Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations.

PubMed

Feltus, F A; Hart, G E; Schertz, K F; Casa, A M; Kresovich, S; Abraham, S; Klein, P E; Brown, P J; Paterson, A H

2006-05-01

To increase the value of associated molecular tools and also to begin to explore the degree to which interspecific and intraspecific genetic variation in Sorghum is attributable to corresponding genetic loci, we have aligned genetic maps derived from two sorghum populations that share one common parent (Sorghum bicolor L. Moench accession BTx623) but differ in morphological and evolutionarily distant alternate parents (S. propinquum or S. bicolor accession IS3620C). A total of 106 well-distributed DNA markers provide for map alignment, revealing only six nominal differences in marker order that are readily explained by sampling variation or mapping of paralogous loci. We also report a total of 61 new QTLs detected from 17 traits in these crosses. Among eight corresponding traits (some new, some previously published) that could be directly compared between the two maps, QTLs for two (tiller height and tiller number) were found to correspond in a non-random manner (P<0.05). For several other traits, correspondence of subsets of QTLs narrowly missed statistical significance. In particular, several QTLs for leaf senescence were near loci previously mapped for 'stay-green' that have been implicated by others in drought tolerance. These data provide strong validation for the value of molecular tools developed in the interspecific cross for utilization in cultivated sorghum, and begin to separate QTLs that distinguish among Sorghum species from those that are informative within the cultigen (S. bicolor).

Transcription Factor Map Alignment of Promoter Regions

PubMed Central

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

2006-01-01

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

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

PubMed

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

2015-01-01

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

Why do galactic spins flip in the cosmic web? A Theory of Tidal Torques near saddles

NASA Astrophysics Data System (ADS)

Pichon, Christophe; Codis, Sandrine; Pogosyan, Dmitry; Dubois, Yohan; Desjacques, Vincent; Devriendt, Julien

2016-10-01

Filaments of the cosmic web drive spin acquisition of disc galaxies. The point process of filament-type saddle represent best this environment and can be used to revisit the Tidal Torque Theory in the context of an anisotropic peak (saddle) background split. The constrained misalignment between the tidal tensor and the Hessian of the density field generated in the vicinity of filament saddle points simply explains the corresponding transverse and longitudinal point-reflection symmetric geometry of spin distribution. It predicts in particular an azimuthal orientation of the spins of more massive galaxies and spin alignment with the filament for less massive galaxies. Its scale dependence also allows us to relate the transition mass corresponding to the alignment of dark matter halos' spin relative to the direction of their neighboring filament to this geometry, and to predict accordingly it's scaling with the mass of non linearity, as was measured in simulations.

AlignNemo: a local network alignment method to integrate homology and topology.

PubMed

Ciriello, Giovanni; Mina, Marco; Guzzi, Pietro H; Cannataro, Mario; Guerra, Concettina

2012-01-01

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

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

PubMed

Zhang, Zhongqi

2012-04-01

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

Design and fabrication of a self-aligned parallel-plate-type silicon micromirror minimizing the effect of misalignment

NASA Astrophysics Data System (ADS)

Yoo, Byung-Wook; Park, Jae-Hyoung; Jin, Joo-Young; Jang, Yun-Ho; Kim, Yong-Kweon

2009-05-01

This paper describes a self-alignment method whereby a mirror actuation voltage, corresponding to a specific tilting angle, is unvarying in terms of misalignment during fabrication. A deep silicon etching process is proposed to penetrate the top silicon layer (the micromirror layer) and an amorphous silicon layer (the addressing electrode layer) together, through an aluminum mask pattern, in order to minimize the misalignment effect on the micromirror actuation. The size of a fabricated mirror plate is 250 × 250 × 4 µm3. A pair of amorphous silicon electrodes under the mirror plate is about half the size of the mirror plate individually. Numerical analysis associated with calculating the pull-in voltage and the bonding misalignment is performed to verify the self-alignment concepts focused upon in this paper. Curves of the applied voltage versus the tilt angle of the self-aligned micromirror are observed using a position sensing detector in order to compare the measurement results with MATLAB analysis of the expected static deflections. Although a 3.7 µm misalignment is found between the mirror plate and the electrodes, in the direction perpendicular to the shallow trench of the electrodes, before the self-alignment process, the measured pull-in voltage has been found to be 103.4 V on average; this differs from the pull-in voltage of a perfectly aligned micromirror by only 0.67%. Regardless of the unpredictable misalignments in repetitive photolithography and bonding, the tilting angles corresponding to the driving voltages are proved to be uniform along the single axis as well as conform to the results of analytical analysis.

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

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

Zemla, A T; Zhou, C E

2007-07-24

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

Unsupervised image matching based on manifold alignment.

PubMed

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

2012-08-01

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

Giant honeybees ( Apis dorsata) mob wasps away from the nest by directed visual patterns

NASA Astrophysics Data System (ADS)

Kastberger, Gerald; Weihmann, Frank; Zierler, Martina; Hötzl, Thomas

2014-11-01

The open nesting behaviour of giant honeybees ( Apis dorsata) accounts for the evolution of a series of defence strategies to protect the colonies from predation. In particular, the concerted action of shimmering behaviour is known to effectively confuse and repel predators. In shimmering, bees on the nest surface flip their abdomens in a highly coordinated manner to generate Mexican wave-like patterns. The paper documents a further-going capacity of this kind of collective defence: the visual patterns of shimmering waves align regarding their directional characteristics with the projected flight manoeuvres of the wasps when preying in front of the bees' nest. The honeybees take here advantage of a threefold asymmetry intrinsic to the prey-predator interaction: (a) the visual patterns of shimmering turn faster than the wasps on their flight path, (b) they "follow" the wasps more persistently (up to 100 ms) than the wasps "follow" the shimmering patterns (up to 40 ms) and (c) the shimmering patterns align with the wasps' flight in all directions at the same strength, whereas the wasps have some preference for horizontal correspondence. The findings give evidence that shimmering honeybees utilize directional alignment to enforce their repelling power against preying wasps. This phenomenon can be identified as predator driving which is generally associated with mobbing behaviour (particularly known in selfish herds of vertebrate species), which is, until now, not reported in insects.

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

PubMed

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

2016-03-23

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

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

PubMed

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

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

Spatiotemporal character of the Bobylev-Pikin flexoelectric instability in a twisted nematic bent-core liquid crystal exposed to very low frequency fields.

PubMed

Krishnamurthy, K S

2014-05-01

The Bobylev-Pikin striped-pattern state induced by a homogeneous electric field is a volume flexoelectric instability, originating in the midregion of a planarly aligned nematic liquid crystal layer. We find that the instability acquires a spatiotemporal character upon excitation by a low frequency (0.5 Hz) square wave field. This is demonstrated using a bent-core liquid crystal, initially in the 90°-twisted planar configuration. The flexoelectric modulation appears close to the cathode at each polarity reversal and, at low voltage amplitudes, decays completely as the field becomes steady. Correspondingly, at successive polarity changes, the stripe direction switches between the alignment directions at the two substrates. For large voltages, the stripes formed nearly along the alignment direction at the cathode gradually reorient toward the midplane director. These observations are generally attributed to inhomogeneous and time-dependent field conditions that come to exist after each polarity reversal. Polarity dependence of the instability is attributed to the formation of intrinsic double layers that bring about an asymmetry in surface fields. Momentary field elevation near the cathode following a voltage sign reversal and concomitant gradient flexoelectric polarization are considered the key factors in accounting for the surfacelike modulation observed at low voltages.

Automatic tool alignment in a backscatter X-ray scanning system

DOEpatents

Garretson, Justin; Hobart, Clinton G.; Gladwell, Thomas S.; Monda, Mark J.

2015-11-17

Technologies pertaining to backscatter x-ray scanning systems are described herein. The backscatter x-ray scanning system includes an x-ray source, which directs collimated x-rays along a plurality of output vectors towards a target. A detector detects diffusely reflected x-rays subsequent to respective collimated x-rays impacting the target, and outputs signals indicative of parameters of the detected x-rays. An image processing system generates an x-ray image based upon parameters of the detected x-rays, wherein each pixel in the image corresponds to a respective output vector. A user selects a particular portion of the image, and a medical device is positioned such that its directional axis is coincident with the output vector corresponding to at least one pixel in the portion of the image.

