRI and US sequences, allowing to temporally align multimodal cardiac imaging sequences. Overall, a generic, fast and accurate method for temporal synchronization of MRI and US sequences of the same patient was introduced. This approach could be straightforwardly used for the correct temporal alignment of pre-operative MRI information and intra-operative US images.

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

Heuristic reusable dynamic programming: efficient updates of local sequence alignment.

PubMed

Hong, Changjin; Tewfik, Ahmed H

2009-01-01

Recomputation of the previously evaluated similarity results between biological sequences becomes inevitable when researchers realize errors in their sequenced data or when the researchers have to compare nearly similar sequences, e.g., in a family of proteins. We present an efficient scheme for updating local sequence alignments with an affine gap model. In principle, using the previous matching result between two amino acid sequences, we perform a forward-backward alignment to generate heuristic searching bands which are bounded by a set of suboptimal paths. Given a correctly updated sequence, we initially predict a new score of the alignment path for each contour to select the best candidates among them. Then, we run the Smith-Waterman algorithm in this confined space. Furthermore, our heuristic alignment for an updated sequence shows that it can be further accelerated by using reusable dynamic programming (rDP), our prior work. In this study, we successfully validate "relative node tolerance bound" (RNTB) in the pruned searching space. Furthermore, we improve the computational performance by quantifying the successful RNTB tolerance probability and switch to rDP on perturbation-resilient columns only. In our searching space derived by a threshold value of 90 percent of the optimal alignment score, we find that 98.3 percent of contours contain correctly updated paths. We also find that our method consumes only 25.36 percent of the runtime cost of sparse dynamic programming (sDP) method, and to only 2.55 percent of that of a normal dynamic programming with the Smith-Waterman algorithm.

Mechanisms of the Anterior Cruciate Ligament Injury in Sports Activities: A Twenty-Year Clinical Research of 1,700 Athletes

PubMed Central

Kobayashi, Hirokazu; Kanamura, Tomonao; Koshida, Sentaro; Miyashita, Koji; Okado, Tsuruo; Shimizu, Takuya; Yokoe, Kiyoshi

2010-01-01

The mechanisms of anterior cruciate ligament (ACL) injuries are still inconclusive from an epidemiological standpoint. An epidemiological approach in a large sample group over an appropriate period of years will be necessary to enhance the current knowledge of the ACL injury mechanism. The objective of the study was to investigate the ACL injury occurrence in a large sample over twenty years and demonstrate the relationships between the ACL injury occurrence and the dynamic knee alignment at the time of the injury. We investigated the activity, the injury mechanism, and the dynamic knee alignment at the time of the injury in 1,718 patients diagnosed as having the ACL injuries. Regarding the activity at the time of the injury, “competition ”was the most common, accounting for about half of all the injuries. The current result also showed that the noncontact injury was the most common, which was observed especially in many female athletes. Finally, the dynamic alignment of “Knee-in & Toe- out ”(i.e. dynamic knee valgus) was the most common, accounting for about half. These results enhance our understanding of the ACL injury mechanism and may be used to guide future injury prevention strategies. Key points We investigated the situation of ACL injury occurrence, especially dynamic alignments at the time of injury, in 1,718 patients who had visited our institution for surgery and physical therapy for twenty years. Our epidemiological study of the large patient group revealed that “knee-in & toe-out ”alignment was the most frequently seen at the time of the ACL injury. From an epidemiological standpoint, we need to pay much attention to avoiding “Knee-in & Toe-out ”alignment during sports activities. PMID:24149795

Kinematic Model of Transient Shape-Induced Anisotropy in Dense Granular Flow

NASA Astrophysics Data System (ADS)

Nadler, B.; Guillard, F.; Einav, I.

2018-05-01

Nonspherical particles are ubiquitous in nature and industry, yet previous theoretical models of granular media are mostly limited to systems of spherical particles. The problem is that in systems of nonspherical anisotropic particles, dynamic particle alignment critically affects their mechanical response. To study the tendency of such particles to align, we propose a simple kinematic model that relates the flow to the evolution of particle alignment with respect to each other. The validity of the proposed model is supported by comparison with particle-based simulations for various particle shapes ranging from elongated rice-like (prolate) to flattened lentil-like (oblate) particles. The model shows good agreement with the simulations for both steady-state and transient responses, and advances the development of comprehensive constitutive models for shape-anisotropic particles.

Mechanism of cell alignment in groups of Myxococcus xanthus bacteria

NASA Astrophysics Data System (ADS)

Balgam, Rajesh; Igoshin, Oleg

2015-03-01

Myxococcus xanthus is a model for studying self-organization in bacteria. These flexible cylindrical bacteria move along. In groups, M. xanthus cells align themselves into dynamic cell clusters but the mechanism underlying their formation is unknown. It has been shown that steric interactions can cause alignment in self-propelled hard rods but it is not clear how flexibility and reversals affect the alignment and cluster formation. We have investigated cell alignment process using our biophysical model of M. xanthus cell in an agent-based simulation framework under realistic cell flexibility values. We observed that flexible model cells can form aligned cell clusters when reversals are suppressed but these clusters disappeared when reversals frequency becomes similar to the observed value. However, M. xanthus cells follow slime (polysaccharide gel like material) trails left by other cells and we show that implementing this into our model rescues cell clustering for reversing cells. Our results show that slime following along with periodic cell reversals act as positive feedback to reinforce existing slime trails and recruit more cells. Furthermore, we have observed that mechanical cell alignment combined with slime following is sufficient to explain the distinct clustering patterns of reversing and non-reversing cells as observed in recent experiments. This work is supported by NSF MCB 0845919 and 1411780.

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…

Positioning (Mis)Aligned: The (Un)Making of Intercultural Asynchronous Computer-Mediated Communication

ERIC Educational Resources Information Center

Wu, Zhiwei

2018-01-01

Framed from positioning theory and dynamic systems theory, the paper reports on a naturalistic study involving four Chinese participants and their American peers in an intercultural asynchronous computer-mediated communication (ACMC) activity. Based on the moment-by-moment analysis and triangulation of forum posts, reflective essays, and…

Automatic Construction of English/Chinese Parallel Corpora.

ERIC Educational Resources Information Center

Yang, Christopher C.; Li, Kar Wing

2003-01-01

Discussion of multilingual corpora and cross-lingual information retrieval focuses on research that constructed English/Chinese parallel corpus automatically from the World Wide Web. Presents an alignment method which is based on dynamic programming to identify one-to-one Chinese and English title pairs and discusses results of experiments…

LIMAO: Cross-platform software for simulating laser-induced alignment and orientation dynamics of linear-, symmetric- and asymmetric tops

NASA Astrophysics Data System (ADS)

Szidarovszky, Tamás; Jono, Maho; Yamanouchi, Kaoru

2018-07-01

A user-friendly and cross-platform software called Laser-Induced Molecular Alignment and Orientation simulator (LIMAO) has been developed. The program can be used to simulate within the rigid rotor approximation the rotational dynamics of gas phase molecules induced by linearly polarized intense laser fields at a given temperature. The software is implemented in the Java and Mathematica programming languages. The primary aim of LIMAO is to aid experimental scientists in predicting and analyzing experimental data representing laser-induced spatial alignment and orientation of molecules.

Dynamic programming algorithms for biological sequence comparison.

PubMed

Pearson, W R; Miller, W

1992-01-01

Efficient dynamic programming algorithms are available for a broad class of protein and DNA sequence comparison problems. These algorithms require computer time proportional to the product of the lengths of the two sequences being compared [O(N2)] but require memory space proportional only to the sum of these lengths [O(N)]. Although the requirement for O(N2) time limits use of the algorithms to the largest computers when searching protein and DNA sequence databases, many other applications of these algorithms, such as calculation of distances for evolutionary trees and comparison of a new sequence to a library of sequence profiles, are well within the capabilities of desktop computers. In particular, the results of library searches with rapid searching programs, such as FASTA or BLAST, should be confirmed by performing a rigorous optimal alignment. Whereas rapid methods do not overlook significant sequence similarities, FASTA limits the number of gaps that can be inserted into an alignment, so that a rigorous alignment may extend the alignment substantially in some cases. BLAST does not allow gaps in the local regions that it reports; a calculation that allows gaps is very likely to extend the alignment substantially. Although a Monte Carlo evaluation of the statistical significance of a similarity score with a rigorous algorithm is much slower than the heuristic approach used by the RDF2 program, the dynamic programming approach should take less than 1 hr on a 386-based PC or desktop Unix workstation. For descriptive purposes, we have limited our discussion to methods for calculating similarity scores and distances that use gap penalties of the form g = rk. Nevertheless, programs for the more general case (g = q+rk) are readily available. Versions of these programs that run either on Unix workstations, IBM-PC class computers, or the Macintosh can be obtained from either of the authors.

Further Validation of Simulated Dynamic Interface Testing Techniques as a Tool in the Forecasting of Air Vehicle Deck Limits

DTIC Science & Technology

2010-01-01

UAV Autonomy program which includes intelligent reasoning for autonomy, technologies to enhance see and avoid capabilities, object identification ...along the ship’s base recovery course (BRC). The pilot then flies toward the stern of the ship, aligning his approach path with the ship’s lineup line...quiescent point identification . CONCLUSIONS The primary goal for conducting dynamic interface analysis is to expand existing operating envelopes and

Multi-exposure high dynamic range image synthesis with camera shake correction

NASA Astrophysics Data System (ADS)

Li, Xudong; Chen, Yongfu; Jiang, Hongzhi; Zhao, Huijie

2017-10-01

Machine vision plays an important part in industrial online inspection. Owing to the nonuniform illuminance conditions and variable working distances, the captured image tends to be over-exposed or under-exposed. As a result, when processing the image such as crack inspection, the algorithm complexity and computing time increase. Multiexposure high dynamic range (HDR) image synthesis is used to improve the quality of the captured image, whose dynamic range is limited. Inevitably, camera shake will result in ghost effect, which blurs the synthesis image to some extent. However, existed exposure fusion algorithms assume that the input images are either perfectly aligned or captured in the same scene. These assumptions limit the application. At present, widely used registration based on Scale Invariant Feature Transform (SIFT) is usually time consuming. In order to rapidly obtain a high quality HDR image without ghost effect, we come up with an efficient Low Dynamic Range (LDR) images capturing approach and propose a registration method based on ORiented Brief (ORB) and histogram equalization which can eliminate the illumination differences between the LDR images. The fusion is performed after alignment. The experiment results demonstrate that the proposed method is robust to illumination changes and local geometric distortion. Comparing with other exposure fusion methods, our method is more efficient and can produce HDR images without ghost effect by registering and fusing four multi-exposure images.

Adaptable liquid crystal elastomers with transesterification-based bond exchange reactions.

PubMed

Hanzon, Drew W; Traugutt, Nicholas A; McBride, Matthew K; Bowman, Christopher N; Yakacki, Christopher M; Yu, Kai

2018-02-14

Adaptable liquid crystal elastomers (LCEs) have recently emerged to provide a new and robust method to program monodomain LCE samples. When a constant stress is applied with active bond exchange reactions (BERs), polymer chains and mesogens gradually align in the strain direction. Mesogen alignment is maintained after removing the BER stimulus (e.g. by lowering the temperature) and the programmed LCE samples exhibit free-standing two-way shape switching behavior. Here, a new adaptable main-chain LCE system was developed with thermally induced transesterification BERs. The network combines the conventional properties of LCEs, such as an isotropic phase transition and soft elasticity, with the dynamic features of adaptable network polymers, which are malleable to stress relaxation due to the BERs. Polarized Fourier transform infrared measurements confirmed the alignment of polymer chains and mesogens after strain-induced programming. The influence of the creep stress, temperature, and time on the strain amplitude of two-way shape switching was examined. The LCE network demonstrates an innovative feature of reprogrammability, where the reversible shape-switching memory of programmed LCEs is readily deleted by free-standing heating as random BERs disrupt the mesogen alignment, so LCEs are reprogrammed after returning to the polydomain state. Due to the dynamic nature of the LCE network, it also exhibits a surface welding effect and can be fully dissolved in the organic solvent, which might be utilized for green and sustainable recycling of LCEs.

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

PubMed Central

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

2006-01-01

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

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

USDA-ARS?s Scientific Manuscript database

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

Disruption of sheet-like structures in Alfvénic turbulence by magnetic reconnection

NASA Astrophysics Data System (ADS)

Mallet, A.; Schekochihin, A. A.; Chandran, B. D. G.

2017-07-01

We propose a mechanism whereby the intense, sheet-like structures naturally formed by dynamically aligning Alfvénic turbulence are destroyed by magnetic reconnection at a scale \\hat{λ }_D, larger than the dissipation scale predicted by models of intermittent, dynamically aligning turbulence. The reconnection process proceeds in several stages: first, a linear tearing mode with N magnetic islands grows and saturates, and then the X-points between these islands collapse into secondary current sheets, which then reconnect until the original structure is destroyed. This effectively imposes an upper limit on the anisotropy of the structures within the perpendicular plane, which means that at scale \\hat{λ }_D the turbulent dynamics change: at scales larger than \\hat{λ }_D, the turbulence exhibits scale-dependent dynamic alignment and a spectral index approximately equal to -3/2, while at scales smaller than \\hat{λ }_D, the turbulent structures undergo a succession of disruptions due to reconnection, limiting dynamic alignment, steepening the effective spectral index and changing the final dissipation scale. The scaling of \\hat{λ }_D with the Lundquist (magnetic Reynolds) number S_{L_\\perp } depends on the order of the statistics being considered, and on the specific model of intermittency; the transition between the two regimes in the energy spectrum is predicted at approximately \\hat{λ }_D˜ S_{L_\\perp }^{-0.6}. The spectral index below \\hat{λ }_D is bounded between -5/3 and -2.3. The final dissipation scale is at \\hat{λ }_{η ,∞}˜ S_{L_\\perp }^{-3/4}, the same as the Kolmogorov scale arising in theories of turbulence that do not involve scale-dependent dynamic alignment.

Elastic Characterization of Transversely Isotropic Soft Materials by Dynamic Shear and Asymmetric Indentation

PubMed Central

Namani, R.; Feng, Y.; Okamoto, R. J.; Jesuraj, N.; Sakiyama-Elbert, S. E.; Genin, G. M.; Bayly, P. V.

2012-01-01

The mechanical characterization of soft anisotropic materials is a fundamental challenge because of difficulties in applying mechanical loads to soft matter and the need to combine information from multiple tests. A method to characterize the linear elastic properties of transversely isotropic soft materials is proposed, based on the combination of dynamic shear testing (DST) and asymmetric indentation. The procedure was demonstrated by characterizing a nearly incompressible transversely isotropic soft material. A soft gel with controlled anisotropy was obtained by polymerizing a mixture of fibrinogen and thrombin solutions in a high field magnet (B = 11.7 T); fibrils in the resulting gel were predominantly aligned parallel to the magnetic field. Aligned fibrin gels were subject to dynamic (20–40 Hz) shear deformation in two orthogonal directions. The shear storage modulus was 1.08 ± 0. 42 kPa (mean ± std. dev.) for shear in a plane parallel to the dominant fiber direction, and 0.58 ± 0.21 kPa for shear in the plane of isotropy. Gels were indented by a rectangular tip of a large aspect ratio, aligned either parallel or perpendicular to the normal to the plane of transverse isotropy. Aligned fibrin gels appeared stiffer when indented with the long axis of a rectangular tip perpendicular to the dominant fiber direction. Three-dimensional numerical simulations of asymmetric indentation were used to determine the relationship between direction-dependent differences in indentation stiffness and material parameters. This approach enables the estimation of a complete set of parameters for an incompressible, transversely isotropic, linear elastic material. PMID:22757501

Study on Dynamic Alignment Technology of COIL Resonator

NASA Astrophysics Data System (ADS)

Xiong, M. D.; Zou, X. J.; Guo, J. H.; Jia, S. N.; Zhang2, Z. B.

2006-10-01

The performance of great power chemical oxygen-iodine laser (COIL) beam is decided mostly by resonator mirror maladjustment and environment vibration. To improve the performance of light beam, an auto-alignment device is used in COIL resonator, the device can keep COIL resonator collimating by adjusting the optical components of resonator. So the coupling model of COIL resonator is present. The multivariable self study fuzzy uncoupling arithmetic and six-dimensional micro drive technology are used to design a six-input-three-output uncoupling controller, resulting in the realization of the high precision dynamic alignment. The experiments indicate that the collimating range of this system is 8 mrad, precision is 5 urad and frequency response is 20Hz, which meet the demand of resonator alignment system.

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.

Self-organized sorting limits behavioral variability in swarms

PubMed Central

Copenhagen, Katherine; Quint, David A.; Gopinathan, Ajay

2016-01-01

Swarming is a phenomenon where collective motion arises from simple local interactions between typically identical individuals. Here, we investigate the effects of variability in behavior among the agents in finite swarms with both alignment and cohesive interactions. We show that swarming is abolished above a critical fraction of non-aligners who do not participate in alignment. In certain regimes, however, swarms above the critical threshold can dynamically reorganize and sort out excess non-aligners to maintain the average fraction close to the critical value. This persists even in swarms with a distribution of alignment interactions, suggesting a simple, robust and efficient mechanism that allows heterogeneously mixed populations to naturally regulate their composition and remain in a collective swarming state or even differentiate among behavioral phenotypes. We show that, for evolving swarms, this self-organized sorting behavior can couple to the evolutionary dynamics leading to new evolutionarily stable equilibrium populations set by the physical swarm parameters. PMID:27550316

Self-organized sorting limits behavioral variability in swarms

NASA Astrophysics Data System (ADS)

Copenhagen, Katherine; Quint, David A.; Gopinathan, Ajay

2016-08-01

Swarming is a phenomenon where collective motion arises from simple local interactions between typically identical individuals. Here, we investigate the effects of variability in behavior among the agents in finite swarms with both alignment and cohesive interactions. We show that swarming is abolished above a critical fraction of non-aligners who do not participate in alignment. In certain regimes, however, swarms above the critical threshold can dynamically reorganize and sort out excess non-aligners to maintain the average fraction close to the critical value. This persists even in swarms with a distribution of alignment interactions, suggesting a simple, robust and efficient mechanism that allows heterogeneously mixed populations to naturally regulate their composition and remain in a collective swarming state or even differentiate among behavioral phenotypes. We show that, for evolving swarms, this self-organized sorting behavior can couple to the evolutionary dynamics leading to new evolutionarily stable equilibrium populations set by the physical swarm parameters.

Relationships between field-aligned currents, electric fields, and particle precipitation as observed by Dynamics Explorer-2

NASA Technical Reports Server (NTRS)

Sugiura, M.; Iyemori, T.; Hoffman, R. A.; Maynard, N. C.; Burch, J. L.; Winningham, J. D.

1984-01-01

The relationships between field-aligned currents, electric fields, and particle fluxes are determined using observations from the polar orbiting low-altitude satellite Dynamics Explorer-2. It is shown that the north-south electric field and the east-west magnetic field components are usually highly correlated in the field-aligned current regions. This proportionality observationally proves that the field-aligned current equals the divergence of the height-integrated ionospheric Pedersen current in the meridional plane to a high degree of approximation. As a general rule, in the evening sector the upward field-aligned currents flow in the boundary plasma sheet region and the downward currents flow in the central plasma sheet region. The current densities determined independently from the plasma and magnetic field measurements are compared. Although the current densities deduced from the two methods are in general agreement, the degree and extent of the agreement vary in individual cases.

Relationships between field-aligned currents, electric fields and particle precipitation as observed by dynamics Explorer-2

NASA Technical Reports Server (NTRS)

Sugiura, M.; Iyemori, T.; Hoffman, R. A.; Maynard, N. C.; Burch, J. L.; Winningham, J. D.

1983-01-01

The relationships between field-aligned currents, electric fields, and particle fluxes are determined using observations from the polar orbiting low-altitude satellite Dynamics Explorer-2. It is shown that the north-south electric field and the east-west magnetic field components are usually highly correlated in the field-aligned current regions. This proportionality observationally proves that the field-aligned current equals the divergence of the height-integrated ionospheric Pedersen current in the meridional plane to a high degree of approximation. As a general rule, in the evening sector the upward field-aligned currents flow in the boundary plasma sheet region and the downward currents flow in the central plasma sheet region. The current densities determined independently from the plasma and magnetic field measurements are compared. Although the current densities deduced from the two methods are in general agreement, the degree and extent of the agreement vary in individual cases.

The impact of static stress change, dynamic stress change, and the background stress on aftershock focal mechanisms

USGS Publications Warehouse

Hardebeck, Jeanne L.

2014-01-01

The focal mechanisms of earthquakes in Southern California before and after four M ≥ 6.7 main shocks provide insight into how fault systems respond to stress and changes in stress. The main shock static stress changes have two observed impacts on the seismicity: changing the focal mechanisms in a given location to favor those aligned with the static stress change and changing the spatial distribution of seismicity to favor locations where the static stress change aligns with the background stress. The aftershock focal mechanisms are significantly aligned with the static stress changes for absolute stress changes of ≥ 0.02 MPa, for up to ~20 years following the main shock. The dynamic stress changes have similar, although smaller, effects on the local focal mechanisms and the spatial seismicity distribution. Dynamic stress effects are best observed at long periods (30–60 s) and for metrics based on repeated stress cycling in the same direction. This implies that dynamic triggering operates, at least in part, through cyclic shear stress loading in the direction of fault slip. The background stress also strongly controls both the preshock and aftershock mechanisms. While most aftershock mechanisms are well oriented in the background stress field, 10% of aftershocks are identified as poorly oriented outliers, which may indicate limited heterogeneity in the postmain shock stress field. The fault plane orientations of the outliers are well oriented in the background stress, while their slip directions are not, implying that the background stress restricts the distribution of available fault planes.

Resolving the multiple sequence alignment problem using biogeography-based optimization with multiple populations.

PubMed

Zemali, El-Amine; Boukra, Abdelmadjid

2015-08-01

The multiple sequence alignment (MSA) is one of the most challenging problems in bioinformatics, it involves discovering similarity between a set of protein or DNA sequences. This paper introduces a new method for the MSA problem called biogeography-based optimization with multiple populations (BBOMP). It is based on a recent metaheuristic inspired from the mathematics of biogeography named biogeography-based optimization (BBO). To improve the exploration ability of BBO, we have introduced a new concept allowing better exploration of the search space. It consists of manipulating multiple populations having each one its own parameters. These parameters are used to build up progressive alignments allowing more diversity. At each iteration, the best found solution is injected in each population. Moreover, to improve solution quality, six operators are defined. These operators are selected with a dynamic probability which changes according to the operators efficiency. In order to test proposed approach performance, we have considered a set of datasets from Balibase 2.0 and compared it with many recent algorithms such as GAPAM, MSA-GA, QEAMSA and RBT-GA. The results show that the proposed approach achieves better average score than the previously cited methods.

Microfluidic flow rate detection based on integrated optical fiber cantilever.

PubMed

Lien, Victor; Vollmer, Frank

2007-10-01

We demonstrate an integrated microfluidic flow sensor with ultra-wide dynamic range, suitable for high throughput applications such as flow cytometry and particle sorting/counting. A fiber-tip cantilever transduces flow rates to optical signal readout, and we demonstrate a dynamic range from 0 to 1500 microL min(-1) for operation in water. Fiber-optic sensor alignment is guided by preformed microfluidic channels, and the dynamic range can be adjusted in a one-step chemical etch. An overall non-linear response is attributed to the far-field angular distribution of single-mode fiber output.

The Self-Organizing Psyche: Nonlinear and Neurobiological Contributions to Psychoanalysis

NASA Astrophysics Data System (ADS)

Stein, A. H.

Sigmund Freud attempted to align nineteenth century biology (and the dynamically conservative, continuous, Newtonian mechanics that underlie it) with discontinuous conscious experience. His tactics both set the future course for psychoanalytic development and introduced seemingly intractable complications into its metapsychology. In large part, these arose from what we now recognize were biological errors and dynamical oversimplifications amid his physical assumptions. Their correction, brought about by integrating nonlinear dynamics and neuro-biological research findings with W. Bion's reading of metapsychology, fundamentally supports a psychoanalysis based upon D. W. Winnicott's ideas surrounding play within transitional space.

EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

PubMed Central

Nahum, Laila A; Reynolds, Matthew T; Wang, Zhengyuan O; Faith, Jeremiah J; Jonna, Rahul; Jiang, Zhi J; Meyer, Thomas J; Pollock, David D

2006-01-01

Background Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; ) to begin to address this. Description EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs. Conclusion EGenBio was designed to serve as a platform for tools and resources to ease combined analysis in evolution, genomics, and biodiversity. PMID:17118150

A Mathematical Optimization Problem in Bioinformatics

ERIC Educational Resources Information Center

Heyer, Laurie J.

2008-01-01

This article describes the sequence alignment problem in bioinformatics. Through examples, we formulate sequence alignment as an optimization problem and show how to compute the optimal alignment with dynamic programming. The examples and sample exercises have been used by the author in a specialized course in bioinformatics, but could be adapted…

Carrier dynamics and recombination mechanisms in staggered-alignment heterostructures

NASA Astrophysics Data System (ADS)

Wilson, Barbara A.

1988-08-01

The experimental and theoretical work on carrier dynamics and recombination mechanisms in semiconductor heterostructures with staggered type II alignments is reviewed. Examples from the literature are discussed for each of the III-V, II-VI, and IV-VI systems, as well as cross-column examples, with a focus on AlGaAs structures. The key optical properties which have benn identified as signatures of staggered-alignment behavior are summarized. A discussion of other epitaxial systems likely to exhibit staggered lineups is presented, and additional experimental and theoretical work is suggested, which could increase understanding of staggered-system behavior.

Image registration and analysis for quantitative myocardial perfusion: application to dynamic circular cardiac CT.

PubMed

Isola, A A; Schmitt, H; van Stevendaal, U; Begemann, P G; Coulon, P; Boussel, L; Grass, M

2011-09-21

Large area detector computed tomography systems with fast rotating gantries enable volumetric dynamic cardiac perfusion studies. Prospectively, ECG-triggered acquisitions limit the data acquisition to a predefined cardiac phase and thereby reduce x-ray dose and limit motion artefacts. Even in the case of highly accurate prospective triggering and stable heart rate, spatial misalignment of the cardiac volumes acquired and reconstructed per cardiac cycle may occur due to small motion pattern variations from cycle to cycle. These misalignments reduce the accuracy of the quantitative analysis of myocardial perfusion parameters on a per voxel basis. An image-based solution to this problem is elastic 3D image registration of dynamic volume sequences with variable contrast, as it is introduced in this contribution. After circular cone-beam CT reconstruction of cardiac volumes covering large areas of the myocardial tissue, the complete series is aligned with respect to a chosen reference volume. The results of the registration process and the perfusion analysis with and without registration are evaluated quantitatively in this paper. The spatial alignment leads to improved quantification of myocardial perfusion for three different pig data sets.

Modeling extracellular matrix (ECM) alterations in ovarian cancer by multiphoton excited fabrication of stromal models (Conference Presentation)

NASA Astrophysics Data System (ADS)

Campagnola, Paul J.; Ajeti, Visar; Lara, Jorge; Eliceiri, Kevin W.; Patankar, Mansh

2016-04-01

A profound remodeling of the extracellular matrix (ECM) occurs in human ovarian cancer but it unknown how this affects tumor growth, where this understanding could lead to better diagnostics and therapeutic approaches. We investigate the role of these ECM alterations by using multiphoton excited (MPE) polymerization to fabricate biomimetic models to investigate operative cell-matrix interactions in invasion/metastasis. First, we create nano/microstructured gradients mimicking the basal lamina to study adhesion/migration dynamics of ovarian cancer cells of differing metastatic potential. We find a strong haptotactic response that depends on both contact guidance and ECM binding cues. While we found enhanced migration for more invasive cells, the specifics of alignment and directed migration also depend on cell polarity. We further use MPE fabrication to create collagen scaffolds with complex, 3D submicron morphology. The stromal scaffold designs are derived directly from "blueprints" based on SHG images of normal, high risk, and malignant ovarian tissues. The models are seeded with different cancer cell lines and this allows decoupling of the roles of cell characteristics (metastatic potential) and ECM structure and composition (normal vs cancer) on adhesion/migration dynamics. We found the malignant stroma structure promotes enhanced migration and proliferation and also cytoskeletal alignment. Creating synthetic models based on fibers patterns further allows decoupling the topographic roles of the fibers themselves vs their alignment within the tissue. These models cannot be synthesized by other conventional fabrication methods and we suggest the MPE image-based fabrication method will enable a variety of studies in cancer biology.

Spontaneous flow in polar active fluids: the effect of a phenomenological self propulsion-like term.

PubMed

Bonelli, Francesco; Gonnella, Giuseppe; Tiribocchi, Adriano; Marenduzzo, Davide

2016-01-01

We present hybrid lattice Boltzmann simulations of extensile and contractile active fluids where we incorporate phenomenologically the tendency of active particles such as cell and bacteria, to move, or swim, along the local orientation. Quite surprisingly, we show that the interplay between alignment and activity can lead to completely different results, according to geometry (periodic boundary conditions or confinement between flat walls) and nature of the activity (extensile or contractile). An interesting generic outcome is that the alignment interaction can transform stationary active patterns into continuously moving ones: the dynamics of these evolving patterns can be oscillatory or chaotic according to the strength of the alignment term. Our results suggest that flow-polarisation alignment can have important consequences on the collective dynamics of active fluids and active gel.

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

NASA Astrophysics Data System (ADS)

Oh, Seungjun; Hayakawa, Ryoma; Pan, Chengjun; Sugiyasu, Kazunori; Wakayama, Yutaka

2016-08-01

Nanowires of semiconducting poly(3-hexylthiophene) (P3HT) were produced by a nanochannel-template technique. Polymer chain alignment in P3HT nanowires was investigated as a function of nanochannel widths (W) and polymer chain lengths (L). We found that the ratio between chain length and channel width (L/W) was a key parameter as regards promoting polymer chain alignment. Clear dichroism was observed in polarized ultraviolet-visible (UV-Vis) absorption spectra only at a ratio of approximately L/W = 2, indicating that the L/W ratio must be optimized to achieve uniaxial chain alignment in the nanochannel direction. We speculate that an appropriate L/W ratio is effective in confining the geometries and conformations of polymer chains. This discussion was supported by theoretical simulations based on molecular dynamics. That is, the geometry of the polymer chains, including the distance and tilting angles of the chains in relation to the nanochannel surface, was dominant in determining the longitudinal alignment along the nanochannels. Thus prepared highly aligned polymer nanowire is advantageous for electrical carrier transport and has great potential for improving the device performance of field-effect transistors. In fact, a one-order improvement in carrier mobility was observed in a P3HT nanowire transistor.

Relationship between nanotopographical alignment and stem cell fate with live imaging and shape analysis

NASA Astrophysics Data System (ADS)

Newman, Peter; Galenano-Niño, Jorge Luis; Graney, Pamela; Razal, Joselito M.; Minett, Andrew I.; Ribas, João; Ovalle-Robles, Raquel; Biro, Maté; Zreiqat, Hala

2016-12-01

The topography of a biomaterial regulates cellular interactions and determine stem cell fate. A complete understanding of how topographical properties affect cell behavior will allow the rational design of material surfaces that elicit specified biological functions once placed in the body. To this end, we fabricate substrates with aligned or randomly organized fibrous nanostructured topographies. Culturing adipose-derived stem cells (ASCs), we explore the dynamic relationship between the alignment of topography, cell shape and cell differentiation to osteogenic and myogenic lineages. We show aligned topographies differentiate cells towards a satellite cell muscle progenitor state - a distinct cell myogenic lineage responsible for postnatal growth and repair of muscle. We analyze cell shape between the different topographies, using fluorescent time-lapse imaging over 21 days. In contrast to previous work, this allows the direct measurement of cell shape at a given time rather than defining the morphology of the underlying topography and neglecting cell shape. We report quantitative metrics of the time-based morphological behaviors of cell shape in response to differing topographies. This analysis offers insights into the relationship between topography, cell shape and cell differentiation. Cells differentiating towards a myogenic fate on aligned topographies adopt a characteristic elongated shape as well as the alignment of cells.

Intermediate Greek EFL Learners' Attitudes to On-Line Teaching Practices: A Blended Task-Based English Language Learning Approach

ERIC Educational Resources Information Center

Liontou, Trisevgeni

2015-01-01

This paper reports on a one-year longitudinal study that adopted a blended teaching approach based on designing and implementing an online EFL course to be used by Greek students aged 13-14 years old along their more traditional face-to-face lessons. The reason for creating a more dynamic learning environment aligned with the rest of the…

Individual responses to alignment perturbations in socket reaction moments while walking in transtibial prostheses.

PubMed

Kobayashi, Toshiki; Orendurff, Michael S; Zhang, Ming; Boone, David A

2014-05-01

The alignment of transtibial prostheses has a systematic effect on the mean socket reaction moments in amputees. However, understanding their individual differences in response to alignment perturbations is also important for prosthetists to fully utilize the socket reaction moments for dynamic alignment in each unique patient. The aim of this study was to investigate individual responses to alignment perturbations in transtibial prostheses with solid-ankle-cushion-heel feet. A custom instrumented prosthesis alignment component was used to measure the socket reaction moments while walking in 11 amputees with transtibial prostheses under 17 alignment conditions, including 3° and 6° of flexion, extension, abduction, and adduction of the socket, 5mm and 10mm of anterior, posterior, lateral, and medial translation of the socket, and an initial baseline alignment. Coronal moments at 30% of stance and maximum sagittal moments were extracted for comparisons from each amputee. In the coronal plane, varus moment at 30% of stance was generally reduced by adduction or medial translation of the socket in all the amputees. In the sagittal plane, extension moment was generally increased by posterior translation or flexion of the socket; however, this was not necessarily the case for all the amputees. Individual responses to alignment perturbations are not always consistent, and prosthetists would need to be aware of this variance when addressing individual socket reaction moments during dynamic alignment in clinical setting. Copyright © 2014 Elsevier Ltd. All rights reserved.

Preparation of Monodomain Liquid Crystal Elastomers and Liquid Crystal Elastomer Nanocomposites.

PubMed

Kim, Hojin; Zhu, Bohan; Chen, Huiying; Adetiba, Oluwatomiyin; Agrawal, Aditya; Ajayan, Pulickel; Jacot, Jeffrey G; Verduzco, Rafael

2016-02-06

LCEs are shape-responsive materials with fully reversible shape change and potential applications in medicine, tissue engineering, artificial muscles, and as soft robots. Here, we demonstrate the preparation of shape-responsive liquid crystal elastomers (LCEs) and LCE nanocomposites along with characterization of their shape-responsiveness, mechanical properties, and microstructure. Two types of LCEs - polysiloxane-based and epoxy-based - are synthesized, aligned, and characterized. Polysiloxane-based LCEs are prepared through two crosslinking steps, the second under an applied load, resulting in monodomain LCEs. Polysiloxane LCE nanocomposites are prepared through the addition of conductive carbon black nanoparticles, both throughout the bulk of the LCE and to the LCE surface. Epoxy-based LCEs are prepared through a reversible esterification reaction. Epoxy-based LCEs are aligned through the application of a uniaxial load at elevated (160 °C) temperatures. Aligned LCEs and LCE nanocomposites are characterized with respect to reversible strain, mechanical stiffness, and liquid crystal ordering using a combination of imaging, two-dimensional X-ray diffraction measurements, differential scanning calorimetry, and dynamic mechanical analysis. LCEs and LCE nanocomposites can be stimulated with heat and/or electrical potential to controllably generate strains in cell culture media, and we demonstrate the application of LCEs as shape-responsive substrates for cell culture using a custom-made apparatus.

Dynamic Knee Alignment and Collateral Knee Laxity and Its Variations in Normal Humans

PubMed Central

Deep, Kamal; Picard, Frederic; Clarke, Jon V.

2015-01-01

Alignment of normal, arthritic, and replaced human knees is a much debated subject as is the collateral ligamentous laxity. Traditional quantitative values have been challenged. Methods used to measure these are also not without flaws. Authors review the recent literature and a novel method of measurement of these values has been included. This method includes use of computer navigation technique in clinic setting for assessment of the normal or affected knee before the surgery. Computer navigation has been known for achievement of alignment accuracy during knee surgery. Now its use in clinic setting has added to the inventory of measurement methods. Authors dispel the common myth of straight mechanical axis in normal knees and also look at quantification of amount of collateral knee laxity. Based on the scientific studies, it has been shown that the mean alignment is in varus in normal knees. It changes from lying non-weight-bearing position to standing weight-bearing position in both coronal and the sagittal planes. It also varies with gender and race. The collateral laxity is also different for males and females. Further studies are needed to define the ideal alignment and collateral laxity which the surgeon should aim for individual knees. PMID:26636090

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.

Dynamic Tensile Loading Improves the Functional Properties of Mesenchymal Stem Cell-Laden Nanofiber-Based Fibrocartilage

PubMed Central

Baker, Brendon M.; Shah, Roshan P.; Huang, Alice H.

2011-01-01

Fibrocartilaginous tissues such as the meniscus serve critical load-bearing roles, relying on arrays of collagen fibers to resist tensile loads experienced with normal activity. As these structures are frequently injured and possess limited healing capacity, there exists great demand for tissue-engineered replacements. Toward recreating the structural features of these anisotropic tissues in vitro, we employ scaffolds composed of co-aligned nanofibers that direct mesenchymal stem cell (MSC) orientation and the formation of organized extracellular matrix (ECM). Concomitant with ECM synthesis, the mechanical properties of constructs increase with free-swelling culture, but ultimately failed to achieve equivalence with meniscal fibrocartilage. As mechanical forces are essential to the development and maintenance of musculoskeletal tissues, this work examined the effect of cyclic tensile loading on MSC-laden nanofibrous constructs. We hypothesized that loading would modulate the transcriptional behavior of MSCs, spur the deposition of ECM, and lead to enhancements in construct mechanical properties compared to free-swelling controls. Fiber-aligned scaffolds were seeded with MSCs and dynamically loaded daily in tension or maintained as nonloaded controls for 4 weeks. With mechanical stimulation, fibrous gene expression increased, collagen deposition increased, and the tensile modulus increased by 16% relative to controls. These results show that dynamic tensile loading enhances the maturation of MSC-laden aligned nanofibrous constructs, suggesting that recapitulation of the structural and mechanical environment of load-bearing tissues results in increases in functional properties that can be exploited for tissue engineering applications. PMID:21247342

Dynamic tensile loading improves the functional properties of mesenchymal stem cell-laden nanofiber-based fibrocartilage.

PubMed

Baker, Brendon M; Shah, Roshan P; Huang, Alice H; Mauck, Robert L

2011-05-01

Fibrocartilaginous tissues such as the meniscus serve critical load-bearing roles, relying on arrays of collagen fibers to resist tensile loads experienced with normal activity. As these structures are frequently injured and possess limited healing capacity, there exists great demand for tissue-engineered replacements. Toward recreating the structural features of these anisotropic tissues in vitro, we employ scaffolds composed of co-aligned nanofibers that direct mesenchymal stem cell (MSC) orientation and the formation of organized extracellular matrix (ECM). Concomitant with ECM synthesis, the mechanical properties of constructs increase with free-swelling culture, but ultimately failed to achieve equivalence with meniscal fibrocartilage. As mechanical forces are essential to the development and maintenance of musculoskeletal tissues, this work examined the effect of cyclic tensile loading on MSC-laden nanofibrous constructs. We hypothesized that loading would modulate the transcriptional behavior of MSCs, spur the deposition of ECM, and lead to enhancements in construct mechanical properties compared to free-swelling controls. Fiber-aligned scaffolds were seeded with MSCs and dynamically loaded daily in tension or maintained as nonloaded controls for 4 weeks. With mechanical stimulation, fibrous gene expression increased, collagen deposition increased, and the tensile modulus increased by 16% relative to controls. These results show that dynamic tensile loading enhances the maturation of MSC-laden aligned nanofibrous constructs, suggesting that recapitulation of the structural and mechanical environment of load-bearing tissues results in increases in functional properties that can be exploited for tissue engineering applications.

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.

Dynamic trunk stabilization: a conceptual back injury prevention program for volleyball athletes.

PubMed

Smith, Chad E; Nyland, John; Caudill, Paul; Brosky, Joseph; Caborn, David N M

2008-11-01

The sport of volleyball creates considerable dynamic trunk stability demands. Back injury occurs all too frequently in volleyball, particularly among female athletes. The purpose of this clinical commentary is to review functional anatomy, muscle coactivation strategies, assessment of trunk muscle performance, and the characteristics of effective exercises for the trunk or core. From this information, a conceptual progressive 3-phase volleyball-specific training program is presented to improve dynamic trunk stability and to potentially reduce the incidence of back injury among volleyball athletes. Phase 1 addresses low-velocity motor control, kinesthetic awareness, and endurance, with the clinician providing cues to teach achievement of biomechanically neutral spine alignment. Phase 2 focuses on progressively higher velocity dynamic multiplanar endurance, coordination, and strength-power challenges integrating upper and lower extremity movements, while maintaining neutral spine alignment. Phase 3 integrates volleyball-specific skill simulations by breaking down composite movement patterns into their component parts, with differing dynamic trunk stability requirements, while maintaining neutral spine alignment. Prospective research is needed to validate the efficacy of this program.

A short note on dynamic programming in a band.

PubMed

Gibrat, Jean-François

2018-06-15

Third generation sequencing technologies generate long reads that exhibit high error rates, in particular for insertions and deletions which are usually the most difficult errors to cope with. The only exact algorithm capable of aligning sequences with insertions and deletions is a dynamic programming algorithm. In this note, for the sake of efficiency, we consider dynamic programming in a band. We show how to choose the band width in function of the long reads' error rates, thus obtaining an [Formula: see text] algorithm in space and time. We also propose a procedure to decide whether this algorithm, when applied to semi-global alignments, provides the optimal score. We suggest that dynamic programming in a band is well suited to the problem of aligning long reads between themselves and can be used as a core component of methods for obtaining a consensus sequence from the long reads alone. The function implementing the dynamic programming algorithm in a band is available, as a standalone program, at: https://forgemia.inra.fr/jean-francois.gibrat/BAND_DYN_PROG.git.

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.

Investigation of Rhodopsin Dynamics in its Signaling State by Solid-State Deuterium NMR Spectroscopy

PubMed Central

Struts, Andrey V.; Chawla, Udeep; Perera, Suchithranga M.D.C.; Brown, Michael F.

2017-01-01

Site-directed deuterium NMR spectroscopy is a valuable tool to study the structural dynamics of biomolecules in cases where solution NMR is inapplicable. Solid-state 2H NMR spectral studies of aligned membrane samples of rhodopsin with selectively labeled retinal provide information on structural changes of the chromophore in different protein states. In addition, solid-state 2H NMR relaxation time measurements allow one to study the dynamics of the ligand during the transition from the inactive to the active state. Here we describe the methodological aspects of solid-state 2H NMR spectroscopy for functional studies of rhodopsin, with an emphasis on the dynamics of the retinal cofactor. We provide complete protocols for the preparation of NMR samples of rhodopsin with 11-cis-retinal selectively deuterated at the methyl groups in aligned membranes. In addition, we review optimized conditions for trapping the rhodopsin photointermediates; and lastly we address the challenging problem of trapping the signaling state of rhodopsin in aligned membrane films. PMID:25697522

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.

Vertically Aligned Carbon Nanofiber based Biosensor Platform for Glucose Sensor

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

Al Mamun, Khandaker A.; Tulip, Fahmida S.; MacArthur, Kimberly

2014-03-01

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

Dynamical differences of hemoglobin and the ionotropic glutamate receptor in different states revealed by a new dynamics alignment method.