Automatic tool alignment in a backscatter x-ray scanning system

DOEpatents

Garretson, Justin; Hobart, Clinton G.; Gladwell, Thomas S.; Monda, Mark J.

2015-06-16

Technologies pertaining to backscatter x-ray scanning systems are described herein. The backscatter x-ray scanning system includes an x-ray source, which directs collimated x-rays along a plurality of output vectors towards a target. A detector detects diffusely reflected x-rays subsequent to respective collimated x-rays impacting the target, and outputs signals indicative of parameters of the detected x-rays. An image processing system generates an x-ray image based upon parameters of the detected x-rays, wherein each pixel in the image corresponds to a respective output vector. A user selects a particular portion of the image, and a tool is positioned such that its directional axis is coincident with the output vector corresponding to at least one pixel in the portion of the image.

High power density capacitor and method of fabrication

DOEpatents

Tuncer, Enis

2012-11-20

A ductile preform for making a drawn capacitor includes a plurality of electrically insulating, ductile insulator plates and a plurality of electrically conductive, ductile capacitor plates. Each insulator plate is stacked vertically on a respective capacitor plate and each capacitor plate is stacked on a corresponding insulator plate in alignment with only one edge so that other edges are not in alignment and so that each insulator plate extends beyond the other edges. One or more electrically insulating, ductile spacers are disposed in horizontal alignment with each capacitor plate along the other edges and the pattern is repeated so that alternating capacitor plates are stacked on alternating opposite edges of the insulator plates. A final insulator plate is positioned at an extremity of the preform. The preform may then be drawn to fuse the components and decrease the dimensions of the preform that are perpendicular to the direction of the draw.

Pathway-engineering for highly-aligned block copolymer arrays.

PubMed

Choo, Youngwoo; Majewski, Paweł W; Fukuto, Masafumi; Osuji, Chinedum O; Yager, Kevin G

2017-12-21

While the ultimate driving force in self-assembly is energy minimization and the corresponding evolution towards equilibrium, kinetic effects can also play a very strong role. These kinetic effects, such as trapping in metastable states, slow coarsening kinetics, and pathway-dependent assembly, are often viewed as complications to be overcome. Here, we instead exploit these effects to engineer a desired final nano-structure in a block copolymer thin film, by selecting a particular ordering pathway through the self-assembly energy landscape. In particular, we combine photothermal shearing with high-temperature annealing to yield hexagonal arrays of block copolymer cylinders that are aligned in a single prescribed direction over macroscopic sample dimensions. Photothermal shearing is first used to generate a highly-aligned horizontal cylinder state, with subsequent thermal processing used to reorient the morphology to the vertical cylinder state in a templated manner. Finally, we demonstrate the successful transfer of engineered morphologies into inorganic replicas.

Self-induced polar order of active Brownian particles in a harmonic trap.

PubMed

Hennes, Marc; Wolff, Katrin; Stark, Holger

2014-06-13

Hydrodynamically interacting active particles in an external harmonic potential form a self-assembled fluid pump at large enough Péclet numbers. Here, we give a quantitative criterion for the formation of the pump and show that particle orientations align in the self-induced flow field in surprising analogy to ferromagnetic order where the active Péclet number plays the role of inverse temperature. The particle orientations follow a Boltzmann distribution Φ(p) ∼ exp(Ap(z)) where the ordering mean field A scales with the active Péclet number and polar order parameter. The mean flow field in which the particles' swimming directions align corresponds to a regularized Stokeslet with strength proportional to swimming speed. Analytic mean-field results are compared with results from Brownian dynamics simulations with hydrodynamic interactions included and are found to capture the self-induced alignment very well.

Multiscale registration algorithm for alignment of meshes

NASA Astrophysics Data System (ADS)

Vadde, Srikanth; Kamarthi, Sagar V.; Gupta, Surendra M.

2004-03-01

Taking a multi-resolution approach, this research work proposes an effective algorithm for aligning a pair of scans obtained by scanning an object's surface from two adjacent views. This algorithm first encases each scan in the pair with an array of cubes of equal and fixed size. For each scan in the pair a surrogate scan is created by the centroids of the cubes that encase the scan. The Gaussian curvatures of points across the surrogate scan pair are compared to find the surrogate corresponding points. If the difference between the Gaussian curvatures of any two points on the surrogate scan pair is less than a predetermined threshold, then those two points are accepted as a pair of surrogate corresponding points. The rotation and translation values between the surrogate scan pair are determined by using a set of surrogate corresponding points. Using the same rotation and translation values the original scan pairs are aligned. The resulting registration (or alignment) error is computed to check the accuracy of the scan alignment. When the registration error becomes acceptably small, the algorithm is terminated. Otherwise the above process is continued with cubes of smaller and smaller sizes until the algorithm is terminated. However at each finer resolution the search space for finding the surrogate corresponding points is restricted to the regions in the neighborhood of the surrogate points that were at found at the preceding coarser level. The surrogate corresponding points, as the resolution becomes finer and finer, converge to the true corresponding points on the original scans. This approach offers three main benefits: it improves the chances of finding the true corresponding points on the scans, minimize the adverse effects of noise in the scans, and reduce the computational load for finding the corresponding points.

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.

Aligning Solution-Derived Carbon Nanotube Film with Full Surface Coverage for High-Performance Electronics Applications.

PubMed

Zhu, Ma-Guang; Si, Jia; Zhang, Zhiyong; Peng, Lian-Mao

2018-06-01

The main challenge for application of solution-derived carbon nanotubes (CNTs) in high performance field-effect transistor (FET) is how to align CNTs into an array with high density and full surface coverage. A directional shrinking transfer method is developed to realize high density aligned array based on randomly orientated CNT network film. Through transferring a solution-derived CNT network film onto a stretched retractable film followed by a shrinking process, alignment degree and density of CNT film increase with the shrinking multiple. The quadruply shrunk CNT films present well alignment, which is identified by the polarized Raman spectroscopy and electrical transport measurements. Based on the high quality and high density aligned CNT array, the fabricated FETs with channel length of 300 nm present ultrahigh performance including on-state current I on of 290 µA µm -1 (V ds = -1.5 V and V gs = -2 V) and peak transconductance g m of 150 µS µm -1 , which are, respectively, among the highest corresponding values in the reported CNT array FETs. High quality and high semiconducting purity CNT arrays with high density and full coverage obtained through this method promote the development of high performance CNT-based electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Accuracy in breast shape alignment with 3D surface fitting algorithms.

PubMed

Riboldi, Marco; Gierga, David P; Chen, George T Y; Baroni, Guido

2009-04-01

Surface imaging is in use in radiotherapy clinical practice for patient setup optimization and monitoring. Breast alignment is accomplished by searching for a tentative spatial correspondence between the reference and daily surface shape models. In this study, the authors quantify whole breast shape alignment by relying on texture features digitized on 3D surface models. Texture feature localization was validated through repeated measurements in a silicone breast phantom, mounted on a high precision mechanical stage. Clinical investigations on breast shape alignment included 133 fractions in 18 patients treated with accelerated partial breast irradiation. The breast shape was detected with a 3D video based surface imaging system so that breathing was compensated. An in-house algorithm for breast alignment, based on surface fitting constrained by nipple matching (constrained surface fitting), was applied. Results were compared with a commercial software where no constraints are utilized (unconstrained surface fitting). Texture feature localization was validated within 2 mm in each anatomical direction. Clinical data show that unconstrained surface fitting achieves adequate accuracy in most cases, though nipple mismatch is considerably higher than residual surface distances (3.9 mm vs 0.6 mm on average). Outliers beyond 1 cm can be experienced as the result of a degenerate surface fit, where unconstrained surface fitting is not sufficient to establish spatial correspondence. In the constrained surface fitting algorithm, average surface mismatch within 1 mm was obtained when nipple position was forced to match in the [1.5; 5] mm range. In conclusion, optimal results can be obtained by trading off the desired overall surface congruence vs matching of selected landmarks (constraint). Constrained surface fitting is put forward to represent an improvement in setup accuracy for those applications where whole breast positional reproducibility is an issue.

Alignment limit of the NMSSM Higgs sector

DOE PAGES

Carena, Marcela; Haber, Howard E.; Low, Ian; ...