PubMed

Tobi, Dror

2017-08-01

A new algorithm for comparison of protein dynamics is presented. Compared protein structures are superposed and their modes of motions are calculated using the anisotropic network model. The obtained modes are aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. Dynamical comparison of hemoglobin in the T and R2 states reveals that the dynamics of the allosteric effector 2,3-bisphosphoglycerate binding site is different in the two states. These differences can contribute to the selectivity of the effector to the T state. Similar comparison of the ionotropic glutamate receptor in the kainate+(R,R)-2b and ZK bound states reveals that the kainate+(R,R)-2b bound states slow modes describe upward motions of ligand binding domain and the transmembrane domain regions. Such motions may lead to the opening of the receptor. The upper lobes of the LBDs of the ZK bound state have a smaller interface with the amino terminal domains above them and have a better ability to move together. The present study exemplifies the use of dynamics comparison as a tool to study protein function. Proteins 2017; 85:1507-1517. © 2014 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Organizational Strategy and Business Environment Effects Based on a Computation Method

NASA Astrophysics Data System (ADS)

Reklitis, Panagiotis; Konstantopoulos, Nikolaos; Trivellas, Panagiotis

2007-12-01

According to many researchers of organizational theory, a great number of problems encountered by the manufacturing firms are due to their ineffectiveness to respond to significant changes of their external environment and align their competitive strategy accordingly. From this point of view, the pursuit of the appropriate generic strategy is vital for firms facing a dynamic and highly competitive environment. In the present paper, we adopt Porter's typology to operationalise organizational strategy (cost leadership, innovative and marketing differentiation, and focus) considering changes in the external business environment (dynamism, complexity and munificence). Although simulation of social events is a quite difficult task, since there are so many considerations (not all well understood) involved, in the present study we developed a dynamic system based on the conceptual framework of strategy-environment associations.

Magnetically aligned phospholipid bilayers in weak magnetic fields: optimization, mechanism, and advantages for X-band EPR studies.

PubMed

Cardon, Thomas B; Tiburu, Elvis K; Lorigan, Gary A

2003-03-01

Our lab is developing a spin-labeled EPR spectroscopic technique complementary to solid-state NMR studies to study the structure, orientation, and dynamics of uniaxially aligned integral membrane proteins inserted into magnetically aligned discotic phospholipid bilayers, or bicelles. The focus of this study is to optimize and understand the mechanisms involved in the magnetic alignment process of bicelle disks in weak magnetic fields. Developing experimental conditions for optimized magnetic alignment of bicelles in low magnetic fields may prove useful to study the dynamics of membrane proteins and its interactions with lipids, drugs, steroids, signaling events, other proteins, etc. In weak magnetic fields, the magnetic alignment of Tm(3+)-doped bicelle disks was thermodynamically and kinetically very sensitive to experimental conditions. Tm(3+)-doped bicelles were magnetically aligned using the following optimized procedure: the temperature was slowly raised at a rate of 1.9K/min from an initial temperature being between 298 and 307K to a final temperature of 318K in the presence of a static magnetic field of 6300G. The spin probe 3beta-doxyl-5alpha-cholestane (cholestane) was inserted into the bicelle disks and utilized to monitor bicelle alignment by analyzing the anisotropic hyperfine splitting for the corresponding EPR spectra. The phases of the bicelles were determined using solid-state 2H NMR spectroscopy and compared with the corresponding EPR spectra. Macroscopic alignment commenced in the liquid crystalline nematic phase (307K), continued to increase upon slowly raising the temperature, and was well-aligned in the liquid crystalline lamellar smectic phase (318K).

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

PubMed Central

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

2006-01-01

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

Effect of electric field induced alignment and dispersion of functionalized carbon nanotubes on properties of natural rubber

NASA Astrophysics Data System (ADS)

Gao, Jiangshan; He, Yan; Gong, Xiubin

2018-06-01

The original equipment and method for orienting multi-walled carbon nanotubes (MWCNTs) in natural rubber (NR) by alternating current (AC) electric field were reported in the present study. MWCNTs with various volume fractions were dispersed in the mixture latex which composed of natural rubber, additives and methylbenzene. The application of AC electric field during nanocomposites curing process was used to induce the formation of aligned conductive nanotube networks between the electrodes. The aligned MWCNTs in the composites have a better orientation performance and dispersion quality than these of random MWCNTs by analyzing TEM and SEM images. The effects of MWCNTs anisotropy on thermal conductivity, dielectric properties, and dynamic mechanical properties of NR were studied. The mean value of thermal conductivity of composites loading with aligned MWCNTs was 8.67% higher than that of composites with random MWCNTs due to the anisotropy of aligned MWCNTs. The compounds with aligned MWCNTs possessed low dielectric constant, loss tangents and conductivity, namely a good insulativity. The compounds loading with aligned MWCNTs had lower loss modulus and better dynamic mechanical properties than those with random MWCNTs. This method can make full use of the high thermal conductivity of MWCNTs axis, and expand the application areas of natural rubber like conducting heat in a certain direction with a high efficiency.

Experience from the in-flight calibration of the Extreme Ultraviolet Explorer (EUVE) and Upper Atmosphere Research Satellite (UARS) fixed head star trackers (FHSTs)

NASA Technical Reports Server (NTRS)

Lee, Michael

1995-01-01

Since the original post-launch calibration of the FHSTs (Fixed Head Star Trackers) on EUVE (Extreme Ultraviolet Explorer) and UARS (Upper Atmosphere Research Satellite), the Flight Dynamics task has continued to analyze the FHST performance. The algorithm used for inflight alignment of spacecraft sensors is described and the equations for the errors in the relative alignment for the simple 2 star tracker case are shown. Simulated data and real data are used to compute the covariance of the relative alignment errors. Several methods for correcting the alignment are compared and results analyzed. The specific problems seen on orbit with UARS and EUVE are then discussed. UARS has experienced anomalous tracker performance on an FHST resulting in continuous variation in apparent tracker alignment. On EUVE, the FHST residuals from the attitude determination algorithm showed a dependence on the direction of roll during survey mode. This dependence is traced back to time tagging errors and the original post launch alignment is found to be in error due to the impact of the time tagging errors on the alignment algorithm. The methods used by the FDF (Flight Dynamics Facility) to correct for these problems is described.

The relative phases of basal ganglia activities dynamically shape effective connectivity in Parkinson's disease.

PubMed

Cagnan, Hayriye; Duff, Eugene Paul; Brown, Peter

2015-06-01

Optimal phase alignment between oscillatory neural circuits is hypothesized to optimize information flow and enhance system performance. This theory is known as communication-through-coherence. The basal ganglia motor circuit exhibits exaggerated oscillatory and coherent activity patterns in Parkinson's disease. Such activity patterns are linked to compromised motor system performance as evinced by bradykinesia, rigidity and tremor, suggesting that network function might actually deteriorate once a certain level of net synchrony is exceeded in the motor circuit. Here, we characterize the processes underscoring excessive synchronization and its termination. To this end, we analysed local field potential recordings from the subthalamic nucleus and globus pallidus of five patients with Parkinson's disease (four male and one female, aged 37-64 years). We observed that certain phase alignments between subthalamic nucleus and globus pallidus amplified local neural synchrony in the beta frequency band while others either suppressed it or did not induce any significant change with respect to surrogates. The increase in local beta synchrony directly correlated with how long the two nuclei locked to beta-amplifying phase alignments. Crucially, administration of the dopamine prodrug, levodopa, reduced the frequency and duration of periods during which subthalamic and pallidal populations were phase-locked to beta-amplifying alignments. Conversely ON dopamine, the total duration over which subthalamic and pallidal populations were aligned to phases that left beta-amplitude unchanged with respect to surrogates increased. Thus dopaminergic input shifted circuit dynamics from persistent periods of locking to amplifying phase alignments, associated with compromised motoric function, to more dynamic phase alignment and improved motoric function. This effect of dopamine on local circuit resonance suggests means by which novel electrical interventions might prevent resonance-related pathological circuit interactions. © The Author (2015). Published by Oxford University Press on behalf of the Guarantors of Brain.

Alignment-Independent Comparisons of Human Gastrointestinal Tract Microbial Communities in a Multidimensional 16S rRNA Gene Evolutionary Space▿

PubMed Central

Rudi, Knut; Zimonja, Monika; Kvenshagen, Bente; Rugtveit, Jarle; Midtvedt, Tore; Eggesbø, Merete

2007-01-01

We present a novel approach for comparing 16S rRNA gene clone libraries that is independent of both DNA sequence alignment and definition of bacterial phylogroups. These steps are the major bottlenecks in current microbial comparative analyses. We used direct comparisons of taxon density distributions in an absolute evolutionary coordinate space. The coordinate space was generated by using alignment-independent bilinear multivariate modeling. Statistical analyses for clone library comparisons were based on multivariate analysis of variance, partial least-squares regression, and permutations. Clone libraries from both adult and infant gastrointestinal tract microbial communities were used as biological models. We reanalyzed a library consisting of 11,831 clones covering complete colons from three healthy adults in addition to a smaller 390-clone library from infant feces. We show that it is possible to extract detailed information about microbial community structures using our alignment-independent method. Our density distribution analysis is also very efficient with respect to computer operation time, meeting the future requirements of large-scale screenings to understand the diversity and dynamics of microbial communities. PMID:17337554

Crystal genes in a marginal glass-forming system of Ni 50Zr 50

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

Wen, T. Q.; Tang, L.; Sun, Y.

Glass-forming motifs with B2 traits are found. A perfect Ni-centered B33 motif deteriorates the glass-forming ability of Ni 50Zr 50. The marginal glass-forming ability (GFA) of binary Ni-Zr system is an issue to be explained considering the numerous bulk metallic glasses (BMGs) found in the Cu-Zr system. Using molecular dynamics, the structures and dynamics of Ni 50Zr 50 metallic liquid and glass are investigated at the atomistic level. To achieve a well-relaxed glassy sample, sub-T g annealing method is applied and the final sample is closer to the experiments than the models prepared by continuous cooling. With the state-of-the-art structuralmore » analysis tools such as cluster alignment and pair-wise alignment methods, two glass-forming motifs with some mixed traits of the metastable B2 crystalline phase and the crystalline Ni-centered B33 motif are found to be dominant in the undercooled liquid and glass samples. A new chemical order characterization on each short-range order (SRO) structure is accomplished based on the cluster alignment method. The significant amount of the crystalline motif and the few icosahedra in the glassy sample deteriorate the GFA.« less

Crystal genes in a marginal glass-forming system of Ni 50Zr 50

DOE PAGES

Wen, T. Q.; Tang, L.; Sun, Y.; ...

2017-10-17

Glass-forming motifs with B2 traits are found. A perfect Ni-centered B33 motif deteriorates the glass-forming ability of Ni 50Zr 50. The marginal glass-forming ability (GFA) of binary Ni-Zr system is an issue to be explained considering the numerous bulk metallic glasses (BMGs) found in the Cu-Zr system. Using molecular dynamics, the structures and dynamics of Ni 50Zr 50 metallic liquid and glass are investigated at the atomistic level. To achieve a well-relaxed glassy sample, sub-T g annealing method is applied and the final sample is closer to the experiments than the models prepared by continuous cooling. With the state-of-the-art structuralmore » analysis tools such as cluster alignment and pair-wise alignment methods, two glass-forming motifs with some mixed traits of the metastable B2 crystalline phase and the crystalline Ni-centered B33 motif are found to be dominant in the undercooled liquid and glass samples. A new chemical order characterization on each short-range order (SRO) structure is accomplished based on the cluster alignment method. The significant amount of the crystalline motif and the few icosahedra in the glassy sample deteriorate the GFA.« less

Time Alignment as a Necessary Step in the Analysis of Sleep Probabilistic Curves

NASA Astrophysics Data System (ADS)

Rošt'áková, Zuzana; Rosipal, Roman

2018-02-01

Sleep can be characterised as a dynamic process that has a finite set of sleep stages during the night. The standard Rechtschaffen and Kales sleep model produces discrete representation of sleep and does not take into account its dynamic structure. In contrast, the continuous sleep representation provided by the probabilistic sleep model accounts for the dynamics of the sleep process. However, analysis of the sleep probabilistic curves is problematic when time misalignment is present. In this study, we highlight the necessity of curve synchronisation before further analysis. Original and in time aligned sleep probabilistic curves were transformed into a finite dimensional vector space, and their ability to predict subjects' age or daily measures is evaluated. We conclude that curve alignment significantly improves the prediction of the daily measures, especially in the case of the S2-related sleep states or slow wave sleep.

Modified compensation algorithm of lever-arm effect and flexural deformation for polar shipborne transfer alignment based on improved adaptive Kalman filter

NASA Astrophysics Data System (ADS)

Wang, Tongda; Cheng, Jianhua; Guan, Dongxue; Kang, Yingyao; Zhang, Wei

2017-09-01

Due to the lever-arm effect and flexural deformation in the practical application of transfer alignment (TA), the TA performance is decreased. The existing polar TA algorithm only compensates a fixed lever-arm without considering the dynamic lever-arm caused by flexural deformation; traditional non-polar TA algorithms also have some limitations. Thus, the performance of existing compensation algorithms is unsatisfactory. In this paper, a modified compensation algorithm of the lever-arm effect and flexural deformation is proposed to promote the accuracy and speed of the polar TA. On the basis of a dynamic lever-arm model and a noise compensation method for flexural deformation, polar TA equations are derived in grid frames. Based on the velocity-plus-attitude matching method, the filter models of polar TA are designed. An adaptive Kalman filter (AKF) is improved to promote the robustness and accuracy of the system, and then applied to the estimation of the misalignment angles. Simulation and experiment results have demonstrated that the modified compensation algorithm based on the improved AKF for polar TA can effectively compensate the lever-arm effect and flexural deformation, and then improve the accuracy and speed of TA in the polar region.

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.

Model for the orientational ordering of the plant microtubule cortical array

NASA Astrophysics Data System (ADS)

Hawkins, Rhoda J.; Tindemans, Simon H.; Mulder, Bela M.

2010-07-01

The plant microtubule cortical array is a striking feature of all growing plant cells. It consists of a more or less homogeneously distributed array of highly aligned microtubules connected to the inner side of the plasma membrane and oriented transversely to the cell growth axis. Here, we formulate a continuum model to describe the origin of orientational order in such confined arrays of dynamical microtubules. The model is based on recent experimental observations that show that a growing cortical microtubule can interact through angle dependent collisions with pre-existing microtubules that can lead either to co-alignment of the growth, retraction through catastrophe induction or crossing over the encountered microtubule. We identify a single control parameter, which is fully determined by the nucleation rate and intrinsic dynamics of individual microtubules. We solve the model analytically in the stationary isotropic phase, discuss the limits of stability of this isotropic phase, and explicitly solve for the ordered stationary states in a simplified version of the model.

Using Information Communication Technologies to Develop Dynamic Curriculum Frameworks for Diverse Cohorts: A Case Study from Event Management

ERIC Educational Resources Information Center

Hadley, Bree Jamila

2012-01-01

This article investigates the role of information communication technologies (ICTs) in establishing a well-aligned, authentic learning environment for a diverse cohort of non-cognate and cognate students studying event management in a higher education context. Based on a case study which examined the way ICTs assisted in accommodating diverse…

Quantitative phase microscopy for cellular dynamics based on transport of intensity equation.

PubMed

Li, Ying; Di, Jianglei; Ma, Chaojie; Zhang, Jiwei; Zhong, Jinzhan; Wang, Kaiqiang; Xi, Teli; Zhao, Jianlin

2018-01-08

We demonstrate a simple method for quantitative phase imaging of tiny transparent objects such as living cells based on the transport of intensity equation. The experiments are performed using an inverted bright field microscope upgraded with a flipping imaging module, which enables to simultaneously create two laterally separated images with unequal defocus distances. This add-on module does not include any lenses or gratings and is cost-effective and easy-to-alignment. The validity of this method is confirmed by the measurement of microlens array and human osteoblastic cells in culture, indicating its potential in the applications of dynamically measuring living cells and other transparent specimens in a quantitative, non-invasive and label-free manner.

Effects of Matrix Alignment and Mechanical Constraints on Cellular Behavior in 3D Engineered Microtissues

NASA Astrophysics Data System (ADS)

Bose, Prasenjit; Eyckmans, Jeroen; Chen, Christopher; Reich, Daniel

The adhesion of cells to the extracellular matrix (ECM) plays a crucial role in a variety of cellular functions. The main building blocks of the ECM are 3D networks of fibrous proteins whose structure and alignments varies with tissue type. However, the impact of ECM alignment on cellular behaviors such as cell adhesion, spreading, extension and mechanics remains poorly understood. We present results on the development of a microtissue-based system that enables control of the structure, orientation, and degree of fibrillar alignment in 3D fibroblast-populated collagen gels. The tissues self-assemble from cell-laden collagen gels placed in micro-fabricated wells containing sets of elastic pillars. The contractile action of the cells leads to controlled alignment of the fibrous collagen, depending on the number and location of the pillars in each well. The pillars are elastic, and are utilized to measure the contractile forces of the microtissues, and by incorporating magnetic material in selected pillars, time-varying forces can be applied to the tissues for dynamic stimulation and measurement of mechanical properties. Results on the effects of varying pillar shape, spacing, location, and stiffness on microtissue organization and contractility will be presented. This work is supported by NSF CMMI-1463011.

Tetrahedron deformation and alignment of perceived vorticity and strain in a turbulent flow

NASA Astrophysics Data System (ADS)

Pumir, Alain; Bodenschatz, Eberhard; Xu, Haitao

2013-03-01

We describe the structure and dynamics of turbulence by the scale-dependent perceived velocity gradient tensor as supported by following four tracers, i.e., fluid particles, that initially form a regular tetrahedron. We report results from experiments in a von Kármán swirling water flow and from numerical simulations of the incompressible Navier-Stokes equation. We analyze the statistics and the dynamics of the perceived rate of strain tensor and vorticity for initially regular tetrahedron of size r0 from the dissipative to the integral scale. Just as for the true velocity gradient, at any instant, the perceived vorticity is also preferentially aligned with the intermediate eigenvector of the perceived rate of strain. However, in the perceived rate of strain eigenframe fixed at a given time t = 0, the perceived vorticity evolves in time such as to align with the strongest eigendirection at t = 0. This also applies to the true velocity gradient. The experimental data at the higher Reynolds number suggests the existence of a self-similar regime in the inertial range. In particular, the dynamics of alignment of the perceived vorticity and strain can be rescaled by t0, the turbulence time scale of the flow when the scale r0 is in the inertial range. For smaller Reynolds numbers we found the dynamics to be scale dependent.

Terminator field-aligned current system: A new finding from model-assimilated data set (MADS)

NASA Astrophysics Data System (ADS)

Zhu, L.; Schunk, R. W.; Scherliess, L.; Sojka, J. J.; Gardner, L. C.; Eccles, J. V.; Rice, D.

2013-12-01

Physics-based data assimilation models have been recognized by the space science community as the most accurate approach to specify and forecast the space weather of the solar-terrestrial environment. The model-assimilated data sets (MADS) produced by these models constitute an internally consistent time series of global three-dimensional fields whose accuracy can be estimated. Because of its internal consistency of physics and completeness of descriptions on the status of global systems, the MADS has also been a powerful tool to identify the systematic errors in measurements, reveal the missing physics in physical models, and discover the important dynamical physical processes that are inadequately observed or missed by measurements due to observational limitations. In the past years, we developed a data assimilation model for the high-latitude ionospheric plasma dynamics and electrodynamics. With a set of physical models, an ensemble Kalman filter, and the ingestion of data from multiple observations, the data assimilation model can produce a self-consistent time-series of the complete descriptions of the global high-latitude ionosphere, which includes the convection electric field, horizontal and field-aligned currents, conductivity, as well as 3-D plasma densities and temperatures, In this presentation, we will show a new field-aligned current system discovered from the analysis of the MADS produced by our data assimilation model. This new current system appears and develops near the ionospheric terminator. The dynamical features of this current system will be described and its connection to the active role of the ionosphere in the M-I coupling will be discussed.

Multi-channel dynamics in high harmonic generation of aligned CO2: ab initio analysis with time-dependent B-spline algebraic diagrammatic construction.

PubMed

Ruberti, M; Decleva, P; Averbukh, V

2018-03-28

Here we present a fully ab initio study of the high-order harmonic generation (HHG) spectrum of aligned CO 2 molecules. The calculations have been performed by using the molecular time-dependent (TD) B-spline algebraic diagrammatic construction (ADC) method. We quantitatively study how the sub-cycle laser-driven multi-channel dynamics, as reflected in the position of the dynamical minimum in the HHG spectrum, is affected by the full inclusion of both correlation-driven and laser-driven dipole interchannel couplings. We calculate channel-resolved spectral intensities as well as the phase differences between contributions of the different ionization-recombination channels to the total HHG spectrum. Our results show that electron correlation effectively controls the relative contributions of the different channels to the total HHG spectrum, leading to the opening of the new ones (1 2 Π u , 1 2 Σ), previously disregarded for the aligned molecular setup. We conclude that inclusion of many-electron effects into the theoretical interpretation of molecular HHG spectra is essential in order to correctly extract ultrafast electron dynamics using HHG spectroscopy.

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.

PubMed

Liao, Weinan; Ren, Jie; Wang, Kun; Wang, Shun; Zeng, Feng; Wang, Ying; Sun, Fengzhu

2016-11-23

The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC). Under a fixed high order of MC, the parameters might not be accurately estimated owing to the limitation of sequencing depth. In our study, we investigate an alternative to FOMC to model background sequences with the data-driven Variable Length Markov Chain (VLMC) in metatranscriptomic data. The VLMC originally designed for long sequences was extended to apply to high-throughput sequencing reads and the strategies to estimate the corresponding parameters were developed. The flexible number of parameters in VLMC avoids estimating the vast number of parameters of high-order MC under limited sequencing depth. Different from the manual selection in FOMC, VLMC determines the MC order adaptively. Several beta diversity measures based on VLMC were applied to compare the bacterial RNA-Seq and metatranscriptomic datasets. Experiments show that VLMC outperforms FOMC to model the background sequences in transcriptomic and metatranscriptomic samples. A software pipeline is available at https://d2vlmc.codeplex.com.

Dynamic Scattering Mode LCDs

NASA Astrophysics Data System (ADS)

Bahadur, Birendra

The following sections are included: * INTRODUCTION * CELL DESIGNING * EXPERIMENTAL OBSERVATIONS IN NEMATICS RELATED WITH DYNAMIC SCATTERING * Experimental Observations at D.C. Field and Electrode Effects * Experimental Observation at Low Frequency A.C. Fields * Homogeneously Aligned Nematic Regime * Williams Domains * Dynamic Scattering * Experimental Observation at High Frequency A.C. Field * Other Experimental Observations * THEORETICAL INTERPRETATIONS * Felici Model * Carr-Helfrich Model * D.C. Excitation * Dubois-Violette, de Gennes and Parodi Model * Low Freqency or Conductive Regime * High Frequency or Dielectric Regime * DYNAMIC SCATTERING IN SMECRIC A PHASE * ELECTRO-OPTICAL CHARACTERISTICS AND LIMITATIONS * Contrast Ratio vs. Voltage, Viewing Angle, Cell Gap, Wavelength and Temperature * Display Current vs. Voltage, Cell Gap and Temperature * Switching Time * Effect of Alignment * Effect of Conductivity, Temperature and Frequency * Addressing of DSM LCDs * Limitations of DSM LCDs * ACKNOWLEDGEMENTS * REFERENCES

Paramagnetic alignment of small grains: A novel method for measuring interstellar magnetic fields

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

Hoang, Thiem; Martin, P. G.; Lazarian, A.

2014-07-20

We present a novel method to measure the strength of interstellar magnetic fields using ultraviolet (UV) polarization of starlight that is in part produced by weakly aligned, small dust grains. We begin with calculating the degrees of the paramagnetic alignment of small (size a ∼ 0.01 μm) and very small (a ∼ 0.001 μm) grains in the interstellar magnetic field due to the Davis-Greenstein relaxation and resonance relaxation. To calculate the degrees of paramagnetic alignment, we use Langevin equations and take into account various interaction processes essential for the rotational dynamics of small grains. We find that the alignment ofmore » small grains is necessary to reproduce the observed polarization in the UV, although the polarization arising from these small grains is negligible at the optical and infrared (IR) wavelengths. Based on fitting theoretical models to observed extinction and polarization curves, we find that the best-fit model for the case with the peak wavelength of polarization λ{sub max} < 0.55 μm requires a higher degree of alignment of small grains than for the typical case with λ{sub max} = 0.55 μm. We interpret the correlation between the systematic increase of the UV polarization relative to maximum polarization (i.e., of p(6 μm{sup –1})/p{sub max}) with λ{sub max}{sup −1} for cases of low λ{sub max} by appealing to the higher degree of alignment of small grains. We utilize the correlation of the paramagnetic alignment of small grains with the magnetic field strength B to suggest a new way to measure B using the observable parameters λ{sub max} and p(6 μm{sup –1})/p{sub max}.« less

Development and alignment of undergraduate medical curricula in a web-based, dynamic Learning Opportunities, Objectives and Outcome Platform (LOOOP).

PubMed

Balzer, Felix; Hautz, Wolf E; Spies, Claudia; Bietenbeck, Andreas; Dittmar, Martin; Sugiharto, Firman; Lehmann, Lars; Eisenmann, Dorothea; Bubser, Florian; Stieg, Markus; Hanfler, Sven; Georg, Waltraud; Tekian, Ara; Ahlers, Olaf

2016-01-01

This study presents a web-based method and its interface ensuring alignment of all parts of a curriculum map including competencies, objectives, teaching and assessment methods, workload and patient availability. Needs, acceptance and effectiveness are shown through a nine-year study. After a comprehensive needs assessment, the curriculum map and a web-based interface "Learning Opportunities, Objectives and Outcome Platform" (LOOOP) were developed according to Harden's conceptual framework of 10-steps for curriculum mapping. The outcome was measured by surveys and results of interdisciplinary MCQ-assessments. The usage rates and functionalities were analysed. The implementation of LOOOP was significantly associated with improved perception of the curriculum structure by teachers and students, quality of defined objectives and their alignment with teaching and assessment, usage by students to prepare examinations and their scores in interdisciplinary MCQ-assessment. Additionally, LOOOP improved the curriculum coordination by faculty, and assisted departments for identifying patient availability for clinical training. LOOOP is well accepted among students and teachers, has positive effect on curriculum development, facilitates effective utilisation of educational resources and improves student's outcomes. Currently, LOOOP is used in five undergraduate medical curricula including 85,000 mapped learning opportunities (lectures, seminars), 5000 registered users (students, teachers) and 380,000 yearly page-visits.

Railway Tunnel Clearance Inspection Method Based on 3D Point Cloud from Mobile Laser Scanning

PubMed Central

Zhou, Yuhui; Wang, Shaohua; Mei, Xi; Yin, Wangling; Lin, Chunfeng; Mao, Qingzhou

2017-01-01

Railway tunnel clearance is directly related to the safe operation of trains and upgrading of freight capacity. As more and more railway are put into operation and the operation is continuously becoming faster, the railway tunnel clearance inspection should be more precise and efficient. In view of the problems existing in traditional tunnel clearance inspection methods, such as low density, slow speed and a lot of manual operations, this paper proposes a tunnel clearance inspection approach based on 3D point clouds obtained by a mobile laser scanning system (MLS). First, a dynamic coordinate system for railway tunnel clearance inspection has been proposed. A rail line extraction algorithm based on 3D linear fitting is implemented from the segmented point cloud to establish a dynamic clearance coordinate system. Second, a method to seamlessly connect all rail segments based on the railway clearance restrictions, and a seamless rail alignment is formed sequentially from the middle tunnel section to both ends. Finally, based on the rail alignment and the track clearance coordinate system, different types of clearance frames are introduced for intrusion operation with the tunnel section to realize the tunnel clearance inspection. By taking the Shuanghekou Tunnel of the Chengdu–Kunming Railway as an example, when the clearance inspection is carried out by the method mentioned herein, its precision can reach 0.03 m, and difference types of clearances can be effectively calculated. This method has a wide application prospects. PMID:28880232

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets.

PubMed

Hoffmann, Nils; Keck, Matthias; Neuweger, Heiko; Wilhelm, Mathias; Högy, Petra; Niehaus, Karsten; Stoye, Jens

2012-08-27

Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). These hyphenated methods provide high-dimensional data. Comparing such data manually to find corresponding signals is a laborious task, as each experiment usually consists of thousands of individual scans, each containing hundreds or even thousands of distinct signals. In order to allow for successful identification of metabolites or proteins within such data, especially in the context of metabolomics and proteomics, an accurate alignment and matching of corresponding features between two or more experiments is required. Such a matching algorithm should capture fluctuations in the chromatographic system which lead to non-linear distortions on the time axis, as well as systematic changes in recorded intensities. Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning and comparing the complete raw data containing all available features. In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE) and center-star multiple alignment by pairwise partitioned dynamic time warping (CeMAPP-DTW). We show how the similarity-based peak group matching method BIPACE may be used for multiple alignment calculation individually and how it can be used as a preprocessing step for the pairwise alignments performed by CeMAPP-DTW. We evaluate the algorithms individually and in combination on a previously published small GC-MS dataset studying the Leishmania parasite and on a larger GC-MS dataset studying grains of wheat (Triticum aestivum). We have shown that BIPACE achieves very high precision and recall and a very low number of false positive peak assignments on both evaluation datasets. CeMAPP-DTW finds a high number of true positives when executed on its own, but achieves even better results when BIPACE is used to constrain its search space. The source code of both algorithms is included in the OpenSource software framework Maltcms, which is available from http://maltcms.sf.net. The evaluation scripts of the present study are available from the same source.

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets

PubMed Central

2012-01-01

Background Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). These hyphenated methods provide high-dimensional data. Comparing such data manually to find corresponding signals is a laborious task, as each experiment usually consists of thousands of individual scans, each containing hundreds or even thousands of distinct signals. In order to allow for successful identification of metabolites or proteins within such data, especially in the context of metabolomics and proteomics, an accurate alignment and matching of corresponding features between two or more experiments is required. Such a matching algorithm should capture fluctuations in the chromatographic system which lead to non-linear distortions on the time axis, as well as systematic changes in recorded intensities. Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning and comparing the complete raw data containing all available features. Results In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE) and center-star multiple alignment by pairwise partitioned dynamic time warping (CeMAPP-DTW). We show how the similarity-based peak group matching method BIPACE may be used for multiple alignment calculation individually and how it can be used as a preprocessing step for the pairwise alignments performed by CeMAPP-DTW. We evaluate the algorithms individually and in combination on a previously published small GC-MS dataset studying the Leishmania parasite and on a larger GC-MS dataset studying grains of wheat (Triticum aestivum). Conclusions We have shown that BIPACE achieves very high precision and recall and a very low number of false positive peak assignments on both evaluation datasets. CeMAPP-DTW finds a high number of true positives when executed on its own, but achieves even better results when BIPACE is used to constrain its search space. The source code of both algorithms is included in the OpenSource software framework Maltcms, which is available from http://maltcms.sf.net. The evaluation scripts of the present study are available from the same source. PMID:22920415

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

PubMed

Ibarra, Ignacio L; Melo, Francisco

2010-07-01

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

GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

PubMed

Alser, Mohammed; Hassan, Hasan; Xin, Hongyi; Ergin, Oguz; Mutlu, Onur; Alkan, Can

2017-11-01

High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms. We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average >96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10. https://github.com/BilkentCompGen/GateKeeper. mohammedalser@bilkent.edu.tr or onur.mutlu@inf.ethz.ch or calkan@cs.bilkent.edu.tr. 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

6DOF Testing of the SLS Inertial Navigation Unit

NASA Technical Reports Server (NTRS)

Geohagan, Kevin; Bernard, Bill; Oliver, T. Emerson; Leggett, Jared; Strickland, Dennis

2018-01-01

The Navigation System on the NASA Space Launch System (SLS) Block 1 vehicle performs initial alignment of the Inertial Navigation System (INS) navigation frame through gyrocompass alignment (GCA). Because the navigation architecture for the SLS Block 1 vehicle is a purely inertial system, the accuracy of the achieved orbit relative to mission requirements is very sensitive to initial alignment accuracy. The assessment of this sensitivity and many others via simulation is a part of the SLS Model-Based Design and Model-Based Requirements approach. As a part of the aforementioned, 6DOF Monte Carlo simulation is used in large part to develop and demonstrate verification of program requirements. To facilitate this and the GN&C flight software design process, an SLS-Program-controlled Design Math Model (DMM) of the SLS INS was developed by the SLS Navigation Team. The SLS INS model implements all of the key functions of the hardware-namely, GCA, inertial navigation, and FDIR (Fault Detection, Isolation, and Recovery)-in support of SLS GN&C design requirements verification. Despite the strong sensitivity to initial alignment, GCA accuracy requirements were not verified by test due to program cost and schedule constraints. Instead, the system relies upon assessments performed using the SLS INS model. In order to verify SLS program requirements by analysis, the SLS INS model is verified and validated against flight hardware. In lieu of direct testing of GCA accuracy in support of requirement verification, the SLS Navigation Team proposed and conducted an engineering test to, among other things, validate the GCA performance and overall behavior of the SLS INS model through comparison with test data. This paper will detail dynamic hardware testing of the SLS INS, conducted by the SLS Navigation Team at Marshall Space Flight Center's 6DOF Table Facility, in support of GCA performance characterization and INS model validation. A 6-DOF motion platform was used to produce 6DOF pad twist and sway dynamics while a simulated SLS flight computer communicated with the INS. Tests conducted include an evaluation of GCA algorithm robustness to increasingly dynamic pad environments, an examination of GCA algorithm stability and accuracy over long durations, and a long-duration static test to gather enough data for Allan Variance analysis. Test setup, execution, and data analysis will be discussed, including analysis performed in support of SLS INS model validation.

Rigid-body motion correction of the liver in image reconstruction for golden-angle stack-of-stars DCE MRI.

PubMed

Johansson, Adam; Balter, James; Cao, Yue

2018-03-01

Respiratory motion can affect pharmacokinetic perfusion parameters quantified from liver dynamic contrast-enhanced MRI. Image registration can be used to align dynamic images after reconstruction. However, intra-image motion blur remains after alignment and can alter the shape of contrast-agent uptake curves. We introduce a method to correct for inter- and intra-image motion during image reconstruction. Sixteen liver dynamic contrast-enhanced MRI examinations of nine subjects were performed using a golden-angle stack-of-stars sequence. For each examination, an image time series with high temporal resolution but severe streak artifacts was reconstructed. Images were aligned using region-limited rigid image registration within a region of interest covering the liver. The transformations resulting from alignment were used to correct raw data for motion by modulating and rotating acquired lines in k-space. The corrected data were then reconstructed using view sharing. Portal-venous input functions extracted from motion-corrected images had significantly greater peak signal enhancements (mean increase: 16%, t-test, P <  0.001) than those from images aligned using image registration after reconstruction. In addition, portal-venous perfusion maps estimated from motion-corrected images showed fewer artifacts close to the edge of the liver. Motion-corrected image reconstruction restores uptake curves distorted by motion. Motion correction also reduces motion artifacts in estimated perfusion parameter maps. Magn Reson Med 79:1345-1353, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

XGC developments for a more efficient XGC-GENE code coupling

NASA Astrophysics Data System (ADS)

Dominski, Julien; Hager, Robert; Ku, Seung-Hoe; Chang, Cs

2017-10-01

In the Exascale Computing Program, the High-Fidelity Whole Device Modeling project initially aims at delivering a tightly-coupled simulation of plasma neoclassical and turbulence dynamics from the core to the edge of the tokamak. To permit such simulations, the gyrokinetic codes GENE and XGC will be coupled together. Numerical efforts are made to improve the numerical schemes agreement in the coupling region. One of the difficulties of coupling those codes together is the incompatibility of their grids. GENE is a continuum grid-based code and XGC is a Particle-In-Cell code using unstructured triangular mesh. A field-aligned filter is thus implemented in XGC. Even if XGC originally had an approximately field-following mesh, this field-aligned filter permits to have a perturbation discretization closer to the one solved in the field-aligned code GENE. Additionally, new XGC gyro-averaging matrices are implemented on a velocity grid adapted to the plasma properties, thus ensuring same accuracy from the core to the edge regions.

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

Three-dimensional dynamic deformation monitoring using a laser-scanning system

NASA Astrophysics Data System (ADS)

Al-Hanbali, Nedal N.; Teskey, William F.

1994-10-01

Non-contact dynamic deformation monitoring (e.g. with a laser scanning system) is very useful in monitoring changes in alignment and changes in size and shape of coupled operating machines. If relative movements between coupled operating machines are large, excessive wear in the machines or unplanned shutdowns due to machinery failure will occur. The purpose of non-contact dynamic deformation monitoring is to identify the causes of large movements and point to remedial action that can be taken to prevent them. The laser scanning system is a laser-based 3D vision system. The system-technique is based on an auto- synchronized triangulation scanning scheme. The system provides accurate, fast, and reliable 3D measurements and can measure objects between 0.5 m to 100 m with a field of view of 40 degree(s) X 50 degree(s). The system is flexible in terms of providing control over the scanned area and depth. The system also provides the user with the intensity image in addition to the depth coded image. This paper reports on the preliminary testing of this system to monitor surface movements and target (point) movements. The monitoring resolution achieved for an operating motorized alignment test rig in the lab was 1 mm for surface movements and 0.50 m for target movements. Raw data manipulation, local calibration, and the method of relating measurements to control points will be discussed. Possibilities for improving the resolution and recommendations for future development will also be presented.

Electronic properties of semiconductor-water interfaces: Predictions from ab-initio molecular dynamics and many-body perturbation theory

NASA Astrophysics Data System (ADS)

Pham, Tuan Anh

2015-03-01

Photoelectrochemical cells offer a promising avenue for hydrogen production from water and sunlight. The efficiency of these devices depends on the electronic structure of the interface between the photoelectrode and liquid water, including the alignment between the semiconductor band edges and the water redox potential. In this talk, we will present the results of first principles calculations of semiconductor-water interfaces that are obtained with a combination of density functional theory (DFT)-based molecular dynamics simulations and many-body perturbation theory (MBPT). First, we will discuss the development of an MBPT approach that is aimed at improving the efficiency and accuracy of existing methodologies while still being applicable to complex heterogeneous interfaces consisting of hundreds of atoms. We will then present studies of the electronic structure of liquid water and aqueous solutions using MBPT, which represent an essential step in establishing a quantitative framework for computing the energy alignment at semiconductor-water interfaces. Finally, using a combination of DFT-based molecular dynamics simulations and MBPT, we will describe the relationship between interfacial structure, electronic properties of semiconductors and their reactivity in aqueous solutions through a number of examples, including functionalized Si surfaces and GaP/InP surfaces in contact with liquid water. T.A.P was supported by the U.S. Department of Energy at the Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and by the Lawrence Fellowship Program.

A generalized global alignment algorithm.

PubMed

Huang, Xiaoqiu; Chao, Kun-Mao

2003-01-22

Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.

Extremely High Thermal Conductivity of Aligned Carbon Nanotube-Polyethylene Composites.

PubMed

Liao, Quanwen; Liu, Zhichun; Liu, Wei; Deng, Chengcheng; Yang, Nuo

2015-11-10

The ultra-low thermal conductivity of bulk polymers may be enhanced by combining them with high thermal conductivity materials such as carbon nanotubes. Different from random doping, we find that the aligned carbon nanotube-polyethylene composites has a high thermal conductivity by non-equilibrium molecular dynamics simulations. The analyses indicate that the aligned composite not only take advantage of the high thermal conduction of carbon nanotubes, but enhance thermal conduction of polyethylene chains.

A study of the dynamic tire properties over a range of tire constructions

NASA Technical Reports Server (NTRS)

Nybakken, G. H.; Dodge, R. N.; Clark, S. K.

1973-01-01

The dynamic properties of four model aircraft tires of various construction were evaluated experimentally and compared with available theory. The experimental investigation consisted of measuring the cornering force and the self-aligning torque developed by the tires undergoing sinusoidal steering inputs while operating on a small scale, road-wheel tire testing apparatus. The force and moment data from the different tires are compared with both finite- and point-contact patch string theory predictions. In general, agreement between finite contact patch theory and experimental observation is good. A modified string theory is also presented in which coefficients for cornering force and self-aligning torque are determined separately. This theory improves the correspondence between the experimental and analytical data, particularly on tires with relatively high self-aligning torques.

Miniaturized GPS/MEMS IMU integrated board

NASA Technical Reports Server (NTRS)

Lin, Ching-Fang (Inventor)

2012-01-01

This invention documents the efforts on the research and development of a miniaturized GPS/MEMS IMU integrated navigation system. A miniaturized GPS/MEMS IMU integrated navigation system is presented; Laser Dynamic Range Imager (LDRI) based alignment algorithm for space applications is discussed. Two navigation cameras are also included to measure the range and range rate which can be integrated into the GPS/MEMS IMU system to enhance the navigation solution.

Radial SI latches vibration test data review

NASA Technical Reports Server (NTRS)

Harrison, P. M.; Smith, J. L.

1984-01-01

Dynamic testing of the Space Telescope Scientific Instrument Radial Latches was performed as specified by the designated test criteria. No structural failures were observed during the test. The alignment stability of the instrument simulator was within required tolerances after testing. Particulates were discovered around the latch bases, after testing, due to wearing at the B and C latch interface surfaces. This report covers criteria derivation, testing, and test results.

Relaxation processes in a low-order three-dimensional magnetohydrodynamics model

NASA Technical Reports Server (NTRS)

Stribling, Troy; Matthaeus, William H.

1991-01-01

The time asymptotic behavior of a Galerkin model of 3D magnetohydrodynamics (MHD) has been interpreted using the selective decay and dynamic alignment relaxation theories. A large number of simulations has been performed that scan a parameter space defined by the rugged ideal invariants, including energy, cross helicity, and magnetic helicity. It is concluded that time asymptotic state can be interpreted as a relaxation to minimum energy. A simple decay model, based on absolute equilibrium theory, is found to predict a mapping of initial onto time asymptotic states, and to accurately describe the long time behavior of the runs when magnetic helicity is present. Attention is also given to two processes, operating on time scales shorter than selective decay and dynamic alignment, in which the ratio of kinetic to magnetic energy relaxes to values 0(1). The faster of the two processes takes states initially dominant in magnetic energy to a state of near-equipartition between kinetic and magnetic energy through power law growth of kinetic energy. The other process takes states initially dominant in kinetic energy to the near-equipartitioned state through exponential growth of magnetic energy.

Ultrasound monitoring of inter-knee distances during gait.

PubMed

Lai, Daniel T H; Wrigley, Tim V; Palaniswami, M

2009-01-01

Knee osteoarthritis is an extremely common, debilitating disease associated with pain and loss of function. There is considerable interest in monitoring lower limb alignment due to its close association with joint overload leading to disease progression. The effects of gait modifications that can lower joint loading are of particular interest. Here we describe an ultrasound-based system for monitoring an important aspect of dynamic lower limb alignment, the inter-knee distance during walking. Monitoring this gait parameter should facilitate studies in reducing knee loading, a primary risk factor of knee osteoarthritis progression. The portable device is composed of an ultrasound sensor connected to an Intel iMote2 equipped with Bluetooth wireless capability. Static tests and calibration results show that the sensor possesses an effective beam envelope of 120 degrees, with maximum distance errors of 10% at the envelope edges. Dynamic walking trials reveal close correlation of inter-knee distance trends between that measured by an optical system (Optotrak Certus NDI) and the sensor device. The maximum average root mean square error was found to be 1.46 cm. Future work will focus on improving the accuracy of the device.

A priori testing of subgrid-scale models for large-eddy simulation of the atmospheric boundary layer

NASA Astrophysics Data System (ADS)

Juneja, Anurag; Brasseur, James G.

1996-11-01

Subgrid-scale models are generally developed assuming homogeneous isotropic turbulence with the filter cutoff lying in the inertial range. In the surface layer and capping inversion regions of the atmospheric boundary layer, the turbulence is strongly anisotropic and, in general, influenced by both buoyancy and shear. Furthermore, the integral scale motions are under-resolved in these regions. Herein we perform direct numerical simulations of shear and buoyancy-generated homogeneous anisotropic turbulence to compute and analyze the actual subgrid-resolved-scale (SGS-RS) dynamics as the filter cutoff moves into the energy-containing scales. These are compared with the SGS-RS dynamics predicted by Smagorinsky-based models with a focus on motivating improved closures. We find that, in general, the underlying assumption of such models, that the anisotropic part of the subgrid stress tensor be aligned with the resolved strain rate tensor, is a poor approximation. Similarly, we find poor alignment between the actual and predicted stress divergence, and find low correlations between the actual and modeled subgrid-scale contribution to the pressure and pressure gradient. Details will be given in the talk.