2016-02-17

The Next-to-Minimal Supersymmetric extension of the Standard Model (NMSSM) with a Higgs boson of mass 125 GeV can be compatible with stop masses of order of the electroweak scale, thereby reducing the degree of fine-tuning necessary to achieve electroweak symmetry breaking. Moreover, in an attractive region of the NMSSM parameter space, corresponding to the \\alignment limit" in which one of the neutral Higgs fields lies approximately in the same direction in field space as the doublet Higgs vacuum expectation value, the observed Higgs boson is predicted to have Standard- Model-like properties. We derive analytical expressions for the alignment conditions andmore » show that they point toward a more natural region of parameter space for electroweak symmetry breaking, while allowing for perturbativity of the theory up to the Planck scale. Additionally, the alignment limit in the NMSSM leads to a well defined spectrum in the Higgs and Higgsino sectors, and yields a rich and interesting Higgs boson phenomenology that can be tested at the LHC. Here, we discuss the most promising channels for discovery and present several benchmark points for further study.« less

Does Test Item Performance Increase with Test-to-Standards Alignment?

ERIC Educational Resources Information Center

Traynor, Anne

2017-01-01

Variation in test performance among examinees from different regions or national jurisdictions is often partially attributed to differences in the degree of content correspondence between local school or training program curricula, and the test of interest. This posited relationship between test-curriculum correspondence, or "alignment,"…

Sino-American Military Relations: Determinants of Policy and Corresponding Military Responsiveness

DTIC Science & Technology

2007-03-01

military medicine, administration, and a host of non -combat related areas10 Similar priorities and methods can be seen in official documents such as the...with the national foreign policy, the PLA conducts military cooperation that is non -aligned, non -confrontational and not directed against any third...benefit. It takes part in bilateral or multilateral joint military exercises in non -traditional security fields so as to enhance the joint

Magnetic domain formation in monolayer nanoparticle films

NASA Astrophysics Data System (ADS)

Maranville, Brian; Krycka, Kathryn; Borchers, Julie; Hogg, Charles; Majetich, Sara; Ijiri, Yumi

2009-03-01

Self-assembled magnetic nanoparticle films offer promise as data storage media, but an understanding of the interactions is missing. Modified Langmuir-Blodgett methods were used to prepare monolayer films of 7 and 11 nm diameter Fe3O4 nanoparticles with large structural domains. Small-angle neutron scattering (SANS) shows a peak at a wavevector Q corresponding to the particle size and spacing, and scattering at intermediate Q indicating possible long-range correlations. We extend to lower Q with off-specular neutron reflectivity, achieving high intensity by sacrificing resolution along one in-plane direction y while retaining high resolution in the other in-plane direction x and the normal direction z. We measure in saturation and zero field to extract magnetic scattering. In high fields, the specular scattering (Qx=0) is increased, consistent with aligned moments. Preliminary results show weak magnetic scattering for nonzero Qx . Since the maximal Qx roughly corresponds to the lowest Q in SANS, the combination of these techniques allows us to quantify field-dependent magnetic domain size.

Vortex generation and wave-vortex interaction over a concave plate with roughness and suction

NASA Technical Reports Server (NTRS)

Bertolotti, Fabio

1993-01-01

The generation and amplification of vortices by surface homogeneities, both in the form of surface waviness and of wall-normal velocity, is investigated using the nonlinear parabolic stability equations. Transients and issues of algebraic growth are avoided through the use of a similarity solution as initial condition for the vortex. In the absence of curvature, the vortex decays as the square root of 1/x when flowing over streamwise aligned riblets of constant height, and grows as the square root of x when flowing over a corresponding streamwise aligned variation of blowing/suction transpiration velocity. However, in the presence of wall inhomogeneities having both streamwise and spanwise periodicity, the growth of the vortex can be much larger. In the presence of curvature, the vortex develops into a Gortler vortex. The 'direct' and 'indirect' interaction mechanisms possible in wave-vortex interaction are presented. The 'direct' interaction does not lead to strong resonance with the flow conditions investigated. The 'indirect' interaction leads to K-type transition.

Aspect sensitive E- and F-region SPEAR-enhanced incoherent backscatter observed by the EISCAT Svalbard radar

NASA Astrophysics Data System (ADS)

Dhillon, R. S.; Robinson, T. R.; Yeoman, T. K.

2009-01-01

Previous studies of the aspect sensitivity of heater-enhanced incoherent radar backscatter in the high-latitude ionosphere have demonstrated the directional dependence of incoherent scatter signatures corresponding to artificially excited electrostatic waves, together with consistent field-aligned signatures that may be related to the presence of artificial field-aligned irregularities. These earlier high-latitude results have provided motivation for repeating the investigation in the different geophysical conditions that obtain in the polar cap ionosphere. The Space Plasma Exploration by Active Radar (SPEAR) facility is located within the polar cap and has provided observations of RF-enhanced ion and plasma line spectra recorded by the EISCAT Svalbard UHF incoherent scatter radar system (ESR), which is collocated with SPEAR. In this paper, we present observations of aspect sensitive E- and F-region SPEAR-induced ion and plasma line enhancements that indicate excitation of both the purely growing mode and the parametric decay instability, together with sporadic E-layer results that may indicate the presence of cavitons. We note consistent enhancements from field-aligned, vertical and also from 5° south of field-aligned. We attribute the prevalence of vertical scatter to the importance of the Spitze region, and of that from field-aligned to possible wave/irregularity coupling.

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

PubMed

Eernisse, D J

1992-04-01

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

The 2016 south Alboran earthquake (Mw = 6.4): A reactivation of the Ibero-Maghrebian region?

NASA Astrophysics Data System (ADS)

Buforn, E.; Pro, C.; Sanz de Galdeano, C.; Cantavella, J. V.; Cesca, S.; Caldeira, B.; Udías, A.; Mattesini, M.

2017-08-01

On 25 January 2016, an earthquake of magnitude Mw = 6.4 occurred at the southern part of the Alboran Sea, between southern Spain and northern Morocco. This shock was preceded by a foreshock (Mw = 5.1) and followed by a long aftershock sequence. Focal mechanism of main shock has been estimated from slip inversion of body waves at teleseismic distances. Solution corresponds to left-lateral strike-slip motion, showing a complex bilateral rupture, formed by two sub-events, with most energy propagating along a plane oriented N30°E plane dipping to the NW. Relocation of larger events of the aftershock series, show two alignments of epicentres in NE-SW and NNE-SSW direction that intersect at the epicentre of the main shock. We have estimated the focal mechanisms of the largest aftershocks from moment tensor inversion at regional distances. We have obtained two families of focal mechanisms corresponding to strike slip for the NNE-SSW alignment and thrusting motion for the NE-SW alignment. Among the faults present in the area the Al Idrisi fault (or fault zone) may be a good candidate for the source of this earthquake. The study of Coulomb Failure Stress shows that it is possible that the 2016 earthquake was triggered by the previous nearby earthquakes of 1994 (Mw = 5.8) and 2004 (Mw = 6.3). The possible seismic reactivation of the central part of the Ibero-Maghrebian region is an open question, but it is clear that the occurrence of the 2016 earthquake confirms that from 1994 the seismicity of central part of IMR is increasing and that focal mechanism of largest earthquakes in this central part correspond to complex ruptures (or zone of fault).

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…

Comparison between Different Methods for Biomechanical Assessment of Ex Vivo Fracture Callus Stiffness in Small Animal Bone Healing Studies

PubMed Central

Steiner, Malte; Volkheimer, David; Meyers, Nicholaus; Wehner, Tim; Wilke, Hans-Joachim; Claes, Lutz; Ignatius, Anita

2015-01-01

For ex vivo measurements of fracture callus stiffness in small animals, different test methods, such as torsion or bending tests, are established. Each method provides advantages and disadvantages, and it is still debated which of those is most sensitive to experimental conditions (i.e. specimen alignment, directional dependency, asymmetric behavior). The aim of this study was to experimentally compare six different testing methods regarding their robustness against experimental errors. Therefore, standardized specimens were created by selective laser sintering (SLS), mimicking size, directional behavior, and embedding variations of respective rat long bone specimens. For the latter, five different geometries were created which show shifted or tilted specimen alignments. The mechanical tests included three-point bending, four-point bending, cantilever bending, axial compression, constrained torsion, and unconstrained torsion. All three different bending tests showed the same principal behavior. They were highly dependent on the rotational direction of the maximum fracture callus expansion relative to the loading direction (creating experimental errors of more than 60%), however small angular deviations (<15°) were negligible. Differences in the experimental results between the bending tests originate in their respective location of maximal bending moment induction. Compared to four-point bending, three-point bending is easier to apply on small rat and mouse bones under realistic testing conditions and yields robust measurements, provided low variation of the callus shape among the tested specimens. Axial compressive testing was highly sensitive to embedding variations, and therefore cannot be recommended. Although it is experimentally difficult to realize, unconstrained torsion testing was found to be the most robust method, since it was independent of both rotational alignment and embedding uncertainties. Constrained torsional testing showed small errors (up to 16.8%, compared to corresponding alignment under unconstrained torsion) due to a parallel offset between the specimens’ axis of gravity and the torsional axis of rotation. PMID:25781027

Structure and statistics of turbulent flow over riblets

NASA Astrophysics Data System (ADS)

Henderson, R. D.; Crawford, C. H.; Karniadakis, G. E.

1993-01-01

In this paper we present comparisons of turbulence statistics obtained from direct numerical simulation of flow over streamwise aligned triangular riblets with experimental results. We also present visualizations of the instantaneous velocity field inside and around the riblet valleys. In light of the behavior of the statistics and flowfields inside the riblet valleys, we investigate previously reported physical mechanisms for the drag reducing effect of riblets; our results here support the hypothesis of flow anchoring by the riblet valleys and the corresponding inhibition of spanwise flow motions.

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.

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

NASA Technical Reports Server (NTRS)

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

2016-01-01

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

Rice Crop Monitoring Using Microwave and Optical Remotely Sensed Image Data

NASA Astrophysics Data System (ADS)

Suga, Y.; Konishi, T.; Takeuchi, S.; Kitano, Y.; Ito, S.

Hiroshima Institute of Technology HIT is operating the direct down-links of microwave and optical satellite data in Japan This study focuses on the validation for rice crop monitoring using microwave and optical remotely sensed image data acquired by satellites referring to ground truth data such as height of crop ratio of crop vegetation cover and leaf area index in the test sites of Japan ENVISAT-1 ASAR data has a capability to capture regularly and to monitor during the rice growing cycle by alternating cross polarization mode images However ASAR data is influenced by several parameters such as landcover structure direction and alignment of rice crop fields in the test sites In this study the validation was carried out combined with microwave and optical satellite image data and ground truth data regarding rice crop fields to investigate the above parameters Multi-temporal multi-direction descending and ascending and multi-angle ASAR alternating cross polarization mode images were used to investigate rice crop growing cycle LANDSAT data were used to detect landcover structure direction and alignment of rice crop fields corresponding to the backscatter of ASAR As the result of this study it was indicated that rice crop growth can be precisely monitored using multiple remotely sensed data and ground truth data considering with spatial spectral temporal and radiometric resolutions

Compromise and Conciliation: Frame Alignment Theory in the Argument Class.

ERIC Educational Resources Information Center

Vandenberg, Peter

"Frame alignment"--the conscious process of creating correspondence between one's own "frame" (ways of making meaning out circumstances) and someone else's--is a necessary condition for participation in organized social movements. Frame alignment processes may offer a generative and useful alternative to the reductive…

High-speed peak matching algorithm for retention time alignment of gas chromatographic data for chemometric analysis.

PubMed

Johnson, Kevin J; Wright, Bob W; Jarman, Kristin H; Synovec, Robert E

2003-05-09

A rapid retention time alignment algorithm was developed as a preprocessing utility to be used prior to chemometric analysis of large datasets of diesel fuel profiles obtained using gas chromatography (GC). Retention time variation from chromatogram-to-chromatogram has been a significant impediment against the use of chemometric techniques in the analysis of chromatographic data due to the inability of current chemometric techniques to correctly model information that shifts from variable to variable within a dataset. The alignment algorithm developed is shown to increase the efficacy of pattern recognition methods applied to diesel fuel chromatograms by retaining chemical selectivity while reducing chromatogram-to-chromatogram retention time variations and to do so on a time scale that makes analysis of large sets of chromatographic data practical. Two sets of diesel fuel gas chromatograms were studied using the novel alignment algorithm followed by principal component analysis (PCA). In the first study, retention times for corresponding chromatographic peaks in 60 chromatograms varied by as much as 300 ms between chromatograms before alignment. In the second study of 42 chromatograms, the retention time shifting exhibited was on the order of 10 s between corresponding chromatographic peaks, and required a coarse retention time correction prior to alignment with the algorithm. In both cases, an increase in retention time precision afforded by the algorithm was clearly visible in plots of overlaid chromatograms before and then after applying the retention time alignment algorithm. Using the alignment algorithm, the standard deviation for corresponding peak retention times following alignment was 17 ms throughout a given chromatogram, corresponding to a relative standard deviation of 0.003% at an average retention time of 8 min. This level of retention time precision is a 5-fold improvement over the retention time precision initially provided by a state-of-the-art GC instrument equipped with electronic pressure control and was critical to the performance of the chemometric analysis. This increase in retention time precision does not come at the expense of chemical selectivity, since the PCA results suggest that essentially all of the chemical selectivity is preserved. Cluster resolution between dissimilar groups of diesel fuel chromatograms in a two-dimensional scores space generated with PCA is shown to substantially increase after alignment. The alignment method is robust against missing or extra peaks relative to a target chromatogram used in the alignment, and operates at high speed, requiring roughly 1 s of computation time per GC chromatogram.

Guidance of dorsal root ganglion neurites and Schwann cells by isolated Schwann cell topography on poly(dimethyl siloxane) conduits and films

NASA Astrophysics Data System (ADS)

Richardson, J. A.; Rementer, C. W.; Bruder, Jan M.; Hoffman-Kim, D.

2011-08-01

Biomimetic replicas of cellular topography have been utilized to direct neurite outgrowth. Here, we cultured postnatal rat dorsal root ganglion (DRG) explants in the presence of Schwann cell (SC) topography to determine the influence of SC topography on neurite outgrowth. Four distinct poly(dimethyl siloxane) conduits were fabricated within which DRG explants were cultured. To determine the contribution of SC topographical features to neurite guidance, the extent of neurite outgrowth into unpatterned conduits, conduits with randomly oriented SC replicas, and conduits with SC replicas parallel or perpendicular to the conduit long axis was measured. Neurite directionality and outgrowth from DRG were also quantified on two-dimensional SC replicas with orientations corresponding to the four conduit conditions. Additionally, live SC migration and neurite extension from DRG on SC replicas were examined as a first step toward quantification of the interactions between live SC and navigating neurites on SC replicas. DRG neurite outgrowth and morphology within conduits and on two-dimensional SC replicas were directed by the underlying SC topographical features. Maximal neurite outgrowth and alignment to the underlying features were observed into parallel conduits and on parallel two-dimensional substrates, whereas the least extent of outgrowth was observed into perpendicular conduits and on perpendicular two-dimensional replica conditions. Additionally, neurites on perpendicular conditions turned to extend along the direction of underlying SC topography. Neurite outgrowth exceeded SC migration in the direction of the underlying anisotropic SC replica after two days in culture. This finding confirms the critical role that SC have in guiding neurite outgrowth and suggests that the mechanism of neurite alignment to SC replicas depends on direct contact with cellular topography. These results suggest that SC topographical replicas may be used to direct and optimize neurite alignment, and emphasize the importance of SC features in neurite guidance.

Speech Accommodation without Priming: The Case of Pitch

ERIC Educational Resources Information Center

Gijssels, Tom; Casasanto, Laura Staum; Jasmin, Kyle; Hagoort, Peter; Casasanto, Daniel

2016-01-01

People often accommodate to each other's speech by aligning their linguistic production with their partner's. According to an influential theory, the Interactive Alignment Model, alignment is the result of priming. When people perceive an utterance, the corresponding linguistic representations are primed and become easier to produce. Here we…

Reverse alignment "mirror image" visualization as a laparoscopic training tool improves task performance.