Assessing the statistical robustness of inter- and intra-basinal carbon isotope chemostratigraphic correlation

NASA Astrophysics Data System (ADS)

Hay, C.; Creveling, J. R.; Huybers, P. J.

2016-12-01

Excursions in the stable carbon isotopic composition of carbonate rocks (δ13Ccarb) can facilitate correlation of Precambrian and Phanerozoic sedimentary successions at a higher temporal resolution than radiometric and biostratigraphic frameworks typically afford. Within the bounds of litho- and biostratigraphic constraints, stratigraphers often correlate isotopic patterns between distant stratigraphic sections through visual alignment of local maxima and minima of isotopic values. The reproducibility of this method can prove challenging and, thus, evaluating the statistical robustness of intrabasinal composite carbon isotope curves, and global correlations to these reference curves, remains difficult. To assess the reproducibility of stratigraphic alignment of δ13Ccarb data, and correlations between carbon isotope excursions, we employ a numerical dynamic time warping methodology that stretches and squeezes the time axis of a record to obtain an optimal correlation (in a least-squares sense) between time-uncertain series of data. In particular, we assess various alignments between series of Early Cambrian δ13Ccarb data with respect to plausible matches. We first show that an alignment of these records obtained visually, and published previously, is broadly reproducible using dynamic time warping. Alternative alignments with similar goodness of fits are also obtainable, and their stratigraphic plausibility are discussed. This approach should be generalizable to an algorithm for the purposes of developing a library of plausible alignments between multiple time-uncertain stratigraphic records.

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

PubMed

Zhou, Carol L Ecale

2015-01-01

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

Mediolateral force distribution at the knee joint shifts across activities and is driven by tibiofemoral alignment.

PubMed

Kutzner, I; Bender, A; Dymke, J; Duda, G; von Roth, P; Bergmann, G

2017-06-01

Tibiofemoral alignment is important to determine the rate of progression of osteoarthritis and implant survival after total knee arthroplasty (TKA). Normally, surgeons aim for neutral tibiofemoral alignment following TKA, but this has been questioned in recent years. The aim of this study was to evaluate whether varus or valgus alignment indeed leads to increased medial or lateral tibiofemoral forces during static and dynamic weight-bearing activities. Tibiofemoral contact forces and moments were measured in nine patients with instrumented knee implants. Medial force ratios were analysed during nine daily activities, including activities with single-limb support (e.g. walking) and double-limb support (e.g. knee bend). Hip-knee-ankle angles in the frontal plane were analysed using full-leg coronal radiographs. The medial force ratio strongly correlated with the tibiofemoral alignment in the static condition of one-legged stance (R² = 0.88) and dynamic single-limb loading (R² = 0.59) with varus malalignment leading to increased medial force ratios of up to 88%. In contrast, the correlation between leg alignment and magnitude of medial compartment force was much less pronounced. A lateral shift of force occurred during activities with double-limb support and higher knee flexion angles. The medial force ratio depends on both the tibiofemoral alignment and the nature of the activity involved. It cannot be generalised to a single value. Higher medial ratios during single-limb loading are associated with varus malalignment in TKA. The current trend towards a 'constitutional varus' after joint replacement, in terms of overall tibiofemoral alignment, should be considered carefully with respect to the increased medial force ratio. Cite this article: Bone Joint J 2017;99-B:779-87. ©2017 The British Editorial Society of Bone & Joint Surgery.

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.

Self-Alignment MEMS IMU Method Based on the Rotation Modulation Technique on a Swing Base

PubMed Central

Chen, Zhiyong; Yang, Haotian; Wang, Chengbin; Lin, Zhihui; Guo, Meifeng

2018-01-01

The micro-electro-mechanical-system (MEMS) inertial measurement unit (IMU) has been widely used in the field of inertial navigation due to its small size, low cost, and light weight, but aligning MEMS IMUs remains a challenge for researchers. MEMS IMUs have been conventionally aligned on a static base, requiring other sensors, such as magnetometers or satellites, to provide auxiliary information, which limits its application range to some extent. Therefore, improving the alignment accuracy of MEMS IMU as much as possible under swing conditions is of considerable value. This paper proposes an alignment method based on the rotation modulation technique (RMT), which is completely self-aligned, unlike the existing alignment techniques. The effect of the inertial sensor errors is mitigated by rotating the IMU. Then, inertial frame-based alignment using the rotation modulation technique (RMT-IFBA) achieved coarse alignment on the swing base. The strong tracking filter (STF) further improved the alignment accuracy. The performance of the proposed method was validated with a physical experiment, and the results of the alignment showed that the standard deviations of pitch, roll, and heading angle were 0.0140°, 0.0097°, and 0.91°, respectively, which verified the practicality and efficacy of the proposed method for the self-alignment of the MEMS IMU on a swing base. PMID:29649150

Correction of static axial alignment in children with knee varus or valgus deformities through guided growth: Does it also correct dynamic frontal plane moments during walking?

PubMed

Böhm, Harald; Stief, Felix; Sander, Klaus; Hösl, Matthias; Döderlein, Leonhard

2015-09-01

Malaligned knees are predisposed to the development and progression of unicompartmental degenerations because of the excessive load placed on one side of the knee. Therefore, guided growth in skeletally immature patients is recommended. Indication for correction of varus/valgus deformities are based on static weight bearing radiographs. However, the dynamic knee abduction moment during walking showed only a weak correlation to malalignment determined by static radiographs. Therefore, the aim of the study was to measure the effects of guided growth on the normalization of frontal plane knee joint moments during walking. 15 legs of 8 patients (11-15 years) with idiopathic axial varus or valgus malalignment were analyzed. 16 typically developed peers served as controls. Instrumented gait analysis and clinical assessment were performed the day before implantation and explantation of eight-plates. Correlation between static mechanical tibiofemoral axis angle (MAA) and dynamic frontal plane knee joint moments and their change by guided growth were performed. The changes in dynamic knee moment in the frontal plane following guided growth showed high and significant correlation to the changes in static MAA (R=0.97, p<0.001). Contrary to the correlation of the changes, there was no correlation between static and dynamic measures in both sessions. In consequence two patients that had a natural knee moment before treatment showed a more pathological one after treatment. In conclusion, the changes in the dynamic load situation during walking can be predicted from the changes in static alignment. If pre-surgical gait analysis reveals a natural load situation, despite a static varus or valgus deformity, the intervention must be critically discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Predicting areas of sustainable error growth in quasigeostrophic flows using perturbation alignment properties

NASA Astrophysics Data System (ADS)

Rivière, G.; Hua, B. L.

2004-10-01

A new perturbation initialization method is used to quantify error growth due to inaccuracies of the forecast model initial conditions in a quasigeostrophic box ocean model describing a wind-driven double gyre circulation. This method is based on recent analytical results on Lagrangian alignment dynamics of the perturbation velocity vector in quasigeostrophic flows. More specifically, it consists in initializing a unique perturbation from the sole knowledge of the control flow properties at the initial time of the forecast and whose velocity vector orientation satisfies a Lagrangian equilibrium criterion. This Alignment-based Initialization method is hereafter denoted as the AI method.In terms of spatial distribution of the errors, we have compared favorably the AI error forecast with the mean error obtained with a Monte-Carlo ensemble prediction. It is shown that the AI forecast is on average as efficient as the error forecast initialized with the leading singular vector for the palenstrophy norm, and significantly more efficient than that for total energy and enstrophy norms. Furthermore, a more precise examination shows that the AI forecast is systematically relevant for all control flows whereas the palenstrophy singular vector forecast leads sometimes to very good scores and sometimes to very bad ones.A principal component analysis at the final time of the forecast shows that the AI mode spatial structure is comparable to that of the first eigenvector of the error covariance matrix for a "bred mode" ensemble. Furthermore, the kinetic energy of the AI mode grows at the same constant rate as that of the "bred modes" from the initial time to the final time of the forecast and is therefore characterized by a sustained phase of error growth. In this sense, the AI mode based on Lagrangian dynamics of the perturbation velocity orientation provides a rationale of the "bred mode" behavior.

Beam/seam alignment control for electron beam welding

DOEpatents

Burkhardt, Jr., James H.; Henry, J. James; Davenport, Clyde M.

1980-01-01

This invention relates to a dynamic beam/seam alignment control system for electron beam welds utilizing video apparatus. The system includes automatic control of workpiece illumination, near infrared illumination of the workpiece to limit the range of illumination and camera sensitivity adjustment, curve fitting of seam position data to obtain an accurate measure of beam/seam alignment, and automatic beam detection and calculation of the threshold beam level from the peak beam level of the preceding video line to locate the beam or seam edges.

Isosteric And Non-Isosteric Base Pairs In RNA Motifs: Molecular Dynamics And Bioinformatics Study Of The Sarcin-Ricin Internal Loop

PubMed Central

Havrila, Marek; Réblová, Kamila; Zirbel, Craig L.; Leontis, Neocles B.; Šponer, Jiří

2013-01-01

The Sarcin-Ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, i.e., in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of SR motif. SHAPE probing experiment was also performed to confirm fidelity of MD simulations. We identified 57 instances of the SR motif in a non-redundant subset of the RNA X-ray structure database and analyzed their basepairing, base-phosphate, and backbone-backbone interactions. We extracted sequences aligned to these instances from large ribosomal RNA alignments to determine frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. Non isosteric base substitutions led to unstable structures, but so did isosteric substitutions which were unable to make key base-phosphate interactions. MD technique explains why some potentially isosteric SR motifs are not realized during evolution. We also found that inability to form stable cWW geometry is an important factor in case of the first base pair of the flexible region of the SR motif. Comparison of structural, bioinformatics, SHAPE probing and MD simulation data reveals that explicit solvent MD simulations neatly reflect viability of different sequence variants of the SR motif. Thus, MD simulations can efficiently complement bioinformatics tools in studies of conservation patterns of RNA motifs and provide atomistic insight into the role of their different signature interactions. PMID:24144333

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

Rigid Facial Motion Influences Featural, But Not Holistic, Face Processing

PubMed Central

Xiao, Naiqi; Quinn, Paul C.; Ge, Liezhong; Lee, Kang

2012-01-01

We report three experiments in which we investigated the effect of rigid facial motion on face processing. Specifically, we used the face composite effect to examine whether rigid facial motion influences primarily featural or holistic processing of faces. In Experiments 1, 2, and 3, participants were first familiarized with dynamic displays in which a target face turned from one side to another; then at test, participants judged whether the top half of a composite face (the top half of the target face aligned or misaligned with the bottom half of a foil face) belonged to the target face. We compared performance in the dynamic condition to various static control conditions in Experiments 1, 2, and 3, which differed from each other in terms of the display order of the multiple static images or the inter stimulus interval (ISI) between the images. We found that the size of the face composite effect in the dynamic condition was significantly smaller than that in the static conditions. In other words, the dynamic face display influenced participants to process the target faces in a part-based manner and consequently their recognition of the upper portion of the composite face at test became less interfered with by the aligned lower part of the foil face. The findings from the present experiments provide the strongest evidence to date to suggest that the rigid facial motion mainly influences facial featural, but not holistic, processing. PMID:22342561

Real-time high-resolution measurement of collagen alignment in dynamically loaded soft tissue.

PubMed

York, Timothy; Kahan, Lindsey; Lake, Spencer P; Gruev, Viktor

2014-06-01

A technique for creating maps of the direction and strength of fiber alignment in collagenous soft tissues is presented. The method uses a division of focal plane polarimeter to measure circularly polarized light transmitted through the tissue. The architecture of the sensor allows measurement of the retardance and fiber alignment at the full frame rate of the sensor without any moving optics. The technique compares favorably to the standard method of using a rotating polarizer. How the new technique enables real-time capture of the full angular spread of fiber alignment and retardance under various cyclic loading conditions is illustrated.

Competing mechanisms and scaling laws for carbon nanotube scission by ultrasonication.

PubMed

Pagani, Guido; Green, Micah J; Poulin, Philippe; Pasquali, Matteo

2012-07-17

Dispersion of carbon nanotubes (CNTs) into liquids typically requires ultrasonication to exfoliate individuals CNTs from bundles. Experiments show that CNT length drops with sonication time (or energy) as a power law t(-m). Yet the breakage mechanism is not well understood, and the experimentally reported power law exponent m ranges from approximately 0.2 to 0.5. Here we simulate the motion of CNTs around cavitating bubbles by coupling brownian dynamics with the Rayleigh-Plesset equation. We observe that, during bubble growth, CNTs align tangentially to the bubble surface. Surprisingly, we find two dynamical regimes during the collapse: shorter CNTs align radially, longer ones buckle. We compute the phase diagram for CNT collapse dynamics as a function of CNT length, stiffness, and initial distance from the bubble nuclei and determine the transition from aligning to buckling. We conclude that, depending on their length, CNTs can break due to either buckling or stretching. These two mechanisms yield different power laws for the length decay (0.25 and 0.5, respectively), reconciling the apparent discrepancy in the experimental data.

A Model for Determining Optimal Governance Structure in DoD Acquisition Projects in a Performance-Based Environment

DTIC Science & Technology

2010-04-30

combating market dynamism (Aldrich, 1979; Child, 1972), which is a result of evolving technology, shifting prices, or variance in product availability... principles : (1) human beings are bounded rationally, and (2), as a result of being rationally bound, will always choose to further their own self... principles to govern the relationship among the buyers and suppliers. Our conceptual model aligns the alternative governance structures derived

Aligning Sales Curriculum Content and Pedagogy with Practitioners' Needs

ERIC Educational Resources Information Center

Newberry, Robert; Collins, Marianne K.

2015-01-01

Meeting the instructional needs of both students and sales practitioners is a common challenge for sales educators. The dynamic and ever evolving nature of the sales landscape, in conjunction with the need to align sales curriculum with relevant business practices is the focus of this article. Building on previous research, this study investigates…

Dynamic evaluation of anterior dental alignment in a sample of 8- to 11-year-old children.

PubMed

Lombardo, Luca; Berveglieri, Chiara; Guarneri, Antonio; Siciliani, Giuseppe

2012-06-01

To describe perceptions related to different anterior dental alignments in a sample of 106 children aged between 8- and 11-years-old. We employed dynamic media (videos) showing a smile in four different arrangements (ideal incisal occlusion - N, median diastema - D, incisal crowding - A, protruding incisors - P), with and without general contextual attractiveness. The perception is the same both for the whole face and for the frontal smile alone and there are no significant differences between the answers from male and female interviews. Smiles with normal alignment gain higher scores for esthetics and are associated with more positive qualities. In contrast, smiles with proclined and crowded teeth obtain lower scores. Analysis of the results showed that there are no significant differences between perceptions, sensations and judgments related to smiles presented either as part of the whole face or in only the lower facial third: general facial attractiveness does not influence evaluations of the smile. The study confirms the general tendency to award higher scores to smiles with normal alignment. Copyright © 2012 CEO. Published by Elsevier Masson SAS. All rights reserved.

What can the past of pay-for-performance tell us about the future of Value-Based Purchasing in Medicare?

PubMed

Ryan, Andrew M; Damberg, Cheryl L

2013-06-01

The Medicare program has implemented pay-for-performance (P4P), or Value-Based Purchasing, for inpatient care and for Medicare Advantage plans, and plans to implement a program for physicians in 2015. In this paper, we review evidence on the effectiveness of P4P and identify design criteria deemed to be best practice in P4P. We then assess the extent to which Medicare's existing and planned Value-Based Purchasing programs align with these best practices. Of the seven identified best practices in P4P program design, the Hospital Value-Based Purchasing program is strongly aligned with two of the best practices, moderately aligned with three, weakly aligned with one, and has unclear alignment with one best practice. The Physician Value-Based Purchasing Modifier is strongly aligned with two of the best practices, moderately aligned with one, weakly aligned with three, and has unclear alignment with one of the best practices. The Medicare Advantage Quality Bonus Program is strongly aligned with four of the best practices, moderately aligned with two, and weakly aligned with one of the best practices. We identify enduring gaps in P4P literature as it relates to Medicare's plans for Value-Based Purchasing and discuss important issues in the future of these implementations in Medicare. Copyright © 2013 Elsevier Inc. All rights reserved.

Frontiers of controlling energy levels at interfaces

NASA Astrophysics Data System (ADS)

Koch, Norbert

The alignment of electron energy levels at interfaces between semiconductors, dielectrics, and electrodes determines the function and efficiency of all electronic and optoelectronic devices. Reliable guidelines for predicting the level alignment for a given material combination and methods to adjust the intrinsic energy landscape are needed to enable efficient engineering approaches. These are sufficiently understood for established electronic materials, e.g., Si, but for the increasing number of emerging materials, e.g., organic and 2D semiconductors, perovskites, this is work in progress. The intrinsic level alignment and the underlying mechanisms at interfaces between organic and inorganic semiconductors are discussed first. Next, methods to alter the level alignment are introduced, which all base on proper charge density rearrangement at a heterojunction. As interface modification agents we use molecular electron acceptors and donors, as well as molecular photochromic switches that add a dynamic aspect and allow device multifunctionality. For 2D semiconductors surface transfer doping with molecular acceptors/donors transpires as viable method to locally tune the Fermi-level position in the energy gap. The fundamental electronic properties of a prototypical 1D interface between intrinsic and p-doped 2D semiconductor regions are derived from local (scanning probe) and area-averaged (photoemission) spectroscopy experiments. Future research opportunities for attaining unsurpassed interface control through charge density management are discussed.

Effects of flow on the dynamics of a ferromagnetic nematic liquid crystal

NASA Astrophysics Data System (ADS)

Potisk, Tilen; Pleiner, Harald; Svenšek, Daniel; Brand, Helmut R.

2018-04-01

We investigate the effects of flow on the dynamics of ferromagnetic nematic liquid crystals. As a model, we study the coupled dynamics of the magnetization, M , the director field, n , associated with the liquid crystalline orientational order, and the velocity field, v . We evaluate how simple shear flow in a ferromagnetic nematic is modified in the presence of small external magnetic fields, and we make experimentally testable predictions for the resulting effective shear viscosity: an increase by a factor of 2 in a magnetic field of about 20 mT. Flow alignment, a characteristic feature of classical uniaxial nematic liquid crystals, is analyzed for ferromagnetic nematics for the two cases of magnetization in or perpendicular to the shear plane. In the former case, we find that small in-plane magnetic fields are sufficient to suppress tumbling and thus that the boundary between flow alignment and tumbling can be controlled easily. In the latter case, we furthermore find a possibility of flow alignment in a regime for which one obtains tumbling for the pure nematic component. We derive the analogs of the three Miesowicz viscosities well-known from usual nematic liquid crystals, corresponding to nine different configurations. Combinations of these can be used to determine several dynamic coefficients experimentally.

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.

Classification of biosensor time series using dynamic time warping: applications in screening cancer cells with characteristic biomarkers.

PubMed

Rai, Shesh N; Trainor, Patrick J; Khosravi, Farhad; Kloecker, Goetz; Panchapakesan, Balaji

2016-01-01

The development of biosensors that produce time series data will facilitate improvements in biomedical diagnostics and in personalized medicine. The time series produced by these devices often contains characteristic features arising from biochemical interactions between the sample and the sensor. To use such characteristic features for determining sample class, similarity-based classifiers can be utilized. However, the construction of such classifiers is complicated by the variability in the time domains of such series that renders the traditional distance metrics such as Euclidean distance ineffective in distinguishing between biological variance and time domain variance. The dynamic time warping (DTW) algorithm is a sequence alignment algorithm that can be used to align two or more series to facilitate quantifying similarity. In this article, we evaluated the performance of DTW distance-based similarity classifiers for classifying time series that mimics electrical signals produced by nanotube biosensors. Simulation studies demonstrated the positive performance of such classifiers in discriminating between time series containing characteristic features that are obscured by noise in the intensity and time domains. We then applied a DTW distance-based k -nearest neighbors classifier to distinguish the presence/absence of mesenchymal biomarker in cancer cells in buffy coats in a blinded test. Using a train-test approach, we find that the classifier had high sensitivity (90.9%) and specificity (81.8%) in differentiating between EpCAM-positive MCF7 cells spiked in buffy coats and those in plain buffy coats.

Evaluation of an image-based tracking workflow with Kalman filtering for automatic image plane alignment in interventional MRI.

PubMed

Neumann, M; Cuvillon, L; Breton, E; de Matheli, M

2013-01-01

Recently, a workflow for magnetic resonance (MR) image plane alignment based on tracking in real-time MR images was introduced. The workflow is based on a tracking device composed of 2 resonant micro-coils and a passive marker, and allows for tracking of the passive marker in clinical real-time images and automatic (re-)initialization using the microcoils. As the Kalman filter has proven its benefit as an estimator and predictor, it is well suited for use in tracking applications. In this paper, a Kalman filter is integrated in the previously developed workflow in order to predict position and orientation of the tracking device. Measurement noise covariances of the Kalman filter are dynamically changed in order to take into account that, according to the image plane orientation, only a subset of the 3D pose components is available. The improved tracking performance of the Kalman extended workflow could be quantified in simulation results. Also, a first experiment in the MRI scanner was performed but without quantitative results yet.

Evaluation of the interaction of cyclin-dependent kinase 5 with activator p25 and with p25-derived inhibitor CIP.

PubMed

Cardone, Antonio; Albers, R Wayne; Sriram, Ram D; Pant, Harish C

2010-05-01

A high-affinity inhibitor protein called CIP, produced by small truncations of p35, was experimentally identified. P35 is a physiological activator of the cyclin-dependent kinase cdk5. P25 is derived from proteolytic truncation of p35 within "stressed" neurons, and it is associated with the hyperphosphorylation of specific neuronal proteins, typically occurring in neurodegenerative diseases such as Alzheimer's. Here, we report a study of the binding mechanisms of the cdk5-p25 and cdk5-CIP complexes. This provides a better understanding of the source of the inhibitory activity of the protein CIP. We use a geometry-based technique to test the hypothesis that p25's truncation increases the flexibility of CIP and thus prevents cdk5 from reaching its active conformation. Our study is based on a geometry-based alignment algorithm, which aligns two given protein conformations with respect to their interfaces. Our results support the flexibility hypothesis and will be used as a basis for targeted molecular dynamics simulations.

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

PubMed Central

Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang

2011-01-01

I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and FG-MD, were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of beta-proteins are still needed to further improve the I-TASSER pipeline. PMID:22069036

Energy absorption ability of buckyball C720 at low impact speed: a numerical study based on molecular dynamics

PubMed Central

2013-01-01

The dynamic impact response of giant buckyball C720 is investigated by using molecular dynamics simulations. The non-recoverable deformation of C720 makes it an ideal candidate for high-performance energy absorption. Firstly, mechanical behaviors under dynamic impact and low-speed crushing are simulated and modeled, which clarifies the buckling-related energy absorption mechanism. One-dimensional C720 arrays (both vertical and horizontal alignments) are studied at various impact speeds, which show that the energy absorption ability is dominated by the impact energy per buckyball and less sensitive to the number and arrangement direction of buckyballs. Three-dimensional stacking of buckyballs in simple cubic, body-centered cubic, hexagonal, and face-centered cubic forms are investigated. Stacking form with higher occupation density yields higher energy absorption. The present study may shed lights on employing C720 assembly as an advanced energy absorption system against low-speed impacts. PMID:23360618

Orbit Alignment in Triple Stars

NASA Astrophysics Data System (ADS)

Tokovinin, Andrei

2017-08-01

The statistics of the angle Φ between orbital angular momenta in hierarchical triple systems with known inner visual or astrometric orbits are studied. A correlation between apparent revolution directions proves the partial orbit alignment known from earlier works. The alignment is strong in triples with outer projected separation less than ˜50 au, where the average Φ is about 20^\\circ . In contrast, outer orbits wider than 1000 au are not aligned with the inner orbits. It is established that the orbit alignment decreases with the increasing mass of the primary component. The average eccentricity of inner orbits in well-aligned triples is smaller than in randomly aligned ones. These findings highlight the role of dissipative interactions with gas in defining the orbital architecture of low-mass triple systems. On the other hand, chaotic dynamics apparently played a role in shaping more massive hierarchies. The analysis of projected configurations and triples with known inner and outer orbits indicates that the distribution of Φ is likely bimodal, where 80% of triples have {{Φ }}< 70^\\circ and the remaining ones are randomly aligned.

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.

Effect of Alignment on L2 Written Production

ERIC Educational Resources Information Center

Wang, Chuming; Wang, Min

2015-01-01

This article aims to uncover how L2 writing is affected by alignment, a socio-cognitive process involving dynamic coordination and adaptation. For this, two studies were conducted. Study 1 required two groups of 24 learners of English as a foreign language (EFL) to continue in English two stories with their endings removed, both of which had a…

Second Language Developmental Dynamics: How Dynamic Systems Theory Accounts for Issues in Second Language Learning

ERIC Educational Resources Information Center

Rosmawati

2014-01-01

Dynamic systems theory (DST) is presented in this article as a suitable approach to research the acquisition of second language (L2) because of its close alignment with the process of second language learning. Through a process of identifying and comparing the characteristics of a dynamic system with the process of L2 learning, this article…

Alignment and integration of complex networks by hypergraph-based spectral clustering

NASA Astrophysics Data System (ADS)

Michoel, Tom; Nachtergaele, Bruno

2012-11-01

Complex networks possess a rich, multiscale structure reflecting the dynamical and functional organization of the systems they model. Often there is a need to analyze multiple networks simultaneously, to model a system by more than one type of interaction, or to go beyond simple pairwise interactions, but currently there is a lack of theoretical and computational methods to address these problems. Here we introduce a framework for clustering and community detection in such systems using hypergraph representations. Our main result is a generalization of the Perron-Frobenius theorem from which we derive spectral clustering algorithms for directed and undirected hypergraphs. We illustrate our approach with applications for local and global alignment of protein-protein interaction networks between multiple species, for tripartite community detection in folksonomies, and for detecting clusters of overlapping regulatory pathways in directed networks.

Alignment and integration of complex networks by hypergraph-based spectral clustering.

PubMed

Michoel, Tom; Nachtergaele, Bruno

2012-11-01

Complex networks possess a rich, multiscale structure reflecting the dynamical and functional organization of the systems they model. Often there is a need to analyze multiple networks simultaneously, to model a system by more than one type of interaction, or to go beyond simple pairwise interactions, but currently there is a lack of theoretical and computational methods to address these problems. Here we introduce a framework for clustering and community detection in such systems using hypergraph representations. Our main result is a generalization of the Perron-Frobenius theorem from which we derive spectral clustering algorithms for directed and undirected hypergraphs. We illustrate our approach with applications for local and global alignment of protein-protein interaction networks between multiple species, for tripartite community detection in folksonomies, and for detecting clusters of overlapping regulatory pathways in directed networks.

Alignment of cell division axes in directed epithelial cell migration

NASA Astrophysics Data System (ADS)

Marel, Anna-Kristina; Podewitz, Nils; Zorn, Matthias; Oskar Rädler, Joachim; Elgeti, Jens

2014-11-01

Cell division is an essential dynamic event in tissue remodeling during wound healing, cancer and embryogenesis. In collective migration, tensile stresses affect cell shape and polarity, hence, the orientation of the cell division axis is expected to depend on cellular flow patterns. Here, we study the degree of orientation of cell division axes in migrating and resting epithelial cell sheets. We use microstructured channels to create a defined scenario of directed cell invasion and compare this situation to resting but proliferating cell monolayers. In experiments, we find a strong alignment of the axis due to directed flow while resting sheets show very weak global order, but local flow gradients still correlate strongly with the cell division axis. We compare experimental results with a previously published mesoscopic particle based simulation model. Most of the observed effects are reproduced by the simulations.

WEB-server for search of a periodicity in amino acid and nucleotide sequences

NASA Astrophysics Data System (ADS)

E Frenkel, F.; Skryabin, K. G.; Korotkov, E. V.

2017-12-01

A new web server (http://victoria.biengi.ac.ru/splinter/login.php) was designed and developed to search for periodicity in nucleotide and amino acid sequences. The web server operation is based upon a new mathematical method of searching for multiple alignments, which is founded on the position weight matrices optimization, as well as on implementation of the two-dimensional dynamic programming. This approach allows the construction of multiple alignments of the indistinctly similar amino acid and nucleotide sequences that accumulated more than 1.5 substitutions per a single amino acid or a nucleotide without performing the sequences paired comparisons. The article examines the principles of the web server operation and two examples of studying amino acid and nucleotide sequences, as well as information that could be obtained using the web server.

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.

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

PubMed Central

Röst, Hannes L.; Liu, Yansheng; D’Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C.; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi

2016-01-01

Large scale, quantitative proteomic studies have become essential for the analysis of clinical cohorts, large perturbation experiments and systems biology studies. While next-generation mass spectrometric techniques such as SWATH-MS have substantially increased throughput and reproducibility, ensuring consistent quantification of thousands of peptide analytes across multiple LC-MS/MS runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we have developed the TRIC software which utilizes fragment ion data to perform cross-run alignment, consistent peak-picking and quantification for high throughput targeted proteomics. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate peak elution information from all LC-MS/MS runs acquired in a study. When compared to state-of-the-art SWATH-MS data analysis, the algorithm was able to reduce the identification error by more than 3-fold at constant recall, while correcting for highly non-linear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem (iPS) cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups and substantially increased the quantitative completeness and biological information in the data, providing insights into protein dynamics of iPS cells. Overall, this study demonstrates the importance of consistent quantification in highly challenging experimental setups, and proposes an algorithm to automate this task, constituting the last missing piece in a pipeline for automated analysis of massively parallel targeted proteomics datasets. PMID:27479329

On-command on/off switching of progenitor cell and cancer cell polarized motility and aligned morphology via a cytocompatible shape memory polymer scaffold.

PubMed

Wang, Jing; Quach, Andy; Brasch, Megan E; Turner, Christopher E; Henderson, James H

2017-09-01

In vitro biomaterial models have enabled advances in understanding the role of extracellular matrix (ECM) architecture in the control of cell motility and polarity. Most models are, however, static and cannot mimic dynamic aspects of in vivo ECM remodeling and function. To address this limitation, we present an electrospun shape memory polymer scaffold that can change fiber alignment on command under cytocompatible conditions. Cellular response was studied using the human fibrosarcoma cell line HT-1080 and the murine mesenchymal stem cell line C3H/10T1/2. The results demonstrate successful on-command on/off switching of cell polarized motility and alignment. Decrease in fiber alignment causes a change from polarized motility along the direction of fiber alignment to non-polarized motility and from aligned to unaligned morphology, while increase in fiber alignment causes a change from non-polarized to polarized motility along the direction of fiber alignment and from unaligned to aligned morphology. In addition, the findings are consistent with the hypothesis that increased fiber alignment causes increased cell velocity, while decreased fiber alignment causes decreased cell velocity. On-command on/off switching of cell polarized motility and alignment is anticipated to enable new study of directed cell motility in tumor metastasis, in cell homing, and in tissue engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Vacuum selection on axionic landscapes

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

Wang, Gaoyuan; Battefeld, Thorsten, E-mail: gaoyuan.wang@stud.uni-goettingen.de, E-mail: tbattefe@astro.physik.uni-goettingen.de

2016-04-01

We compute the distribution of minima that are reached dynamically on multi-field axionic landscapes, both numerically and analytically. Such landscapes are well suited for inflationary model building due to the presence of shift symmetries and possible alignment effects (the KNP mechanism). The resulting distribution of dynamically reached minima differs considerably from the naive expectation based on counting all vacua. These differences are more pronounced in the presence of many fields due to dynamical selection effects: while low lying minima are preferred as fields roll down the potential, trajectories are also more likely to get trapped by one of the manymore » nearby minima. We show that common analytic arguments based on random matrix theory in the large D-limit to estimate the distribution of minima are insufficient for quantitative arguments pertaining to the dynamically reached ones. This discrepancy is not restricted to axionic potentials. We provide an empirical expression for the expectation value of such dynamically reached minimas' height and argue that the cosmological constant problem is not alleviated in the absence of anthropic arguments. We further comment on the likelihood of inflation on axionic landscapes in the large D-limit.« less

SYNCHRONIZATION OF HETEROGENEOUS OSCILLATORS UNDER NETWORK MODIFICATIONS: PERTURBATION AND OPTIMIZATION OF THE SYNCHRONY ALIGNMENT FUNCTION

PubMed Central

Taylor, Dane; Skardal, Per Sebastian; Sun, Jie

2016-01-01

Synchronization is central to many complex systems in engineering physics (e.g., the power-grid, Josephson junction circuits, and electro-chemical oscillators) and biology (e.g., neuronal, circadian, and cardiac rhythms). Despite these widespread applications—for which proper functionality depends sensitively on the extent of synchronization—there remains a lack of understanding for how systems can best evolve and adapt to enhance or inhibit synchronization. We study how network modifications affect the synchronization properties of network-coupled dynamical systems that have heterogeneous node dynamics (e.g., phase oscillators with non-identical frequencies), which is often the case for real-world systems. Our approach relies on a synchrony alignment function (SAF) that quantifies the interplay between heterogeneity of the network and of the oscillators and provides an objective measure for a system’s ability to synchronize. We conduct a spectral perturbation analysis of the SAF for structural network modifications including the addition and removal of edges, which subsequently ranks the edges according to their importance to synchronization. Based on this analysis, we develop gradient-descent algorithms to efficiently solve optimization problems that aim to maximize phase synchronization via network modifications. We support these and other results with numerical experiments. PMID:27872501

Immersion and dry scanner extensions for sub-10nm production nodes

NASA Astrophysics Data System (ADS)

Weichselbaum, Stefan; Bornebroek, Frank; de Kort, Toine; Droste, Richard; de Graaf, Roelof F.; van Ballegoij, Rob; Botter, Herman; McLaren, Matthew G.; de Boeij, Wim P.

2015-03-01

Progressing towards the 10nm and 7nm imaging node, pattern-placement and layer-to-layer overlay requirements keep on scaling down and drives system improvements in immersion (ArFi) and dry (ArF/KrF) scanners. A series of module enhancements in the NXT platform have been introduced; among others, the scanner is equipped with exposure stages with better dynamics and thermal control. Grid accuracy improvements with respect to calibration, setup, stability, and layout dependency tighten MMO performance and enable mix and match scanner operation. The same platform improvements also benefit focus control. Improvements in detectability and reproducibility of low contrast alignment marks enhance the alignment solution window for 10nm logic processes and beyond. The system's architecture allows dynamic use of high-order scanner optimization based on advanced actuators of projection lens and scanning stages. This enables a holistic optimization approach for the scanner, the mask, and the patterning process. Productivity scanner design modifications esp. stage speeds and optimization in metrology schemes provide lower layer costs for customers using immersion lithography as well as conventional dry technology. Imaging, overlay, focus, and productivity data is presented, that demonstrates 10nm and 7nm node litho-capability for both (immersion & dry) platforms.

On Multi-Dimensional Unstructured Mesh Adaption

NASA Technical Reports Server (NTRS)

Wood, William A.; Kleb, William L.

1999-01-01

Anisotropic unstructured mesh adaption is developed for a truly multi-dimensional upwind fluctuation splitting scheme, as applied to scalar advection-diffusion. The adaption is performed locally using edge swapping, point insertion/deletion, and nodal displacements. Comparisons are made versus the current state of the art for aggressive anisotropic unstructured adaption, which is based on a posteriori error estimates. Demonstration of both schemes to model problems, with features representative of compressible gas dynamics, show the present method to be superior to the a posteriori adaption for linear advection. The performance of the two methods is more similar when applied to nonlinear advection, with a difference in the treatment of shocks. The a posteriori adaption can excessively cluster points to a shock, while the present multi-dimensional scheme tends to merely align with a shock, using fewer nodes. As a consequence of this alignment tendency, an implementation of eigenvalue limiting for the suppression of expansion shocks is developed for the multi-dimensional distribution scheme. The differences in the treatment of shocks by the adaption schemes, along with the inherently low levels of artificial dissipation in the fluctuation splitting solver, suggest the present method is a strong candidate for applications to compressible gas dynamics.

The Impact of Structural Heterogeneity on Excitation-Inhibition Balance in Cortical Networks.

PubMed

Landau, Itamar D; Egger, Robert; Dercksen, Vincent J; Oberlaender, Marcel; Sompolinsky, Haim

2016-12-07

Models of cortical dynamics often assume a homogeneous connectivity structure. However, we show that heterogeneous input connectivity can prevent the dynamic balance between excitation and inhibition, a hallmark of cortical dynamics, and yield unrealistically sparse and temporally regular firing. Anatomically based estimates of the connectivity of layer 4 (L4) rat barrel cortex and numerical simulations of this circuit indicate that the local network possesses substantial heterogeneity in input connectivity, sufficient to disrupt excitation-inhibition balance. We show that homeostatic plasticity in inhibitory synapses can align the functional connectivity to compensate for structural heterogeneity. Alternatively, spike-frequency adaptation can give rise to a novel state in which local firing rates adjust dynamically so that adaptation currents and synaptic inputs are balanced. This theory is supported by simulations of L4 barrel cortex during spontaneous and stimulus-evoked conditions. Our study shows how synaptic and cellular mechanisms yield fluctuation-driven dynamics despite structural heterogeneity in cortical circuits. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Magnetic Alignment of Block Copolymer Microdomains by Intrinsic Chain Anisotropy.

PubMed

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

2015-12-18

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

Taking directions: the role of microtubule-bound nucleation in the self-organization of the plant cortical array

NASA Astrophysics Data System (ADS)

Deinum, Eva E.; Tindemans, Simon H.; Mulder, Bela M.

2011-10-01

The highly aligned cortical microtubule array of interphase plant cells is a key regulator of anisotropic cell expansion. Recent computational and analytical work has shown that the non-equilibrium self-organization of this structure can be understood on the basis of experimentally observed collisional interactions between dynamic microtubules attached to the plasma membrane. Most of these approaches assumed that new microtubules are homogeneously and isotropically nucleated on the cortical surface. Experimental evidence, however, shows that nucleation mostly occurs from other microtubules and under specific relative angles. Here, we investigate the impact of directed microtubule-bound nucleations on the alignment process using computer simulations. The results show that microtubule-bound nucleations can increase the degree of alignment achieved, decrease the timescale of the ordering process and widen the regime of dynamic parameters for which the system can self-organize. We establish that the major determinant of this effect is the degree of co-alignment of the nucleations with the parent microtubule. The specific role of sideways branching nucleations appears to allow stronger alignment while maintaining a measure of overall spatial homogeneity. Finally, we investigate the suggestion that observed persistent rotation of microtubule domains can be explained through a handedness bias in microtubule-bound nucleations, showing that this is possible only for an extreme bias and over a limited range of parameters.

FtsZ rings and helices: physical mechanisms for the dynamic alignment of biopolymers in rod-shaped bacteria.

PubMed

Fischer-Friedrich, Elisabeth; Friedrich, Benjamin M; Gov, Nir S

2012-02-01

In many bacterial species, the protein FtsZ forms a cytoskeletal ring that marks the future division site and scaffolds the division machinery. In rod-shaped bacteria, most frequently membrane-attached FtsZ rings or ring fragments are reported and occasionally helices. By contrast, axial FtsZ clusters have never been reported. In this paper, we investigate theoretically how dynamic FtsZ aggregates align in rod-shaped bacteria. We study systematically different physical mechanisms that affect the alignment of FtsZ polymers using a computational model that relies on autocatalytic aggregation of FtsZ filaments at the membrane. Our study identifies a general tool kit of physical and geometrical mechanisms by which rod-shaped cells align biopolymer aggregates. Our analysis compares the relative impact of each mechanism on the circumferential alignment of FtsZ as observed in rod-shaped bacteria. We determine spontaneous curvature of FtsZ polymers and axial confinement of FtsZ on the membrane as the strongest factors. Including Min oscillations in our model, we find that these stabilize axial and helical clusters on short time scales, but promote the formation of an FtsZ ring at the cell middle at longer times. This effect could provide an explanation to the long standing puzzle of transiently observed oscillating FtsZ helices in Escherichia coli cells prior to cell division.

Vertically aligned carbon nanofiber as nano-neuron interface for monitoring neural function.

PubMed

Yu, Zhe; McKnight, Timothy E; Ericson, M Nance; Melechko, Anatoli V; Simpson, Michael L; Morrison, Barclay

2012-05-01

Neural chips, which are capable of simultaneous multisite neural recording and stimulation, have been used to detect and modulate neural activity for almost thirty years. As neural interfaces, neural chips provide dynamic functional information for neural decoding and neural control. By improving sensitivity and spatial resolution, nano-scale electrodes may revolutionize neural detection and modulation at cellular and molecular levels as nano-neuron interfaces. We developed a carbon-nanofiber neural chip with lithographically defined arrays of vertically aligned carbon nanofiber electrodes and demonstrated its capability of both stimulating and monitoring electrophysiological signals from brain tissues in vitro and monitoring dynamic information of neuroplasticity. This novel nano-neuron interface may potentially serve as a precise, informative, biocompatible, and dual-mode neural interface for monitoring of both neuroelectrical and neurochemical activity at the single-cell level and even inside the cell. The authors demonstrate the utility of a neural chip with lithographically defined arrays of vertically aligned carbon nanofiber electrodes. The new device can be used to stimulate and/or monitor signals from brain tissue in vitro and for monitoring dynamic information of neuroplasticity both intracellularly and at the single cell level including neuroelectrical and neurochemical activities. Copyright © 2012 Elsevier Inc. All rights reserved.

Topography on a subcellular scale modulates cellular adhesions and actin stress fiber dynamics in tumor associated fibroblasts

NASA Astrophysics Data System (ADS)

Azatov, Mikheil; Sun, Xiaoyu; Suberi, Alexandra; Fourkas, John T.; Upadhyaya, Arpita

2017-12-01

Cells can sense and adapt to mechanical properties of their environment. The local geometry of the extracellular matrix, such as its topography, has been shown to modulate cell morphology, migration, and proliferation. Here we investigate the effect of micro/nanotopography on the morphology and cytoskeletal dynamics of human pancreatic tumor-associated fibroblast cells (TAFs). We use arrays of parallel nanoridges with variable spacings on a subcellular scale to investigate the response of TAFs to the topography of their environment. We find that cell shape and stress fiber organization both align along the direction of the nanoridges. Our analysis reveals a strong bimodal relationship between the degree of alignment and the spacing of the nanoridges. Furthermore, focal adhesions align along ridges and form preferentially on top of the ridges. Tracking actin stress fiber movement reveals enhanced dynamics of stress fibers on topographically patterned surfaces. We find that components of the actin cytoskeleton move preferentially along the ridges with a significantly higher velocity along the ridges than on a flat surface. Our results suggest that a complex interplay between the actin cytoskeleton and focal adhesions coordinates the cellular response to micro/nanotopography.

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

Alpha LAMP Integration Facility

NASA Technical Reports Server (NTRS)

Oshiro, Richard; Sowers, Dennis; Gargiulo, Joe; Mcgahey, Mark

1994-01-01

This paper describes the activity recently completed to meet the simulated space environment requirements for the ground-based testing of an integrated Space Based Laser (SBL) system experiment. The need to maintain optical alignment in the challenging dynamic environment of the pressure recovery system required to simulate space dominated the design requirements. A robust system design was established which minimized the total program costs, most notably by reducing the cost of integrating the components of the experiment. The components of the experiment are integrated on an optical bench in a clean area adjacent to the vacuum chamber and moved on air bearings into the chamber for testing.

Space Technology 5 Multipoint Observations of Temporal and Spatial Variability of Field-Aligned Currents

NASA Technical Reports Server (NTRS)

Le, G.; Wang, Y.; Slavin, J. A.; Strangeway, R. L.

2009-01-01

Space Technology 5 (ST5) is a constellation mission consisting of three microsatellites. It provides the first multipoint magnetic field measurements in low Earth orbit, which enables us to separate spatial and temporal variations. In this paper, we present a study of the temporal variability of field-aligned currents using the ST5 data. We examine the field-aligned current observations during and after a geomagnetic storm and compare the magnetic field profiles at the three spacecraft. The multipoint data demonstrate that mesoscale current structures, commonly embedded within large-scale current sheets, are very dynamic with highly variable current density and/or polarity in approx.10 min time scales. On the other hand, the data also show that the time scales for the currents to be relatively stable are approx.1 min for mesoscale currents and approx.10 min for large-scale currents. These temporal features are very likely associated with dynamic variations of their charge carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of mesoscale field-aligned currents are found to be consistent with those of auroral parallel electric field.