PubMed

Dunnican, Ward J; Singh, T Paul; Ata, Ashar; Bendana, Emma E; Conlee, Thomas D; Dolce, Charles J; Ramakrishnan, Rakesh

2010-06-01

Reverse alignment (mirror image) visualization is a disconcerting situation occasionally faced during laparoscopic operations. This occurs when the camera faces back at the surgeon in the opposite direction from which the surgeon's body and instruments are facing. Most surgeons will attempt to optimize trocar and camera placement to avoid this situation. The authors' objective was to determine whether the intentional use of reverse alignment visualization during laparoscopic training would improve performance. A standard box trainer was configured for reverse alignment, and 34 medical students and junior surgical residents were randomized to train with either forward alignment (DIRECT) or reverse alignment (MIRROR) visualization. Enrollees were tested on both modalities before and after a 4-week structured training program specific to their modality. Student's t test was used to determine differences in task performance between the 2 groups. Twenty-one participants completed the study (10 DIRECT, 11 MIRROR). There were no significant differences in performance time between DIRECT or MIRROR participants during forward or reverse alignment initial testing. At final testing, DIRECT participants had improved times only in forward alignment performance; they demonstrated no significant improvement in reverse alignment performance. MIRROR participants had significant time improvement in both forward and reverse alignment performance at final testing. Reverse alignment imaging for laparoscopic training improves task performance for both reverse alignment and forward alignment tasks. This may be translated into improved performance in the operating room when faced with reverse alignment situations. Minimal lab training can account for drastic adaptation to this environment.

Use of a W-band polarimeter to measure microphysical characteristics of clouds

NASA Astrophysics Data System (ADS)

Galloway, John Charles

1997-08-01

This dissertation presents W-Band measurements of the copolar correlation co-efficient and Doppler spectrum taken from the University of Wyoming King Air research airplane. These measurements demonstrate the utility of making W-Band polarimetric and Doppler spectrum measurements from an airborne platform in investigations of cloud microphysical properties. Comparison of copolar correlation coefficient measurements with aircraft in situ probe measurements verifies that polarimetric measurements indicate phase transitions, and hydrometeor alignment in ice clouds. Melting layers in clouds were measured by the W-Band system on board the King Air during 1992 and 1994. Both measurements established the use of the linear depolarization ratio, LDR, to locate the melting layer using an airborne W-Band system. The measurement during 1994 allowed direct comparison of the magnitude of the copolar correlation coefficient with the values of LDR. The relation between the measurements corresponds with a predicted relationship between the two parameters for observation of particles exhibiting isotropy in the plane of polarization. Measurements of needle crystals at horizontal and vertical incidence provided further evidence that the copolar correlation coefficient values agreed with the expected response from hydrometeors possessing a preferred alignment for the side looking case, and hydrometeors without a preferred alignment for the vertical incidence case. Observation of significant specific differential phase at vertical incidence, the first reported at W-Band, corresponded to a significant increase in differential reflectivity overhead, which was most likely produced by hydrometeor alignment driven by cloud electrification. Comparison of the drop size distributions estimated using the Doppler spectra with those measured by the wingtip probes on the King Air reveals that the radar system is better suited under some liquid cloud conditions to provide microphysical measurements of the cloud or precipitation than the probes. The radiometric calibration of the radar system determines the accuracy of the drop size distribution estimate. The results presented here indicate that the procedure used to absolutely calibrate the W-Band radar system successfully characterized the reflectivity measurements to the extent required to obtain close correspondence between the radar and probe measurements of the drop size distribution.

The Effectiveness of Aligned Developmental Feedback on the Overhand Throw in Third-Grade Students

ERIC Educational Resources Information Center

Cohen, Rona; Goodway, Jacqueline D.; Lidor, Ronnie

2012-01-01

Background: To improve student performance, teachers need to evaluate the developmental level of the child and to deliver feedback statements that correspond with the student's ability to process the information delivered. Therefore, feedback aligned with the developmental level of the child (aligned developmental feedback--ADF) is sometimes…

The Generation of the Distant Kuiper Belt by Planet Nine from an Initially Broad Perihelion Distribution

NASA Astrophysics Data System (ADS)

Khain, Tali; Batygin, Konstantin; Brown, Michael E.

2018-04-01

The observation that the orbits of long-period Kuiper Belt objects are anomalously clustered in physical space has recently prompted the Planet Nine hypothesis - the proposed existence of a distant and eccentric planetary member of our Solar System. Within the framework of this model, a Neptune-like perturber sculpts the orbital distribution of distant Kuiper Belt objects through a complex interplay of resonant and secular effects, such that the surviving orbits get organized into apsidally aligned and anti-aligned configurations with respect to Planet Nine's orbit. We present results on the role of Kuiper Belt initial conditions on the evolution of the outer Solar System using numerical simulations. Intriguingly, we find that the final perihelion distance distribution depends strongly on the primordial state of the system, and demonstrate that a bimodal structure corresponding to the existence of both aligned and anti-aligned clusters is only reproduced if the initial perihelion distribution is assumed to extend well beyond 36 AU. The bimodality in the final perihelion distance distribution is due to the permanently stable objects, with the lower perihelion peak corresponding to the anti-aligned orbits and the higher perihelion peak corresponding to the aligned orbits. We identify the mechanisms that enable the persistent stability of these objects and locate the regions of phase space in which they reside. The obtained results contextualize the Planet Nine hypothesis within the broader narrative of solar system formation, and offer further insight into the observational search for Planet Nine.

Landmark matching based retinal image alignment by enforcing sparsity in correspondence matrix.

PubMed

Zheng, Yuanjie; Daniel, Ebenezer; Hunter, Allan A; Xiao, Rui; Gao, Jianbin; Li, Hongsheng; Maguire, Maureen G; Brainard, David H; Gee, James C

2014-08-01

Retinal image alignment is fundamental to many applications in diagnosis of eye diseases. In this paper, we address the problem of landmark matching based retinal image alignment. We propose a novel landmark matching formulation by enforcing sparsity in the correspondence matrix and offer its solutions based on linear programming. The proposed formulation not only enables a joint estimation of the landmark correspondences and a predefined transformation model but also combines the benefits of the softassign strategy (Chui and Rangarajan, 2003) and the combinatorial optimization of linear programming. We also introduced a set of reinforced self-similarities descriptors which can better characterize local photometric and geometric properties of the retinal image. Theoretical analysis and experimental results with both fundus color images and angiogram images show the superior performances of our algorithms to several state-of-the-art techniques. Copyright © 2013 Elsevier B.V. All rights reserved.

Registration algorithm research for three dimensional medical image

NASA Astrophysics Data System (ADS)

Zhao, Jianping; Yang, Huamin; Ding, Ying

2008-03-01

The development of CT and MRI etc. technique offers the means by which we can research directly human internal structure. In clinic, usually various imaging results of a patient are combined for analysis. At present, in the most case, doctors make a diagnosis by observing some slice images of human body. As complexity and configuration diversity of the structure of human body organ, and as well unpredictiveness of focus location and configuration, it is difficult to imagine the cubic configuration of organs and their relationship from these 2D slices without corresponding specialty knowledge and practical experience. So it isn't satisfied with preferable requests of medical diagnosis that only aligning two 2D images to get one 2D slice image. As a result we need extend registration t problem to 3D image. As the quantity of 3D volume data are much more, it undoubtedly increases calculation quantity for aligning two 3D images accurately. It forces us to find some good methods that can achieve better effect on precision and satisfy the demand for time. So in this paper digitally reconstructed radiograph (DRR) image method is proposed to solve correlative problems. Ray tracking two 3D images and digitally reconstruct to create two 2D images, by aligning 2D data to realize to align 3D data.

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

PubMed

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

2015-11-01

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

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.

Evaluation of ERTS imagery for spectral geological mapping in diverse terranes of New York State

NASA Technical Reports Server (NTRS)

Isachsen, Y. W.; Fakundiny, R. H.; Forster, S. W.

1974-01-01

Linear anomalies dominate the new geological information derived from ERTS-1 imagery, total lengths now exceeding 6000 km. Experimentation with a variety of viewing techniques suggests that conventional photogeologic analyses of band 7 results in the location of more than 97 percent of all linears found. The maxima on rose diagrams for ERTS-1 anomalies correspond well with those for mapped faults and topographic lineaments, despite a difference in relative magnitudes of maxima thought due to solar illumination direction. A multiscale analysis of linears showed that single topographic linears at 1:2,500,000 became segmented at 1:1,000,000, aligned zones of shorter parallel, en echelon, or conjugate linears at 1:500,000, and still shorter linears lacking obvious alignment at 1:250,000. Visible glacial features include individual drumlins, best seen in winter imagery, drumlinoids, eskers, ice-marginal drainage channels, glacial lake shorelines and sand plains, and end moraines.

A novel post-weld-shift measurement and compensation technique in butterfly-type laser module packages

NASA Astrophysics Data System (ADS)

Hsu, Yi-Cheng, Sr.; Tsai, Y. C.; Hung, Y. S.; Cheng, W. H.

2005-08-01

One of the greatest challenges in the packaging of laser modules using laser welding technique is to use a reliable and accurate joining process. However, during welding, due to the material property difference between welded components, the rapid solidification of the welded region and the associated material shrinkage often introduced a post-weld-shift (PWS) between welded components. For a typical single-mode fiber application, if the PWS induced fiber alignment shift by the laser welding joining process is even a few micrometers, up to 50 % or greater loss in the coupled power may occur. The fiber alignment shift of the PWS effect in the laser welding process has a significant impact on the laser module package yield. Therefore, a detailed understanding of the effects of PWS on the fiber alignment shifts in laser-welded laser module packages and then the compensation of the fiber alignment shifts due to PWS effects are the key research subjects in laser welding techniques for optoelectronic packaging applications. Previously, the power losses due to PWS in butterfly-type laser module packages have been qualitatively corrected by applying the laser hammering technique to the direction of the detected shift. Therefore, by applying an elastic deformation to the welded components and by observing the corresponding power variation, the direction and magnitude of the PWS may be predicted. Despite numerous studies on improving the fabrication yields of laser module packaging using the PWS correction in laser welding techniques by a qualitative estimate, limited information is available for the quantitative understanding of the PWS induced fiber alignment shift which can be useful in designing and fabricating high-yield and high-performance laser module packages. The purpose of this paper is to present a quantitative probing of the PWS induced fiber alignment shift in laser-welded butterfly-type laser module packaging by employing a novel technique of a high-magnification camera with image capture system (HMCICS). The benefit of using the HMCICS technique to determine the fiber alignment shift are quantitatively measure and compensate the PWS direction and magnitude during the laser-welded laser module packages. This study makes it possible to probe the nonlinear behavior of the PWS by using a novel HMCICS technique that results in a real time quantitative compensation of the PWS in butterfly-type laser module packages, when compared to the currently available qualitatively estimated techniques to correct the PWS2. Therefore, the reliable butterfly-type laser modules with high yield and high performance used in lightwave transmission systems may thus be developed and fabricated.

SU-E-J-258: Inter- and Intra-Fraction Setup Stability and Couch Change Tolerance for Image Guided Radiation Therapy

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

Teboh, Forbang R; Agee, M; Rowe, L

2014-06-01

Purpose: Immobilization devices combine rigid patient fixation as well as comfort and play a key role providing the stability required for accurate radiation delivery. In the setup step, couch re-positioning needed to align the patient is derived via registration of acquired versus reference image. For subsequent fractions, replicating the initial setup should yield identical alignment errors when compared to the reference. This is not always the case and further couch re-positioning can be needed. An important quality assurance measure is to set couch tolerances beyond which additional investigations are needed. The purpose of this work was to study the inter-fractionmore » couch changes needed to re-align the patient and the intra-fraction stability of the alignment as a guide to establish the couch tolerances. Methods: Data from twelve patients treated on the Accuray CyberKnife (CK) system for fractionated intracranial radiotherapy and immobilized with Aquaplast RT, U-frame, F-Head-Support (Qfix, PA, USA) was used. Each fraction involved image acquisitions and registration with the reference to re-align the patient. The absolute couch position corresponding to the approved setup alignment was recorded per fraction. Intra-fraction set-up corrections were recorded throughout the treatment. Results: The average approved setup alignment was 0.03±0.28mm, 0.15±0.22mm, 0.06±0.31mm in the L/R, A/P, S/I directions respectively and 0.00±0.35degrees, 0.03±0.32degrees, 0.08±0.45degrees for roll, pitch and yaw respectively. The inter-fraction reproducibility of the couch position was 6.65mm, 10.55mm, and 4.77mm in the L/R, A/P and S/I directions respectively and 0.82degrees, 0.71degrees for roll and pitch respectively. Intra-fraction monitoring showed small average errors of 0.21±0.21mm, 0.00±0.08mm, 0.23±0.22mm in the L/R, A/P, S/I directions respectively and 0.03±0.12degrees, 0.04±0.25degrees, and 0.13±0.15degrees in the roll, pitch and yaw respectively. Conclusion: The inter-fraction reproducibility should serve as a guide to couch tolerances, specific to a site and immobilization. More patients need to be included to make general conclusions.« less

Intrinsic alignments of galaxies in the EAGLE and cosmo-OWLS simulations

NASA Astrophysics Data System (ADS)

Velliscig, Marco; Cacciato, Marcello; Schaye, Joop; Hoekstra, Henk; Bower, Richard G.; Crain, Robert A.; van Daalen, Marcel P.; Furlong, Michelle; McCarthy, I. G.; Schaller, Matthieu; Theuns, Tom

2015-12-01

We report results for the alignments of galaxies in the EAGLE and cosmo-OWLS hydrodynamical cosmological simulations as a function of galaxy separation (-1 ≤ log10(r/[ h-1 Mpc]) ≤ 2) and halo mass (10.7 ≤ log10(M200/[h-1 M⊙]) ≤ 15). We focus on two classes of alignments: the orientations of galaxies with respect to either the directions to, or the orientations of, surrounding galaxies. We find that the strength of the alignment is a strongly decreasing function of the distance between galaxies. For galaxies hosted by the most massive haloes in our simulations the alignment can remain significant up to ˜100 Mpc. Galaxies hosted by more massive haloes show stronger alignment. At a fixed halo mass, more aspherical or prolate galaxies exhibit stronger alignments. The spatial distribution of satellites is anisotropic and significantly aligned with the major axis of the main host halo. The major axes of satellite galaxies, when all stars are considered, are preferentially aligned towards the centre of the main host halo. The predicted projected direction-orientation alignment, ɛg+(rp), is in broad agreement with recent observations. We find that the orientation-orientation alignment is weaker than the orientation-direction alignment on all scales. Overall, the strength of galaxy alignments depends strongly on the subset of stars that are used to measure the orientations of galaxies and it is always weaker than the alignment of dark matter haloes. Thus, alignment models that use halo orientation as a direct proxy for galaxy orientation overestimate the impact of intrinsic galaxy alignments.

Anisotropic piezoresistivity characteristics of aligned carbon nanotube-polymer nanocomposites

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

A novel automated method for doing registration and 3D reconstruction from multi-modal RGB/IR image sequences

NASA Astrophysics Data System (ADS)

Kirby, Richard; Whitaker, Ross

2016-09-01

In recent years, the use of multi-modal camera rigs consisting of an RGB sensor and an infrared (IR) sensor have become increasingly popular for use in surveillance and robotics applications. The advantages of using multi-modal camera rigs include improved foreground/background segmentation, wider range of lighting conditions under which the system works, and richer information (e.g. visible light and heat signature) for target identification. However, the traditional computer vision method of mapping pairs of images using pixel intensities or image features is often not possible with an RGB/IR image pair. We introduce a novel method to overcome the lack of common features in RGB/IR image pairs by using a variational methods optimization algorithm to map the optical flow fields computed from different wavelength images. This results in the alignment of the flow fields, which in turn produce correspondences similar to those found in a stereo RGB/RGB camera rig using pixel intensities or image features. In addition to aligning the different wavelength images, these correspondences are used to generate dense disparity and depth maps. We obtain accuracies similar to other multi-modal image alignment methodologies as long as the scene contains sufficient depth variations, although a direct comparison is not possible because of the lack of standard image sets from moving multi-modal camera rigs. We test our method on synthetic optical flow fields and on real image sequences that we created with a multi-modal binocular stereo RGB/IR camera rig. We determine our method's accuracy by comparing against a ground truth.

The Generation of the Distant Kuiper Belt by Planet Nine from an Initially Broad Perihelion Distribution

NASA Astrophysics Data System (ADS)

Khain, Tali; Batygin, Konstantin; Brown, Michael E.