Disentangling the Role of Entanglement Density and Molecular Alignment in the Mechanical Response of Glassy Polymers

NASA Astrophysics Data System (ADS)

O'Connor, Thomas; Robbins, Mark

Glassy polymers are a ubiquitous part of modern life, but much about their mechanical properties remains poorly understood. Since chains in glassy states are hindered from exploring their conformational entropy, they can't be understood with common entropic network models. Additionally, glassy states are highly sensitive to material history and nonequilibrium distributions of chain alignment and entanglement can be produced during material processing. Understanding how these far-from equilibrium states impact mechanical properties is analytically challenging but essential to optimizing processing methods. We use molecular dynamics simulations to study the yield and strain hardening of glassy polymers as separate functions of the degree of molecular alignment and inter-chain entanglement. We vary chain alignment and entanglement with three different preparation protocols that mimic common processing conditions in and out of solution. We compare our results to common mechanical models of amorphous polymers and assess their applicability to different experimental processing conditions. This research was performed within the Center for Materials in Extreme Dynamic Environments (CMEDE) under the Hopkins Extreme Materials Institute at Johns Hopkins University. Financial support was provided by Grant W911NF-12-2-0022.

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

PubMed

Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

2005-01-01

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

Electrostatically Induced Carbon Nanotube Alignment for Polymer Composite Applications

NASA Astrophysics Data System (ADS)

Chapkin, Wesley Aaron

We have developed a non-invasive technique utilizing polarized Raman spectroscopy to measure changes in carbon nanotube (CNT) alignment in situ and in real time in a polymer matrix. With this technique, we have confirmed the prediction of faster alignment for CNTs in higher electric fields. Real-time polarized Raman spectroscopy also allows us to demonstrate the loss of CNT alignment that occurs after the electric field is removed, which reveals the need for fast polymerization steps or the continued application of the aligning force during polymerization to lock in CNT alignment. Through a study on the effect of polymer viscosity on the rate of CNT alignment, we have determined that shear viscosity serves as the controlling mechanism for CNT rotation. This finding matches literature modeling of rigid rod mobility in a polymer melt and demonstrates that the rotational mobility of CNTs can be explained by a continuum model even though the diameters of single-walled CNTs are 1-2 nm. The viscosity dependence indicates that the manipulation of temperature (and indirectly viscosity) will have a direct effect on the rate of CNT alignment, which could prove useful in expediting the manufacturing of CNT-reinforced composites cured at elevated temperatures. Using real-time polarized Raman spectroscopy, we also demonstrate that electric fields of various strengths lead not only to different speeds of CNT rotation but also to different degrees of alignment. We hypothesize that this difference in achievable alignment results from discrete populations of nanotubes based on their length. The results are then explained by balancing the alignment energy for a given electric field strength with the randomizing thermal energy of the system. By studying the alignment dynamics of different CNT length distributions, we show that different degrees of alignment achieved as a function of the applied electric field strength are directly related to the square of the nanotube length. This finding matches an electrostatic potential energy model for CNT rotation. Lastly, we investigate the effects of conductive carbon fibers on electrostatically induced alignment of CNTs within carbon fiber composites. The relative electric field strength throughout the composite is modeled using COMSOL Multiphysics. We show the ability to generate enhanced electric field gradients within the gaps between carbon fibers for various fiber orientations. Using polarized Raman spectroscopy, increased levels of CNT alignment are observed between carbon fiber tows, which is consistent with the modeled higher electric field strengths in these regions. These findings could potentially lead to the development of carbon fiber composites with CNT additions that selectively enhance the composite properties outside the carbon fiber interphase in the neat epoxy.

A Novel Adaptive H∞ Filtering Method with Delay Compensation for the Transfer Alignment of Strapdown Inertial Navigation Systems.

PubMed

Lyu, Weiwei; Cheng, Xianghong

2017-11-28

Transfer alignment is always a key technology in a strapdown inertial navigation system (SINS) because of its rapidity and accuracy. In this paper a transfer alignment model is established, which contains the SINS error model and the measurement model. The time delay in the process of transfer alignment is analyzed, and an H∞ filtering method with delay compensation is presented. Then the H∞ filtering theory and the robust mechanism of H∞ filter are deduced and analyzed in detail. In order to improve the transfer alignment accuracy in SINS with time delay, an adaptive H∞ filtering method with delay compensation is proposed. Since the robustness factor plays an important role in the filtering process and has effect on the filtering accuracy, the adaptive H∞ filter with delay compensation can adjust the value of robustness factor adaptively according to the dynamic external environment. The vehicle transfer alignment experiment indicates that by using the adaptive H∞ filtering method with delay compensation, the transfer alignment accuracy and the pure inertial navigation accuracy can be dramatically improved, which demonstrates the superiority of the proposed filtering method.

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.

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.

Pair aligning improved motility of Quincke rollers.

PubMed

Lu, Shi Qing; Zhang, Bing Yue; Zhang, Zhi Chao; Shi, Yan; Zhang, Tian Hui

2018-06-06

Density-dependent speed is studied in a two-dimensional active colloid in which the colloidal particles are propelled by an external electric field via a Quincke rotation. Above the critcal electric field, dense dynamic clusters form spotaneously, in which the particles are highly aligned in velocity and move much faster than isolated units. Detailed observations on pair collision reveal that the alignment of velocity is induced by the long-ranged hydrodynamic interactions and the improvement of speed in the clusters arises from pair aligning in which two particles are closely paired and rotate synchronically. In the aligning state, the short-range in-plane dipole-dipole attraction enhances the rotation torque and gives rises to a larger rolling speed. The pair aligning becomes difficult and unstable at high electric field where the normal dipole-dipole repulsion becomes dominant. As a consequence, the dependence of speed on density becomes weak increasingly upon the increase of the electric field. This result offers an interpretation for the discrepancy between our and previous observations on Quincke rollers.

Active and Passive Radiative Transfer Modeling with Preferentially-Aligned Particles

NASA Technical Reports Server (NTRS)

Adams, Ian Stuart

2017-01-01

The fluid dynamics of falling hydrometeors often results in preferential orientations that can affect both the intensity and polarization of electromagnetic radiation. In order to properly interpret remote sensing observations of ice and snow, such alignments should be considered when constructing databases of scattering particles; however, the inclusion of aligned particles increases the complexity of the scattering data. To demonstrate the use of scattering properties of preferentially-aligned particles, millimeter-wave brightness temperatures and radar observables, including reflectivity and linear depolarization ratio, are modeled using the Atmospheric Radiative Transfer Simulator (ARTS). The necessary scattering parameters for vector radiative transfer, particularly with respect to ARTS, are reviewed, and the exploitation of particle symmetries, as well as scattering reciprocity relationships, are detailed.

Spacecraft alignment estimation. [for onboard sensors

NASA Technical Reports Server (NTRS)

Shuster, Malcolm D.; Bierman, Gerald J.

1988-01-01

A numerically well-behaved factorized methodology is developed for estimating spacecraft sensor alignments from prelaunch and inflight data without the need to compute the spacecraft attitude or angular velocity. Such a methodology permits the estimation of sensor alignments (or other biases) in a framework free of unknown dynamical variables. In actual mission implementation such an algorithm is usually better behaved than one that must compute sensor alignments simultaneously with the spacecraft attitude, for example by means of a Kalman filter. In particular, such a methodology is less sensitive to data dropouts of long duration, and the derived measurement used in the attitude-independent algorithm usually makes data checking and editing of outliers much simpler than would be the case in the filter.

Energy Level Alignment at Aqueous GaN and ZnO Interfaces

NASA Astrophysics Data System (ADS)

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

2014-03-01

Electronic energy level alignment at semiconductor-electrolyte interfaces is fundamental to electrochemical activity. Motivated in particular by the search for new materials that can be more efficient for photocatalysis, we develop a first principles method to calculate this alignment at aqueous interfaces and demonstrate it for the specific case of non-polar GaN and ZnO interfaces with water. In the first step, density functional theory (DFT) based molecular dynamics is used to sample the physical interface structure and to evaluate the electrostatic potential step at the interface. In the second step, the GW approach is used to evaluate the reference electronic energy level separately in the bulk semiconductor (valence band edge energy) and in bulk water (the 1b1 energy level), relative to the internal electrostatic energy reference. Use of the GW approach naturally corrects for errors inherent in the use of Kohn-Sham energy eigenvalues to approximate the electronic excitation energies in each material. With this predicted interface alignment, specific redox levels in water, with potentials known relative to the 1b1 level, can then be compared to the semiconductor band edge positions. Our results will be discussed in the context of experiments in which photoexcited GaN and ZnO drive the hydrogen evolution reaction. Research carried out at Brookhaven National Laboratory under Contract No. DE-AC02-98CH10886 with the U.S. Department of Energy.

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

Relative impact of uniaxial alignment vs. form-induced stress on differentiation of human adipose derived stem cells

PubMed Central

Huang, Samuel; Li, Julie Yi-Shuan; Chien, Shu; Zhang, Kang; Chen, Shaochen

2013-01-01

ADSCs are a great cell source for tissue engineering and regenerative medicine. However, the development of methods to appropriately manipulate these cells in vitro remains a challenge. Here the proliferation and differentiation of ADSCs on microfabricated surfaces with varying geometries were investigated. To create the patterned substrates, a maskless biofabrication method was developed based on dynamic optical projection stereolithography. Proliferation and early differentiation of ADSCs were compared across three distinct multicellular patterns, namely stripes (ST), symmetric fork (SF), and asymmetric fork (AF). The ST pattern was designed for uniaxial cell alignment while the SF and AF pattern were designed with altered cell directionality to different extents. The SF and AF patterns generated similar levels of regional peak stress, which were both significantly higher than those within the ST pattern. No significant difference in ADSC proliferation was observed among the three patterns. In comparison to the ST pattern, higher peak stress levels of the SF and AF patterns were associated with up-regulation of the chondrogenic and osteogenic markers SOX9 and RUNX2. Interestingly, uniaxial cell alignment in the ST pattern seemed to increase the expression of SM22α and smooth muscle α-actin, suggesting an early smooth muscle lineage progression. These results indicate that geometric cues that promote uniaxial alignment might be more potent for myogenesis than those with increased peak stress. Overall, the use of these patterned geometric cues for modulating cell alignment and form-induced stress can serve as a powerful and versatile technique towards controlling differentiation in ADSCs. PMID:24060419

Alignment of time-resolved data from high throughput experiments.

PubMed

Abidi, Nada; Franke, Raimo; Findeisen, Peter; Klawonn, Frank

2016-12-01

To better understand the dynamics of the underlying processes in cells, it is necessary to take measurements over a time course. Modern high-throughput technologies are often used for this purpose to measure the behavior of cell products like metabolites, peptides, proteins, [Formula: see text]RNA or mRNA at different points in time. Compared to classical time series, the number of time points is usually very limited and the measurements are taken at irregular time intervals. The main reasons for this are the costs of the experiments and the fact that the dynamic behavior usually shows a strong reaction and fast changes shortly after a stimulus and then slowly converges to a certain stable state. Another reason might simply be missing values. It is common to repeat the experiments and to have replicates in order to carry out a more reliable analysis. The ideal assumptions that the initial stimulus really started exactly at the same time for all replicates and that the replicates are perfectly synchronized are seldom satisfied. Therefore, there is a need to first adjust or align the time-resolved data before further analysis is carried out. Dynamic time warping (DTW) is considered as one of the common alignment techniques for time series data with equidistant time points. In this paper, we modified the DTW algorithm so that it can align sequences with measurements at different, non-equidistant time points with large gaps in between. This type of data is usually known as time-resolved data characterized by irregular time intervals between measurements as well as non-identical time points for different replicates. This new algorithm can be easily used to align time-resolved data from high-throughput experiments and to come across existing problems such as time scarcity and existing noise in the measurements. We propose a modified method of DTW to adapt requirements imposed by time-resolved data by use of monotone cubic interpolation splines. Our presented approach provides a nonlinear alignment of two sequences that neither need to have equi-distant time points nor measurements at identical time points. The proposed method is evaluated with artificial as well as real data. The software is available as an R package tra (Time-Resolved data Alignment) which is freely available at: http://public.ostfalia.de/klawonn/tra.zip .

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.

Surface tension-driven self-alignment.

PubMed

Mastrangeli, Massimo; Zhou, Quan; Sariola, Veikko; Lambert, Pierre

2017-01-04

Surface tension-driven self-alignment is a passive and highly-accurate positioning mechanism that can significantly simplify and enhance the construction of advanced microsystems. After years of research, demonstrations and developments, the surface engineering and manufacturing technology enabling capillary self-alignment has achieved a degree of maturity conducive to a successful transfer to industrial practice. In view of this transition, a broad and accessible review of the physics, material science and applications of capillary self-alignment is presented. Statics and dynamics of the self-aligning action of deformed liquid bridges are explained through simple models and experiments, and all fundamental aspects of surface patterning and conditioning, of choice, deposition and confinement of liquids, and of component feeding and interconnection to substrates are illustrated through relevant applications in micro- and nanotechnology. A final outline addresses remaining challenges and additional extensions envisioned to further spread the use and fully exploit the potential of the technique.

Magnetic alignment of block copolymer microdomains by intrinsic chain anisotropy

DOE PAGES

Rokhlenko, Yekaterina; Yager, Kevin G.; Gopinadhan, Manesh; ...

2015-12-18

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

Magnetic alignment of block copolymer microdomains by intrinsic chain anisotropy

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

Rokhlenko, Yekaterina; Yager, Kevin G.; Gopinadhan, Manesh

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

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

Pattern formation of frictional fingers in a gravitational potential

NASA Astrophysics Data System (ADS)

Eriksen, Jon Alm; Toussaint, Renaud; Mâløy, Knut Jørgen; Flekkøy, Eirik; Galland, Olivier; Sandnes, Bjørnar

2018-01-01

Aligned finger structures, with a characteristic width, emerge during the slow drainage of a liquid-granular mixture in a tilted Hele-Shaw cell. A transition from vertical to horizontal alignment of the finger structures is observed as the tilting angle and the granular density are varied. An analytical model is presented, demonstrating that the alignment properties are the result of the competition between fluctuating granular stresses and the hydrostatic pressure. The dynamics is reproduced in simulations. We also show how the system explains patterns observed in nature, created during the early stages of a dike formation.

Contribution of the polarization moments of different rank to the integral CPT signal

NASA Astrophysics Data System (ADS)

Taskova, E.; Alipieva, E.; Todorov, G.

2016-01-01

In the present work we investigate the relation of the polarization moments having different ranks with the tensor components which form the observable integral CPT signal, in the presence of a stray magnetic field. A numerical experiment with parameters close to the real ones is performed, using a program based on the irreducible tensor operator formalism1. The integral fluorescent signal is calculated for the non-polarized fluorescence at different laser power excitation. Detailed analysis of the numerical solutions for all tensor components which describe population and alignment allows visualizing the dynamics of their behavior in dependence on the experimental geometry and laboratory magnetic field B'. The dependence of population f00, longitudinal f02 and transverse f22 alignment in the presence of transverse magnetic field is investigated. The shape and sign of the resonance change with laser power.

A Novel Framework for the Comparative Analysis of Biological Networks

PubMed Central

Pache, Roland A.; Aloy, Patrick

2012-01-01

Genome sequencing projects provide nearly complete lists of the individual components present in an organism, but reveal little about how they work together. Follow-up initiatives have deciphered thousands of dynamic and context-dependent interrelationships between gene products that need to be analyzed with novel bioinformatics approaches able to capture their complex emerging properties. Here, we present a novel framework for the alignment and comparative analysis of biological networks of arbitrary topology. Our strategy includes the prediction of likely conserved interactions, based on evolutionary distances, to counter the high number of missing interactions in the current interactome networks, and a fast assessment of the statistical significance of individual alignment solutions, which vastly increases its performance with respect to existing tools. Finally, we illustrate the biological significance of the results through the identification of novel complex components and potential cases of cross-talk between pathways and alternative signaling routes. PMID:22363585

Free-viewpoint video of human actors using multiple handheld Kinects.

PubMed

Ye, Genzhi; Liu, Yebin; Deng, Yue; Hasler, Nils; Ji, Xiangyang; Dai, Qionghai; Theobalt, Christian

2013-10-01

We present an algorithm for creating free-viewpoint video of interacting humans using three handheld Kinect cameras. Our method reconstructs deforming surface geometry and temporal varying texture of humans through estimation of human poses and camera poses for every time step of the RGBZ video. Skeletal configurations and camera poses are found by solving a joint energy minimization problem, which optimizes the alignment of RGBZ data from all cameras, as well as the alignment of human shape templates to the Kinect data. The energy function is based on a combination of geometric correspondence finding, implicit scene segmentation, and correspondence finding using image features. Finally, texture recovery is achieved through jointly optimization on spatio-temporal RGB data using matrix completion. As opposed to previous methods, our algorithm succeeds on free-viewpoint video of human actors under general uncontrolled indoor scenes with potentially dynamic background, and it succeeds even if the cameras are moving.

Advancing patient safety: a framework for accountability and practical action.

PubMed

Wilson, N J; Hatlie, M J

2001-01-01

This article traces the development of the patient safety movement in healthcare from 1997 to the present. It reviews the findings and recommendations in the Institute of Medicine report on medical errors, which issued a call to action. Moving beyond the call to action requires aligning incentives, in both public and private sectors, consistent with complexity theory and the tenets of a systems approach to the reliable delivery of service in dynamic environments in which failure produces severe consequences. Because safety is a fundamental value of healthcare and has money-saving potential, it can be a powerful pathway forcultural change. Thisarticle explains a simple framework that requires alignment among stakeholder groups and communities. It recommends a practical problem-solving approach and explores the roles and responsibilities of each segment within the framework. Finally, it describes a VHA Inc. leadership initiative, based on the framework, to promote change within healthcare systems.

Multi-classification of cell deformation based on object alignment and run length statistic.

PubMed

Li, Heng; Liu, Zhiwen; An, Xing; Shi, Yonggang

2014-01-01

Cellular morphology is widely applied in digital pathology and is essential for improving our understanding of the basic physiological processes of organisms. One of the main issues of application is to develop efficient methods for cell deformation measurement. We propose an innovative indirect approach to analyze dynamic cell morphology in image sequences. The proposed approach considers both the cellular shape change and cytoplasm variation, and takes each frame in the image sequence into account. The cell deformation is measured by the minimum energy function of object alignment, which is invariant to object pose. Then an indirect analysis strategy is employed to overcome the limitation of gradual deformation by run length statistic. We demonstrate the power of the proposed approach with one application: multi-classification of cell deformation. Experimental results show that the proposed method is sensitive to the morphology variation and performs better than standard shape representation methods.

A Method for the Alignment of Heterogeneous Macromolecules from Electron Microscopy

PubMed Central

Shatsky, Maxim; Hall, Richard J.; Brenner, Steven E.; Glaeser, Robert M.

2009-01-01

We propose a feature-based image alignment method for single-particle electron microscopy that is able to accommodate various similarity scoring functions while efficiently sampling the two-dimensional transformational space. We use this image alignment method to evaluate the performance of a scoring function that is based on the Mutual Information (MI) of two images rather than one that is based on the cross-correlation function. We show that alignment using MI for the scoring function has far less model-dependent bias than is found with cross-correlation based alignment. We also demonstrate that MI improves the alignment of some types of heterogeneous data, provided that the signal to noise ratio is relatively high. These results indicate, therefore, that use of MI as the scoring function is well suited for the alignment of class-averages computed from single particle images. Our method is tested on data from three model structures and one real dataset. PMID:19166941

Dynamic Spectrum Sharing with Limited Network State Information

DTIC Science & Technology

2010-11-01

M. L. Honig,"Two-Cell Downlink Noncoherent Cooperation Without Transmitter Phase Alignment", Proc. Globecom Conf., Miami, FL, Dec. 2010. D. Schmidt, W...restrict the number of active streams even though the maximum multiplexing gain is not achieved. 3 Noncoherent Cooperative Broadcasting...study a noncoherent cooperative transmission scheme with two interfering links, which does not require phase alignment. It is assumed that the

Dynamics and allostery of the ionotropic glutamate receptors and the ligand binding domain.

PubMed

Tobi, Dror

2016-02-01

The dynamics of the ligand-binding domain (LBD) and the intact ionotropic glutamate receptor (iGluR) were studied using Gaussian Network Model (GNM) analysis. The dynamics of LBDs with various allosteric modulators is compared using a novel method of multiple alignment of GNM modes of motion. The analysis reveals that allosteric effectors change the dynamics of amino acids at the upper lobe interface of the LBD dimer as well as at the hinge region between the upper- and lower- lobes. For the intact glutamate receptor the analysis show that the clamshell-like movement of the LBD upper and lower lobes is coupled to the bending of the trans-membrane domain (TMD) helices which may open the channel pore. The results offer a new insight on the mechanism of action of allosteric modulators on the iGluR and support the notion of TMD helices bending as a possible mechanism for channel opening. In addition, the study validates the methodology of multiple GNM modes alignment as a useful tool to study allosteric effect and its relation to proteins dynamics. © 2015 Wiley Periodicals, Inc.

Aligned composite structures for mitigation of impact damage and resistance to wear in dynamic environments

DOEpatents

Mulligan, Anthony C.; Rigali, Mark J.; Sutaria, Manish P.; Popovich, Dragan; Halloran, Joseph P.; Fulcher, Michael L.; Cook, Randy C.

2005-12-13

Fibrous monolith composites having architectures that provide increased flaw insensitivity, improved hardness, wear resistance and damage tolerance and methods of manufacture thereof are provided for use in dynamic environments to mitigate impact damage and increase wear resistance.

Aligned composite structures for mitigation of impact damage and resistance to wear in dynamic environments

DOEpatents

Mulligan, Anthony C.; Rigali, Mark J.; Sutaria, Manish P.; Popovich, Dragan; Halloran, Joseph P.; Fulcher, Michael L.; Cook, Randy C.

2009-04-14

Fibrous monolith composites having architectures that provide increased flaw insensitivity, improved hardness, wear resistance and damage tolerance and methods of manufacture thereof are provided for use in dynamic environments to mitigate impact damage and increase wear resistance.

Aligned composite structures for mitigation of impact damage and resistance to wear in dynamic environments

DOEpatents

Rigali, Mark J.; Sutaria, Manish P.; Mulligan, Anthony C.; Popovich, Dragan

2004-03-23

Fibrous monolith composites having architectures that provide increased flaw insensitivity, improved hardness, wear resistance and damage tolerance and methods of manufacture thereof are provided for use in dynamic environments to mitigate impact damage and increase wear resistance.

Alignment of process compliance and monitoring requirements in dynamic business collaborations

NASA Astrophysics Data System (ADS)

Comuzzi, Marco

2017-07-01

Dynamic business collaborations are intrinsically characterised by change because processes can be distributed or outsourced and partners may be substituted by new ones with enhanced or different capabilities. In this context, compliance requirements management becomes particularly challenging. Partners in a collaboration may join and leave dynamically and tasks over which compliance requirements are specified may be consequently distributed or delegated to new partners. This article considers the issue of aligning compliance requirements in a dynamic business collaboration with the monitoring requirements induced on the collaborating partners when change occurs. We first provide a conceptual model of business collaborations and their compliance requirements, introducing the concept of monitoring capabilities induced by compliance requirements. Then, we present a set of mechanisms to ensure consistency between monitoring and compliance requirements in the presence of change, e.g. when tasks are delegated or backsourced in-house. We also discuss a set of metrics to evaluate the status of a collaboration in respect of compliance monitorability. Finally, we discuss a prototype implementation of our framework.

Policy reconciliation for access control in dynamic cross-enterprise collaborations

NASA Astrophysics Data System (ADS)

Preuveneers, D.; Joosen, W.; Ilie-Zudor, E.

2018-03-01

In dynamic cross-enterprise collaborations, different enterprises form a - possibly temporary - business relationship. To integrate their business processes, enterprises may need to grant each other limited access to their information systems. Authentication and authorization are key to secure information handling. However, access control policies often rely on non-standardized attributes to describe the roles and permissions of their employees which convolutes cross-organizational authorization when business relationships evolve quickly. Our framework addresses the managerial overhead of continuous updates to access control policies for enterprise information systems to accommodate disparate attribute usage. By inferring attribute relationships, our framework facilitates attribute and policy reconciliation, and automatically aligns dynamic entitlements during the evaluation of authorization decisions. We validate our framework with a Industry 4.0 motivating scenario on networked production where such dynamic cross-enterprise collaborations are quintessential. The evaluation reveals the capabilities and performance of our framework, and illustrates the feasibility of liberating the security administrator from manually provisioning and aligning attributes, and verifying the consistency of access control policies for cross-enterprise collaborations.

Diffractive imaging of a rotational wavepacket in nitrogen molecules with femtosecond megaelectronvolt electron pulses

DOE PAGES

Yang, Jie; Guehr, Markus; Vecchione, Theodore; ...

2016-04-05

Imaging changes in molecular geometries on their natural femtosecond timescale with sub-Angström spatial precision is one of the critical challenges in the chemical sciences, as the nuclear geometry changes determine the molecular reactivity. For photoexcited molecules, the nuclear dynamics determine the photoenergy conversion path and efficiency. Here we report a gas-phase electron diffraction experiment using megaelectronvolt (MeV) electrons, where we captured the rotational wavepacket dynamics of nonadiabatically laser-aligned nitrogen molecules. We achieved a combination of 100 fs root-mean-squared temporal resolution and sub-Angstrom (0.76 Å) spatial resolution that makes it possible to resolve the position of the nuclei within the molecule.more » In addition, the diffraction patterns reveal the angular distribution of the molecules, which changes from prolate (aligned) to oblate (anti-aligned) in 300 fs. Lastly, our results demonstrate a significant and promising step towards making atomically resolved movies of molecular reactions.« less

Mechanical design of multiple zone plates precision alignment apparatus for hard X-ray focusing in twenty-nanometer scale

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

Shu, Deming; Liu, Jie; Gleber, Sophie C.

An enhanced mechanical design of multiple zone plates precision alignment apparatus for hard x-ray focusing in a twenty-nanometer scale is provided. The precision alignment apparatus includes a zone plate alignment base frame; a plurality of zone plates; and a plurality of zone plate holders, each said zone plate holder for mounting and aligning a respective zone plate for hard x-ray focusing. At least one respective positioning stage drives and positions each respective zone plate holder. Each respective positioning stage is mounted on the zone plate alignment base frame. A respective linkage component connects each respective positioning stage and the respectivemore » zone plate holder. The zone plate alignment base frame, each zone plate holder and each linkage component is formed of a selected material for providing thermal expansion stability and positioning stability for the precision alignment apparatus.« less

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

PubMed

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

2005-12-15

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

Smart grid initialization reduces the computational complexity of multi-objective image registration based on a dual-dynamic transformation model to account for large anatomical differences

NASA Astrophysics Data System (ADS)

Bosman, Peter A. N.; Alderliesten, Tanja

2016-03-01

We recently demonstrated the strong potential of using dual-dynamic transformation models when tackling deformable image registration problems involving large anatomical differences. Dual-dynamic transformation models employ two moving grids instead of the common single moving grid for the target image (and single fixed grid for the source image). We previously employed powerful optimization algorithms to make use of the additional flexibility offered by a dual-dynamic transformation model with good results, directly obtaining insight into the trade-off between important registration objectives as a result of taking a multi-objective approach to optimization. However, optimization has so far been initialized using two regular grids, which still leaves a great potential of dual-dynamic transformation models untapped: a-priori grid alignment with image structures/areas that are expected to deform more. This allows (far) less grid points to be used, compared to using a sufficiently refined regular grid, leading to (far) more efficient optimization, or, equivalently, more accurate results using the same number of grid points. We study the implications of exploiting this potential by experimenting with two new smart grid initialization procedures: one manual expert-based and one automated image-feature-based. We consider a CT test case with large differences in bladder volume with and without a multi-resolution scheme and find a substantial benefit of using smart grid initialization.

Biologically inspired EM image alignment and neural reconstruction.

PubMed

Knowles-Barley, Seymour; Butcher, Nancy J; Meinertzhagen, Ian A; Armstrong, J Douglas

2011-08-15

Three-dimensional reconstruction of consecutive serial-section transmission electron microscopy (ssTEM) images of neural tissue currently requires many hours of manual tracing and annotation. Several computational techniques have already been applied to ssTEM images to facilitate 3D reconstruction and ease this burden. Here, we present an alternative computational approach for ssTEM image analysis. We have used biologically inspired receptive fields as a basis for a ridge detection algorithm to identify cell membranes, synaptic contacts and mitochondria. Detected line segments are used to improve alignment between consecutive images and we have joined small segments of membrane into cell surfaces using a dynamic programming algorithm similar to the Needleman-Wunsch and Smith-Waterman DNA sequence alignment procedures. A shortest path-based approach has been used to close edges and achieve image segmentation. Partial reconstructions were automatically generated and used as a basis for semi-automatic reconstruction of neural tissue. The accuracy of partial reconstructions was evaluated and 96% of membrane could be identified at the cost of 13% false positive detections. An open-source reference implementation is available in the Supplementary information. seymour.kb@ed.ac.uk; douglas.armstrong@ed.ac.uk Supplementary data are available at Bioinformatics online.

Trends in mica–mica adhesion reflect the influence of molecular details on long-range dispersion forces underlying aggregation and coalignment

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

Li, Dongsheng; Chun, Jaehun; Xiao, Dongdong

2017-07-05

Oriented attachment of nanocrystalline subunits is recognized as a common crystallization pathway that is closely related to formation of nanoparticle superlattices, mesocrystals, and other kinetically stabilized structures. Approaching particles have been observed to rotate to achieve co-alignment while separated by nanometer-scale solvent layers. Little is known about the forces that drive co-alignment, particularly in this “solvent-separated” regime. To obtain a mechanistic understanding of this process, we used atomic force microscopy-based dynamic force spectroscopy with tips fabricated from oriented mica to measure the adhesion forces between mica (001) surfaces in electrolyte solutions as a function of orientation, temperature, electrolyte type, andmore » electrolyte concentration. The results reveal a ~60° periodicity as well as a complex dependence on electrolyte concentration and temperature. A continuum model that considers the competition between electrostatic repulsion and van der Waals attraction, augmented by microscopic details that include surface separation, water structure, ion hydration, and charge regulation at the interface, qualitatively reproduces the observed trends and implies that dispersion forces are responsible for establishing co-alignment in the solvent-separated state.« less

Trends in mica–mica adhesion reflect the influence of molecular details on long-range dispersion forces underlying aggregation and coalignment

DOE PAGES

Li, Dongsheng; Chun, Jaehun; Xiao, Dongdong; ...

2017-07-05

Here, oriented attachment of nanocrystalline subunits is recognized as a common crystallization pathway that is closely related to formation of nanoparticle superlattices, mesocrystals, and other kinetically stabilized structures. Approaching particles have been observed to rotate to achieve co-alignment while separated by nanometer-scale solvent layers. Little is known about the forces that drive co-alignment, particularly in this “solvent-separated” regime. To obtain a mechanistic understanding of this process, we used atomic force microscopy-based dynamic force spectroscopy with tips fabricated from oriented mica to measure the adhesion forces between mica (001) surfaces in electrolyte solutions as a function of orientation, temperature, electrolyte type,more » and electrolyte concentration. The results reveal a ~60° periodicity as well as a complex dependence on electrolyte concentration and temperature. A continuum model that considers the competition between electrostatic repulsion and van der Waals attraction, augmented by microscopic details that include surface separation, water structure, ion hydration, and charge regulation at the interface, qualitatively reproduces the observed trends and implies that dispersion forces are responsible for establishing co-alignment in the solvent-separated state.« less

Trends in mica–mica adhesion reflect the influence of molecular details on long-range dispersion forces underlying aggregation and coalignment

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

Li, Dongsheng; Chun, Jaehun; Xiao, Dongdong

Oriented attachment of nanocrystalline subunits is recognized as a common crystallization pathway that is closely related to formation of nanoparticle superlattices, mesocrystals, and other kinetically stabilized structures. Approaching particles have been observed to rotate to achieve co-alignment while separated by nanometer-scale solvent layers. Little is known about the forces that drive co-alignment, particularly in this “solvent-separated” regime. To obtain a mechanistic understanding of this process, we used atomic force microscopy-based dynamic force spectroscopy with tips fabricated from oriented mica to measure the adhesion forces between mica (001) surfaces in electrolyte solutions as a function of orientation, temperature, electrolyte type, andmore » electrolyte concentration. The results reveal a ~60° periodicity as well as a complex dependence on electrolyte concentration and temperature. A continuum model that considers the competition between electrostatic repulsion and van der Waals attraction, augmented by microscopic details that include surface separation, water structure, ion hydration, and charge regulation at the interface, qualitatively reproduces the observed trends and implies that dispersion forces are responsible for establishing co-alignment in the solvent-separated state.« less

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.

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

PubMed

Löytynoja, Ari

2012-01-01

Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.

Single-particle studies of band alignment effects on electron transfer dynamics from semiconductor hetero-nanostructures to single-walled carbon nanotubes.

PubMed

Yuan, Chi-Tsu; Wang, Yong-Gang; Huang, Kuo-Yen; Chen, Ting-Yu; Yu, Pyng; Tang, Jau; Sitt, Amit; Banin, Uri; Millo, Oded

2012-01-24

We utilize single-molecule spectroscopy combined with time-correlated single-photon counting to probe the electron transfer (ET) rates from various types of semiconductor hetero-nanocrystals, having either type-I or type-II band alignment, to single-walled carbon nanotubes. A significantly larger ET rate was observed for type-II ZnSe/CdS dot-in-rod nanostructures as compared to type-I spherical CdSe/ZnS core/shell quantum dots and to CdSe/CdS dot-in-rod structures. Furthermore, such rapid ET dynamics can compete with both Auger and radiative recombination processes, with significance for effective photovoltaic operation. © 2011 American Chemical Society

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

PubMed

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

2012-09-01

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

Hot spot dynamics in carbon nanotube array devices.

PubMed

Engel, Michael; Steiner, Mathias; Seo, Jung-Woo T; Hersam, Mark C; Avouris, Phaedon

2015-03-11

We report on the dynamics of spatial temperature distributions in aligned semiconducting carbon nanotube array devices with submicrometer channel lengths. By using high-resolution optical microscopy in combination with electrical transport measurements, we observe under steady state bias conditions the emergence of time-variable, local temperature maxima with dimensions below 300 nm, and temperatures above 400 K. On the basis of time domain cross-correlation analysis, we investigate how the intensity fluctuations of the thermal radiation patterns are correlated with the overall device current. The analysis reveals the interdependence of electrical current fluctuations and time-variable hot spot formation that limits the overall device performance and, ultimately, may cause device degradation. The findings have implications for the future development of carbon nanotube-based technologies.

3D-QSAR and docking studies on 4-anilinoquinazoline and 4-anilinoquinoline epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors

NASA Astrophysics Data System (ADS)

Assefa, Haregewein; Kamath, Shantaram; Buolamwini, John K.

2003-08-01

The overexpression and/or mutation of the epidermal growth factor receptor (EGFR) tyrosine kinase has been observed in many human solid tumors, and is under intense investigation as a novel anticancer molecular target. Comparative 3D-QSAR analyses using different alignments were undertaken employing comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) for 122 anilinoquinazoline and 50 anilinoquinoline inhibitors of EGFR kinase. The SYBYL multifit alignment rule was applied to three different conformational templates, two obtained from a MacroModel Monte Carlo conformational search, and one from the bound conformation of erlotinib in complex with EGFR in the X-ray crystal structure. In addition, a flexible ligand docking alignment obtained with the GOLD docking program, and a novel flexible receptor-guided consensus dynamics alignment obtained with the DISCOVER program in the INSIGHTII modeling package were also investigated. 3D-QSAR models with q2 values up to 0.70 and r2 values up to 0.97 were obtained. Among the 4-anilinoquinazoline set, the q2 values were similar, but the ability of the different conformational models to predict the activities of an external test set varied considerably. In this regard, the model derived using the X-ray crystallographically determined bioactive conformation of erlotinib afforded the best predictive model. Electrostatic, hydrophobic and H-bond donor descriptors contributed the most to the QSAR models of the 4-anilinoquinazolines, whereas electrostatic, hydrophobic and H-bond acceptor descriptors contributed the most to the 4-anilinoquinoline QSAR, particularly the H-bond acceptor descriptor. A novel receptor-guided consensus dynamics alignment has also been introduced for 3D-QSAR studies. This new alignment method may incorporate to some extent ligand-receptor induced fit effects into 3D-QSAR models.

The shape and dynamics of local attraction

NASA Astrophysics Data System (ADS)

Strömbom, D.; Siljestam, M.; Park, J.; Sumpter, D. J. T.

2015-11-01

Moving animal groups, such as flocks of birds or schools of fish, exhibit a varity of self-organized complex dynamical behaviors and shapes. This kind of flocking behavior has been studied using self-propelled particle models, in which the "particles" interact with their nearest neighbors through repulsion, attraction and alignment responses. In particular, it has been shown that models based on attraction alone can generate a range of dynamic groups in 2D, with periodic boundary conditions, and in the absence of repulsion. Here we investigate the effects of changing these conditions on the type of groups observed in the model. We show that replacing the periodic boundary conditions with a weak global attaction term in 2D, and extending the model to 3D does not significantly change the type of groups observed. We also provide a description of how attraction strength and blind angle determine the groups generated in the 3D version of the model. Finally, we show that adding repulsion do change the type of groups oberved, making them appear and behave more like real moving animal groups. Our results suggest that many biological instances of collective motion may be explained without assuming that animals explicitly align with each other. Instead, complex collective motion is explained by the interplay of attraction and repulsion forces. Supplementary material in the form of four mp4 files available from the Journal web page at http://dx.doi.org/10.1140/epjst/e2015-50093-5

Study of Charge Transport in Vertically Aligned Nitride Nanowire Based Core Shell P-I-N Junctions

DTIC Science & Technology

2016-07-01

Vertically- Aligned Nitride Nanowire Based Core Shell P-I-N Junctions Distribution Statement A. Approved for public release; distribution is...Study of Charge Transport in Vertically- Aligned Nitride Nanowire Based Core Shell P-I-N Junctions Grant Number: HDTRA1-14-1-0003 Principal...Investigator: Abhishek Motayed University of Maryland DISTRIBUTION A: Public Release Study of Charge Transport in Vertically-Aligned Nitride Nanowire

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.

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.

Overcoming the drawback of lower sense margin in tunnel FET based dynamic memory along with enhanced charge retention and scalability

NASA Astrophysics Data System (ADS)

Navlakha, Nupur; Kranti, Abhinav

2017-11-01

The work reports on the use of a planar tri-gate tunnel field effect transistor (TFET) to operate as dynamic memory at 85 °C with an enhanced sense margin (SM). Two symmetric gates (G1) aligned to the source at a partial region of intrinsic film result into better electrostatic control that regulates the read mechanism based on band-to-band tunneling, while the other gate (G2), positioned adjacent to the first front gate is responsible for charge storage and sustenance. The proposed architecture results in an enhanced SM of ˜1.2 μA μm-1 along with a longer retention time (RT) of ˜1.8 s at 85 °C, for a total length of 600 nm. The double gate architecture towards the source increases the tunneling current and also reduces short channel effects, enhancing SM and scalability, thereby overcoming the critical bottleneck faced by TFET based dynamic memories. The work also discusses the impact of overlap/underlap and interface charges on the performance of TFET based dynamic memory. Insights into device operation demonstrate that the choice of appropriate architecture and biases not only limit the trade-off between SM and RT, but also result in improved scalability with drain voltage and total length being scaled down to 0.8 V and 115 nm, respectively.

Robust image registration for multiple exposure high dynamic range image synthesis

NASA Astrophysics Data System (ADS)

Yao, Susu

2011-03-01

Image registration is an important preprocessing technique in high dynamic range (HDR) image synthesis. This paper proposed a robust image registration method for aligning a group of low dynamic range images (LDR) that are captured with different exposure times. Illumination change and photometric distortion between two images would result in inaccurate registration. We propose to transform intensity image data into phase congruency to eliminate the effect of the changes in image brightness and use phase cross correlation in the Fourier transform domain to perform image registration. Considering the presence of non-overlapped regions due to photometric distortion, evolutionary programming is applied to search for the accurate translation parameters so that the accuracy of registration is able to be achieved at a hundredth of a pixel level. The proposed algorithm works well for under and over-exposed image registration. It has been applied to align LDR images for synthesizing high quality HDR images..

Endocytic reawakening of motility in jammed epithelia

NASA Astrophysics Data System (ADS)

Malinverno, Chiara; Corallino, Salvatore; Giavazzi, Fabio; Bergert, Martin; Li, Qingsen; Leoni, Marco; Disanza, Andrea; Frittoli, Emanuela; Oldani, Amanda; Martini, Emanuele; Lendenmann, Tobias; Deflorian, Gianluca; Beznoussenko, Galina V.; Poulikakos, Dimos; Ong, Kok Haur; Uroz, Marina; Trepat, Xavier; Parazzoli, Dario; Maiuri, Paolo; Yu, Weimiao; Ferrari, Aldo; Cerbino, Roberto; Scita, Giorgio

2017-05-01

Dynamics of epithelial monolayers has recently been interpreted in terms of a jamming or rigidity transition. How cells control such phase transitions is, however, unknown. Here we show that RAB5A, a key endocytic protein, is sufficient to induce large-scale, coordinated motility over tens of cells, and ballistic motion in otherwise kinetically arrested monolayers. This is linked to increased traction forces and to the extension of cell protrusions, which align with local velocity. Molecularly, impairing endocytosis, macropinocytosis or increasing fluid efflux abrogates RAB5A-induced collective motility. A simple model based on mechanical junctional tension and an active cell reorientation mechanism for the velocity of self-propelled cells identifies regimes of monolayer dynamics that explain endocytic reawakening of locomotion in terms of a combination of large-scale directed migration and local unjamming. These changes in multicellular dynamics enable collectives to migrate under physical constraints and may be exploited by tumours for interstitial dissemination.

Relationships between static foot alignment and dynamic plantar loads in runners with acute and chronic stages of plantar fasciitis: a cross-sectional study

PubMed Central

Ribeiro, Ana P.; Sacco, Isabel C. N.; Dinato, Roberto C.; João, Silvia M. A.

2016-01-01

BACKGROUND: The risk factors for the development of plantar fasciitis (PF) have been associated with the medial longitudinal arch (MLA), rearfoot alignment and calcaneal overload. However, the relationships between the biomechanical variables have yet to be determined. OBJECTIVE: The goal of this study was to investigate the relationships between the MLA, rearfoot alignment, and dynamic plantar loads in runners with unilateral PF in acute and chronic phases. METHOD: Cross-sectional study which thirty-five runners with unilateral PF were evaluated: 20 in the acute phase (with pain) and 15 with previous chronic PF (without pain). The MLA index and rearfoot alignment were calculated using digital images. The contact area, maximum force, peak pressure, and force-time integral over three plantar areas were acquired with Pedar X insoles while running at 12 km/h, and the loading rates were calculated from the vertical forces. RESULTS: The multiple regression analyses indicated that both the force-time integral (R 2=0.15 for acute phase PF; R 2=0.17 for chronic PF) and maximum force (R 2=0.35 for chronic PF) over the forefoot were predicted by an elevated MLA index. The rearfoot valgus alignment predicted the maximum force over the rearfoot in both PF groups: acute (R 2=0.18) and chronic (R 2=0.45). The rearfoot valgus alignment also predicted higher loading rates in the PF groups: acute (R 2=0.19) and chronic (R 2=0.40). CONCLUSION: The MLA index and the rearfoot alignment were good predictors of plantar loads over the forefoot and rearfoot areas in runners with PF. However, rearfoot valgus was demonstrated to be an important clinical measure, since it was able to predict the maximum force and both loading rates over the rearfoot. PMID:26786073

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.

Space Technology 5 Multi-Point Observations of Temporal Variability of Field-Aligned Currents

NASA Technical Reports Server (NTRS)

Le, Guan; Wang, Yongli; Slavin, James A.; Strangeway, Robert J.