2018-06-01

The observation that the orbits of long-period Kuiper Belt objects (KBOs) are anomalously clustered in physical space has recently prompted the Planet Nine hypothesis—the proposed existence of a distant and eccentric planetary member of our solar system. Within the framework of this model, a Neptune-like perturber sculpts the orbital distribution of distant KBOs through a complex interplay of resonant and secular effects, such that in addition to perihelion-circulating objects, the surviving orbits get organized into apsidally aligned and anti-aligned configurations with respect to Planet Nine’s orbit. In this work, we investigate the role of Kuiper Belt initial conditions on the evolution of the outer solar system using numerical simulations. Intriguingly, we find that the final perihelion distance distribution depends strongly on the primordial state of the system, and we demonstrate that a bimodal structure corresponding to the existence of both aligned and anti-aligned clusters is only reproduced if the initial perihelion distribution is assumed to extend well beyond ∼36 au. The bimodality in the final perihelion distance distribution is due to the existence of permanently stable objects, with the lower perihelion peak corresponding to the anti-aligned orbits and the higher perihelion peak corresponding to the aligned orbits. We identify the mechanisms that enable the persistent stability of these objects and locate the regions of phase space in which they reside. The obtained results contextualize the Planet Nine hypothesis within the broader narrative of solar system formation and offer further insight into the observational search for Planet Nine.

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).

Iterative Most-Likely Point Registration (IMLP): A Robust Algorithm for Computing Optimal Shape Alignment

PubMed Central

Billings, Seth D.; Boctor, Emad M.; Taylor, Russell H.

2015-01-01

We present a probabilistic registration algorithm that robustly solves the problem of rigid-body alignment between two shapes with high accuracy, by aptly modeling measurement noise in each shape, whether isotropic or anisotropic. For point-cloud shapes, the probabilistic framework additionally enables modeling locally-linear surface regions in the vicinity of each point to further improve registration accuracy. The proposed Iterative Most-Likely Point (IMLP) algorithm is formed as a variant of the popular Iterative Closest Point (ICP) algorithm, which iterates between point-correspondence and point-registration steps. IMLP’s probabilistic framework is used to incorporate a generalized noise model into both the correspondence and the registration phases of the algorithm, hence its name as a most-likely point method rather than a closest-point method. To efficiently compute the most-likely correspondences, we devise a novel search strategy based on a principal direction (PD)-tree search. We also propose a new approach to solve the generalized total-least-squares (GTLS) sub-problem of the registration phase, wherein the point correspondences are registered under a generalized noise model. Our GTLS approach has improved accuracy, efficiency, and stability compared to prior methods presented for this problem and offers a straightforward implementation using standard least squares. We evaluate the performance of IMLP relative to a large number of prior algorithms including ICP, a robust variant on ICP, Generalized ICP (GICP), and Coherent Point Drift (CPD), as well as drawing close comparison with the prior anisotropic registration methods of GTLS-ICP and A-ICP. The performance of IMLP is shown to be superior with respect to these algorithms over a wide range of noise conditions, outliers, and misalignments using both mesh and point-cloud representations of various shapes. PMID:25748700

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A

PubMed Central

Ndhlovu, Andrew; Durand, Pierre M.; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. Database URL: http://www.bioinf.wits.ac.za/software/fire/evodb PMID:26140928

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.

PubMed

Ndhlovu, Andrew; Durand, Pierre M; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. © The Author(s) 2015. Published by Oxford University Press.

Flux transfer events - Scale size and interior structure

NASA Technical Reports Server (NTRS)

Saunders, M. A.; Russell, C. T.; Sckopke, N.

1984-01-01

The first direct investigation of the spatial properties of flux transfer events (FTEs) at the earth's dayside magnetopause are reported. Simultaneous magnetometer and plasma data from the ISEE 1 and 2 satellites are combined to show that magnetosheath FTEs can have a scale size of the order of an earth radius in the magnetopause normal direction. It is confirmed that the magnetic field within the events appears to be twisted, this twisting corresponding to a core field-aligned current of a magnitude of a few tens of thousands of A. Also shown is evidence for plasma vorticity in FTEs. The transverse flow and field perturbations accompanying the three events studied obey approximately the Walen relation for a propagating Alfven wave.

Thermionic emission and tunneling at carbon nanotube-organic semiconductor interface.

PubMed

Sarker, Biddut K; Khondaker, Saiful I

2012-06-26

We study the charge carrier injection mechanism across the carbon nanotube (CNT)-organic semiconductor interface using a densely aligned carbon nanotube array as electrode and pentacene as organic semiconductor. The current density-voltage (J-V) characteristics measured at different temperatures show a transition from a thermal emission mechanism at high temperature (above 200 K) to a tunneling mechanism at low temperature (below 200 K). A barrier height of ∼0.16 eV is calculated from the thermal emission regime, which is much lower compared to the metal/pentacene devices. At low temperatures, the J-V curves exhibit a direct tunneling mechanism at low bias, corresponding to a trapezoidal barrier, while at high bias the mechanism is well described by Fowler-Nordheim tunneling, which corresponds to a triangular barrier. A transition from direct tunneling to Fowler-Nordheim tunneling further signifies a small injection barrier at the CNT/pentacene interface. Our results presented here are the first direct experimental evidence of low charge carrier injection barrier between CNT electrodes and an organic semiconductor and are a significant step forward in realizing the overall goal of using CNT electrodes in organic electronics.

Alignment of galaxies relative to their local environment in SDSS-DR8

NASA Astrophysics Data System (ADS)

Hirv, A.; Pelt, J.; Saar, E.; Tago, E.; Tamm, A.; Tempel, E.; Einasto, M.

2017-03-01

Aims: We study the alignment of galaxies relative to their local environment in SDSS-DR8 and, using these data, we discuss evolution scenarios for different types of galaxies. Methods: We defined a vector field of the direction of anisotropy of the local environment of galaxies. We summed the unit direction vectors of all close neighbours of a given galaxy in a particular way to estimate this field. We found the alignment angles between the spin axes of disc galaxies, or the minor axes of elliptical galaxies, and the direction of anisotropy. The distributions of cosines of these angles are compared to the random distributions to analyse the alignment of galaxies. Results: Sab galaxies show perpendicular alignment relative to the direction of anisotropy in a sparse environment, for single galaxies and galaxies of low luminosity. Most of the parallel alignment of Scd galaxies comes from dense regions, from 2...3 member groups and from galaxies with low luminosity. The perpendicular alignment of S0 galaxies does not depend strongly on environmental density nor luminosity; it is detected for single and 2...3 member group galaxies, and for main galaxies of 4...10 member groups. The perpendicular alignment of elliptical galaxies is clearly detected for single galaxies and for members of ≤10 member groups; the alignment increases with environmental density and luminosity. Conclusions: We confirm the existence of fossil tidally induced alignment of Sab galaxies at low z. The alignment of Scd galaxies can be explained via the infall of matter to filaments. S0 galaxies may have encountered relatively massive mergers along the direction of anisotropy. Major mergers along this direction can explain the alignment of elliptical galaxies. Less massive, but repeated mergers are possibly responsible for the formation of elliptical galaxies in sparser areas and for less luminous elliptical galaxies.

Changes in Rod and Frame Test Scores Recorded in Schoolchildren during Development – A Longitudinal Study

PubMed Central

Bagust, Jeff; Docherty, Sharon; Haynes, Wayne; Telford, Richard; Isableu, Brice

2013-01-01

The Rod and Frame Test has been used to assess the degree to which subjects rely on the visual frame of reference to perceive vertical (visual field dependence- independence perceptual style). Early investigations found children exhibited a wide range of alignment errors, which reduced as they matured. These studies used a mechanical Rod and Frame system, and presented only mean values of grouped data. The current study also considered changes in individual performance. Changes in rod alignment accuracy in 419 school children were measured using a computer-based Rod and Frame test. Each child was tested at school Grade 2 and retested in Grades 4 and 6. The results confirmed that children displayed a wide range of alignment errors, which decreased with age but did not reach the expected adult values. Although most children showed a decrease in frame dependency over the 4 years of the study, almost 20% had increased alignment errors suggesting that they were becoming more frame-dependent. Plots of individual variation (SD) against mean error allowed the sample to be divided into 4 groups; the majority with small errors and SDs; a group with small SDs, but alignments clustering around the frame angle of 18°; a group showing large errors in the opposite direction to the frame tilt; and a small number with large SDs whose alignment appeared to be random. The errors in the last 3 groups could largely be explained by alignment of the rod to different aspects of the frame. At corresponding ages females exhibited larger alignment errors than males although this did not reach statistical significance. This study confirms that children rely more heavily on the visual frame of reference for processing spatial orientation cues. Most become less frame-dependent as they mature, but there are considerable individual differences. PMID:23724139

Tentative Identification of Interstellar Dust in the Magnetic Wall of the Heliosphere

NASA Astrophysics Data System (ADS)

Frisch, Priscilla C.