2008-01-01

Space Technology 5 (ST5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that meso-scale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of approximately 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are approximately 1 min for meso-scale currents and approximately 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

Space Technology 5 (ST-5) Observations of Field-Aligned Currents: Temporal Variability

NASA Technical Reports Server (NTRS)

Le, Guan

2010-01-01

Space Technology 5 (ST-5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from STS. The data demonstrate that masoscale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of about 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are about I min for meso-scale currents and about 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

Space Technology 5 Multi-point Observations of Field-aligned Currents: Temporal Variability of Meso-Scale Structures

NASA Technical Reports Server (NTRS)

Le, Guan; Wang, Yongli; Slavin, James A.; Strangeway, Robert J.

2007-01-01

Space Technology 5 (ST5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that meso-scale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of - 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are approx. 1 min for meso-scale currents and approx. 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

Space Technology 5 (ST-5) Multipoint Observations of Temporal and Spatial Variability of Field-Aligned Currents

NASA Technical Reports Server (NTRS)

Le, Guan

2010-01-01

Space Technology 5 (ST-5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that mesoscale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of about 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are about 1 min for meso-scale currents and about 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

Effects of auroral potential drops on plasma sheet dynamics

NASA Astrophysics Data System (ADS)

Xi, Sheng; Lotko, William; Zhang, Binzheng; Wiltberger, Michael; Lyon, John

2016-11-01

The reaction of the magnetosphere-ionosphere system to dynamic auroral potential drops is investigated using the Lyon-Fedder-Mobarry global model including, for the first time in a global simulation, the dissipative load of field-aligned potential drops in the low-altitude boundary condition. This extra load reduces the field-aligned current (j||) supplied by nightside reconnection dynamos. The system adapts by forcing the nightside X line closer to Earth, with a corresponding reduction in current lensing (j||/B = constant) at the ionosphere and additional contraction of the plasma sheet during substorm recovery and steady magnetospheric convection. For steady and moderate solar wind driving and with constant ionospheric conductance, the cross polar cap potential and hemispheric field-aligned current are lower by approximately the ratio of the peak field-aligned potential drop to the cross polar cap potential (10-15%) when potential drops are included. Hemispheric ionospheric Joule dissipation is less by 8%, while the area-integrated, average work done on the fluid by the reconnecting magnetotail field increases by 50% within |y| < 8 RE. Effects on the nightside plasma sheet include (1) an average X line 4 RE closer to Earth; (2) a 12% higher mean reconnection rate; and (3) dawn-dusk asymmetry in reconnection with a 17% higher rate in the premidnight sector.

Hysteretic dynamics of active particles in a periodic orienting field

PubMed Central

Romensky, Maksym; Scholz, Dimitri; Lobaskin, Vladimir

2015-01-01

Active motion of living organisms and artificial self-propelling particles has been an area of intense research at the interface of biology, chemistry and physics. Significant progress in understanding these phenomena has been related to the observation that dynamic self-organization in active systems has much in common with ordering in equilibrium condensed matter such as spontaneous magnetization in ferromagnets. The velocities of active particles may behave similar to magnetic dipoles and develop global alignment, although interactions between the individuals might be completely different. In this work, we show that the dynamics of active particles in external fields can also be described in a way that resembles equilibrium condensed matter. It follows simple general laws, which are independent of the microscopic details of the system. The dynamics is revealed through hysteresis of the mean velocity of active particles subjected to a periodic orienting field. The hysteresis is measured in computer simulations and experiments on unicellular organisms. We find that the ability of the particles to follow the field scales with the ratio of the field variation period to the particles' orientational relaxation time, which, in turn, is related to the particle self-propulsion power and the energy dissipation rate. The collective behaviour of the particles due to aligning interactions manifests itself at low frequencies via increased persistence of the swarm motion when compared with motion of an individual. By contrast, at high field frequencies, the active group fails to develop the alignment and tends to behave like a set of independent individuals even in the presence of interactions. We also report on asymptotic laws for the hysteretic dynamics of active particles, which resemble those in magnetic systems. The generality of the assumptions in the underlying model suggests that the observed laws might apply to a variety of dynamic phenomena from the motion of synthetic active particles to crowd or opinion dynamics. PMID:26040594

Feature-based Alignment of Volumetric Multi-modal Images

PubMed Central

Toews, Matthew; Zöllei, Lilla; Wells, William M.

2014-01-01

This paper proposes a method for aligning image volumes acquired from different imaging modalities (e.g. MR, CT) based on 3D scale-invariant image features. A novel method for encoding invariant feature geometry and appearance is developed, based on the assumption of locally linear intensity relationships, providing a solution to poor repeatability of feature detection in different image modalities. The encoding method is incorporated into a probabilistic feature-based model for multi-modal image alignment. The model parameters are estimated via a group-wise alignment algorithm, that iteratively alternates between estimating a feature-based model from feature data, then realigning feature data to the model, converging to a stable alignment solution with few pre-processing or pre-alignment requirements. The resulting model can be used to align multi-modal image data with the benefits of invariant feature correspondence: globally optimal solutions, high efficiency and low memory usage. The method is tested on the difficult RIRE data set of CT, T1, T2, PD and MP-RAGE brain images of subjects exhibiting significant inter-subject variability due to pathology. PMID:24683955

Acquired prior knowledge modulates audiovisual integration.

PubMed

Van Wanrooij, Marc M; Bremen, Peter; John Van Opstal, A

2010-05-01

Orienting responses to audiovisual events in the environment can benefit markedly by the integration of visual and auditory spatial information. However, logically, audiovisual integration would only be considered successful for stimuli that are spatially and temporally aligned, as these would be emitted by a single object in space-time. As humans do not have prior knowledge about whether novel auditory and visual events do indeed emanate from the same object, such information needs to be extracted from a variety of sources. For example, expectation about alignment or misalignment could modulate the strength of multisensory integration. If evidence from previous trials would repeatedly favour aligned audiovisual inputs, the internal state might also assume alignment for the next trial, and hence react to a new audiovisual event as if it were aligned. To test for such a strategy, subjects oriented a head-fixed pointer as fast as possible to a visual flash that was consistently paired, though not always spatially aligned, with a co-occurring broadband sound. We varied the probability of audiovisual alignment between experiments. Reaction times were consistently lower in blocks containing only aligned audiovisual stimuli than in blocks also containing pseudorandomly presented spatially disparate stimuli. Results demonstrate dynamic updating of the subject's prior expectation of audiovisual congruency. We discuss a model of prior probability estimation to explain the results.

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.

Static beam-based alignment for the Ring-To-Main-Linac of the Compact Linear Collider

NASA Astrophysics Data System (ADS)

Han, Y.; Latina, A.; Ma, L.; Schulte, D.

2017-06-01

The Compact Linear Collider (CLIC) is a future multi-TeV collider for the post-Large Hadron Collider era. It features high-gradient acceleration and ultra-low emittance to achieve its ambitious goals of high collision energy and peak luminosity. Beam-based alignment (BBA) techniques are mandatory for CLIC to preserve the ultra-low emittances from the damping rings to the interaction point. In this paper, a detailed study of BBA techniques has been carried out for the entire 27 km long ``Ring-To-Main-Linac'' (RTML) section of the CLIC, to correct realistic static errors such as element position offsets, angle, magnetic strength and dynamic magnetic centre shifts. The correction strategy is proved to be very effective and leads to a relaxation of the pre-alignment tolerances for the component installation in the tunnel. This is the first time such a large scale and complex lattice has been corrected to match the design budgets. The techniques proposed could be applied to similarly sized facilities, such as the International Linear Collider, where a similar RTML section is used, or free-electron lasers, which, being equipped with linacs and bunch compressors, present challenges similar to those of the CLIC RTML. Moreover, a new technique is investigated for the emittance tuning procedure: the direct measurement of the interactions between the beams and a set of a few consecutive laser wires. The speed of this technique can be faster comparing to the traditional techniques based on emittance reconstructed from beam size measurements at several positions.

A Novel Adaptive H∞ Filtering Method with Delay Compensation for the Transfer Alignment of Strapdown Inertial Navigation Systems

PubMed Central

Lyu, Weiwei

2017-01-01

Transfer alignment is always a key technology in a strapdown inertial navigation system (SINS) because of its rapidity and accuracy. In this paper a transfer alignment model is established, which contains the SINS error model and the measurement model. The time delay in the process of transfer alignment is analyzed, and an H∞ filtering method with delay compensation is presented. Then the H∞ filtering theory and the robust mechanism of H∞ filter are deduced and analyzed in detail. In order to improve the transfer alignment accuracy in SINS with time delay, an adaptive H∞ filtering method with delay compensation is proposed. Since the robustness factor plays an important role in the filtering process and has effect on the filtering accuracy, the adaptive H∞ filter with delay compensation can adjust the value of robustness factor adaptively according to the dynamic external environment. The vehicle transfer alignment experiment indicates that by using the adaptive H∞ filtering method with delay compensation, the transfer alignment accuracy and the pure inertial navigation accuracy can be dramatically improved, which demonstrates the superiority of the proposed filtering method. PMID:29182592

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

PubMed

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

2015-01-01

We have optimized the magnetic alignment of phospholipid bilayered micelles (bicelles) for EPR spectroscopy, by varying lipid composition and temperature. Bicelles have been extensively used in NMR spectroscopy for several decades, in order to obtain aligned samples in a near-native membrane environment and take advantage of the intrinsic sensitivity of magnetic resonance to molecular orientation. Recently, bicelles have also seen increasing use in EPR, which offers superior sensitivity and orientational resolution. However, the low magnetic field strength (less than 1 T) of most conventional EPR spectrometers results in homogeneously oriented bicelles only at a temperature well above physiological. To optimize bicelle composition for magnetic alignment at reduced temperature, we prepared bicelles containing varying ratios of saturated (DMPC) and unsaturated (POPC) phospholipids, using EPR spectra of a spin-labeled fatty acid to assess alignment as a function of lipid composition and temperature. Spectral analysis showed that bicelles containing an equimolar mixture of DMPC and POPC homogeneously align at 298 K, 20 K lower than conventional DMPC-only bicelles. It is now possible to perform EPR studies of membrane protein structure and dynamics in well-aligned bicelles at physiological temperatures and below. Copyright © 2014 Elsevier Inc. All rights reserved.

Understanding Angiography-Based Aneurysm Flow Fields through Comparison with Computational Fluid Dynamics.

PubMed

Cebral, J R; Mut, F; Chung, B J; Spelle, L; Moret, J; van Nijnatten, F; Ruijters, D

2017-06-01

Hemodynamics is thought to be an important factor for aneurysm progression and rupture. Our aim was to evaluate whether flow fields reconstructed from dynamic angiography data can be used to realistically represent the main flow structures in intracranial aneurysms. DSA-based flow reconstructions, obtained during interventional treatment, were compared qualitatively with flow fields obtained from patient-specific computational fluid dynamics models and quantitatively with projections of the computational fluid dynamics fields (by computing a directional similarity of the vector fields) in 15 cerebral aneurysms. The average similarity between the DSA and the projected computational fluid dynamics flow fields was 78% in the parent artery, while it was only 30% in the aneurysm region. Qualitatively, both the DSA and projected computational fluid dynamics flow fields captured the location of the inflow jet, the main vortex structure, the intrasaccular flow split, and the main rotation direction in approximately 60% of the cases. Several factors affect the reconstruction of 2D flow fields from dynamic angiography sequences. The most important factors are the 3-dimensionality of the intrasaccular flow patterns and inflow jets, the alignment of the main vortex structure with the line of sight, the overlapping of surrounding vessels, and possibly frame rate undersampling. Flow visualization with DSA from >1 projection is required for understanding of the 3D intrasaccular flow patterns. Although these DSA-based flow quantification techniques do not capture swirling or secondary flows in the parent artery, they still provide a good representation of the mean axial flow and the corresponding flow rate. © 2017 by American Journal of Neuroradiology.

ViCAR: An Adaptive and Landmark-Free Registration of Time Lapse Image Data from Microfluidics Experiments

PubMed Central

Hattab, Georges; Schlüter, Jan-Philip; Becker, Anke; Nattkemper, Tim W.

2017-01-01

In order to understand gene function in bacterial life cycles, time lapse bioimaging is applied in combination with different marker protocols in so called microfluidics chambers (i.e., a multi-well plate). In one experiment, a series of T images is recorded for one visual field, with a pixel resolution of 60 nm/px. Any (semi-)automatic analysis of the data is hampered by a strong image noise, low contrast and, last but not least, considerable irregular shifts during the acquisition. Image registration corrects such shifts enabling next steps of the analysis (e.g., feature extraction or tracking). Image alignment faces two obstacles in this microscopic context: (a) highly dynamic structural changes in the sample (i.e., colony growth) and (b) an individual data set-specific sample environment which makes the application of landmarks-based alignments almost impossible. We present a computational image registration solution, we refer to as ViCAR: (Vi)sual (C)ues based (A)daptive (R)egistration, for such microfluidics experiments, consisting of (1) the detection of particular polygons (outlined and segmented ones, referred to as visual cues), (2) the adaptive retrieval of three coordinates throughout different sets of frames, and finally (3) an image registration based on the relation of these points correcting both rotation and translation. We tested ViCAR with different data sets and have found that it provides an effective spatial alignment thereby paving the way to extract temporal features pertinent to each resulting bacterial colony. By using ViCAR, we achieved an image registration with 99.9% of image closeness, based on the average rmsd of 4.10−2 pixels, and superior results compared to a state of the art algorithm. PMID:28620411

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

PubMed

Zheng, Qi; Grice, Elizabeth A

2016-10-01

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

Dynamic RSA for the evaluation of inducible micromotion of Oxford UKA during step-up and step-down motion.

PubMed

Horsager, Kristian; Kaptein, Bart L; Rømer, Lone; Jørgensen, Peter B; Stilling, Maiken

2017-06-01

Background and purpose - Implant inducible micromotions have been suggested to reflect the quality of the fixation interface. We investigated the usability of dynamic RSA for evaluation of inducible micromotions of the Oxford Unicompartmental Knee Arthroplasty (UKA) tibial component, and evaluated factors that have been suggested to compromise the fixation, such as fixation method, component alignment, and radiolucent lines (RLLs). Patients and methods - 15 patients (12 men) with a mean age of 69 (55-86) years, with an Oxford UKA (7 cemented), were studied after a mean time in situ of 4.4 (3.6-5.1) years. 4 had tibial RLLs. Each patient was recorded with dynamic RSA (10 frames/second) during a step-up/step-down motion. Inducible micromotions were calculated for the tibial component with respect to the tibia bone. Postoperative component alignment was measured with model-based RSA and RLLs were measured on screened radiographs. Results - All tibial components showed inducible micromotions as a function of the step-cycle motion with a mean subsidence of up to -0.06 mm (95% CI: -0.10 to -0.03). Tibial component inducible micromotions were similar for cemented fixation and cementless fixation. Patients with tibial RLLs had 0.5° (95% CI: 0.18-0.81) greater inducible medio-lateral tilt of the tibial component. There was a correlation between postoperative posterior slope of the tibial plateau and inducible anterior-posterior tilt. Interpretation - All patients had inducible micromotions of the tibial component during step-cycle motion. RLLs and a high posterior slope increased the magnitude of inducible micromotions. This suggests that dynamic RSA is a valuable clinical tool for the evaluation of functional implant fixation.

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.

When does power disparity help or hurt group performance?

PubMed

Tarakci, Murat; Greer, Lindred L; Groenen, Patrick J F

2016-03-01

Power differences are ubiquitous in social settings. However, the question of whether groups with higher or lower power disparity achieve better performance has thus far received conflicting answers. To address this issue, we identify 3 underlying assumptions in the literature that may have led to these divergent findings, including a myopic focus on static hierarchies, an assumption that those at the top of hierarchies are competent at group tasks, and an assumption that equality is not possible. We employ a multimethod set of studies to examine these assumptions and to understand when power disparity will help or harm group performance. First, our agent-based simulation analyses show that by unpacking these common implicit assumptions in power research, we can explain earlier disparate findings--power disparity benefits group performance when it is dynamically aligned with the power holder's task competence, and harms group performance when held constant and/or is not aligned with task competence. Second, our empirical findings in both a field study of fraud investigation groups and a multiround laboratory study corroborate the simulation results. We thereby contribute to research on power by highlighting a dynamic understanding of power in groups and explaining how current implicit assumptions may lead to opposing findings. (c) 2016 APA, all rights reserved).

[Prevention of stress in the workplace].

PubMed

Vaccani, R

2009-01-01

The chronological/logical path goes from the base distinction that classify the stressing phenomena between the two categories, eu-stress and dis-stress. It is underlined the subjective characteristic of stressing processes, the statement that what might be eu-stress for someone can be dis-stress for others. The organizational setting can be considered as a privileged preventive intervention area. Therefore it is suggested this categorization for the stress organizational causes: Causes connected to the organizational system (Incoherencies or structural understaffing, procedural incoherencies); Causes connected to the wrong alignment of competencies; Causes connected to the wrong alignment of aptitudes; Causes connected to the social dynamics of abuse of power. The categories to differentiate the stress organizational causes are proposed to give a useful glossary to design various preventive actions: Preventive actions on the organizational setting; Preventive actions through education; Preventive actions about role redesign; Preventive actions aimed at sustaining ethical social cohabitation. Finally, it is assessed that the approach to organizational stress requires an holistic, multi disciplinary perspective analysis, able to connect the ethic and qualitative characteristic of the markets (closed and open markets) to the organizational setting, to the subject peculiar character at work and its impact with working roles, to the social dynamics derived from hierarchical roles, to the organizational moods, to the individual perceptions, to the clinical paths.

An augmented magnetic navigation system for Transcatheter Aortic Valve Implantation.

PubMed

Luo, Zhe; Cai, Junfeng; Nie, Yuanyuan; Wang, Guotai; Gu, Lixu

2013-01-01

This research proposes an augmented magnetic navigation system for Transcatheter Aortic Valve Implantation (TAVI) employing a magnetic tracking system (MTS) combined with a dynamic aortic model and intra-operative ultrasound (US) images. The dynamic 3D aortic model is constructed based on the preoperative 4D computed tomography (CT), which is animated according to the real time electrocardiograph (ECG) input of patient. And a preoperative planning is performed to determine the target position of the aortic valve prosthesis. The temporal alignment is performed to synchronize the ECG signals, intra-operative US image and tracking information. Afterwards, with the assistance of synchronized ECG signals, the contour of aortic root automatic extracted from short axis US image is registered to the dynamic aortic model by a feature based registration intra-operatively. Then the augmented MTS guides the interventionist to confidently position and deploy the aortic valve prosthesis to target. The system was validated by animal studies on three porcine subjects, the deployment and tilting errors of which are 3.17 ± 0.91 mm and 7.40 ± 2.89° respectively.

Dynamic social networks based on movement

USGS Publications Warehouse

Scharf, Henry; Hooten, Mevin B.; Fosdick, Bailey K.; Johnson, Devin S.; London, Joshua M.; Durban, John W.

2016-01-01

Network modeling techniques provide a means for quantifying social structure in populations of individuals. Data used to define social connectivity are often expensive to collect and based on case-specific, ad hoc criteria. Moreover, in applications involving animal social networks, collection of these data is often opportunistic and can be invasive. Frequently, the social network of interest for a given population is closely related to the way individuals move. Thus, telemetry data, which are minimally invasive and relatively inexpensive to collect, present an alternative source of information. We develop a framework for using telemetry data to infer social relationships among animals. To achieve this, we propose a Bayesian hierarchical model with an underlying dynamic social network controlling movement of individuals via two mechanisms: an attractive effect and an aligning effect. We demonstrate the model and its ability to accurately identify complex social behavior in simulation, and apply our model to telemetry data arising from killer whales. Using auxiliary information about the study population, we investigate model validity and find the inferred dynamic social network is consistent with killer whale ecology and expert knowledge.

Energy partitioning and impulse dispersion in the decorated, tapered, strongly nonlinear granular alignment: A system with many potential applications

NASA Astrophysics Data System (ADS)

Doney, Robert L.; Agui, Juan H.; Sen, Surajit

2009-09-01

Rapid absorption of impulses using light-weight, small, reusable systems is a challenging problem. An axially aligned set of progressively shrinking elastic spheres, a "tapered chain," has been shown to be a versatile and scalable shock absorber in earlier simulational, theoretical, and experimental works by several authors. We have recently shown (see R. L. Doney and S. Sen, Phys. Rev. Lett. 97, 155502 (2006)) that the shock absorption ability of a tapered chain can be dramatically enhanced by placing small interstitial grains between the regular grains in the tapered chain systems. Here we focus on a detailed study of the problem introduced in the above mentioned letter, present extensive dynamical simulations using parameters for a titanium-aluminum-vanadium alloy Ti6Al4V, derive attendant hard-sphere analyses based formulae to describe energy dispersion, and finally discuss some preliminary experimental results using systems with chrome spheres and small Nitinol interstitial grains to present the underlying nonlinear dynamics of this so-called decorated tapered granular alignment. We are specifically interested in small systems, comprised of several grains. This is because in real applications, mass and volume occupied must inevitably be minimized. Our conclusion is that the decorated tapered chain offers enhanced energy dispersion by locking in much of the input energy in the grains of the tapered chain rather than in the small interstitial grains. Thus, the present study offers insights into how the shock absorption capabilities of these systems can be pushed even further by improving energy absorption capabilities of the larger grains in the tapered chains. We envision that these scalable, decorated tapered chains may be used as shock absorbing components in body armor, armored vehicles, building applications and in perhaps even in applications in rehabilitation science.

Sparse alignment for robust tensor learning.

PubMed

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

2014-10-01

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

Onorbit IMU alignment error budget

NASA Technical Reports Server (NTRS)

Corson, R. W.

1980-01-01

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

Physician-Hospital Alignment in Orthopedic Surgery.

PubMed

Bushnell, Brandon D

2015-09-01

The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. Copyright 2015, SLACK Incorporated.

Development of an embedded instrument for autofocus and polarization alignment of polarization maintaining fiber

NASA Astrophysics Data System (ADS)

Feng, Di; Fang, Qimeng; Huang, Huaibo; Zhao, Zhengqi; Song, Ningfang

2017-12-01

The development and implementation of a practical instrument based on an embedded technique for autofocus and polarization alignment of polarization maintaining fiber is presented. For focusing efficiency and stability, an image-based focusing algorithm fully considering the image definition evaluation and the focusing search strategy was used to accomplish autofocus. For improving the alignment accuracy, various image-based algorithms of alignment detection were developed with high calculation speed and strong robustness. The instrument can be operated as a standalone device with real-time processing and convenience operations. The hardware construction, software interface, and image-based algorithms of main modules are described. Additionally, several image simulation experiments were also carried out to analyze the accuracy of the above alignment detection algorithms. Both the simulation results and experiment results indicate that the instrument can achieve the accuracy of polarization alignment <±0.1 deg.

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

ERIC Educational Resources Information Center

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

2009-01-01

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

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

Nonlinear field equations for aligning self-propelled rods.

PubMed

Peshkov, Anton; Aranson, Igor S; Bertin, Eric; Chaté, Hugues; Ginelli, Francesco

2012-12-28

We derive a set of minimal and well-behaved nonlinear field equations describing the collective properties of self-propelled rods from a simple microscopic starting point, the Vicsek model with nematic alignment. Analysis of their linear and nonlinear dynamics shows good agreement with the original microscopic model. In particular, we derive an explicit expression for density-segregated, banded solutions, allowing us to develop a more complete analytic picture of the problem at the nonlinear level.

Dynamical formation of spatially localized arrays of aligned nanowires in plastic films with magnetic anisotropy.

PubMed

Fragouli, Despina; Buonsanti, Raffaella; Bertoni, Giovanni; Sangregorio, Claudio; Innocenti, Claudia; Falqui, Andrea; Gatteschi, Dante; Cozzoli, Pantaleo Davide; Athanassiou, Athanassia; Cingolani, Roberto

2010-04-27

We present a simple technique for magnetic-field-induced formation, assembling, and positioning of magnetic nanowires in a polymer film. Starting from a polymer/iron oxide nanoparticle casted solution that is allowed to dry along with the application of a weak magnetic field, nanocomposite films incorporating aligned nanocrystal-built nanowire arrays are obtained. The control of the dimensions of the nanowires and of their localization across the polymer matrix is achieved by varying the duration of the applied magnetic field, in combination with the evaporation dynamics. These multifunctional anisotropic free-standing nanocomposite films, which demonstrate high magnetic anisotropy, can be used in a wide field of technological applications, ranging from sensors to microfluidics and magnetic devices.

Memory-efficient dynamic programming backtrace and pairwise local sequence alignment.

PubMed

Newberg, Lee A

2008-08-15

A backtrace through a dynamic programming algorithm's intermediate results in search of an optimal path, or to sample paths according to an implied probability distribution, or as the second stage of a forward-backward algorithm, is a task of fundamental importance in computational biology. When there is insufficient space to store all intermediate results in high-speed memory (e.g. cache) existing approaches store selected stages of the computation, and recompute missing values from these checkpoints on an as-needed basis. Here we present an optimal checkpointing strategy, and demonstrate its utility with pairwise local sequence alignment of sequences of length 10,000. Sample C++-code for optimal backtrace is available in the Supplementary Materials. Supplementary data is available at Bioinformatics online.

Phase separation and large deviations of lattice active matter

NASA Astrophysics Data System (ADS)

Whitelam, Stephen; Klymko, Katherine; Mandal, Dibyendu

2018-04-01

Off-lattice active Brownian particles form clusters and undergo phase separation even in the absence of attractions or velocity-alignment mechanisms. Arguments that explain this phenomenon appeal only to the ability of particles to move persistently in a direction that fluctuates, but existing lattice models of hard particles that account for this behavior do not exhibit phase separation. Here we present a lattice model of active matter that exhibits motility-induced phase separation in the absence of velocity alignment. Using direct and rare-event sampling of dynamical trajectories, we show that clustering and phase separation are accompanied by pronounced fluctuations of static and dynamic order parameters. This model provides a complement to off-lattice models for the study of motility-induced phase separation.

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

PubMed Central

Zheng, Qi; Grice, Elizabeth A.

2016-01-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost. PMID:27706155

Multiple alignment analysis on phylogenetic tree of the spread of SARS epidemic using distance method

NASA Astrophysics Data System (ADS)

Amiroch, S.; Pradana, M. S.; Irawan, M. I.; Mukhlash, I.

2017-09-01

Multiple Alignment (MA) is a particularly important tool for studying the viral genome and determine the evolutionary process of the specific virus. Application of MA in the case of the spread of the Severe acute respiratory syndrome (SARS) epidemic is an interesting thing because this virus epidemic a few years ago spread so quickly that medical attention in many countries. Although there has been a lot of software to process multiple sequences, but the use of pairwise alignment to process MA is very important to consider. In previous research, the alignment between the sequences to process MA algorithm, Super Pairwise Alignment, but in this study used a dynamic programming algorithm Needleman wunchs simulated in Matlab. From the analysis of MA obtained and stable region and unstable which indicates the position where the mutation occurs, the system network topology that produced the phylogenetic tree of the SARS epidemic distance method, and system area networks mutation.

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 fiber optic sensor for ophthalmic refractive diagnostics

NASA Technical Reports Server (NTRS)

Ansari, Rafat R.; Dhadwal, Harbans S.; Campbell, Melanie C. W.; Dellavecchia, Michael A.

1992-01-01

This paper demonstrates the application of a lensless fiber optic spectrometer (sensor) to study the onset of cataracts. This new miniaturized and rugged fiber optic probe is based upon dynamic light scattering (DLS) principles. It has no moving parts, no apertures, and requires no optical alignment. It is flexible and easy to use. Results are presented for cold-induced cataract in excised bovine eye lenses, and aging effects in excised human eye lenses. The device can be easily incorporated into a slit-lamp apparatus (ophthalmoscope) for complete eye diagnostics.

High-harmonic spectroscopy of aligned molecules

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

Mixing and demixing of binary mixtures of polar chiral active particles.

PubMed

Ai, Bao-Quan; Shao, Zhi-Gang; Zhong, Wei-Rong

2018-05-17

We study a binary mixture of polar chiral (counterclockwise or clockwise) active particles in a two-dimensional box with periodic boundary conditions. Besides the excluded volume interactions between particles, the particles are also subjected to the polar velocity alignment. From the extensive Brownian dynamics simulations, it is found that the particle configuration (mixing or demixing) is determined by the competition between the chirality difference and the polar velocity alignment. When the chirality difference competes with the polar velocity alignment, the clockwise particles aggregate in one cluster and the counterclockwise particles aggregate in the other cluster; thus, the particles are demixed and can be separated. However, when the chirality difference or the polar velocity alignment is dominant, the particles are mixed. Our findings could be used for the experimental pursuit of the separation of binary mixtures of chiral active particles.

Enzyme activity assays within microstructured optical fibers enabled by automated alignment.

PubMed

Warren-Smith, Stephen C; Nie, Guiying; Schartner, Erik P; Salamonsen, Lois A; Monro, Tanya M

2012-12-01

A fluorescence-based enzyme activity assay has been demonstrated within a small-core microstructured optical fiber (MOF) for the first time. To achieve this, a reflection-based automated alignment system has been developed, which uses feedback and piezoelectric actuators to maintain optical alignment. The auto-alignment system provides optical stability for the time required to perform an activity assay. The chosen assay is based on the enzyme proprotein convertase 5/6 (PC6) and has important applications in women's health.

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

PubMed

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

2006-08-15

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

A Kalman Filter for SINS Self-Alignment Based on Vector Observation.

PubMed

Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Tong, Jinwu

2017-01-29

In this paper, a self-alignment method for strapdown inertial navigation systems based on the q -method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate.

A Kalman Filter for SINS Self-Alignment Based on Vector Observation

PubMed Central

Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Tong, Jinwu

2017-01-01

In this paper, a self-alignment method for strapdown inertial navigation systems based on the q-method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate. PMID:28146059

Sensitivity of medial and lateral knee contact force predictions to frontal plane alignment and contact locations.

PubMed

Saliba, Christopher M; Brandon, Scott C E; Deluzio, Kevin J

2017-05-24

Musculoskeletal models are increasingly used to estimate medial and lateral knee contact forces, which are difficult to measure in vivo. The sensitivity of contact force predictions to modeling parameters is important to the interpretation and implication of results generated by the model. The purpose of this study was to quantify the sensitivity of knee contact force predictions to simultaneous errors in frontal plane knee alignment and contact locations under different dynamic conditions. We scaled a generic musculoskeletal model for N=23 subjects' stature and radiographic knee alignment, then perturbed frontal plane alignment and mediolateral contact locations within experimentally-possible ranges of 10° to -10° and 10 to -10mm, respectively. The sensitivity of first peak, second peak, and mean medial and lateral knee contact forces to knee adduction angle and contact locations was modeled using linear regression. Medial loads increased, and lateral loads decreased, by between 3% and 6% bodyweight for each degree of varus perturbation. Shifting the medial contact point medially increased medial loads and decreased lateral loads by between 1% and 4% bodyweight per millimeter. This study demonstrates that realistic measurement errors of 5mm (contact distance) or 5° (frontal plane alignment) could result in a combined 50% BW error in subject specific contact force estimates. We also show that model sensitivity varies between subjects as a result of differences in gait dynamics. These results demonstrate that predicted knee joint contact forces should be considered as a range of possible values determined by model uncertainty. Copyright © 2017 Elsevier Ltd. All rights reserved.

Solar dynamic power for Space Station Freedom

NASA Technical Reports Server (NTRS)

Labus, Thomas L.; Secunde, Richard R.; Lovely, Ronald G.

1989-01-01

The Space Station Freedom Program is presently planned to consist of two phases. At the completion of Phase 1, Freedom's manned base will consist of a transverse boom with attached manned modules and 75 kW of available electric power supplied by photovoltaic (PV) power sources. In Phase 2, electric power available to the manned base will be increased to 125 kW by the addition of two solar dynamic (SD) power modules, one at each end of the transverse boom. Power for manned base growth beyond Phase 2 will be supplied by additional SD modules. Studies show that SD power for the growth eras will result in life cycle cost savings of $3 to $4 billion when compared to PV-supplied power. In the SD power modules for Space Station Freedom, an offset parabolic concentrator collects and focuses solar energy into a heat receiver. To allow full power operation over the entire orbit, the receiver includes integral thermal energy storage by means of the heat of fusion of a salt mixture. Thermal energy is removed from the receiver and converted to electrical energy by a power conversion unit (PCU) which includes a closed brayton cycle (CBC) heat engine and an alternator. The receiver/PCU/radiator combination will be completely assembled and charged with gas and cooling fluid on earth before launch to orbit. The concentrator subassemblies will be pre-aligned and stowed in the orbiter bay before launch. On orbit, the receiver/PCU/radiator assembly will be installed as a unit. The pre-aligned concentrator panels will then be latched together and the total concentrator attached to the receiver/PCU/radiator by the astronauts. After final electric connections are made and checkout is complete, the SD power module will be ready for operation.

Solar dynamic power for space station freedom

NASA Technical Reports Server (NTRS)

Labus, Thomas L.; Secunde, Richard R.; Lovely, Ronald G.

1989-01-01

The Space Station Freedom Program is presently planned to consist of two phases. At the completion of Phase 1, Freedom's manned base will consist of a transverse boom with attached manned modules and 75 kW of available electric power supplied by photovoltaic (PV) power sources. In Phase 2, electric power available to the manned base will be increased to 125 kW by the addition of two solar dynamic (SD) power modules, one at each end of the transverse boom. Power for manned base growth beyond Phase 2 will be supplied by additional SD modules. Studies show that SD power for the growth eras will result in life cycle cost savings of $3 to $4 billion when compared to PV-supplied power. In the SD power modules for Space Station Freedom, an offset parabolic concentrator collects and focuses solar energy into a heat receiver. To allow full power operation over the entire orbit, the receiver includes integral thermal energy storage by means of the heat of fusion of a salt mixture. Thermal energy is removed from the receiver and converted to electrical energy by a power conversion unit (PCU) which includes a closed brayton cycle (CBC) heat engine and an alternator. The receiver/PCU/radiator combination will be completely assembled and charged with gas and cooling fluid on Earth before launch to orbit. The concentrator subassemblies will be pre-aligned and stowed in the orbiter bay before launch. On orbit, the receiver/PCU/radiator assembly will be installed as a unit. The pre-aligned concentrator panels will then be latched together and the total concentrator attached to the receiver/PCU/radiator by the astronauts. After final electric connections are made and checkout is complete, the SD power module will be ready for operation.

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.

Enhanced critical-current in P-doped BaFe2As2 thin films on metal substrates arising from poorly aligned grain boundaries.

PubMed

Sato, Hikaru; Hiramatsu, Hidenori; Kamiya, Toshio; Hosono, Hideo

2016-11-11

Thin films of the iron-based superconductor BaFe 2 (As 1-x P x ) 2 (Ba122:P) were fabricated on polycrystalline metal-tape substrates with two kinds of in-plane grain boundary alignments (well aligned (4°) and poorly aligned (8°)) by pulsed laser deposition. The poorly aligned substrate is not applicable to cuprate-coated conductors because the in-plane alignment >4° results in exponential decay of the critical current density (J c ). The Ba122:P film exhibited higher J c at 4 K when grown on the poorly aligned substrate than on the well-aligned substrate even though the crystallinity was poorer. It was revealed that the misorientation angles of the poorly aligned samples were less than 6°, which are less than the critical angle of an iron-based superconductor, cobalt-doped BaFe 2 As 2 (~9°), and the observed strong pinning in the Ba122:P is attributed to the high-density grain boundaries with the misorientation angles smaller than the critical angle. This result reveals a distinct advantage over cuprate-coated conductors because well-aligned metal-tape substrates are not necessary for practical applications of the iron-based superconductors.

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

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/.

Postural orientation and equilibrium processes associated with increased postural sway in autism spectrum disorder (ASD).

PubMed

Wang, Zheng; Hallac, Rami R; Conroy, Kaitlin C; White, Stormi P; Kane, Alex A; Collinsworth, Amy L; Sweeney, John A; Mosconi, Matthew W

2016-01-01

Increased postural sway has been repeatedly documented in children with autism spectrum disorder (ASD). Characterizing the control processes underlying this deficit, including postural orientation and equilibrium, may provide key insights into neurophysiological mechanisms associated with ASD. Postural orientation refers to children's ability to actively align their trunk and head with respect to their base of support, while postural equilibrium is an active process whereby children coordinate ankle dorsi-/plantar-flexion and hip abduction/adduction movements to stabilize their upper body. Dynamic engagement of each of these control processes is important for maintaining postural stability, though neither postural orientation nor equilibrium has been studied in ASD. Twenty-two children with ASD and 21 age and performance IQ-matched typically developing (TD) controls completed three standing tests. During static stance, participants were instructed to stand as still as possible. During dynamic stances, participants swayed at a comfortable speed and magnitude in either anterior-posterior (AP) or mediolateral (ML) directions. The center of pressure (COP) standard deviation and trajectory length were examined to determine if children with ASD showed increased postural sway. Postural orientation was assessed using a novel virtual time-to-contact (VTC) approach that characterized spatiotemporal dimensions of children's postural sway (i.e., body alignment) relative to their postural limitation boundary, defined as the maximum extent to which each child could sway in each direction. Postural equilibrium was quantified by evaluating the amount of shared or mutual information of COP time series measured along the AP and ML directions. Consistent with prior studies, children with ASD showed increased postural sway during both static and dynamic stances relative to TD children. In regard to postural orientation processes, children with ASD demonstrated reduced spatial perception of their postural limitation boundary towards target directions and reduced time to correct this error during dynamic postural sways but not during static stance. Regarding postural equilibrium, they showed a compromised ability to decouple ankle dorsi-/plantar-flexion and hip abduction/adduction processes during dynamic stances. These results suggest that deficits in both postural orientation and equilibrium processes contribute to reduced postural stability in ASD. Specifically, increased postural sway in ASD appears to reflect patients' impaired perception of their body movement relative to their own postural limitation boundary as well as a reduced ability to decouple distinct ankle and hip movements to align their body during standing. Our findings that deficits in postural orientation and equilibrium are more pronounced during dynamic compared to static stances suggests that the increased demands of everyday activities in which children must dynamically shift their COP involve more severe postural control deficits in ASD relative to static stance conditions that often are studied. Systematic assessment of dynamic postural control processes in ASD may provide important insights into new treatment targets and neurodevelopmental mechanisms.

Earle K. Plyler Prize Lecture: The Three Pillars of Ultrafast Molecular Science - Time, Phase, Intensity

NASA Astrophysics Data System (ADS)

Stolow, Albert

We discuss the probing and control of molecular wavepacket dynamics in the context of three main `pillars' of light-matter interaction: time, phase, intensity. Time: Using short, coherent laser pulses and perturbative matter-field interactions, we study molecular wavepackets with a focus on the ultrafast non-Born-Oppenheimer dynamics, that is, the coupling of electronic and nuclear motions. Time-Resolved Photoelectron Spectroscopy (TRPES) is a powerful ultrafast probe of these processes in polyatomic molecules because it is sensitive both electronic and vibrational dynamics. Ideally, one would like to observe these ultrafast processes from the molecule's point of view - the Molecular Frame - thereby avoiding loss of information due to orientational averaging. This can be achieved by Time-Resolved Coincidence Imaging Spectroscopy (TRCIS) which images 3D recoil vectors of both photofragments and photoelectrons, in coincidence and as a function of time, permitting direct Molecular Frame imaging of valence electronic dynamics during a molecular dynamics. Phase: Using intermediate strength non-perturbative interactions, we apply the second order (polarizability) Non-Resonant Dynamic Stark Effect (NRDSE) to control molecular dynamics without any net absorption of light. NRDSE is also the interaction underlying molecular alignment and applies to field-free 1D of linear molecules and field-free 3D alignment of general (asymmetric) molecules. Using laser alignment, we can transiently fix a molecule in space, yielding a more general approach to direct Molecular Frame imaging of valence electronic dynamics during a chemical reaction. Intensity: In strong (ionizing) laser fields, a new laser-matter physics emerges for polyatomic systems wherein both the single active electron picture and the adiabatic electron response, both implicit in the standard 3-step models, can fail dramatically. This has important consequences for all attosecond strong field spectroscopies of polyatomic molecules, including high harmonic generation (HHG). We discuss an experimental method, Channel-Resolved Above Threshold Ionization (CRATI), which directly unveils the electronic channels participating in the attosecond molecular strong field ionization response [10]. This work was supported by the National Research Council of Canada and the Natural Sciences & Engineering Research Council.

An Accurate Scalable Template-based Alignment Algorithm

PubMed Central

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

2013-01-01

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

Energy Partitioning and Impulse Dispersion in the Decorated, Tapered, Strongly Nonlinear Granular Alignment: A System with Many Potential Applications

DTIC Science & Technology

2010-03-01

finally discuss some preliminary experimental results using systems with chrome spheres and small Nitinol interstitial grains to present the... Nitinol interstitial grains to present the underlying nonlinear dynamics of this so-called decorated tapered granular alignment. We are specifically...second was the DTC setup. In this case, small Nitinol 2.38 mm diameter particles were in- troduced between the main STC particles so that NDTC=9. 53 The

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

PubMed

Martínez, Leandro

2015-01-01

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

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

PubMed Central

Martínez, Leandro

2015-01-01

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

No condylar lift-off occurs because of excessive lateral soft tissue laxity in neutrally aligned total knee arthroplasty: a computer simulation study.

PubMed

Kuriyama, Shinichi; Ishikawa, Masahiro; Nakamura, Shinichiro; Furu, Moritoshi; Ito, Hiromu; Matsuda, Shuichi

2016-08-01

Condylar lift-off can induce excessive polyethylene wear after total knee arthroplasty (TKA). A computer simulation was used to evaluate the influence of femoral varus alignment and lateral collateral ligament (LCL) laxity on lift-off after single-design TKA. It was hypothesised that proper ligament balancing and coronal alignment would prevent lift-off. The computer model in this study is a dynamic musculoskeletal program that simulates gait up to 60° of knee flexion. The lift-off phenomenon was defined as positive with an intercomponent distance of >2 mm. In neutrally aligned components in the coronal plane, the femoral and tibial components were set perpendicular to the femoral and tibial mechanical axis, respectively. The femoral coronal alignment was changed from neutral to 5° varus in 1° increments. Simultaneously, the LCL length was elongated from 0 to 5 mm in 1-mm increments to provide a model of pathological slack. Within 2° of femoral varus alignment, lift-off did not occur even if the LCL was elongated by up to 5 mm. However, lift-off occurred easily in the stance phase in femoral varus alignments of >3° with slight LCL slack. The contact forces of the tibiofemoral joint were influenced more by femoral varus alignment than by LCL laxity. Aiming for neutral alignment in severely varus knees makes it difficult to achieve appropriate ligament balance. Our study suggests that no lift-off occurs with excessive LCL laxity alone in a neutrally aligned TKA and therefore that varus alignment should be avoided to decrease lift-off after TKA. Case series, Level IV.

A discrete particle model reproducing collective dynamics of a bee swarm.

PubMed

Bernardi, Sara; Colombi, Annachiara; Scianna, Marco

2018-02-01

In this article, we present a microscopic discrete mathematical model describing collective dynamics of a bee swarm. More specifically, each bee is set to move according to individual strategies and social interactions, the former involving the desire to reach a target destination, the latter accounting for repulsive/attractive stimuli and for alignment processes. The insects tend in fact to remain sufficiently close to the rest of the population, while avoiding collisions, and they are able to track and synchronize their movement to the flight of a given set of neighbors within their visual field. The resulting collective behavior of the bee cloud therefore emerges from non-local short/long-range interactions. Differently from similar approaches present in the literature, we here test different alignment mechanisms (i.e., based either on an Euclidean or on a topological neighborhood metric), which have an impact also on the other social components characterizing insect behavior. A series of numerical realizations then shows the phenomenology of the swarm (in terms of pattern configuration, collective productive movement, and flight synchronization) in different regions of the space of free model parameters (i.e., strength of attractive/repulsive forces, extension of the interaction regions). In this respect, constraints in the possible variations of such coefficients are here given both by reasonable empirical observations and by analytical results on some stability characteristics of the defined pairwise interaction kernels, which have to assure a realistic crystalline configuration of the swarm. An analysis of the effect of unconscious random fluctuations of bee dynamics is also provided. Copyright © 2018 Elsevier Ltd. All rights reserved.