2005-10-01

Observations of the weak polarization of light from nearby stars, reported by Tinbergen, are consistent with polarization by small (radius <0.14 μm), interstellar dust grains entrained in the magnetic wall of the heliosphere. The region of maximum polarization is toward ecliptic coordinates (λ, β)~(295deg, 0deg), corresponding to (l, b) = (20°, -21°). The direction of maximum polarization is offset along the ecliptic longitude by ~35° from the nose of the heliosphere and extends to low ecliptic latitudes. An offset is also seen between the region with the best-aligned dust grains, λ~281deg-330deg, and the upwind direction of the undeflected large grains, λ~259deg, β~+8deg, which are observed by Ulysses and Galileo to be flowing into the heliosphere. In the aligned-grain region, the strength of polarization anticorrelates with ecliptic latitude, indicating that the magnetic wall is predominantly at negative ecliptic latitudes. An extension of the magnetic wall to β<0deg, formed by the interstellar magnetic field BIS draped over the heliosphere, is consistent with predictions by Linde (1998). A consistent interpretation follows if the maximum-polarization region traces the heliosphere magnetic wall in a direction approximately perpendicular to BIS, while the region of best-aligned dust samples the region where BIS drapes smoothly over the heliosphere with maximum compression. These data are consistent with BIS being tilted by 60° with respect to the ecliptic plane and parallel to the Galactic plane. Interstellar dust grains captured in the heliosheath may also introduce a weak, but important, large-scale contaminant for the cosmic microwave background signal with a symmetry consistent with the relative tilts of BIS and the ecliptic.

Factors affecting minimum push and pull forces of manual carts.

PubMed

Al-Eisawi, K W; Kerk, C J; Congleton, J J; Amendola, A A; Jenkins, O C; Gaines, W

1999-06-01

The minimum forces needed to manually push or pull a 4-wheel cart of differing weights with similar wheel sizes from a stationary state were measured on four floor materials under different conditions of wheel width, diameter, and orientation. Cart load was increased from 0 to 181.4 kg in increments of 36.3 kg. The floor materials were smooth concrete, tile, asphalt, and industrial carpet. Two wheel widths were tested: 25 and 38 mm. Wheel diameters were 51, 102, and 153 mm. Wheel orientation was tested at four levels: F0R0 (all four wheels aligned in the forward direction), F0R90 (the two front wheels, the wheels furthest from the cart handle, aligned in the forward direction and the two rear wheels, the wheels closest to the cart handle, aligned at 90 degrees to the forward direction), F90R0 (the two front wheels aligned at 90 degrees to the forward direction and the two rear wheels aligned in the forward direction), and F90R90 (all four wheels aligned at 90 degrees to the forward direction). Wheel width did not have a significant effect on the minimum push/pull forces. The minimum push/pull forces were linearly proportional to cart weight, and inversely proportional to wheel diameter. The coefficients of rolling friction were estimated as 2.2, 2.4, 3.3, and 4.5 mm for hard rubber wheels rolling on smooth concrete, tile, asphalt, and industrial carpet floors, respectively. The effect of wheel orientation was not consistent over the tested conditions, but, in general, the smallest minimum push/pull forces were measured with all four wheels aligned in the forward direction, whereas the largest minimum push/pull forces were measured when all four wheels were aligned at 90 degrees to the forward direction. There was no significant difference between the push and pull forces when all four wheels were aligned in the forward direction.

Mechanically Oriented 3D Collagen Hydrogel for Directing Neurite Growth.

PubMed

Antman-Passig, Merav; Levy, Shahar; Gartenberg, Chaim; Schori, Hadas; Shefi, Orit

2017-05-01

Recent studies in the field of neuro-tissue engineering have demonstrated the promising effects of aligned contact guidance cue to scaffolds of enhancement and direction of neuronal growth. In vivo, neurons grow and develop neurites in a complex three-dimensional (3D) extracellular matrix (ECM) surrounding. Studies have utilized hydrogel scaffolds derived from ECM molecules to better simulate natural growth. While many efforts have been made to control neuronal growth on 2D surfaces, the development of 3D scaffolds with an elaborate oriented topography to direct neuronal growth still remains a challenge. In this study, we designed a method for growing neurons in an aligned and oriented 3D collagen hydrogel. We aligned collagen fibers by inducing controlled uniaxial strain on gels. To examine the collagen hydrogel as a suitable scaffold for neuronal growth, we evaluated the physical properties of the hydrogel and measured collagen fiber properties. By combining the neuronal culture in 3D collagen hydrogels with strain-induced alignment, we were able to direct neuronal growth in the direction of the aligned collagen matrix. Quantitative evaluation of neurite extension and directionality within aligned gels was performed. The analysis showed neurite growth aligned with collagen matrix orientation, while maintaining the advantageous 3D growth.

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

PubMed

Bhaduri, Anirban; Pugalenthi, Ganesan; Sowdhamini, Ramanathan

2004-04-02

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

Varus alignment leads to increased forces in the anterior cruciate ligament.

PubMed

van de Pol, Gerrit Jan; Arnold, Markus P; Verdonschot, Nico; van Kampen, Albert

2009-03-01

Varus thrust of the knee is a dynamic increase of an often preexisting varus angle and it is suspected to be a major reason for failure of anterior cruciate ligament reconstructions. However, it is not known if a direct relationship exists between varus thrust and forces in the anterior cruciate ligament. Forces in the anterior cruciate ligament increase with increasing varus alignment, and consequently an anterior cruciate ligament deficiency in a varus-aligned leg leads to more lateral tibiofemoral joint opening. Controlled laboratory study. Six human cadaver legs were axially loaded with 3 different weightbearing lines--a neutral weightbearing line, a weightbearing line that passes through the middle of the medial tibial plateau (50% varus), and a line passing the edge of the medial tibial plateau (100% varus)--that were used to create a varus moment. The resulting lateral tibiofemoral joint opening and corresponding anterior cruciate ligament tension were measured. The tests were repeated with and without the anterior cruciate ligament in place. In the neutral aligned legs, there was no apparent lateral joint opening, and no anterior cruciate ligament tension change was noted. The lateral joint opening increased when the weightbearing line increased from 0% to 50% to 100%. The lateral joint opening was significantly higher in 10 degrees of knee flexion compared with knee extension. In the 100% varus weightbearing line, the anterior cruciate ligament tension was significantly higher (53.9 N) compared with neutral (31 N) or the 50% weightbearing line (37.9 N). A thrust could only be observed in the 100% weightbearing line tests. In the absence of an anterior cruciate ligament, there was more lateral joint opening, although this was only significant in the 100% weightbearing line. There is a direct relationship between varus alignment and anterior cruciate ligament tension. In the absence of an anterior cruciate ligament, the amount of lateral opening tends to increase. With increasing lateral opening, a thrust can sometimes be experimentally observed. A varus alignment in an anterior cruciate ligament-deficient knee does not necessarily lead to a varus thrust and therefore does not always need operative varus alignment correction. However, in an unstable anterior cruciate ligament-deficient knee with a varus thrust, it might be safer to perform a high valgus tibial osteotomy to minimize the risk of an anterior cruciate ligament reconstruction failure.

The direction of stretch-induced cell and stress fiber orientation depends on collagen matrix stress.

PubMed

Tondon, Abhishek; Kaunas, Roland

2014-01-01

Cell structure depends on both matrix strain and stiffness, but their interactive effects are poorly understood. We investigated the interactive roles of matrix properties and stretching patterns on cell structure by uniaxially stretching U2OS cells expressing GFP-actin on silicone rubber sheets supporting either a surface