A coupled duration-focused architecture for real-time music-to-score alignment.

PubMed

Cont, Arshia

2010-06-01

The capacity for real-time synchronization and coordination is a common ability among trained musicians performing a music score that presents an interesting challenge for machine intelligence. Compared to speech recognition, which has influenced many music information retrieval systems, music's temporal dynamics and complexity pose challenging problems to common approximations regarding time modeling of data streams. In this paper, we propose a design for a real-time music-to-score alignment system. Given a live recording of a musician playing a music score, the system is capable of following the musician in real time within the score and decoding the tempo (or pace) of its performance. The proposed design features two coupled audio and tempo agents within a unique probabilistic inference framework that adaptively updates its parameters based on the real-time context. Online decoding is achieved through the collaboration of the coupled agents in a Hidden Hybrid Markov/semi-Markov framework, where prediction feedback of one agent affects the behavior of the other. We perform evaluations for both real-time alignment and the proposed temporal model. An implementation of the presented system has been widely used in real concert situations worldwide and the readers are encouraged to access the actual system and experiment the results.

Active Brownian particles with velocity-alignment and active fluctuations

NASA Astrophysics Data System (ADS)

Großmann, R.; Schimansky-Geier, L.; Romanczuk, P.

2012-07-01

We consider a model of active Brownian particles (ABPs) with velocity alignment in two spatial dimensions with passive and active fluctuations. Here, active fluctuations refers to purely non-equilibrium stochastic forces correlated with the heading of an individual active particle. In the simplest case studied here, they are assumed to be independent stochastic forces parallel (speed noise) and perpendicular (angular noise) to the velocity of the particle. On the other hand, passive fluctuations are defined by a noise vector independent of the direction of motion of a particle, and may account, for example, for thermal fluctuations. We derive a macroscopic description of the ABP gas with velocity-alignment interaction. Here, we start from the individual-based description in terms of stochastic differential equations (Langevin equations) and derive equations of motion for the coarse-grained kinetic variables (density, velocity and temperature) via a moment expansion of the corresponding probability density function. We focus here on the different impact of active and passive fluctuations on onset of collective motion and show how active fluctuations in the active Brownian dynamics can change the phase-transition behaviour of the system. In particular, we show that active angular fluctuations lead to an earlier breakdown of collective motion and to the emergence of a new bistable regime in the mean-field case.

Spatio-temporal alignment of multiple sensors

NASA Astrophysics Data System (ADS)

Zhang, Tinghua; Ni, Guoqiang; Fan, Guihua; Sun, Huayan; Yang, Biao

2018-01-01

Aiming to achieve the spatio-temporal alignment of multi sensor on the same platform for space target observation, a joint spatio-temporal alignment method is proposed. To calibrate the parameters and measure the attitude of cameras, an astronomical calibration method is proposed based on star chart simulation and collinear invariant features of quadrilateral diagonal between the observed star chart. In order to satisfy a temporal correspondence and spatial alignment similarity simultaneously, the method based on the astronomical calibration and attitude measurement in this paper formulates the video alignment to fold the spatial and temporal alignment into a joint alignment framework. The advantage of this method is reinforced by exploiting the similarities and prior knowledge of velocity vector field between adjacent frames, which is calculated by the SIFT Flow algorithm. The proposed method provides the highest spatio-temporal alignment accuracy compared to the state-of-the-art methods on sequences recorded from multi sensor at different times.

Spatial and Temporal Dynamics and Value of Nature-Based Recreation, Estimated via Social Media.

PubMed

Sonter, Laura J; Watson, Keri B; Wood, Spencer A; Ricketts, Taylor H

2016-01-01

Conserved lands provide multiple ecosystem services, including opportunities for nature-based recreation. Managing this service requires understanding the landscape attributes underpinning its provision, and how changes in land management affect its contribution to human wellbeing over time. However, evidence from both spatially explicit and temporally dynamic analyses is scarce, often due to data limitations. In this study, we investigated nature-based recreation within conserved lands in Vermont, USA. We used geotagged photographs uploaded to the photo-sharing website Flickr to quantify visits by in-state and out-of-state visitors, and we multiplied visits by mean trip expenditures to show that conserved lands contributed US $1.8 billion (US $0.18-20.2 at 95% confidence) to Vermont's tourism industry between 2007 and 2014. We found eight landscape attributes explained the pattern of visits to conserved lands; visits were higher in larger conserved lands, with less forest cover, greater trail density and more opportunities for snow sports. Some of these attributes differed from those found in other locations, but all aligned with our understanding of recreation in Vermont. We also found that using temporally static models to inform conservation decisions may have perverse outcomes for nature-based recreation. For example, static models suggest conserved land with less forest cover receive more visits, but temporally dynamic models suggest clearing forests decreases, rather than increases, visits to these sites. Our results illustrate the importance of understanding both the spatial and temporal dynamics of ecosystem services for conservation decision-making.

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.

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

PubMed

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

2015-11-01

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

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

PubMed Central

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

2015-01-01

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

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

NASA Astrophysics Data System (ADS)

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

1999-01-01

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

Directed branch growth in aligned nanowire arrays.

PubMed

Beaudry, Allan L; LaForge, Joshua M; Tucker, Ryan T; Sorge, Jason B; Adamski, Nicholas L; Li, Peng; Taschuk, Michael T; Brett, Michael J

2014-01-01

Branch growth is directed along two, three, or four in-plane directions in vertically aligned nanowire arrays using vapor-liquid-solid glancing angle deposition (VLS-GLAD) flux engineering. In this work, a dynamically controlled collimated vapor flux guides branch placement during the self-catalyzed epitaxial growth of branched indium tin oxide nanowire arrays. The flux is positioned to grow branches on select nanowire facets, enabling fabrication of aligned nanotree arrays with L-, T-, or X-branching. In addition, a flux motion algorithm is designed to selectively elongate branches along one in-plane axis. Nanotrees are found to be aligned across large areas by X-ray diffraction pole figure analysis and through branch length and orientation measurements collected over 140 μm(2) from scanning electron microscopy images for each array. The pathway to guided assembly of nanowire architectures with controlled interconnectivity in three-dimensions using VLS-GLAD is discussed.

Dynamics of Cancer Cell near Collagen Fiber Chain

NASA Astrophysics Data System (ADS)

Kim, Jihan; Sun, Bo

Cell migration is an integrated process that is important in life. Migration is essential for embryonic development as well as homeostatic processes such as wound healing and immune responses. When cell migrates through connective extracellular matrix (ECM), it applies cellular traction force to ECM and senses the rigidity of their local environment. We used human breast cancer cell (MDA-MB-231) which is highly invasive and applies strong traction force to ECM. As cancer cell applies traction force to type I collage-based ECM, it deforms collagen fibers near the surface. Patterns of deforming collagen fibers are significantly different with pairs of cancer cells compared to a single cancer cell. While a pair of cancer cells within 60 um creates aligned collagen fiber chains between them permanently, a single cancer cell does not form any fiber chains. In this experiment we measured a cellular response and an interaction between a pair of cells through the chain. Finally, we analyzed correlation of directions between cancer cell migration and the collagen chain alignment.

Time delay and integration array (TDI) using charge transfer device technology. Phase 2, volume 1: Technical

NASA Technical Reports Server (NTRS)

1977-01-01

The 20x9 TDI array was developed to meet the LANDSAT Thematic Mapper Requirements. This array is based upon a self-aligned, transparent gate, buried channel process. The process features: (1) buried channel, four phase, overlapping gate CCD's for high transfer efficiency without fat zero; (2) self-aligned transistors to minimize clock feedthrough and parasitic capacitance; and (3) transparent tin oxide electrode for high quantum efficiency with front surface irradiation. The requirements placed on the array and the performance achieved are summarized. This data is the result of flat field measurements only, no imaging or dynamic target measurements were made during this program. Measurements were performed with two different test stands. The bench test equipment fabricated for this program operated at the 8 micro sec line time and employed simple sampling of the gated MOSFET output video signal. The second stand employed Correlated Doubled Sampling (CDS) and operated at 79.2 micro sec line time.

Currents and Associated Electron Scattering and Bouncing Near the Diffusion Region at Earth's Magnetopause

NASA Technical Reports Server (NTRS)

Lavraud, B.; Zhang, Y. C.; Vernisse, Y.; Gershman, D. J.; Dorelli, J.; Cassak, P. A.; Dargent, J.; Pollock, C.; Giles, B.; Aunai, N.;

Recapitulating phylogenies using k-mers: from trees to networks.

PubMed

Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

Optimal network alignment with graphlet degree vectors.

PubMed

Milenković, Tijana; Ng, Weng Leong; Hayes, Wayne; Przulj, Natasa

2010-06-30

Important biological information is encoded in the topology of biological networks. Comparative analyses of biological networks are proving to be valuable, as they can lead to transfer of knowledge between species and give deeper insights into biological function, disease, and evolution. We introduce a new method that uses the Hungarian algorithm to produce optimal global alignment between two networks using any cost function. We design a cost function based solely on network topology and use it in our network alignment. Our method can be applied to any two networks, not just biological ones, since it is based only on network topology. We use our new method to align protein-protein interaction networks of two eukaryotic species and demonstrate that our alignment exposes large and topologically complex regions of network similarity. At the same time, our alignment is biologically valid, since many of the aligned protein pairs perform the same biological function. From the alignment, we predict function of yet unannotated proteins, many of which we validate in the literature. Also, we apply our method to find topological similarities between metabolic networks of different species and build phylogenetic trees based on our network alignment score. The phylogenetic trees obtained in this way bear a striking resemblance to the ones obtained by sequence alignments. Our method detects topologically similar regions in large networks that are statistically significant. It does this independent of protein sequence or any other information external to network topology.

Controlling Disorder by Electric Field Directed Reconfiguration of Nanowires to Tune Random Lasing.

PubMed

Donahue, Philip P; Zhang, Chenji; Nye, Nicholas; Miller, Jennifer; Wang, Cheng-Yu; Tang, Rong; Christodoulides, Demetrios; Keating, Christine D; Liu, Zhiwen

2018-06-27

Top-down fabrication is commonly used to provide positioning control of optical structures; yet, it places stringent limitations on component materials and oftentimes, dynamic reconfigurability is challenging to realize. Here we present a reconfigurable nanoparticle platform that can integrate heterogeneous particle assembly of different shapes, sizes, and material compositions. We demonstrate dynamic manipulation of disorder in this platform and use it to controllably enhance or frustrate random laser emission for a suspension of titanium dioxide nanowires in a dye solution. Using an alternating current electric field, we control the nanowire orientation to dynamically control the collective scattering of the sample and thus light confinement. Our theoretical model indicates that an increase of 22% in scattering coefficient can be achieved for the experimentally determined nanowire length distribution upon alignment. As a result, a nearly 20-fold enhancement in lasing intensity was achieved. We illustrate the generality of the approach by demonstrating enhanced lasing for aligned nanowires of other materials including gold, mixed gold/dielectric and vanadium oxide (VxOy).

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.

The Saccharomyces Genome Database Variant Viewer

PubMed Central

Sheppard, Travis K.; Hitz, Benjamin C.; Engel, Stacia R.; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C.; Dalusag, Kyla S.; Demeter, Janos; Hellerstedt, Sage T.; Karra, Kalpana; Nash, Robert S.; Paskov, Kelley M.; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Cherry, J. Michael

2016-01-01

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. PMID:26578556

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.

Text-image alignment for historical handwritten documents

NASA Astrophysics Data System (ADS)

Zinger, S.; Nerbonne, J.; Schomaker, L.

2009-01-01

We describe our work on text-image alignment in context of building a historical document retrieval system. We aim at aligning images of words in handwritten lines with their text transcriptions. The images of handwritten lines are automatically segmented from the scanned pages of historical documents and then manually transcribed. To train automatic routines to detect words in an image of handwritten text, we need a training set - images of words with their transcriptions. We present our results on aligning words from the images of handwritten lines and their corresponding text transcriptions. Alignment based on the longest spaces between portions of handwriting is a baseline. We then show that relative lengths, i.e. proportions of words in their lines, can be used to improve the alignment results considerably. To take into account the relative word length, we define the expressions for the cost function that has to be minimized for aligning text words with their images. We apply right to left alignment as well as alignment based on exhaustive search. The quality assessment of these alignments shows correct results for 69% of words from 100 lines, or 90% of partially correct and correct alignments combined.

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

Controllable 3D architectures of aligned carbon nanotube arrays by multi-step processes

NASA Astrophysics Data System (ADS)

Huang, Shaoming

2003-06-01

An effective way to fabricate large area three-dimensional (3D) aligned CNTs pattern based on pyrolysis of iron(II) phthalocyanine (FePc) by two-step processes is reported. The controllable generation of different lengths and selective growth of the aligned CNT arrays on metal-patterned (e.g., Ag and Au) substrate are the bases for generating such 3D aligned CNTs architectures. By controlling experimental conditions 3D aligned CNT arrays with different lengths/densities and morphologies/structures as well as multi-layered architectures can be fabricated in large scale by multi-step pyrolysis of FePc. These 3D architectures could have interesting properties and be applied for developing novel nanotube-based devices.

A Novel Center Star Multiple Sequence Alignment Algorithm Based on Affine Gap Penalty and K-Band

NASA Astrophysics Data System (ADS)

Zou, Quan; Shan, Xiao; Jiang, Yi

Multiple sequence alignment is one of the most important topics in computational biology, but it cannot deal with the large data so far. As the development of copy-number variant(CNV) and Single Nucleotide Polymorphisms(SNP) research, many researchers want to align numbers of similar sequences for detecting CNV and SNP. In this paper, we propose a novel multiple sequence alignment algorithm based on affine gap penalty and k-band. It can align more quickly and accurately, that will be helpful for mining CNV and SNP. Experiments prove the performance of our algorithm.

An electrical bio-chip to transfer and detect electromagnetic stimulation on the cells based on vertically aligned carbon nanotubes.

PubMed

Rafizadeh-Tafti, Saeed; Haqiqatkhah, Mohammad Hossein; Saviz, Mehrdad; Janmaleki, Mohsen; Faraji Dana, Reza; Zanganeh, Somayeh; Abdolahad, Mohammad

2017-01-01

A highly sensitive impedimetric bio-chip based on vertically aligned multiwall carbon nanotubes (VAMWCNTs), was applied in direct interaction with lung cancer cells. Our tool provided both inducing and monitoring the bioelectrical changes in the cells initiated by electromagnetic (EM) wave stimulation. EM wave of 940MHz frequency with different intensities was used. Here, wave ablation might accumulate electrical charge on the tips of nanotubes penetrated into cell's membrane. The charge might induce ionic exchanges into the cell and cause alterations in electrical states of the membrane. Transmembrane electrostatic/dynamic states would be strongly affected due to such exchanges. Our novel modality was that, the cells' vitality changes caused by charge inductions were electrically detected with the same nanotubes in the architecture of electrodes for impedance measurement. The responses of the sensor were confirmed by electron and florescent microscopy images as well as biological assays. In summation, our method provided an effective biochip for enhancing and detecting external EM stimulation on the cells useful for future diagnostic and therapeutic applications, such as wave-guided drug-resistance breakage. Copyright © 2016 Elsevier B.V. All rights reserved.

Chunk Alignment for Corpus-Based Machine Translation

ERIC Educational Resources Information Center

Kim, Jae Dong

2011-01-01

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

Fine-tuning structural RNA alignments in the twilight zone.

PubMed

Bremges, Andreas; Schirmer, Stefanie; Giegerich, Robert

2010-04-30

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

EAPhy: A Flexible Tool for High-throughput Quality Filtering of Exon-alignments and Data Processing for Phylogenetic Methods.

PubMed

Blom, Mozes P K

2015-08-05

Recently developed molecular methods enable geneticists to target and sequence thousands of orthologous loci and infer evolutionary relationships across the tree of life. Large numbers of genetic markers benefit species tree inference but visual inspection of alignment quality, as traditionally conducted, is challenging with thousands of loci. Furthermore, due to the impracticality of repeated visual inspection with alternative filtering criteria, the potential consequences of using datasets with different degrees of missing data remain nominally explored in most empirical phylogenomic studies. In this short communication, I describe a flexible high-throughput pipeline designed to assess alignment quality and filter exonic sequence data for subsequent inference. The stringency criteria for alignment quality and missing data can be adapted based on the expected level of sequence divergence. Each alignment is automatically evaluated based on the stringency criteria specified, significantly reducing the number of alignments that require visual inspection. By developing a rapid method for alignment filtering and quality assessment, the consistency of phylogenetic estimation based on exonic sequence alignments can be further explored across distinct inference methods, while accounting for different degrees of missing data.

Construction of a stochastic model of track geometry irregularities and validation through experimental measurements of dynamic loading

NASA Astrophysics Data System (ADS)

Panunzio, Alfonso M.; Puel, G.; Cottereau, R.; Simon, S.; Quost, X.

2017-03-01

This paper describes the construction of a stochastic model of urban railway track geometry irregularities, based on experimental data. The considered irregularities are track gauge, superelevation, horizontal and vertical curvatures. They are modelled as random fields whose statistical properties are extracted from a large set of on-track measurements of the geometry of an urban railway network. About 300-1000 terms are used in the Karhunen-Loève/Polynomial Chaos expansions to represent the random fields with appropriate accuracy. The construction of the random fields is then validated by comparing on-track measurements of the contact forces and numerical dynamics simulations for different operational conditions (train velocity and car load) and horizontal layouts (alignment, curve). The dynamics simulations are performed both with and without randomly generated geometrical irregularities for the track. The power spectrum densities obtained from the dynamics simulations with the model of geometrical irregularities compare extremely well with those obtained from the experimental contact forces. Without irregularities, the spectrum is 10-50 dB too low.

Efficient Agent-Based Models for Non-Genomic Evolution

NASA Technical Reports Server (NTRS)

Gupta, Nachi; Agogino, Adrian; Tumer, Kagan

2006-01-01

Modeling dynamical systems composed of aggregations of primitive proteins is critical to the field of astrobiological science involving early evolutionary structures and the origins of life. Unfortunately traditional non-multi-agent methods either require oversimplified models or are slow to converge to adequate solutions. This paper shows how to address these deficiencies by modeling the protein aggregations through a utility based multi-agent system. In this method each agent controls the properties of a set of proteins assigned to that agent. Some of these properties determine the dynamics of the system, such as the ability for some proteins to join or split other proteins, while additional properties determine the aggregation s fitness as a viable primitive cell. We show that over a wide range of starting conditions, there are mechanisins that allow protein aggregations to achieve high values of overall fitness. In addition through the use of agent-specific utilities that remain aligned with the overall global utility, we are able to reach these conclusions with 50 times fewer learning steps.

Feature Based Retention Time Alignment for Improved HDX MS Analysis

NASA Astrophysics Data System (ADS)

Venable, John D.; Scuba, William; Brock, Ansgar

2013-04-01

An algorithm for retention time alignment of mass shifted hydrogen-deuterium exchange (HDX) data based on an iterative distance minimization procedure is described. The algorithm performs pairwise comparisons in an iterative fashion between a list of features from a reference file and a file to be time aligned to calculate a retention time mapping function. Features are characterized by their charge, retention time and mass of the monoisotopic peak. The algorithm is able to align datasets with mass shifted features, which is a prerequisite for aligning hydrogen-deuterium exchange mass spectrometry datasets. Confidence assignments from the fully automated processing of a commercial HDX software package are shown to benefit significantly from retention time alignment prior to extraction of deuterium incorporation values.

Non-thermal emission and dynamical state of massive galaxy clusters from CLASH sample

NASA Astrophysics Data System (ADS)

Pandey-Pommier, M.; Richard, J.; Combes, F.; Edge, A.; Guiderdoni, B.; Narasimha, D.; Bagchi, J.; Jacob, J.

2016-12-01

Massive galaxy clusters are the most violent large scale structures undergoing merger events in the Universe. Based upon their morphological properties in X-rays, they are classified as un-relaxed and relaxed clusters and often host (a fraction of them) different types of non-thermal radio emitting components, viz., 'haloes', 'mini-haloes', 'relics' and 'phoenix' within their Intra Cluster Medium (ICM). The radio haloes show steep (α = -1.2) and ultra steep (α < -1.5) spectral properties at low radio frequencies, giving important insights on the merger (pre or post) state of the cluster. Ultra steep spectrum radio halo emissions are rare and expected to be the dominating population to be discovered via LOFAR and SKA in the future. Further, the distribution of matter (morphological information), alignment of hot X-ray emitting gas from the ICM with the total mass (dark + baryonic matter) and the bright cluster galaxy (BCG) is generally used to study the dynamical state of the cluster. We present here a multi wavelength study on 14 massive clusters from the CLASH survey and show the correlation between the state of their merger in X-ray and spectral properties (1.4 GHz - 150 MHz) at radio wavelengths. Using the optical data we also discuss about the gas-mass alignment, in order to understand the interplay between dark and baryonic matter in massive galaxy clusters.

Morphologies of omega band auroras

NASA Astrophysics Data System (ADS)

Sato, Natsuo; Yukimatu, Akira Sessai; Tanaka, Yoshimasa; Hori, Tomoaki

2017-08-01

We examined the morphological signatures of 315 omega band aurora events observed using the Time History of Events and Macroscale Interactions during Substorm ground-based all-sky imager network over a period of 8 years. We find that omega bands can be classified into the following three subtypes: (1) classical (O-type) omega bands, (2) torch or tongue (T-type) omega bands, and (3) combinations of classical and torch or tongue (O/T-type) omega bands. The statistical results show that T-type bands occur the most frequently (45%), followed by O/T-type bands (35%) and O-type bands (18%). We also examined the morphologies of the omega bands during their formation, from the growth period to the declining period through the maximum period. Interestingly, the omega bands are not stable, but rather exhibit dynamic changes in shape, intensity, and motion. They grow from small-scale bumps (seeds) at the poleward boundary of preexisting east-west-aligned auroras, rather than via the rotation or shear motion of preexisting east-west-aligned auroras, and do not exhibit any shear motion during the periods of auroral activity growth. Furthermore, the auroral luminosity is observed to increase during the declining period, and the total time from the start of the growth period to the end of the declining period is found to be about 20 min. Such dynamical signatures may be important in determining the mechanism responsible for omega band formation.

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

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

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

Learning a Mahalanobis Distance-Based Dynamic Time Warping Measure for Multivariate Time Series Classification.

PubMed

Mei, Jiangyuan; Liu, Meizhu; Wang, Yuan-Fang; Gao, Huijun

2016-06-01

Multivariate time series (MTS) datasets broadly exist in numerous fields, including health care, multimedia, finance, and biometrics. How to classify MTS accurately has become a hot research topic since it is an important element in many computer vision and pattern recognition applications. In this paper, we propose a Mahalanobis distance-based dynamic time warping (DTW) measure for MTS classification. The Mahalanobis distance builds an accurate relationship between each variable and its corresponding category. It is utilized to calculate the local distance between vectors in MTS. Then we use DTW to align those MTS which are out of synchronization or with different lengths. After that, how to learn an accurate Mahalanobis distance function becomes another key problem. This paper establishes a LogDet divergence-based metric learning with triplet constraint model which can learn Mahalanobis matrix with high precision and robustness. Furthermore, the proposed method is applied on nine MTS datasets selected from the University of California, Irvine machine learning repository and Robert T. Olszewski's homepage, and the results demonstrate the improved performance of the proposed approach.

Dynamic Locked Plating of Distal Femur Fractures.

PubMed

Linn, Michael S; McAndrew, Christopher M; Prusaczyk, Beth; Brimmo, Olubusola; Ricci, William M; Gardner, Michael J

2015-10-01

Nonunion after locked bridge plating of comminuted distal femur fractures is not uncommon. "Dynamic" locked plating may create an improved mechanical environment, thereby achieving higher union rates than standard locked plating constructs. Academic Level 1 Trauma Center. Twenty-eight patients with comminuted supracondylar femur fractures treated with either dynamic or standard locked plating. Dynamic plating was achieved using an overdrilling technique of the near cortex to allow for a 0.5-mm "halo" around the screw shaft at the near cortex. Standard locked plating was done based on manufacturer's suggested technique. The patients treated with dynamic plating were matched 1:1 with those treated with standard locked plating based on OTA classification and working length. Three blinded observers made callus measurements on 6-week radiographs using a 4-point ordinal scale. The results were analyzed using a 2-tailed t test and 2-way intraclass correlations. The dynamic plating group had significantly greater callus (2.0; SD, 0.7) compared with the control group (1.3: SD, 0.8, P = 0.048) with substantial agreement amongst observers in both consistency (0.724) and absolute score (0.734). With dynamic plating group, 1 patient failed to unite, versus three in the control group (P = 0.59). The dynamic group had a mean change in coronal plane alignment of 0.5 degrees (SD, 2.6) compared with 0.6 (SD, 3.0) for the control group (P = 0.9) without fixation failure in either group. Overdrilling the near cortex in metaphyseal bridge plating can be adapted to standard implants to create a dynamic construct and increase axial motion. This technique seems to be safe and leads to increased callus formation, which may decrease nonunion rates seen with standard locked plating. Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

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.

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

PubMed

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

2009-07-01

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

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.

Seeing the Song: Left Auditory Structures May Track Auditory-Visual Dynamic Alignment

PubMed Central

Mossbridge, Julia A.; Grabowecky, Marcia; Suzuki, Satoru

2013-01-01

Auditory and visual signals generated by a single source tend to be temporally correlated, such as the synchronous sounds of footsteps and the limb movements of a walker. Continuous tracking and comparison of the dynamics of auditory-visual streams is thus useful for the perceptual binding of information arising from a common source. Although language-related mechanisms have been implicated in the tracking of speech-related auditory-visual signals (e.g., speech sounds and lip movements), it is not well known what sensory mechanisms generally track ongoing auditory-visual synchrony for non-speech signals in a complex auditory-visual environment. To begin to address this question, we used music and visual displays that varied in the dynamics of multiple features (e.g., auditory loudness and pitch; visual luminance, color, size, motion, and organization) across multiple time scales. Auditory activity (monitored using auditory steady-state responses, ASSR) was selectively reduced in the left hemisphere when the music and dynamic visual displays were temporally misaligned. Importantly, ASSR was not affected when attentional engagement with the music was reduced, or when visual displays presented dynamics clearly dissimilar to the music. These results appear to suggest that left-lateralized auditory mechanisms are sensitive to auditory-visual temporal alignment, but perhaps only when the dynamics of auditory and visual streams are similar. These mechanisms may contribute to correct auditory-visual binding in a busy sensory environment. PMID:24194873

Low-energy spectral features of supernova (anti)neutrinos in inverted hierarchy

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

Fogli, G. L.; Marrone, A.; Tamborra, I.

2008-11-01

In the dense supernova core, self-interactions may align the flavor polarization vectors of {nu} and {nu} and induce collective flavor transformations. Different alignment Ansaetze are known to describe approximately the phenomena of synchronized or bipolar oscillations and the split of {nu} energy spectra. We discuss another phenomenon observed in some numerical experiments in inverted hierarchy, showing features akin to a low-energy split of {nu} spectra. The phenomenon appears to be approximately described by another alignment Ansatz which, in the considered scenario, reduces the (nonadiabatic) dynamics of all energy modes to only two {nu} plus two {nu} modes. The associated spectralmore » features, however, appear to be fragile when passing from single to multiangle simulations.« less

Influence of repulsion zone in the directional alignment of self-propelled particles

NASA Astrophysics Data System (ADS)

Cambui, Dorilson

2014-04-01

Collective behavior in animal groups such as schools of fish, swarms of insects or flocks of birds, although a phenomenon widely studied in biological systems, is subject of great interdisciplinary interest. An important tool to describe the dynamics of collective motion and ordered live organisms is the concept of self-propelled particles. Proposed by Vicsek and collaborators, it was considered in this model only as an (single) interaction rule, set as alignment, where particles align to motion the nearest neighbors. In this paper, we have considered a variant of this model by adding a second rule called repulsion zone, where particles repel each other at short distances, in order to investigate the influence of this zone on directional order of the particles.

Learning-based deformable image registration for infant MR images in the first year of life.

PubMed

Hu, Shunbo; Wei, Lifang; Gao, Yaozong; Guo, Yanrong; Wu, Guorong; Shen, Dinggang

2017-01-01

Many brain development studies have been devoted to investigate dynamic structural and functional changes in the first year of life. To quantitatively measure brain development in such a dynamic period, accurate image registration for different infant subjects with possible large age gap is of high demand. Although many state-of-the-art image registration methods have been proposed for young and elderly brain images, very few registration methods work for infant brain images acquired in the first year of life, because of (a) large anatomical changes due to fast brain development and (b) dynamic appearance changes due to white-matter myelination. To address these two difficulties, we propose a learning-based registration method to not only align the anatomical structures but also alleviate the appearance differences between two arbitrary infant MR images (with large age gap) by leveraging the regression forest to predict both the initial displacement vector and appearance changes. Specifically, in the training stage, two regression models are trained separately, with (a) one model learning the relationship between local image appearance (of one development phase) and its displacement toward the template (of another development phase) and (b) another model learning the local appearance changes between the two brain development phases. Then, in the testing stage, to register a new infant image to the template, we first predict both its voxel-wise displacement and appearance changes by the two learned regression models. Since such initializations can alleviate significant appearance and shape differences between new infant image and the template, it is easy to just use a conventional registration method to refine the remaining registration. We apply our proposed registration method to align 24 infant subjects at five different time points (i.e., 2-week-old, 3-month-old, 6-month-old, 9-month-old, and 12-month-old), and achieve more accurate and robust registration results, compared to the state-of-the-art registration methods. The proposed learning-based registration method addresses the challenging task of registering infant brain images and achieves higher registration accuracy compared with other counterpart registration methods. © 2016 American Association of Physicists in Medicine.

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

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

PubMed Central

Lee, Hui Sun; Im, Wonpil

2013-01-01

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

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

ERIC Educational Resources Information Center

Morton, Christopher

2013-01-01

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

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

Accelerating Large Data Analysis By Exploiting Regularities

NASA Technical Reports Server (NTRS)

Moran, Patrick J.; Ellsworth, David

2003-01-01

We present techniques for discovering and exploiting regularity in large curvilinear data sets. The data can be based on a single mesh or a mesh composed of multiple submeshes (also known as zones). Multi-zone data are typical to Computational Fluid Dynamics (CFD) simulations. Regularities include axis-aligned rectilinear and cylindrical meshes as well as cases where one zone is equivalent to a rigid-body transformation of another. Our algorithms can also discover rigid-body motion of meshes in time-series data. Next, we describe a data model where we can utilize the results from the discovery process in order to accelerate large data visualizations. Where possible, we replace general curvilinear zones with rectilinear or cylindrical zones. In rigid-body motion cases we replace a time-series of meshes with a transformed mesh object where a reference mesh is dynamically transformed based on a given time value in order to satisfy geometry requests, on demand. The data model enables us to make these substitutions and dynamic transformations transparently with respect to the visualization algorithms. We present results with large data sets where we combine our mesh replacement and transformation techniques with out-of-core paging in order to achieve significant speed-ups in analysis.

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.

Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

NASA Astrophysics Data System (ADS)

van Eijck, L.; Merzel, F.; Rols, S.; Ollivier, J.; Forsyth, V. T.; Johnson, M. R.

2011-08-01

Quantifying the molecular elasticity of DNA is fundamental to our understanding of its biological functions. Recently different groups, through experiments on tailored DNA samples and numerical models, have reported a range of stretching force constants (0.3 to 3N/m). However, the most direct, microscopic measurement of DNA stiffness is obtained from the dispersion of its vibrations. A new neutron scattering spectrometer and aligned, wet spun samples have enabled such measurements, which provide the first data of collective excitations of DNA and yield a force constant of 83N/m. Structural and dynamic order persists unchanged to within 15 K of the melting point of the sample, precluding the formation of bubbles. These findings are supported by large scale phonon and molecular dynamics calculations, which reconcile hard and soft force constants.

Automated movement correction for dynamic PET/CT images: evaluation with phantom and patient data.

PubMed

Ye, Hu; Wong, Koon-Pong; Wardak, Mirwais; Dahlbom, Magnus; Kepe, Vladimir; Barrio, Jorge R; Nelson, Linda D; Small, Gary W; Huang, Sung-Cheng

2014-01-01

Head movement during a dynamic brain PET/CT imaging results in mismatch between CT and dynamic PET images. It can cause artifacts in CT-based attenuation corrected PET images, thus affecting both the qualitative and quantitative aspects of the dynamic PET images and the derived parametric images. In this study, we developed an automated retrospective image-based movement correction (MC) procedure. The MC method first registered the CT image to each dynamic PET frames, then re-reconstructed the PET frames with CT-based attenuation correction, and finally re-aligned all the PET frames to the same position. We evaluated the MC method's performance on the Hoffman phantom and dynamic FDDNP and FDG PET/CT images of patients with neurodegenerative disease or with poor compliance. Dynamic FDDNP PET/CT images (65 min) were obtained from 12 patients and dynamic FDG PET/CT images (60 min) were obtained from 6 patients. Logan analysis with cerebellum as the reference region was used to generate regional distribution volume ratio (DVR) for FDDNP scan before and after MC. For FDG studies, the image derived input function was used to generate parametric image of FDG uptake constant (Ki) before and after MC. Phantom study showed high accuracy of registration between PET and CT and improved PET images after MC. In patient study, head movement was observed in all subjects, especially in late PET frames with an average displacement of 6.92 mm. The z-direction translation (average maximum = 5.32 mm) and x-axis rotation (average maximum = 5.19 degrees) occurred most frequently. Image artifacts were significantly diminished after MC. There were significant differences (P<0.05) in the FDDNP DVR and FDG Ki values in the parietal and temporal regions after MC. In conclusion, MC applied to dynamic brain FDDNP and FDG PET/CT scans could improve the qualitative and quantitative aspects of images of both tracers.

Automated Movement Correction for Dynamic PET/CT Images: Evaluation with Phantom and Patient Data

PubMed Central

Ye, Hu; Wong, Koon-Pong; Wardak, Mirwais; Dahlbom, Magnus; Kepe, Vladimir; Barrio, Jorge R.; Nelson, Linda D.; Small, Gary W.; Huang, Sung-Cheng

2014-01-01

Head movement during a dynamic brain PET/CT imaging results in mismatch between CT and dynamic PET images. It can cause artifacts in CT-based attenuation corrected PET images, thus affecting both the qualitative and quantitative aspects of the dynamic PET images and the derived parametric images. In this study, we developed an automated retrospective image-based movement correction (MC) procedure. The MC method first registered the CT image to each dynamic PET frames, then re-reconstructed the PET frames with CT-based attenuation correction, and finally re-aligned all the PET frames to the same position. We evaluated the MC method's performance on the Hoffman phantom and dynamic FDDNP and FDG PET/CT images of patients with neurodegenerative disease or with poor compliance. Dynamic FDDNP PET/CT images (65 min) were obtained from 12 patients and dynamic FDG PET/CT images (60 min) were obtained from 6 patients. Logan analysis with cerebellum as the reference region was used to generate regional distribution volume ratio (DVR) for FDDNP scan before and after MC. For FDG studies, the image derived input function was used to generate parametric image of FDG uptake constant (Ki) before and after MC. Phantom study showed high accuracy of registration between PET and CT and improved PET images after MC. In patient study, head movement was observed in all subjects, especially in late PET frames with an average displacement of 6.92 mm. The z-direction translation (average maximum = 5.32 mm) and x-axis rotation (average maximum = 5.19 degrees) occurred most frequently. Image artifacts were significantly diminished after MC. There were significant differences (P<0.05) in the FDDNP DVR and FDG Ki values in the parietal and temporal regions after MC. In conclusion, MC applied to dynamic brain FDDNP and FDG PET/CT scans could improve the qualitative and quantitative aspects of images of both tracers. PMID:25111700

Hydrological and dynamical characterization of Meddies in the Azores region: A paradigm for baroclinic vortex dynamics

NASA Astrophysics Data System (ADS)

Tychensky, A.; Carton, X.

1998-10-01

The Structure des Echanges Mer-Atmosphere, Proprietes des Heterogeneites Oceaniques: Recherche Expérimentale (SEMAPHORE) oceanographic experiment surveyed a 500 × 500 km2 domain south of the Azores from June to November 1993 and collected hydrological data, float trajectories, and current meter recordings. This data exhibited three intrathermocline eddies of Mediterranean water (Meddies), two of them being repeatedly sampled. Their hydrological and dynamical properties are quantified here by an isopycnic analysis. For the three Meddies, intense temperature and salinity anomalies (up to 4°C and 1.1 practical salinity units (psu)) are observed extending vertically over up to 1000 m and centered around 1000 m. Horizontally, these anomalies spread out to radii of 50-60 km, while the maximum azimuthal velocities (30 cm s-1, as computed by geostrophy) lie only at 35-40 km from the central axis. These Meddies followed curved trajectories, with drift velocities up to 7.5 cm s-1, under the influence of the neighboring mesoscale features (cyclonic vortices or Azores Current meanders). The three-dimensional structure of potential vorticity in and around these features evidences their complex interactions. Northwest of the domain, a Meddy was coupled to a subsurface anticyclone, forming an "aligned" vortex. It later interacted with the Azores Current, creating a large-amplitude northward meander by vertical alignment of vorticity. In the southeastern part of the domain, another Meddy was vertically aligned with an anticyclonic meander of the Azores Current and horizontally coupled with a cyclone of large vertical extent. These two features, as well as a small warm and salty fragment in their vicinity, seem to result from the southward crossing of the Meddy under the Azores Current. These observations illustrate previous theoretical studies of baroclinic vortex dynamics.

A bifractal nature of reticular patterns induced by oxygen plasma on polymer films

NASA Astrophysics Data System (ADS)

Bae, Junwan; Lee, I. J.

2015-05-01

Plasma etching was demonstrated to be a promising tool for generating self-organized nano-patterns on various commercial films. Unfortunately, dynamic scaling approach toward fundamental understanding of the formation and growth of the plasma-induced nano-structure has not always been straightforward. The temporal evolution of self-aligned nano-patterns may often evolve with an additional scale-invariance, which leads to breakdown of the well-established dynamic scaling law. The concept of a bifractal interface is successfully applied to reticular patterns induced by oxygen plasma on the surface of polymer films. The reticular pattern, composed of nano-size self-aligned protuberances and underlying structure, develops two types of anomalous dynamic scaling characterized by super-roughening and intrinsic anomalous scaling, respectively. The diffusion and aggregation of short-cleaved chains under the plasma environment are responsible for the regular distribution of the nano-size protuberances. Remarkably, it is uncovered that the dynamic roughening of the underlying structure is governed by a relaxation mechanism described by the Edwards-Wilkinson universality class with a conservative noise. The evidence for the basic phase, characterized by the negative roughness and growth exponents, has been elusive since its first theoretical consideration more than two decades ago.

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

PubMed

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

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

Cryo-EM Image Alignment Based on Nonuniform Fast Fourier Transform

PubMed Central

Yang, Zhengfan; Penczek, Pawel A.

2008-01-01

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

The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

PubMed

Chen, Wenbin; Hendrix, William; Samatova, Nagiza F

2017-12-01

The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem. In this article, we propose an algorithm for the problem of aligning multiple metabolic pathways based on the similarities among reactions, compounds, enzymes, and pathway topology. First, we compute a weight between each pair of like entities in different input pathways based on the entities' similarity score and topological structure using Ay et al.'s methods. We then construct a weighted k-partite graph for the reactions, compounds, and enzymes. We extract a mapping between these entities by solving the maximum-weighted k-partite matching problem by applying a novel heuristic algorithm. By analyzing the alignment results of multiple pathways in different organisms, we show that the alignments found by our algorithm correctly identify common subnetworks among multiple pathways.

Hierarchical Aligned Cluster Analysis for Temporal Clustering of Human Motion.

PubMed

Zhou, Feng; De la Torre, Fernando; Hodgins, Jessica K

2013-03-01

Temporal segmentation of human motion into plausible motion primitives is central to understanding and building computational models of human motion. Several issues contribute to the challenge of discovering motion primitives: the exponential nature of all possible movement combinations, the variability in the temporal scale of human actions, and the complexity of representing articulated motion. We pose the problem of learning motion primitives as one of temporal clustering, and derive an unsupervised hierarchical bottom-up framework called hierarchical aligned cluster analysis (HACA). HACA finds a partition of a given multidimensional time series into m disjoint segments such that each segment belongs to one of k clusters. HACA combines kernel k-means with the generalized dynamic time alignment kernel to cluster time series data. Moreover, it provides a natural framework to find a low-dimensional embedding for time series. HACA is efficiently optimized with a coordinate descent strategy and dynamic programming. Experimental results on motion capture and video data demonstrate the effectiveness of HACA for segmenting complex motions and as a visualization tool. We also compare the performance of HACA to state-of-the-art algorithms for temporal clustering on data of a honey bee dance. The HACA code is available online.

Fine-tuning structural RNA alignments in the twilight zone

PubMed Central

2010-01-01

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

Automation of the targeting and reflective alignment concept

NASA Technical Reports Server (NTRS)

Redfield, Robin C.

1992-01-01

The automated alignment system, described herein, employs a reflective, passive (requiring no power) target and includes a PC-based imaging system and one camera mounted on a six degree of freedom robot manipulator. The system detects and corrects for manipulator misalignment in three translational and three rotational directions by employing the Targeting and Reflective Alignment Concept (TRAC), which simplifies alignment by decoupling translational and rotational alignment control. The concept uses information on the camera and the target's relative position based on video feedback from the camera. These relative positions are converted into alignment errors and minimized by motions of the robot. The system is robust to exogenous lighting by virtue of a subtraction algorithm which enables the camera to only see the target. These capabilities are realized with relatively minimal complexity and expense.

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.

TMRG studies on spin alignment in molecule-based ferrimagnetics [rapid communication

NASA Astrophysics Data System (ADS)

Liu, Q. M.; Yao, K. L.; Liu, Z. L.

2005-05-01

A physical picture of spin alignment in organic molecule-based ferrimagnets is presented from studying the thermal effective magnetic moment of the sublattice by use of the transfer matrix renormalization group. We conclude that the classical antiparallel spin alignment is not the most stable state. The three-spin system tends to parallel alignment when the exchange interaction between the biradical and the monoradical molecules is much weaker than that within the biradical, which can result in the decrease of the effective magnetic moment upon lowering the temperature. More importantly, we give the theoretical evidence that even the antiparallel spin alignment in the biradical monoradical alternating chain does not necessarily lead to ferrimagnetic spin ordering due to the formation of the spin singlet pairs, which suppresses the ferrimagnetic spin alignment.

On the relationship between tumour growth rate and survival in non-small cell lung cancer.

PubMed

Mistry, Hitesh B

2017-01-01

A recurrent question within oncology drug development is predicting phase III outcome for a new treatment using early clinical data. One approach to tackle this problem has been to derive metrics from mathematical models that describe tumour size dynamics termed re-growth rate and time to tumour re-growth. They have shown to be strong predictors of overall survival in numerous studies but there is debate about how these metrics are derived and if they are more predictive than empirical end-points. This work explores the issues raised in using model-derived metric as predictors for survival analyses. Re-growth rate and time to tumour re-growth were calculated for three large clinical studies by forward and reverse alignment. The latter involves re-aligning patients to their time of progression. Hence, it accounts for the time taken to estimate re-growth rate and time to tumour re-growth but also assesses if these predictors correlate to survival from the time of progression. I found that neither re-growth rate nor time to tumour re-growth correlated to survival using reverse alignment. This suggests that the dynamics of tumours up until disease progression has no relationship to survival post progression. For prediction of a phase III trial I found the metrics performed no better than empirical end-points. These results highlight that care must be taken when relating dynamics of tumour imaging to survival and that bench-marking new approaches to existing ones is essential.

Dynamic thermal field-induced gradient soft-shear for highly oriented block copolymer thin films.

PubMed

Singh, Gurpreet; Yager, Kevin G; Berry, Brian; Kim, Ho-Cheol; Karim, Alamgir

2012-11-27

As demand for smaller, more powerful, and energy-efficient devices continues, conventional patterning technologies are pushing up against fundamental limits. Block copolymers (BCPs) are considered prime candidates for a potential solution via directed self-assembly of nanostructures. We introduce here a facile directed self-assembly method to rapidly fabricate unidirectionally aligned BCP nanopatterns at large scale, on rigid or flexible template-free substrates via a thermally induced dynamic gradient soft-shear field. A localized differential thermal expansion at the interface between a BCP film and a confining polydimethylsiloxane (PDMS) layer due to a dynamic thermal field imposes the gradient soft-shear field. PDMS undergoes directional expansion (along the annealing direction) in the heating zone and contracts back in the cooling zone, thus setting up a single cycle of oscillatory shear (maximum lateral shear stress ∼12 × 10(4) Pa) in the system. We successfully apply this process to create unidirectional alignment of BCP thin films over a wide range of thicknesses (nm to μm) and processing speeds (μm/s to mm/s) using both a flat and patterned PDMS layer. Grazing incidence small-angle X-ray scattering measurements show absolutely no sign of isotropic population and reveal ≥99% aligned orientational order with an angular spread Δθ(fwhm) ≤ 5° (full width at half-maximum). This method may pave the way to practical industrial use of hierarchically patterned BCP nanostructures.

CAFE: aCcelerated Alignment-FrEe sequence analysis.

PubMed

Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A; Waterman, Michael S; Sun, Fengzhu

2017-07-03

Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

ERIC Educational Resources Information Center

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

2015-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Development of New Supramolecular Lyotropic Liquid Crystals and Their Application as Alignment Media for Organic Compounds.

PubMed

Leyendecker, Martin; Meyer, Nils-Christopher; Thiele, Christina M

2017-09-11

Most alignment media for the residual dipolar coupling (RDC) based molecular structure determination of small organic compounds consist of rod-like polymers dissolved in organic solvents or of swollen cross-linked polymer gels. Thus far, the synthesis of polymer-based alignment media has been a challenging process, which is often followed by a time-consuming sample preparation. We herein propose the use of non-polymeric alignment media based on benzenetricarboxamides (BTAs), which self-assemble into rod-like supramolecules. Our newly found supramolecular lyotropic liquid crystals (LLCs) are studied in terms of their LLC properties and their suitability as alignment media in NMR spectroscopy. Scalable enantiodifferentiating properties are introduced through a sergeant-and-soldier principle by blending achiral with chiral substituted BTAs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Video-Based Fingerprint Verification

PubMed Central

Qin, Wei; Yin, Yilong; Liu, Lili

2013-01-01

Conventional fingerprint verification systems use only static information. In this paper, fingerprint videos, which contain dynamic information, are utilized for verification. Fingerprint videos are acquired by the same capture device that acquires conventional fingerprint images, and the user experience of providing a fingerprint video is the same as that of providing a single impression. After preprocessing and aligning processes, “inside similarity” and “outside similarity” are defined and calculated to take advantage of both dynamic and static information contained in fingerprint videos. Match scores between two matching fingerprint videos are then calculated by combining the two kinds of similarity. Experimental results show that the proposed video-based method leads to a relative reduction of 60 percent in the equal error rate (EER) in comparison to the conventional single impression-based method. We also analyze the time complexity of our method when different combinations of strategies are used. Our method still outperforms the conventional method, even if both methods have the same time complexity. Finally, experimental results demonstrate that the proposed video-based method can lead to better accuracy than the multiple impressions fusion method, and the proposed method has a much lower false acceptance rate (FAR) when the false rejection rate (FRR) is quite low. PMID:24008283

WEBnm@ v2.0: Web server and services for comparing protein flexibility.

PubMed

Tiwari, Sandhya P; Fuglebakk, Edvin; Hollup, Siv M; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn H; Tekle, Kidane M; Reuter, Nathalie

2014-12-30

Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

Spatial and Temporal Dynamics and Value of Nature-Based Recreation, Estimated via Social Media

PubMed Central

Watson, Keri B.; Wood, Spencer A.; Ricketts, Taylor H.

2016-01-01

Conserved lands provide multiple ecosystem services, including opportunities for nature-based recreation. Managing this service requires understanding the landscape attributes underpinning its provision, and how changes in land management affect its contribution to human wellbeing over time. However, evidence from both spatially explicit and temporally dynamic analyses is scarce, often due to data limitations. In this study, we investigated nature-based recreation within conserved lands in Vermont, USA. We used geotagged photographs uploaded to the photo-sharing website Flickr to quantify visits by in-state and out-of-state visitors, and we multiplied visits by mean trip expenditures to show that conserved lands contributed US $1.8 billion (US $0.18–20.2 at 95% confidence) to Vermont’s tourism industry between 2007 and 2014. We found eight landscape attributes explained the pattern of visits to conserved lands; visits were higher in larger conserved lands, with less forest cover, greater trail density and more opportunities for snow sports. Some of these attributes differed from those found in other locations, but all aligned with our understanding of recreation in Vermont. We also found that using temporally static models to inform conservation decisions may have perverse outcomes for nature-based recreation. For example, static models suggest conserved land with less forest cover receive more visits, but temporally dynamic models suggest clearing forests decreases, rather than increases, visits to these sites. Our results illustrate the importance of understanding both the spatial and temporal dynamics of ecosystem services for conservation decision-making. PMID:27611325

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

Dense-HOG-based drift-reduced 3D face tracking for infant pain monitoring

NASA Astrophysics Data System (ADS)

Saeijs, Ronald W. J. J.; Tjon A Ten, Walther E.; de With, Peter H. N.

2017-03-01

This paper presents a new algorithm for 3D face tracking intended for clinical infant pain monitoring. The algorithm uses a cylinder head model and 3D head pose recovery by alignment of dynamically extracted templates based on dense-HOG features. The algorithm includes extensions for drift reduction, using re-registration in combination with multi-pose state estimation by means of a square-root unscented Kalman filter. The paper reports experimental results on videos of moving infants in hospital who are relaxed or in pain. Results show good tracking behavior for poses up to 50 degrees from upright-frontal. In terms of eye location error relative to inter-ocular distance, the mean tracking error is below 9%.

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

PubMed

Kawabata, Takeshi; Nakamura, Haruki

2014-07-28

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

ModeRNA: a tool for comparative modeling of RNA 3D structure

PubMed Central

Rother, Magdalena; Rother, Kristian; Puton, Tomasz; Bujnicki, Janusz M.

2011-01-01

RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available. PMID:21300639

Simulation-based comprehensive benchmarking of RNA-seq aligners

PubMed Central

Baruzzo, Giacomo; Hayer, Katharina E; Kim, Eun Ji; Di Camillo, Barbara; FitzGerald, Garret A; Grant, Gregory R

2018-01-01

Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters. We found that performance varied by genome complexity, and accuracy and popularity were poorly correlated. The most widely cited tool underperforms for most metrics, particularly when using default settings. PMID:27941783

DE 1 observations of type 1 counterstreaming electrons and field-aligned currents

NASA Technical Reports Server (NTRS)

Lin, C. S.; Burch, J. L.; Barfield, J. N.; Sugiura, M.; Nielsen, E.

1984-01-01

Dynamics Explorer 1 satellite observations of plasma and magnetic fields during type one counterstreaming electron events are presented. Counterstreaming electrons are observed at high altitudes in the region of field-aligned current. The total current density computed from the plasma data in the 18-10,000 eV energy range is generally about 1-2 micro-A/sq m. For the downward current, low-energy electrons contribute more than 40 percent of the total plasma current density integrated above 18 eV. For the upward current, such electrons contribute less than 50 percent of that current density. Electron beams in the field-aligned direction are occasionally detected. The pitch angle distributions of counterstreaming electrons are generally enhanced at both small and large pitch angles. STARE simultaneous observations for one DE 1 pass indicated that the field-aligned current was closed through Pedersen currents in the ionosphere. The directions of the ionospheric current systems are consistent with the DE 1 observations at high altitudes.

Direction-specific interaction forces underlying zinc oxide crystal growth by oriented attachment

DOE PAGES

Zhang, X.; Shen, Z.; Liu, J.; ...

2017-10-10

Here, crystallization by particle attachment is impacting our understanding of natural mineralization processes and holds promise for novel materials design. When particles assemble in crystallographic registry, expulsion of the intervening solvent and particle coalescence is enabled by near-perfect co-alignment via interparticle forces that remain poorly quantified. Here we report measurement and simulation of these nanoscale aligning forces for the ZnO(0001)-ZnO(000¯1) system in aqueous solution. Dynamic force spectroscopy using nanoengineered single crystal probes reveals an attractive force with 60o rotational periodicity. Calculated distance and orientation-dependent potentials of mean force show several attractive free energy wells distinguished by numbers of intervening watermore » layers, which reach a minimum when aligned. The calculated activation energy to separate the attractively bound solvated interfaces perfectly reproduces the measured 60o periodicity, revealing the key role of intervening water structuring as a basis to generate the interparticle torque that completes alignment and enables coalescence.« less

Direction-specific interaction forces underlying zinc oxide crystal growth by oriented attachment

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

Zhang, X.; Shen, Z.; Liu, J.

Here, crystallization by particle attachment is impacting our understanding of natural mineralization processes and holds promise for novel materials design. When particles assemble in crystallographic registry, expulsion of the intervening solvent and particle coalescence is enabled by near-perfect co-alignment via interparticle forces that remain poorly quantified. Here we report measurement and simulation of these nanoscale aligning forces for the ZnO(0001)-ZnO(000¯1) system in aqueous solution. Dynamic force spectroscopy using nanoengineered single crystal probes reveals an attractive force with 60o rotational periodicity. Calculated distance and orientation-dependent potentials of mean force show several attractive free energy wells distinguished by numbers of intervening watermore » layers, which reach a minimum when aligned. The calculated activation energy to separate the attractively bound solvated interfaces perfectly reproduces the measured 60o periodicity, revealing the key role of intervening water structuring as a basis to generate the interparticle torque that completes alignment and enables coalescence.« less

Guided growth of horizontal GaN nanowires on quartz and their transfer to other substrates.

PubMed

Goren-Ruck, Lior; Tsivion, David; Schvartzman, Mark; Popovitz-Biro, Ronit; Joselevich, Ernesto

2014-03-25

The guided growth of horizontal nanowires has so far been demonstrated on a limited number of substrates. In most cases, the nanowires are covalently bonded to the substrate where they grow and cannot be transferred to other substrates. Here we demonstrate the guided growth of well-aligned horizontal GaN nanowires on quartz and their subsequent transfer to silicon wafers by selective etching of the quartz while maintaining their alignment. The guided growth was observed on different planes of quartz with varying degrees of alignment. We characterized the crystallographic orientations of the nanowires and proposed a new mechanism of "dynamic graphoepitaxy" for their guided growth on quartz. The transfer of the guided nanowires enabled the fabrication of back-gated field-effect transistors from aligned nanowire arrays on oxidized silicon wafers and the production of crossbar arrays. The guided growth of transferrable nanowires opens up the possibility of massively parallel integration of nanowires into functional systems on virtually any desired substrate.

Detecting fiducials affected by trombone delay in ARC and the main laser alignment at the National Ignition Facility

NASA Astrophysics Data System (ADS)

Awwal, Abdul A. S.; Bliss, Erlan S.; Miller Kamm, Victoria; Leach, Richard R.; Roberts, Randy; Rushford, Michael C.; Lowe-Webb, Roger; Wilhelmsen, Karl

2015-09-01

Four of the 192 beams of the National Ignition Facility (NIF) are currently being diverted into the Advanced Radiographic Capability (ARC) system to generate a sequence of short (1-50 picoseconds) 1053 nm laser pulses. When focused onto high Z wires in vacuum, these pulses create high energy x-ray pulses capable of penetrating the dense, imploding fusion fuel plasma during ignition scale experiments. The transmitted x-rays imaged with x-ray diagnostics can create movie radiographs that are expected to provide unprecedented insight into the implosion dynamics. The resulting images will serve as a diagnostic for tuning the experimental parameters towards successful fusion reactions. Beam delays introduced into the ARC pulses via independent, free-space optical trombones create the desired x-ray image sequence, or movie. However, these beam delays cause optical distortion of various alignment fiducials viewed by alignment sensors in the NIF and ARC beamlines. This work describes how the position of circular alignment fiducials is estimated in the presence of distortion.

Patterned Cell Alignment in Response to Macroscale Curvature

NASA Astrophysics Data System (ADS)

Bade, Nathan; Kamien, Randall; Assoian, Richard; Stebe, Kathleen

The formation of spatial behavior patterns in tissues is a long-standing problem in biology. Decades of research have focused on understanding how biochemical signaling and morphogen gradients establish cell patterns during development and tissue morphogenesis. Here, we show that geometry and physical cues can drive organization and pattern formation. We find that mouse embryonic fibroblasts and human vascular smooth muscle cells sense curvature differently when in monolayers than when isolated on surfaces with various amounts of Gaussian curvature. While the long, apical stress fibers within these cells align in the direction of minimum curvature on cylindrical substrates, a subpopulation of stress fibers beneath the nucleus aligns in the circumferential direction and is bent maximally. We find dramatic reorganization of the actin cytoskeleton upon activation of RhoA, which is associated with increased contractility of the fibers. Thus, stress fiber alignment is likely a result of a complex balance between energy penalties associated with stress fiber bending, contractility, and the dynamics of F-actin assembly.

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

Dynamic test results for the CASES ground experiment

NASA Technical Reports Server (NTRS)

Bukley, Angelia P.; Patterson, Alan F.; Jones, Victoria L.

1993-01-01

The Controls, Astrophysics, and Structures Experiment in Space (CASES) Ground Test Facility (GTF) has been developed at Marshall Space Flight Center (MSFC) to provide a facility for the investigation of Controls/Structures Interaction (CSI) phenomena, to support ground testing of a potential shuttle-based CASES flight experiment, and to perform limited boom deployment and retraction dynamics studies. The primary objectives of the ground experiment are to investigate CSI on a test article representative of a Large Space Structure (LSS); provide a platform for Guest Investigators (GI's) to conduct CSI studies; to test and evaluate LSS control methodologies, system identification (ID) techniques, failure mode analysis; and to compare ground test predictions and flight results. The proposed CASES flight experiment consists of a 32 meter deployable/retractable boom at the end of which is an occulting plate. The control objective of the experiment is to maintain alignment of the tip plate (occulter) with a detector located at the base of the boom in the orbiter bay. The tip plate is pointed towards a star, the sun, or the galactic center to collect high-energy X-rays emitted by these sources. The tip plate, boom, and detector comprise a Fourier telescope. The occulting holes in the tip plate are approximately one millimeter in diameter making the alignment requirements quite stringent. Control authority is provided by bidirectional linear thrusters located at the boom tip and Angular Momentum Exchange Devices (AMED's) located at mid-boom and at the tip. The experiment embodies a number of CSI control problems including vibration suppression, pointing a long flexible structure, and disturbance rejection. The CASES GTF is representative of the proposed flight experiment with identical control objectives.

GenoMycDB: a database for comparative analysis of mycobacterial genes and genomes.

PubMed

Catanho, Marcos; Mascarenhas, Daniel; Degrave, Wim; Miranda, Antonio Basílio de

2006-03-31

Several databases and computational tools have been created with the aim of organizing, integrating and analyzing the wealth of information generated by large-scale sequencing projects of mycobacterial genomes and those of other organisms. However, with very few exceptions, these databases and tools do not allow for massive and/or dynamic comparison of these data. GenoMycDB (http://www.dbbm.fiocruz.br/GenoMycDB) is a relational database built for large-scale comparative analyses of completely sequenced mycobacterial genomes, based on their predicted protein content. Its central structure is composed of the results obtained after pair-wise sequence alignments among all the predicted proteins coded by the genomes of six mycobacteria: Mycobacterium tuberculosis (strains H37Rv and CDC1551), M. bovis AF2122/97, M. avium subsp. paratuberculosis K10, M. leprae TN, and M. smegmatis MC2 155. The database stores the computed similarity parameters of every aligned pair, providing for each protein sequence the predicted subcellular localization, the assigned cluster of orthologous groups, the features of the corresponding gene, and links to several important databases. Tables containing pairs or groups of potential homologs between selected species/strains can be produced dynamically by user-defined criteria, based on one or multiple sequence similarity parameters. In addition, searches can be restricted according to the predicted subcellular localization of the protein, the DNA strand of the corresponding gene and/or the description of the protein. Massive data search and/or retrieval are available, and different ways of exporting the result are offered. GenoMycDB provides an on-line resource for the functional classification of mycobacterial proteins as well as for the analysis of genome structure, organization, and evolution.

Connecting Lab-Based Attosecond Science with FEL research

ScienceCinema

Vrakking, Marc

2017-12-09

In the last few years laboratory-scale femtosecond laser-based research using XUV light has developed dramatically following the successful development of attosecond laser pulses by means of high-harmonic generation. Using attosecond laser pulses, studies of electron dynamics on the natural timescale that electronic processes occur in atoms, molecules and solids can be contemplated, providing unprecedented insight into the fundamental role that electrons play in photo-induced processes. In my talk I will briefly review the present status of the attosecond science research field in terms of present and foreseen capabilities, and discuss a few recent applications, including a first example of the use of attosecond laser pulses in molecular science. In addition, I will discuss very recent results of experiments where photoionization of dynamically aligned molecules is investigated using a high-harmonics XUV source. Photoionization of aligned molecules becomes all the more interesting if the experiment is performed using x-ray photons. Following the absorption of x-rays, ejected photoelectrons can be used as a probe of the (time-evolving) molecular structure, making use of intra-molecular electron diffraction. This amounts, as some have stated, to “illuminating the molecule from within”. I will present the present status of our experiments on this topic making use of the FLASH free electron laser in Hamburg. Future progress in this research field not only depends on the availability of better and more powerful light sources, but also requires sophisticated detector strategies. In my talk I will explain how we are trying to meet some of the experimental challenges by using the Medipix family of detectors, which we have already used for time- and space-resolved imaging of electrons and ions.

Estimating Critical Values for Strength of Alignment among Curriculum, Assessments, and Instruction

ERIC Educational Resources Information Center

Fulmer, Gavin W.

2010-01-01

School accountability decisions based on standardized tests hinge on the degree of alignment of the test with a state's standards. Yet no established criteria were available for judging strength of alignment. Previous studies of alignment among tests, standards, and teachers' instruction have yielded mixed results that are difficult to interpret…

Estimating Critical Values for Strength of Alignment among Curriculum, Assessments, and Instruction

ERIC Educational Resources Information Center

Fulmer, Gavin W.

2011-01-01

School accountability decisions based on standardized tests hinge on the degree of alignment of the test with the state's standards documents. Yet, there exist no established criteria for judging strength of alignment. Previous measures of alignment among tests, standards, and teachers' instruction have yielded mixed results that are difficult to…

Gauging Item Alignment through Online Systems While Controlling for Rater Effects

ERIC Educational Resources Information Center

Anderson, Daniel; Irvin, Shawn; Alonzo, Julie; Tindal, Gerald A.

2015-01-01

The alignment of test items to content standards is critical to the validity of decisions made from standards-based tests. Generally, alignment is determined based on judgments made by a panel of content experts with either ratings averaged or via a consensus reached through discussion. When the pool of items to be reviewed is large, or the…

Evol and ProDy for bridging protein sequence evolution and structural dynamics

PubMed Central

Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R.; Bahar, Ivet

2014-01-01

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. Availability and implementation: ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/. Contact: bahar@pitt.edu PMID:24849577

A unified model for transfer alignment at random misalignment angles based on second-order EKF

NASA Astrophysics Data System (ADS)

Cui, Xiao; Mei, Chunbo; Qin, Yongyuan; Yan, Gongmin; Liu, Zhenbo

2017-04-01

In the transfer alignment process of inertial navigation systems (INSs), the conventional linear error model based on the small misalignment angle assumption cannot be applied to large misalignment situations. Furthermore, the nonlinear model based on the large misalignment angle suffers from redundant computation with nonlinear filters. This paper presents a unified model for transfer alignment suitable for arbitrary misalignment angles. The alignment problem is transformed into an estimation of the relative attitude between the master INS (MINS) and the slave INS (SINS), by decomposing the attitude matrix of the latter. Based on the Rodriguez parameters, a unified alignment model in the inertial frame with the linear state-space equation and a second order nonlinear measurement equation are established, without making any assumptions about the misalignment angles. Furthermore, we employ the Taylor series expansions on the second-order nonlinear measurement equation to implement the second-order extended Kalman filter (EKF2). Monte-Carlo simulations demonstrate that the initial alignment can be fulfilled within 10 s, with higher accuracy and much smaller computational cost compared with the traditional unscented Kalman filter (UKF) at large misalignment angles.

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

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

PubMed

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

2015-01-01

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

Stakeholder Alignment and Changing Geospatial Information Capabilities

NASA Astrophysics Data System (ADS)

Winter, S.; Cutcher-Gershenfeld, J.; King, J. L.

2015-12-01

Changing geospatial information capabilities can have major economic and social effects on activities such as drought monitoring, weather forecasts, agricultural productivity projections, water and air quality assessments, the effects of forestry practices and so on. Whose interests are served by such changes? Two common mistakes are assuming stability in the community of stakeholders and consistency in stakeholder behavior. Stakeholder communities can reconfigure dramatically as some leave the discussion, others enter, and circumstances shift — all resulting in dynamic points of alignment and misalignment . New stakeholders can bring new interests, and existing stakeholders can change their positions. Stakeholders and their interests need to be be considered as geospatial information capabilities change, but this is easier said than done. New ways of thinking about stakeholder alignment in light of changes in capability are presented.

Coupling of magnetopause-boundary layer to the polar ionosphere

NASA Technical Reports Server (NTRS)

Wei, C. Q.; Lee, L. C.

1993-01-01

The plasma dynamics in the low-latitude boundary layer and its coupling to the polar ionosphere under boundary conditions at the magnetopause are investigated. In the presence of a driven plasma flow along the magnetopause, the Kelvin-Helmholtz instability can develop, leading to the formation and growth of plasma vortices in the boundary layer. The finite ionospheric conductivity leads to the decay of these vortices. The competing effect of the formation and decay of vortices leads to the formation of strong vortices only in a limited region. Several enhanced field-aligned power density regions associated with the boundary layer vortices and the upward field-aligned current (FAC) filaments can be found along the postnoon auroral oval. These enhanced field-aligned power density regions may account for the observed auroral bright spots.

Femtosecond-laser-induced nonadiabatic alignment in photoexcited pyrimidine

NASA Astrophysics Data System (ADS)

Li, Shuai; Ling, Fengzi; Wang, Yanmei; Long, Jinyou; Deng, Xulan; Jin, Bing; Zhang, Bing

2017-09-01

The rotational wave-packet dynamics in electronically excited pyrimidine induced by a femtosecond laser pulse at 321.5 nm has been studied by time-resolved mass spectroscopy and photoelectron velocity-map imaging. The rotational revival features at 81.3 ps, which are the direct manifestation of field-free nonadiabatic alignment, are clearly observed in both the time-dependent ion yields and photoelectron angular distributions. In particular, the out-of-phase recurrences in the parent-ion and fragment-ions transients indicate the different directions of the ionization transition-dipole moments for the generation of the parent ion and fragment ions. By tuning the polarization of the probe light parallel or perpendicular to that of the pump light, we demonstrate the potential application of nonadiabatic alignment to manipulate the branching ratio of photoionization products.

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 > ).

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.

Auroral activity associated with Kelvin-Helmholtz instability at the inner edge of the low-latitude boundary layer

NASA Technical Reports Server (NTRS)

Farrugia, C. J.; Sandholt, P. E.; Burlaga, L. F.

1994-01-01

Auroral activity occurred in the late afternoon sector (approx. 16 MLT) in the northern hemisphere during the passage at Earth of an interplanetary magnetic cloud on January 14, 1988. The auroral activity consisted of a very dynamic display which was preceded and followed by quiet auroral displays. During the quiet displays, discrete rayed arcs aligned along the geomagnetic L shells were observed. In the active stage, rapidly evolving spiral forms centered on magnetic zenith were evident. The activity persisted for many minutes and was characterized by the absence of directed motion. They were strongly suggestive of intense filaments of upward field-aligned currents embedded in the large-scale region 1 current system. Distortions of the flux ropes as they connect from the equatorial magnetosphere to the ionosphere were witnessed. We assess as possible generating mechanisms three nonlocal sources known to be associated with field-aligned currents. Of these, partial compressions of the magnetosphere due to variations of solar wind dynamic pressure seem an unlikely source. The possibility that the auroral forms are due to reconnection is investigated but is excluded because the active aurora were observed on the closed field line region just equatorward of the convection reversal boundary. To support this conclusion further, we apply recent results on the mapping of ionospheric regions to the equatorial plane based on the Tsyganenko 1989 model (Kaufmann et al., 1993). We find that for comparable magnetic activity the aurora map to the equatorial plane at X(sub GSM) = approx. 3 R(sub E) and approx. 2 R(sub E) inward of the magnetopause, that is, the inner edge of the boundary layer close to dusk. Since the auroral forms are manifestly associated with magnetic field shear, a vortical motion at the equatorial end of the flux rope is indicated, making the Kelvin-Helmholtz instability acting at the inner edge of the low-latitude boundary layer the most probable generating source.

Transitions between homogeneous phases of polar active liquids

NASA Astrophysics Data System (ADS)

Dauchot, Olivier; Nguyen Thu Lam, Khanh Dang; Schindler, Michael; EC2M Team; PCT Team

2015-03-01

Polar active liquids, composed of aligning self-propelled particle exhibit large scale collective motion. Simulations of Vicsek-like models of constant-speed point particles, aligning with their neighbors in the presence of noise, have revealed the existence of a transition towards a true long range order polar-motion phase. Generically, the homogenous polar state is unstable; non-linear propagative structures develop; and the transition is discontinuous. The long range dynamics of these systems has been successfully captured using various scheme of kinetic theories. However the complexity of the dynamics close to the transition has somewhat hindered more basics questions. Is there a simple way to predict the existence and the order of a transition to collective motion for a given microscopic dynamics? What would be the physically meaningful and relevant quantity to answer this question? Here, we tackle these questions, restricting ourselves to the study of the homogeneous phases of polar active liquids in the low density limit and obtain a very intuitive understanding of the conditions which particle interaction must satisfy to induce a transition towards collective motion.

Configuring and Characterizing X-Rays for Laser-Driven Compression Experiments at the Dynamic Compression Sector

NASA Astrophysics Data System (ADS)

Li, Y.; Capatina, D.; D'Amico, K.; Eng, P.; Hawreliak, J.; Graber, T.; Rickerson, D.; Klug, J.; Rigg, P. A.; Gupta, Y. M.

2017-06-01

Coupling laser-driven compression experiments to the x-ray beam at the Dynamic Compression Sector (DCS) at the Advanced Photon Source (APS) of Argonne National Laboratory requires state-of-the-art x-ray focusing, pulse isolation, and diagnostics capabilities. The 100J UV pulsed laser system can be fired once every 20 minutes so precise alignment and focusing of the x-rays on each new sample must be fast and reproducible. Multiple Kirkpatrick-Baez (KB) mirrors are used to achieve a focal spot size as small as 50 μm at the target, while the strategic placement of scintillating screens, cameras, and detectors allows for fast diagnosis of the beam shape, intensity, and alignment of the sample to the x-ray beam. In addition, a series of x-ray choppers and shutters are used to ensure that the sample is exposed to only a single x-ray pulse ( 80ps) during the dynamic compression event and require highly precise synchronization. Details of the technical requirements, layout, and performance of these instruments will be presented. Work supported by DOE/NNSA.

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

PubMed

Tajima, K

1988-11-01

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

Propagation and stability characteristics of a 500-m-long laser-based fiducial line for high-precision alignment of long-distance linear accelerators.

PubMed

Suwada, Tsuyoshi; Satoh, Masanori; Telada, Souichi; Minoshima, Kaoru

2013-09-01

A laser-based alignment system with a He-Ne laser has been newly developed in order to precisely align accelerator units at the KEKB injector linac. The laser beam was first implemented as a 500-m-long fiducial straight line for alignment measurements. We experimentally investigated the propagation and stability characteristics of the laser beam passing through laser pipes in vacuum. The pointing stability at the last fiducial point was successfully obtained with the transverse displacements of ±40 μm level in one standard deviation by applying a feedback control. This pointing stability corresponds to an angle of ±0.08 μrad. This report contains a detailed description of the experimental investigation for the propagation and stability characteristics of the laser beam in the laser-based alignment system for long-distance linear accelerators.

Orbital Verification of the CXO High-Resolution Mirror Assembly Alignment and Vignetting

NASA Technical Reports Server (NTRS)

Gaetz, T. J.; Jerius, D.; Edgar, R. J.; VanSpeybroeck, L. P.; Schwartz, D. A.; Markevitch, M.; Schulz, N. S.

2000-01-01

Prior to launch, the High Resolution Mirror Assembly (HRMA) of the Chandra X-ray Observatory underwent extensive ground testing at the X-ray Calibration Facility (XRCF) at the Marshall Space Flight Center in Huntsville. Observations made during the post-launch Orbital Activation and Calibration period, allow the on-orbit condition of the X-ray optics to be assessed. Based on these ground-based and on-orbit data, we examine the alignment of the x-ray optics based on the PSF, and the boresight and alignment of the optical axis alignment relative to the detectors. We examine the vignetting and the single reflection ghost suppression properties of the telescope. Slight imperfections in alignment lead to a small azimuthal dependence of the off-axis area; the morphology of off-axis images also shows an additional small azimuthal dependence varying as 1/2 the off-axis azimuth angle.

Propagation and stability characteristics of a 500-m-long laser-based fiducial line for high-precision alignment of long-distance linear accelerators

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

Suwada, Tsuyoshi; Satoh, Masanori; Telada, Souichi

2013-09-15

A laser-based alignment system with a He-Ne laser has been newly developed in order to precisely align accelerator units at the KEKB injector linac. The laser beam was first implemented as a 500-m-long fiducial straight line for alignment measurements. We experimentally investigated the propagation and stability characteristics of the laser beam passing through laser pipes in vacuum. The pointing stability at the last fiducial point was successfully obtained with the transverse displacements of ±40 μm level in one standard deviation by applying a feedback control. This pointing stability corresponds to an angle of ±0.08 μrad. This report contains a detailedmore » description of the experimental investigation for the propagation and stability characteristics of the laser beam in the laser-based alignment system for long-distance linear accelerators.« less

Improved alignment evaluation and optimization : final report.

DOT National Transportation Integrated Search

2007-09-11

This report outlines the development of an enhanced highway alignment evaluation and optimization : model. A GIS-based software tool is prepared for alignment optimization that uses genetic algorithms for : optimal search. The software is capable of ...

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.

VCGDB: a dynamic genome database of the Chinese population

PubMed Central

2014-01-01

Background The data released by the 1000 Genomes Project contain an increasing number of genome sequences from different nations and populations with a large number of genetic variations. As a result, the focus of human genome studies is changing from single and static to complex and dynamic. The currently available human reference genome (GRCh37) is based on sequencing data from 13 anonymous Caucasian volunteers, which might limit the scope of genomics, transcriptomics, epigenetics, and genome wide association studies. Description We used the massive amount of sequencing data published by the 1000 Genomes Project Consortium to construct the Virtual Chinese Genome Database (VCGDB), a dynamic genome database of the Chinese population based on the whole genome sequencing data of 194 individuals. VCGDB provides dynamic genomic information, which contains 35 million single nucleotide variations (SNVs), 0.5 million insertions/deletions (indels), and 29 million rare variations, together with genomic annotation information. VCGDB also provides a highly interactive user-friendly virtual Chinese genome browser (VCGBrowser) with functions like seamless zooming and real-time searching. In addition, we have established three population-specific consensus Chinese reference genomes that are compatible with mainstream alignment software. Conclusions VCGDB offers a feasible strategy for processing big data to keep pace with the biological data explosion by providing a robust resource for genomics studies; in particular, studies aimed at finding regions of the genome associated with diseases. PMID:24708222

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

PubMed

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

2002-11-12

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

Introducing difference recurrence relations for faster semi-global alignment of long sequences.

PubMed

Suzuki, Hajime; Kasahara, Masahiro

2018-02-19

The read length of single-molecule DNA sequencers is reaching 1 Mb. Popular alignment software tools widely used for analyzing such long reads often take advantage of single-instruction multiple-data (SIMD) operations to accelerate calculation of dynamic programming (DP) matrices in the Smith-Waterman-Gotoh (SWG) algorithm with a fixed alignment start position at the origin. Nonetheless, 16-bit or 32-bit integers are necessary for storing the values in a DP matrix when sequences to be aligned are long; this situation hampers the use of the full SIMD width of modern processors. We proposed a faster semi-global alignment algorithm, "difference recurrence relations," that runs more rapidly than the state-of-the-art algorithm by a factor of 2.1. Instead of calculating and storing all the values in a DP matrix directly, our algorithm computes and stores mainly the differences between the values of adjacent cells in the matrix. Although the SWG algorithm and our algorithm can output exactly the same result, our algorithm mainly involves 8-bit integer operations, enabling us to exploit the full width of SIMD operations (e.g., 32) on modern processors. We also developed a library, libgaba, so that developers can easily integrate our algorithm into alignment programs. Our novel algorithm and optimized library implementation will facilitate accelerating nucleotide long-read analysis algorithms that use pairwise alignment stages. The library is implemented in the C programming language and available at https://github.com/ocxtal/libgaba .

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

Sattarivand, Mike; Summers, Clare; Robar, James

Purpose: To evaluate the validity of using spine as a surrogate for tumor positioning with ExacTrac stereoscopic imaging in lung stereotactic body radiation therapy (SBRT). Methods: Using the Novalis ExacTrac x-ray system, 39 lung SBRT patients (182 treatments) were aligned before treatment with 6 degrees (6D) of freedom couch (3 translations, 3 rotations) based on spine matching on stereoscopic images. The couch was shifted to treatment isocenter and pre-treatment CBCT was performed based on a soft tissue match around tumor volume. The CBCT data were used to measure residual errors following ExacTrac alignment. The thresholds for re-aligning the patients basedmore » on CBCT were 3mm shift or 3° rotation (in any 6D). In order to evaluate the effect of tumor location on residual errors, correlations between tumor distance from spine and individual residual errors were calculated. Results: Residual errors were up to 0.5±2.4mm. Using 3mm/3° thresholds, 80/182 (44%) of the treatments required re-alignment based on CBCT soft tissue matching following ExacTrac spine alignment. Most mismatches were in sup-inf, ant-post, and roll directions which had larger standard deviations. No correlation was found between tumor distance from spine and individual residual errors. Conclusion: ExacTrac stereoscopic imaging offers a quick pre-treatment patient alignment. However, bone matching based on spine is not reliable for aligning lung SBRT patients who require soft tissue image registration from CBCT. Spine can be a poor surrogate for lung SBRT patient alignment even for proximal tumor volumes.« less

Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.

PubMed

Dong, Zheng; Zhou, Hongyu; Tao, Peng

2018-02-01

PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics. © 2017 The Protein Society.

From Guide to Practice: Improving Your After School Science Program to Increase Student Academic Achievement

NASA Astrophysics Data System (ADS)

Taylor, J.

2013-12-01

Numerous science organizations, such as NASA, offer educational outreach activities geared towards after school. For some programs, the primary goal is to grow students' love of science. For others, the programs are also intended to increase academic achievement. For those programs looking to support student learning in out-of-school time environments, aligning the program with learning during the classroom day can be a challenge. The Institute for Education Sciences, What Works Clearinghouse, put together a 'Practice Guide' for maximizing learning time beyond the regular school day. These practice guides provide concrete recommendations for educators supported by research. While this guide is not specific to any content or subject-area, the recommendations provided align very well with science education. After school science is often viewed as a fun, dynamic environment for students. Indeed, one of the recommendations to ensure time is structured according to students' needs is to provide relevant and interesting experiences. Given that our after school programs provide such creative environments for students, what other components are needed to promote increased academic achievement? The recommendations provided to academic achievement, include: 1. Align Instruction, 2. Maximize Attendance and Participation, 3. Adapt Instruction, 4. Provide Engaging Experiences, and 5. Evaluate Program. In this session we will examine these five recommendations presented in the Practice Guide, discuss how these strategies align with science programs, and examine what questions each program should address in order to provide experiences that lend themselves to maximizing instruction. Roadblocks and solutions for overcoming challenges in each of the five areas will be presented. Jessica Taylor will present this research based on her role as an author on the Practice Guide, 'Improving Academic Achievement in Out-of-School Time' and her experience working in various informal science programs for NASA.

Iterative pass optimization of sequence data

NASA Technical Reports Server (NTRS)

Wheeler, Ward C.

2003-01-01

The problem of determining the minimum-cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete. This "tree alignment" problem has motivated the considerable effort placed in multiple sequence alignment procedures. Wheeler in 1996 proposed a heuristic method, direct optimization, to calculate cladogram costs without the intervention of multiple sequence alignment. This method, though more efficient in time and more effective in cladogram length than many alignment-based procedures, greedily optimizes nodes based on descendent information only. In their proposal of an exact multiple alignment solution, Sankoff et al. in 1976 described a heuristic procedure--the iterative improvement method--to create alignments at internal nodes by solving a series of median problems. The combination of a three-sequence direct optimization with iterative improvement and a branch-length-based cladogram cost procedure, provides an algorithm that frequently results in superior (i.e., lower) cladogram costs. This iterative pass optimization is both computation and memory intensive, but economies can be made to reduce this burden. An example in arthropod systematics is discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

Blob dynamics in TORPEX poloidal null configurations

NASA Astrophysics Data System (ADS)

Shanahan, B. W.; Dudson, B. D.

2016-12-01

3D blob dynamics are simulated in X-point magnetic configurations in the TORPEX device via a non-field-aligned coordinate system, using an isothermal model which evolves density, vorticity, parallel velocity and parallel current density. By modifying the parallel gradient operator to include perpendicular perturbations from poloidal field coils, numerical singularities associated with field aligned coordinates are avoided. A comparison with a previously developed analytical model (Avino 2016 Phys. Rev. Lett. 116 105001) is performed and an agreement is found with minimal modification. Experimental comparison determines that the null region can cause an acceleration of filaments due to increasing connection length, but this acceleration is small relative to other effects, which we quantify. Experimental measurements (Avino 2016 Phys. Rev. Lett. 116 105001) are reproduced, and the dominant acceleration mechanism is identified as that of a developing dipole in a moving background. Contributions from increasing connection length close to the null point are a small correction.

The Saccharomyces Genome Database Variant Viewer.

PubMed

Sheppard, Travis K; Hitz, Benjamin C; Engel, Stacia R; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C; Dalusag, Kyla S; Demeter, Janos; Hellerstedt, Sage T; Karra, Kalpana; Nash, Robert S; Paskov, Kelley M; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Cherry, J Michael

2016-01-04

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dynamical patterns in nematic active matter on a sphere

NASA Astrophysics Data System (ADS)

Henkes, Silke; Marchetti, M. Cristina; Sknepnek, Rastko

2018-04-01

Using simulations of self-propelled agents with short-range repulsion and nematic alignment, we explore the dynamical phases of a dense active nematic confined to the surface of a sphere. We map the nonequilibrium phase diagram as a function of curvature, alignment strength, and activity. Our model reproduces several phases seen in recent experiments on active microtubule bundles confined the surfaces of vesicles. At low driving, we recover the equilibrium nematic ground state with four +1 /2 defects. As the driving is increased, geodesic forces drive the transition to a polar band wrapping around an equator, with large empty spherical caps corresponding to two +1 defects at the poles. Upon further increasing activity, the bands fold onto themselves, and the system eventually transitions to a turbulent state marked by the proliferation of pairs of topological defects. We highlight the key role of the nematic persistence length in controlling pattern formation in these confined systems with positive Gaussian curvature.

International Space Station Future Correlation Analysis Improvements

NASA Technical Reports Server (NTRS)

Laible, Michael R.; Pinnamaneni, Murthy; Sugavanam, Sujatha; Grygier, Michael

2018-01-01

Ongoing modal analyses and model correlation are performed on different configurations of the International Space Station (ISS). These analyses utilize on-orbit dynamic measurements collected using four main ISS instrumentation systems: External Wireless Instrumentation System (EWIS), Internal Wireless Instrumentation System (IWIS), Space Acceleration Measurement System (SAMS), and Structural Dynamic Measurement System (SDMS). Remote Sensor Units (RSUs) are network relay stations that acquire flight data from sensors. Measured data is stored in the Remote Sensor Unit (RSU) until it receives a command to download data via RF to the Network Control Unit (NCU). Since each RSU has its own clock, it is necessary to synchronize measurements before analysis. Imprecise synchronization impacts analysis results. A study was performed to evaluate three different synchronization techniques: (i) measurements visually aligned to analytical time-response data using model comparison, (ii) Frequency Domain Decomposition (FDD), and (iii) lag from cross-correlation to align measurements. This paper presents the results of this study.

Introducing Evidence Through Research "Push": Using Theory and Qualitative Methods.

PubMed

Morden, Andrew; Ong, Bie Nio; Brooks, Lauren; Jinks, Clare; Porcheret, Mark; Edwards, John J; Dziedzic, Krysia S

2015-11-01

A multitude of factors can influence the uptake and implementation of complex interventions in health care. A plethora of theories and frameworks recognize the need to establish relationships, understand organizational dynamics, address context and contingency, and engage key decision makers. Less attention is paid to how theories that emphasize relational contexts can actually be deployed to guide the implementation of an intervention. The purpose of the article is to demonstrate the potential role of qualitative research aligned with theory to inform complex interventions. We detail a study underpinned by theory and qualitative research that (a) ensured key actors made sense of the complex intervention at the earliest stage of adoption and (b) aided initial engagement with the intervention. We conclude that using theoretical approaches aligned with qualitative research can provide insights into the context and dynamics of health care settings that in turn can be used to aid intervention implementation. © The Author(s) 2015.

Global dynamics of selective attention and its lapses in primary auditory cortex.

PubMed

Lakatos, Peter; Barczak, Annamaria; Neymotin, Samuel A; McGinnis, Tammy; Ross, Deborah; Javitt, Daniel C; O'Connell, Monica Noelle

2016-12-01

Previous research demonstrated that while selectively attending to relevant aspects of the external world, the brain extracts pertinent information by aligning its neuronal oscillations to key time points of stimuli or their sampling by sensory organs. This alignment mechanism is termed oscillatory entrainment. We investigated the global, long-timescale dynamics of this mechanism in the primary auditory cortex of nonhuman primates, and hypothesized that lapses of entrainment would correspond to lapses of attention. By examining electrophysiological and behavioral measures, we observed that besides the lack of entrainment by external stimuli, attentional lapses were also characterized by high-amplitude alpha oscillations, with alpha frequency structuring of neuronal ensemble and single-unit operations. Entrainment and alpha-oscillation-dominated periods were strongly anticorrelated and fluctuated rhythmically at an ultra-slow rate. Our results indicate that these two distinct brain states represent externally versus internally oriented computational resources engaged by large-scale task-positive and task-negative functional networks.

Vertically aligned carbon nanofiber as nano-neuron interface for monitoring neural function

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

Ericson, Milton Nance; McKnight, Timothy E; Melechko, Anatoli Vasilievich

2012-01-01

Neural chips, which are capable of simultaneous, multi-site neural recording and stimulation, have been used to detect and modulate neural activity for almost 30 years. As a neural interface, neural chips provide dynamic functional information for neural decoding and neural control. By improving sensitivity and spatial resolution, nano-scale electrodes may revolutionize neural detection and modulation at cellular and molecular levels as nano-neuron interfaces. We developed a carbon-nanofiber neural chip with lithographically defined arrays of vertically aligned carbon nanofiber electrodes and demonstrated its capability of both stimulating and monitoring electrophysiological signals from brain tissues in vitro and monitoring dynamic information ofmore » neuroplasticity. This novel nano-neuron interface can potentially serve as a precise, informative, biocompatible, and dual-mode neural interface for monitoring of both neuroelectrical and neurochemical activity at the single cell level and even inside the cell.« less

Alignment of Standards and Assessment: A Theoretical and Empirical Study of Methods for Alignment

ERIC Educational Resources Information Center

Nasstrom, Gunilla; Henriksson, Widar

2008-01-01

Introduction: In a standards-based school-system alignment of policy documents with standards and assessment is important. To be able to evaluate whether schools and students have reached the standards, the assessment should focus on the standards. Different models and methods can be used for measuring alignment, i.e. the correspondence between…

Is the aligning prism measured with the Mallett unit correlated with fusional vergence reserves?

PubMed

Conway, Miriam L; Thomas, Jennifer; Subramanian, Ahalya

2012-01-01

The Mallett Unit is a clinical test designed to detect the fixation disparity that is most likely to occur in the presence of a decompensated heterophoria. It measures the associated phoria, which is the "aligning prism" needed to nullify the subjective disparity. The technique has gained widespread acceptance within professions such as optometry, for investigating suspected cases of decompensating heterophoria; it is, however, rarely used by orthoptists and ophthalmologists. The aim of this study was to investigate whether fusional vergence reserves, measured routinely by both orthoptists and ophthalmologists to detect heterophoria decompensation, were correlated with aligning prism (associated phoria) in a normal clinical population. Aligning prism (using the Mallett Unit) and fusional vergence reserves (using a prism bar) were measured in 500 participants (mean 41.63 years; standard deviation 11.86 years) at 40 cm and 6 m. At 40 cm a strong correlation (p<0.001) between base in aligning prism (Exo FD) and positive fusional reserves was found. Of the participants with zero aligning prism 30% had reduced fusional reserves. At 6 m a weak correlation between base out aligning prism (Eso FD) and negative fusional reserves was found to break (p = 0.01) and to recovery (p = 0.048). Of the participants with zero aligning prism 12% reported reduced fusional reserves. For near vision testing, the strong inverse correlation between base in aligning prism (Exo FD) and fusional vergence reserves supports the notion that both measures are indicators of decompensation of heterophoria. For distance vision testing and for those patients reporting zero aligning prism further research is required to determine why the relationship appears to be weak/non-existent?

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.

Is the Aligning Prism Measured with the Mallett Unit Correlated with Fusional Vergence Reserves?

PubMed Central

Conway, Miriam L.; Thomas, Jennifer; Subramanian, Ahalya

2012-01-01

Background The Mallett Unit is a clinical test designed to detect the fixation disparity that is most likely to occur in the presence of a decompensated heterophoria. It measures the associated phoria, which is the “aligning prism” needed to nullify the subjective disparity. The technique has gained widespread acceptance within professions such as optometry, for investigating suspected cases of decompensating heterophoria; it is, however, rarely used by orthoptists and ophthalmologists. The aim of this study was to investigate whether fusional vergence reserves, measured routinely by both orthoptists and ophthalmologists to detect heterophoria decompensation, were correlated with aligning prism (associated phoria) in a normal clinical population. Methodology/Principal Findings Aligning prism (using the Mallett Unit) and fusional vergence reserves (using a prism bar) were measured in 500 participants (mean 41.63 years; standard deviation 11.86 years) at 40 cm and 6 m. At 40 cm a strong correlation (p<0.001) between base in aligning prism (Exo FD) and positive fusional reserves was found. Of the participants with zero aligning prism 30% had reduced fusional reserves. At 6 m a weak correlation between base out aligning prism (Eso FD) and negative fusional reserves was found to break (p = 0.01) and to recovery (p = 0.048). Of the participants with zero aligning prism 12% reported reduced fusional reserves. Conclusions/Significance For near vision testing, the strong inverse correlation between base in aligning prism (Exo FD) and fusional vergence reserves supports the notion that both measures are indicators of decompensation of heterophoria. For distance vision testing and for those patients reporting zero aligning prism further research is required to determine why the relationship appears to be weak/non-existent? PMID:22905174

AGILE: Autonomous Global Integrated Language Exploitation

DTIC Science & Technology

2009-12-01

combination, including METEOR-based alignment (with stemming and WordNet synonym matching) and GIZA ++ based alignment. So far, we have not seen any...parse trees and a detailed analysis of how function words operate in translation. This program lets us fix alignment errors that systems like GIZA ...correlates better with Pyramid than with Responsiveness scoring (i.e., it is a more precise, careful, measure) • BE generally outperforms ROUGE

Controlled Synthesis and Functionalization of Vertically-Aligned Carbon Nanotubes for Multifunctional Applications

DTIC Science & Technology

2015-05-07

6 1.6 Lithium - Ion Batteries Based on Vertically-Aligned Carbon Nanotube Electrodes and Ionic...Cl, Br, or I) Prepared by Ball-Milling and Used as Anode Materials for Lithium - Ion Batteries ……………....................23 3.4 Well-Defined Two...9 1.6 Lithium - Ion Batteries Based on Vertically-Aligned Carbon Nanotube Electrodes and Ionic Liquid Electrolytes

Six health care trends that will reshape the patient-provider dynamic.

PubMed

Liao, Joshua M; Emanuel, Ezekiel J; Navathe, Amol S

2016-09-01

Six trends - movement towards value-based payment, rapid adoption of digital health technology, care delivery in non-traditional settings, development of individualized clinical guidelines, increased transparency, and growing cultural awareness about the harms of medical overuse - are driving the US health care system towards a future defined by quality- and patient-centric care. Health care organizations are responding to these changes by implementing provider and workforce changes, pursuing stronger payer-provider integration, and accelerating the use of digital technology and data. While these efforts can also improve the clinical relationship and create positive system redesign among health care organizations, they require alignment between organizational and physician incentives that can inadvertently harm the dynamic between patients and providers. Organizations can utilize several strategies to preserve the patient-physician relationship and advance the positive benefits of new organizational strategies while guarding against unintended consequences. Copyright © 2016 Elsevier Inc. All rights reserved.

Kerman's Problem in the Continuum

NASA Astrophysics Data System (ADS)

Macchiavelli, A. O.; Casten, R. F.; Clark, R. M.; Campbell, C. M.; Crawford, H. L.; Cromaz, M.; Fallon, P.; Jones, M. D.; Salathe, M.

2017-09-01

In 1956 Kerman published a seminal paper on rotational perturbations in nuclei. Since then, Coriolis and rotational alignment effects have been extensively studied and are rather well understood. With the development of exotic beam facilities and advanced instrumentation it is becoming possible to access regions of deformation in the nuclear chart, near the neutron drip-line. Here, the effects of weak binding are expected to play an important role, affecting the dynamics of the nuclear motion. In this work we study Kerman's problem when the single-particle levels involved are resonant states. We will present results showing the behavior of the kinematic and dynamic moments of inertia as a function of the state widths. Connection to possible experiments will be discussed. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Nuclear Physics under Contract No. DE-AC02-05CH11231 (LBNL).

Ultra-sensitive all-fibre photothermal spectroscopy with large dynamic range

PubMed Central

Jin, Wei; Cao, Yingchun; Yang, Fan; Ho, Hoi Lut

2015-01-01

Photothermal interferometry is an ultra-sensitive spectroscopic means for trace chemical detection in gas- and liquid-phase materials. Previous photothermal interferometry systems used free-space optics and have limitations in efficiency of light–matter interaction, size and optical alignment, and integration into photonic circuits. Here we exploit photothermal-induced phase change in a gas-filled hollow-core photonic bandgap fibre, and demonstrate an all-fibre acetylene gas sensor with a noise equivalent concentration of 2 p.p.b. (2.3 × 10−9 cm−1 in absorption coefficient) and an unprecedented dynamic range of nearly six orders of magnitude. The realization of photothermal interferometry with low-cost near infrared semiconductor lasers and fibre-based technology allows a class of optical sensors with compact size, ultra sensitivity and selectivity, applicability to harsh environment, and capability for remote and multiplexed multi-point detection and distributed sensing. PMID:25866015

Towards an Ontology for Reef Islands

NASA Astrophysics Data System (ADS)

Duce, Stephanie

Reef islands are complex, dynamic and vulnerable environments with a diverse range of stake holders. Communication and data sharing between these different groups of stake holders is often difficult. An ontology for the reef island domain would improve the understanding of reef island geomorphology and improve communication between stake holders as well as forming a platform from which to move towards interoperability and the application of Information Technology to forecast and monitor these environments. This paper develops a small, prototypical reef island domain ontology, based on informal, natural language relations, aligned to the DOLCE upper-level ontology, for 20 fundamental terms within the domain. A subset of these terms and their relations are discussed in detail. This approach reveals and discusses challenges which must be overcome in the creation of a reef island domain ontology and which could be relevant to other ontologies in dynamic geospatial domains.

Cooling rate dependence of structural order in Ni 62 Nb 38 metallic glass

DOE PAGES

Wen, Tongqi; Sun, Yang; Ye, Beilin; ...

2018-01-31

In this article, molecular dynamics (MD) simulations are performed to study the structure of Ni 62Nb 38 bulk metallic glass at the atomistic level. Structural analysis based on the cluster alignment method is carried out and a new Ni-centered distorted-icosahedra (DISICO) motif is excavated. We show that the short-range order and medium-range order in the glass are enhanced with lower cooling rate. Almost 50% of the clusters around the Ni atoms in the well-annealed Ni 62Nb 38 glass sample from our MD simulations can be classified as DISICO. It is revealed that the structural distortion with respect to the perfectmore » icosahedra is driven by chemical ordering in the distorted region of the DISICO motif. The relationship between the structure, energy, and dynamics in this glass-forming alloy during the cooling and annealing processes is also established.« less

Metallic Glass Wire Based Localization of Kinesin/Microtubule Bio-molecular Motility System

NASA Astrophysics Data System (ADS)

Kim, K.; Sikora, A.; Yaginuma, S.; Nakayama, K. S.; Nakazawa, H.; Umetsu, M.; Hwang, W.; Teizer, W.

2014-03-01

We report electrophoretic accumulation of microtubules along metallic glass (Pd42.5Cu30Ni7.5P20) wires free-standing in solution. Microtubules are dynamic cytoskeletal filaments. Kinesin is a cytoskeletal motor protein. Functions of these bio-molecules are central to various dynamic cellular processes. Functional artificial organization of bio-molecules is a prerequisite for transferring their native functions into device applications. Fluorescence microscopy at the individual-microtubule level reveals microtubules aligning along the wire axis during the electrophoretic migration. Casein-treated electrodes are effective for releasing trapped microtubules upon removal of the external field. Furthermore, we demonstrate gliding motion of microtubules on kinesin-treated metallic glass wires. The reversible manner in the local adsorption of microtubules, the flexibility of wire electrodes, and the compatibility between the wire electrode and the bio-molecules are beneficial for spatio-temporal manipulation of the motility machinery in 3 dimensions.

Cooling rate dependence of structural order in Ni 62 Nb 38 metallic glass

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

Wen, Tongqi; Sun, Yang; Ye, Beilin

In this article, molecular dynamics (MD) simulations are performed to study the structure of Ni 62Nb 38 bulk metallic glass at the atomistic level. Structural analysis based on the cluster alignment method is carried out and a new Ni-centered distorted-icosahedra (DISICO) motif is excavated. We show that the short-range order and medium-range order in the glass are enhanced with lower cooling rate. Almost 50% of the clusters around the Ni atoms in the well-annealed Ni 62Nb 38 glass sample from our MD simulations can be classified as DISICO. It is revealed that the structural distortion with respect to the perfectmore » icosahedra is driven by chemical ordering in the distorted region of the DISICO motif. The relationship between the structure, energy, and dynamics in this glass-forming alloy during the cooling and annealing processes is also established.« less

Solar dynamic power module design

NASA Technical Reports Server (NTRS)

Secunde, Richard R.; Labus, Thomas L.; Lovely, Ronald G.

1989-01-01

Studies have shown that use of solar dynamic (SD) power for the growth eras of the Space Station Freedom program will result in life cycle cost savings when compared to power supplied by photovoltaic sources. In the SD power module, a concentrator collects and focuses solar energy into a heat receiver which has integral thermal energy storage. A power conversion unit (PCU) based on the closed Brayton thermodynamic cycle removes thermal energy from the receiver and converts that energy to electrical energy. Since the closed Brayton cycle is a single phase gas cycle, the conversion hardware (heat exchangers, turbine, compressor, etc.) can be designed for operation in low earth orbit, and tested with confidence in test facilities on earth before launch into space. The concentrator subassemblies will be aligned and the receiver/PCU/radiator combination completely assembled and charged with gas and cooling liquid on earth before launch to, and assembly on orbit.

Cooling rate dependence of structural order in Ni62Nb38 metallic glass

NASA Astrophysics Data System (ADS)

Wen, Tongqi; Sun, Yang; Ye, Beilin; Tang, Ling; Yang, Zejin; Ho, Kai-Ming; Wang, Cai-Zhuang; Wang, Nan

2018-01-01

Molecular dynamics (MD) simulations are performed to study the structure of Ni62Nb38 bulk metallic glass at the atomistic level. Structural analysis based on the cluster alignment method is carried out and a new Ni-centered distorted-icosahedra (DISICO) motif is excavated. We show that the short-range order and medium-range order in the glass are enhanced with lower cooling rate. Almost 50% of the clusters around the Ni atoms in the well-annealed Ni62Nb38 glass sample from our MD simulations can be classified as DISICO. It is revealed that the structural distortion with respect to the perfect icosahedra is driven by chemical ordering in the distorted region of the DISICO motif. The relationship between the structure, energy, and dynamics in this glass-forming alloy during the cooling and annealing processes is also established.

Huddle-coaching: a dynamic intervention for trainees and staff to support team-based care.

PubMed

Shunk, Rebecca; Dulay, Maya; Chou, Calvin L; Janson, Susan; O'Brien, Bridget C

2014-02-01

Many outpatient clinics where health professionals train will transition to a team-based medical home model over the next several years. Therefore, training programs need innovative approaches to prepare and incorporate trainees into team-based delivery systems. To address this need, educators at the San Francisco Veterans Affairs (VA) Medical Center included trainees in preclinic team "huddles," or briefing meetings to facilitate care coordination, and developed an interprofessional huddle-coaching program for nurse practitioner students and internal medicine residents who function as primary providers for patient panels in VA outpatient primary care clinics. The program aimed to support trainees' partnerships with staff and full participation in the VA's Patient Aligned Care Teams. The huddle-coaching program focuses on structuring the huddle process via scheduling, checklists, and designated huddle coaches; building relationships among team members through team-building activities; and teaching core skills to support collaborative practice. A multifaceted evaluation of the program showed positive results. Participants rated training sessions and team-building activities favorably. In interviews, trainees valued their team members and identified improvements in efficiency and quality of patient care as a result of the team-based approach. Huddle checklists and scores on the Team Development Measure indicated progress in team processes and relationships as the year progressed. These findings suggest that the huddle-coaching program was a worthwhile investment in trainee development that also supported the clinic's larger mission to deliver team-based, patient-aligned care. As more training sites shift to team-based care, the huddle-coaching program offers a strategy for successfully incorporating trainees.

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.

Effect of multi-dimensional ultraviolet light exposure on the growth of pentacene film and application to organic field-effect transistors.

PubMed

Bae, Jin-Hyuk; Lee, Sin-Doo; Choi, Jong Sun; Park, Jaehoon

2012-05-01

We report on the multi-dimensional alignment of pentacene molecules on a poly(methyl methacrylate)-based photosensitive polymer (PMMA-polymer) and its effect on the electrical performance of the pentacene-based field-effect transistor (FET). Pentacene molecules are shown to be preferentially aligned on the linearly polarized ultraviolet (LPUV)-exposed PMMA-polymer layer, which is contrast to an isotropic alignment on the bare PMMA-polymer layer. Multi-dimensional alignment of pentacene molecules in the film could be achieved by adjusting the direction of LPUV exposed to the PMMA-polymer. The control of pentacene molecular alignment is found to be promising for the field-effect mobility enhancement in the pentacene FET.

Fuzzy adaptive strong tracking scaled unscented Kalman filter for initial alignment of large misalignment angles

NASA Astrophysics Data System (ADS)

Li, Jing; Song, Ningfang; Yang, Gongliu; Jiang, Rui

2016-07-01

In the initial alignment process of strapdown inertial navigation system (SINS), large misalignment angles always bring nonlinear problem, which can usually be processed using the scaled unscented Kalman filter (SUKF). In this paper, the problem of large misalignment angles in SINS alignment is further investigated, and the strong tracking scaled unscented Kalman filter (STSUKF) is proposed with fixed parameters to improve convergence speed, while these parameters are artificially constructed and uncertain in real application. To further improve the alignment stability and reduce the parameters selection, this paper proposes a fuzzy adaptive strategy combined with STSUKF (FUZZY-STSUKF). As a result, initial alignment scheme of large misalignment angles based on FUZZY-STSUKF is designed and verified by simulations and turntable experiment. The results show that the scheme improves the accuracy and convergence speed of SINS initial alignment compared with those based on SUKF and STSUKF.

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

Orientation and Order in Shear-Aligned Thin Films of Cylinder-Forming Block Copolymers

NASA Astrophysics Data System (ADS)

Register, Richard

The regularity and tunability of the nanoscale structure in block copolymers makes their thin films attractive as nanolithographic templates; however, in the absence of a guiding field, self-assembly produces a polygrain structure with no particular orientation and a high density of defects. As demonstrated in the elegant studies of Ed Kramer and coworkers, graphoepitaxy can provide local control over domain orientation, with a dramatic reduction in defect density. Alternatively, cylindrical microdomains lying in the plane of the film can be aligned over macroscopic areas by applying shear stress at the film surface. In non-sheared films of polystyrene-poly(n-hexylmethacrylate) diblocks, PS-PHMA, the PS cylinder axis orientation relative to the surface switches from parallel to perpendicular as a function of film thickness; this oscillation is damped out as the fraction of the PS block increases, away from the sphere-cylinder phase boundary. In aligned films, thicknesses which possess the highest coverage of parallel cylinders prior to shear show the highest quality of alignment post-shear, as measured by the in-plane orientational order parameter. In well-aligned samples of optimal thickness, the quality of alignment is limited by isolated dislocations, whose density is highest at high PS contents, and by undulations in the cylinders' trajectories, whose impact is most severe at low PS contents; consequently, polymers whose compositions lie in the middle of the cylinder-forming region exhibit the highest quality of alignment. The dynamics of the alignment process are also investigated, and fit to a melting-recrystallization model which allows for the determination of two key alignment parameters: the critical stress needed for alignment, and an orientation rate constant. For films containing a monolayer of cylindrical domains, as PS weight fraction or overall molecular weight increases, the critical stress increases moderately, while the rate of alignment drastically decreases. As the number of layers of cylinders in the film increases, the critical stress decreases modestly, while the rate remains unchanged; substrate wetting condition has no measurable influence on alignment response. [Work of Raleigh Davis, in collaboration with Paul Chaikin.

The SRI24 multichannel brain atlas: construction and applications

NASA Astrophysics Data System (ADS)

Rohlfing, Torsten; Zahr, Natalie M.; Sullivan, Edith V.; Pfefferbaum, Adolf

2008-03-01

We present a new standard atlas of the human brain based on magnetic resonance images. The atlas was generated using unbiased population registration from high-resolution images obtained by multichannel-coil acquisition at 3T in a group of 24 normal subjects. The final atlas comprises three anatomical channels (T I-weighted, early and late spin echo), three diffusion-related channels (fractional anisotropy, mean diffusivity, diffusion-weighted image), and three tissue probability maps (CSF, gray matter, white matter). The atlas is dynamic in that it is implicitly represented by nonrigid transformations between the 24 subject images, as well as distortion-correction alignments between the image channels in each subject. The atlas can, therefore, be generated at essentially arbitrary image resolutions and orientations (e.g., AC/PC aligned), without compounding interpolation artifacts. We demonstrate in this paper two different applications of the atlas: (a) region definition by label propagation in a fiber tracking study is enabled by the increased sharpness of our atlas compared with other available atlases, and (b) spatial normalization is enabled by its average shape property. In summary, our atlas has unique features and will be made available to the scientific community as a resource and reference system for future imaging-based studies of the human brain.

Design of and normative data for a new computer based test of ocular torsion.

PubMed

Vaswani, Reena S; Mudgil, Ananth V

2004-01-01

To evaluate a new clinically practical and dynamic test for quantifying torsional binocular eye alignment changes which may occur in the change from monocular to binocular viewing conditions. The test was developed using a computer with Lotus Freelance Software, binoculars with prisms and colored filters. The subject looks through binoculars at the computer screen two meters away. For monocular vision, six concentric blue circles, a blue horizontal line and a tilted red line were displayed on the screen. For binocular vision, white circles replaced blue circles. The subject was asked to orient the lines parallel to each other. The difference in tilt (degrees) between the subjective parallel and fixed horizontal position is the torsional alignment of the eye. The time to administer the test was approximately two minutes. In 70 Normal subjects, average age 16 years, the mean degree of cyclodeviation tilt in the right eye was 0.6 degrees for monocular viewing conditions and 0.7 degrees for binocular viewing conditions, with a standard deviation of approximately one degree. There was no "statistically significant" difference between monocular and binocular viewing. This computer based test is a simple, computerized, non-invasive test that has a potential for use in the diagnosis of cyclovertical strabismus. Currently, there is no commercially available test for this purpose.

Quantifying the relationship between the plasmapause and the inner boundary of small-scale field-aligned currents, as deduced from Swarm observations

NASA Astrophysics Data System (ADS)

Heilig, Balázs; Lühr, Hermann

2018-04-01

This paper presents a statistical study of the equatorward boundary of small-scale field-aligned currents (SSFACs) and investigates the relation between this boundary and the plasmapause (PP). The PP data used for validation were derived from in situ electron density observations of NASA's Van Allen Probes. We confirmed the findings of a previous study by the same authors obtained from the observations of the CHAMP satellite SSFAC and the NASA IMAGE satellite PP detections, namely that the two boundaries respond similarly to changes in geomagnetic activity, and they are closely located in the near midnight MLT sector, suggesting a dynamic linkage. Dayside PP correlates with the delayed time history of the SSFAC boundary. We interpreted this behaviour as a direct consequence of co-rotation: the new PP, formed on the night side, propagates to the dayside by rotating with Earth. This finding paves the way toward an efficient PP monitoring tool based on an SSFAC index derived from vector magnetic field observations at low-Earth orbit.

Dynamic in-situ sensing of fluid-dispersed 2D materials integrated on microfluidic Si chip.

PubMed

Hogan, Benjamin T; Dyakov, Sergey A; Brennan, Lorcan J; Younesy, Salma; Perova, Tatiana S; Gun'ko, Yurii K; Craciun, Monica F; Baldycheva, Anna

2017-02-10

In this work, we propose a novel approach for wafer-scale integration of 2D materials on CMOS photonic chip utilising methods of synthetic chemistry and microfluidics technology. We have successfully demonstrated that this approach can be used for integration of any fluid-dispersed 2D nano-objects on silicon-on-insulator photonics platform. We demonstrate for the first time that the design of an optofluidic waveguide system can be optimised to enable simultaneous in-situ Raman spectroscopy monitoring of 2D dispersed flakes during the device operation. Moreover, for the first time, we have successfully demonstrated the possibility of label-free 2D flake detection via selective enhancement of the Stokes Raman signal at specific wavelengths. We discovered an ultra-high signal sensitivity to the xyz alignment of 2D flakes within the optofluidic waveguide. This in turn enables precise in-situ alignment detection, for the first practicable realisation of 3D photonic microstructure shaping based on 2D-fluid composites and CMOS photonics platform, while also representing a useful technological tool for the control of liquid phase deposition of 2D materials.

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

PubMed

Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

2013-01-01

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

Misalignment in Gas Foil Journal Bearings: An Experimental Study

NASA Technical Reports Server (NTRS)

Howard, Samuel A.

2008-01-01

As gas foil journal bearings become more prevalent in production machines, such as small gas turbine propulsion systems and microturbines, system-level performance issues must be identified and quantified in order to provide for successful design practices. Several examples of system-level design parameters that are not fully understood in foil bearing systems are thermal management schemes, alignment requirements, balance requirements, thrust load balancing, and others. In order to address some of these deficiencies and begin to develop guidelines, this paper presents a preliminary experimental investigation of the misalignment tolerance of gas foil journal bearing systems. Using a notional gas foil bearing supported rotor and a laser-based shaft alignment system, increasing levels of misalignment are imparted to the bearing supports while monitoring temperature at the bearing edges. The amount of misalignment that induces bearing failure is identified and compared to other conventional bearing types such as cylindrical roller bearings and angular contact ball bearings. Additionally, the dynamic response of the rotor indicates that the gas foil bearing force coefficients may be affected by misalignment.

Orbital misalignment of the Neptune-mass exoplanet GJ 436b with the spin of its cool star

NASA Astrophysics Data System (ADS)

Bourrier, Vincent; Lovis, Christophe; Beust, Hervé; Ehrenreich, David; Henry, Gregory W.; Astudillo-Defru, Nicola; Allart, Romain; Bonfils, Xavier; Ségransan, Damien; Delfosse, Xavier; Cegla, Heather M.; Wyttenbach, Aurélien; Heng, Kevin; Lavie, Baptiste; Pepe, Francesco

2018-01-01

The angle between the spin of a star and the orbital planes of its planets traces the history of the planetary system. Exoplanets orbiting close to cool stars are expected to be on circular, aligned orbits because of strong tidal interactions with the stellar convective envelope. Spin–orbit alignment can be measured when the planet transits its star, but such ground-based spectroscopic measurements are challenging for cool, slowly rotating stars. Here we report the three-dimensional characterization of the trajectory of an exoplanet around an M dwarf star, derived by mapping the spectrum of the stellar photosphere along the chord transited by the planet. We find that the eccentric orbit of the Neptune-mass exoplanet GJ 436b is nearly perpendicular to the stellar equator. Both eccentricity and misalignment, surprising around a cool star, can result from dynamical interactions (via Kozai migration) with a yet-undetected outer companion. This inward migration of GJ 436b could have triggered the atmospheric escape that now sustains its giant exosphere.

Coherent clusters of inertial particles in homogeneous turbulence

NASA Astrophysics Data System (ADS)

Baker, Lucia; Frankel, Ari; Mani, Ali; Coletti, Filippo

2016-11-01

Clustering of heavy particles in turbulent flows manifests itself in a broad spectrum of physical phenomena, including sediment transport, cloud formation, and spray combustion. However, a clear topological definition of particle cluster has been lacking, limiting our ability to describe their features and dynamics. Here we introduce a definition of coherent cluster based on self-similarity, and apply it to the distribution of heavy particles in direct numerical simulations of homogeneous isotropic turbulence. We consider a range of particle Stokes numbers, with and without the effect of gravity. Clusters show self-similarity at length scales larger than twice the Kolmogorov length, with a specific fractal dimension. In the absence of gravity, clusters demonstrate a tendency to sample regions of the flow where strain is dominant over vorticity, and to align themselves with the local vorticity vector; when gravity is present, the clusters tend to align themselves with gravity, and their fall speed is different from the average settling velocity. This approach yields observations which are consistent with findings obtained from previous studies while opening new avenues for analysis of the topology and evolution of particle clusters in a wealth of applications.

Web-4D-QSAR: A web-based application to generate 4D-QSAR descriptors.

PubMed

Ataide Martins, João Paulo; Rougeth de Oliveira, Marco Antônio; Oliveira de Queiroz, Mário Sérgio

2018-06-05

A web-based application is developed to generate 4D-QSAR descriptors using the LQTA-QSAR methodology, based on molecular dynamics (MD) trajectories and topology information retrieved from the GROMACS package. The LQTAGrid module calculates the intermolecular interaction energies at each grid point, considering probes and all aligned conformations resulting from MD simulations. These interaction energies are the independent variables or descriptors employed in a QSAR analysis. A friendly front end web interface, built using the Django framework and Python programming language, integrates all steps of the LQTA-QSAR methodology in a way that is transparent to the user, and in the backend, GROMACS and LQTAGrid are executed to generate 4D-QSAR descriptors to be used later in the process of QSAR model building. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Towards A Self Adaptive System for Social Wellness.

PubMed

Khattak, Asad Masood; Khan, Wajahat Ali; Pervez, Zeeshan; Iqbal, Farkhund; Lee, Sungyoung

2016-04-13

Advancements in science and technology have highlighted the importance of robust healthcare services, lifestyle services and personalized recommendations. For this purpose patient daily life activity recognition, profile information, and patient personal experience are required. In this research work we focus on the improvement in general health and life status of the elderly through the use of an innovative services to align dietary intake with daily life and health activity information. Dynamic provisioning of personalized healthcare and life-care services are based on the patient daily life activities recognized using smart phone. To achieve this, an ontology-based approach is proposed, where all the daily life activities and patient profile information are modeled in ontology. Then the semantic context is exploited with an inference mechanism that enables fine-grained situation analysis for personalized service recommendations. A generic system architecture is proposed that facilitates context information storage and exchange, profile information, and the newly recognized activities. The system exploits the patient's situation using semantic inference and provides recommendations for appropriate nutrition and activity related services. The proposed system is extensively evaluated for the claims and for its dynamic nature. The experimental results are very encouraging and have shown better accuracy than the existing system. The proposed system has also performed better in terms of the system support for a dynamic knowledge-base and the personalized recommendations.

Web-based resources for mass-spectrometry-based metabolomics: a user's guide.

PubMed

Tohge, Takayuki; Fernie, Alisdair R

2009-03-01

In recent years, a plethora of web-based tools aimed at supporting mass-spectrometry-based metabolite profiling and metabolomics applications have appeared. Given the huge hurdles presented by the chemical diversity and dynamic range of the metabolites present in the plant kingdom, profiling the levels of a broad range of metabolites is highly challenging. Given the scale and costs involved in defining the plant metabolome, it is imperative that data are effectively shared between laboratories pursuing this goal. However, ensuring accurate comparison of samples run on the same machine within the same laboratory, let alone cross-machine and cross-laboratory comparisons, requires both careful experimentation and data interpretation. In this review, we present an overview of currently available software that aids either in peak identification or in the related field of peak alignment as well as those with utility in defining structural information of compounds and metabolic pathways.

Can CT-based patient-matched instrumentation achieve consistent rotational alignment in knee arthroplasty?

PubMed

Tibesku, C O; Innocenti, B; Wong, P; Salehi, A; Labey, L

2012-02-01

Long-term success of contemporary total knee replacements relies to a large extent on proper implant alignment. This study was undertaken to test whether specimen-matched cutting blocks based on computed axial tomography (CT) scans could provide accurate rotational alignment of the femoral component. CT scans of five fresh frozen full leg cadaver specimens, equipped with infrared reflective markers, were used to produce a specimen-matched femoral cutting block. Using those blocks, the bone cuts were made to implant a bi-compartmental femoral component. Rotational alignment of the components in the horizontal plane was determined using an optical measurement system and compared with all relevant rotational reference axes identified on the CT scans. Average rotational alignment for the bi-compartmental component in the horizontal plane was 1.9° (range 0°-6.3°; standard deviation 2.6°). One specimen that showed the highest deviation from the planned alignment also featured a completely degraded medial articular surface. The CT-based specimen-matched cutting blocks achieved good rotational alignment accuracy except for one specimen with badly damaged cartilage. In such cases, imaging techniques that visualize the cartilage layer might be more suitable to design cutting blocks, as they will provide a better fit and increased surface support.

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

PubMed Central

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

2014-01-01

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

Synthesis and supramolecular assembly of biomimetic polymers

NASA Astrophysics Data System (ADS)

Marciel, Amanda Brittany

A grand challenge in materials chemistry is the synthesis of macromolecules and polymers with precise shapes and architectures. Polymer microstructure and architecture strongly affect the resulting functionality of advanced materials, yet understanding the static and dynamic properties of these complex macromolecules in bulk has been difficult due to their inherit polydispersity. Single molecule studies have provided a wealth of information on linear flexible and semi-flexible polymers in dilute solutions. However, few investigations have focused on industrially relevant complex topologies (e.g., star, comb, hyperbranched polymers) in industrially relevant solution conditions (e.g., semi-dilute, concentrated). Therefore, from this perspective there is a strong need to synthesize precision complex architectures for bulk studies as well as complex architectures compatible with current single molecule techniques to study static and dynamic polymer properties. In this way, we developed a hybrid synthetic strategy to produce branched polymer architectures based on chemically modified DNA. Overall, this approach enables control of backbone length and flexibility, as well as branch grafting density and chemical identity. We utilized a two-step scheme based on enzymatic incorporation of non-natural nucleotides containing bioorthogonal dibenzocyclooctyne (DBCO) functional groups along the main polymer backbone, followed by copper-free "click" chemistry to graft synthetic polymer branches or oligonucleotide branches to the DNA backbone, thereby allowing for the synthesis of a variety of polymer architectures, including three-arm stars, H-polymers, graft block copolymers, and comb polymers for materials assembly and single molecule studies. Bulk materials properties are also affected by industrial processing conditions that alter polymer morphology. Therefore, in an alternative strategy we developed a microfluidic-based approach to assemble highly aligned synthetic oligopeptides nanostructures using microscale extensional flows. This strategy enabled reproducible, reliable fabrication of aligned hierarchical constructs that do not form spontaneously in solution. In this way, fluidic-directed assembly of supramolecular structures allows for unprecedented manipulation at the nano- and mesoscale, which has the potential to provide rapid and efficient control of functional materials properties.

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

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

PubMed Central

Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

2013-01-01

Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

Optical attenuation mechanism upgrades, MOBLAS, and TLRS systems

NASA Technical Reports Server (NTRS)

Eichinger, Richard; Johnson, Toni; Malitson, Paul; Oldham, Thomas; Stewart, Loyal

1993-01-01

This poster presentation describes the Optical Attenuation Mechanism (OAM) Upgrades to the MOBLAS and TLRS Crustal Dynamics Satellite Laser Ranging (CDSLR) systems. The upgrades were for the purposes of preparing these systems to laser range to the TOPEX/POSEIDON spacecraft when it will be launched in the summer of 1992. The OAM permits the laser receiver to operate over the expected large signal dynamic range from TOPEX/POSEIDON and it reduces the number of pre- and post-calibrations for each satellite during multi-satellite tracking operations. It further simplifies the calibration bias corrections that had been made due to the pass-to-pass variation of the photomultiplier supply voltage and the transmit filter glass thickness. The upgrade incorporated improvements to the optical alignment capability of each CDSLR system through the addition of a CCD camera into the MOBLAS receive telescope and an alignment telescope onto the TLRS optical table. The OAM is stepper motor and microprocessor based; and the system can be controlled either manually by a control switch panel or computer controlled via an EIA RS-232C serial interface. The OAM has a neutral density (ND) range of 0.0 to 4.0 and the positioning is absolute referenced in steps of 0.1 ND. Both the fixed transmit filter and the daylight filter are solenoid actuated with digital inputs and outputs to and from the OAM microprocessor. During automated operation, the operator has the option to overide the remote control and control the OAM system via a local control switch panel.

Simulation study of the initial crystallization processes of poly(3-hexylthiophene) in solution: ordering dynamics of main chains and side chains.

PubMed

Takizawa, Yuumi; Shimomura, Takeshi; Miura, Toshiaki

2013-05-23

We study the initial nucleation dynamics of poly(3-hexylthiophene) (P3HT) in solution, focusing on the relationship between the ordering process of main chains and that of side chains. We carried out Langevin dynamics simulation and found that the initial nucleation processes consist of three steps: the ordering of ring orientation, the ordering of main-chain vectors, and the ordering of side chains. At the start, the normal vectors of thiophene rings aligned in a very short time, followed by alignment of main-chain end-to-end vectors. The flexible side-chain ordering took almost 5 times longer than the rigid-main-chain ordering. The simulation results indicated that the ordering of side chains was induced after the formation of the regular stack structure of main chains. This slow ordering dynamics of flexible side chains is one of the factors that cause anisotropic nuclei growth, which would be closely related to the formation of nanofiber structures without external flow field. Our simulation results revealed how the combined structure of the planar and rigid-main-chain backbones and the sparse flexible side chains lead to specific ordering behaviors that are not observed in ordinary linear polymer crystallization processes.

Defense Meteorological Satellite Program Data in Dynamic Auroral Boundary Coordinates: New insights into Polar Cap and Auroral Dynamics

NASA Astrophysics Data System (ADS)

Knipp, D.

2016-12-01

Using reprocessed (Level-2) data from the Defense Meteorology Satellite Program magnetometer (SSM) and particle precipitation (SSJ) instruments we determine the boundaries of the central plasma sheet auroral oval, and then consider the relative locations and intensities of field aligned currents. Large-scale field-aligned currents (FAC) are determined using the Minimum Variance Analysis technique, and their influence is then removed from the magnetic perturbations allowing us to estimate intensity and scale-size of the smaller-scale currents. When sorted by dynamic auroral boundary coordinates we find that large- scale Region 1 (R1) FAC are often within the polar cap and Region 2 (R2) FAC show a strong dawn-dusk asymmetry (as in Ohtani et al., 2010). We find that mesoscale FAC are stronger in the summer and are most consistently present in the vicinity of dawnside (downward) R1 FAC. Further, mesoscale FAC are confined to auroral latitudes and above on the dawnside, but can be subaroural on the dusk side. Hotspots of mesoscale FAC occur in pre-midnight regions especially during summer. Finally, we show how this information can be combined with measurements from above and below the ionosphere-thermosphere to help explain significant perturbations in polar cap dynamics.

CENP-E Kinesin Interacts with SKAP Protein to Orchestrate Accurate Chromosome Segregation in Mitosis*

PubMed Central

Huang, Yuejia; Wang, Wenwen; Yao, Phil; Wang, Xiwei; Liu, Xing; Zhuang, Xiaoxuan; Yan, Feng; Zhou, Jinhua; Du, Jian; Ward, Tarsha; Zou, Hanfa; Zhang, Jiancun; Fang, Guowei; Ding, Xia; Dou, Zhen; Yao, Xuebiao

2012-01-01

Mitotic chromosome segregation is orchestrated by the dynamic interaction of spindle microtubules with the kinetochore. Although previous studies show that the mitotic kinesin CENP-E forms a link between attachment of the spindle microtubule to the kinetochore and the mitotic checkpoint signaling cascade, the molecular mechanism underlying dynamic kinetochore-microtubule interactions in mammalian cells remains elusive. Here, we identify a novel interaction between CENP-E and SKAP that functions synergistically in governing dynamic kinetochore-microtubule interactions. SKAP binds to the C-terminal tail of CENP-E in vitro and is essential for an accurate kinetochore-microtubule attachment in vivo. Immunoelectron microscopic analysis indicates that SKAP is a constituent of the kinetochore corona fibers of mammalian centromeres. Depletion of SKAP or CENP-E by RNA interference results in a dramatic reduction of inter-kinetochore tension, which causes chromosome mis-segregation with a prolonged delay in achieving metaphase alignment. Importantly, SKAP binds to microtubules in vitro, and this interaction is synergized by CENP-E. Based on these findings, we propose that SKAP cooperates with CENP-E to orchestrate dynamic kinetochore-microtubule interaction for faithful chromosome segregation. PMID:22110139

Knee Joint Loading during Gait in Healthy Controls and Individuals with Knee Osteoarthritis

PubMed Central

Kumar, Deepak; Manal, Kurt T.; Rudolph, Katherine S.

2013-01-01

Objective People with knee osteoarthritis (OA) are thought to walk with high loads at the knee which are yet to be quantfied using modeling techniques that account for subject specific EMG patterns, kinematics and kinetics. The objective was to estimate medial and lateral loading for people with knee OA and controls using an approach that is sensitive to subject specific muscle activation patterns. Methods 16 OA and 12 control (C) subjects walked while kinematic, kinetic and EMG data were collected. Muscle forces were calculated using an EMG-Driven model and loading was calculated by balancing the external moments with internal muscle and contact forces Results OA subjects walked slower and had greater laxity, static and dynamic varus alignment, less flexion and greater knee adduction moment (KAM). Loading (normalized to body weight) was no different between the groups but OA subjects had greater absolute medial load than controls and maintained a greater %total load on the medial compartment. These patterns were associated with body mass, sagittal and frontal plane moments, static alignment and close to signficance for dynamic alignment. Lateral compartment unloading during mid-late stance was observed in 50% of OA subjects. Conclusions Loading for control subjects was similar to data from instrumented prostheses. Knee OA subjects had high medial contact loads in early stance and half of the OA cohort demonstared lateral compartment lift-off. Results suggest that interventions aimed at reducing body weight and dynamic malalignment might be effective in reducing medial compartment loading and establishing normal medio-lateral load sharing patterns. PMID:23182814

Regular and reverse nanoscale stick-slip behavior: Modeling and experiments

NASA Astrophysics Data System (ADS)

Landolsi, Fakhreddine; Sun, Yuekai; Lu, Hao; Ghorbel, Fathi H.; Lou, Jun

2010-02-01

We recently proposed a new nanoscale friction model based on the bristle interpretation of single asperity contacts. The model is mathematically continuous and dynamic which makes it suitable for implementation in nanomanipulation and nanorobotic modeling. In the present paper, friction force microscope (FFM) scans of muscovite mica samples and vertically aligned multi-wall carbon nanotubes (VAMWCNTs) arrays are conducted. The choice of these materials is motivated by the fact that they exibit different stick-slip behaviors. The corresponding experimental and simulation results are compared. Our nanoscale friction model is shown to represent both the regular and reverse frictional sawtooth characteristics of the muscovite mica and the VAMWCNTs, respectively.

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

Magnetic field alignment of coil-coil diblock copolymers and blends via intrinsic chain anisotropy

NASA Astrophysics Data System (ADS)

Rokhlenko, Yekaterina; Majewski, Pawel; Larson, Steven; Yager, Kevin; Gopalan, Padma; Avgeropoulos, Apostolos; Chan, Edwin; Osuji, Chinedum

Magnetic fields can control alignment of self-assembled soft materials such as block copolymers provided there is a suitably large magnetic susceptibility anisotropy present in the system. Recent results have highlighted the existence of a non-trivial intrinsic anisotropy in coil-coil diblock copolymers, specifically in lamellar-forming PS-b-P4VP, which enables alignment at field strengths of a few tesla in systems lacking mesogenic components. Alignment is predicated on correlation in the orientation of end-end vectors implied by the localization of block junctions at the microdomain interface and is observed on cooling across the order-disorder transition in the presence of the field. For appropriate combinations of field strength and grain size, we can leverage intrinsic chain anisotropy to magnetically direct self-assembly of many non-mesogenic systems, including other coil-coil BCPs like PS-b-PDMS and PS-b-PMMA, blends of BCPs of disparate morphologies and MWs, and blends of BCPs with homopolymers. This is noteworthy as blends of PS-b-P4VP with PEO provide a route to form functional materials such as nanoporous films by dissolution of PEO, or aligned ion conduction materials. We survey these various systems using TEM and in-situ X-ray scattering to study the phase behavior and temperature-, time- and field- dependent dynamics of alignment.

On the Alignment of Strain, Vorticity and Scalar Gradient in Turbulent, Buoyant, Nonpremixed Flames

NASA Technical Reports Server (NTRS)

Boratav, O. N.; Elghobashi, S. E.; Zhong, R.

1999-01-01

The alignment of vorticity and scalar gradient with the eigendirections of the rate of strain tensor is investigated in turbulent buoyant nonpremixed horizontal and vertical flames. The uniqueness of a buoyant nonpremixed flame is that it contains regions with distinct alignment characteristics. The strain-enstrophy angle Psi is used to identify these regions. Examination of the vorticity field and the vorticity production in these different regions indicates that Psi and consequently the alignment properties near the flame surface identified by the mixture fraction band F approximately equals F(sub st) differ from those in the fuel region, F > F(sub st) and the oxidizer region, F < F(sub st). The F approximately equals F(sub st) band shows strain-dominance resulting in vorticity/alpha alignment while F > F(sub st) (and F < F(sub st) for the vertical flame) band(s) show(s) vorticity/beta alignment. The implication of this result is that the scalar dissipation, epsilon(sub F), attains its maximum value always near F approximately equals F(sub st). These results are also discussed within the framework of recent dynamical results [Galanti et al., Nonlinearity 10, 1675 (1997)] suggesting that the Navier-Stokes equations evolved towards an attracting solution. It is shown that the properties of such an attracting solution are also consistent with our results of buoyant turbulent nonpremixed flames.

Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment

PubMed Central

Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L.; Yao, Xuebiao

2015-01-01

The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C–MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression. PMID:26240331

Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment.

PubMed

Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L; Yao, Xuebiao

2015-08-18

The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C-MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression.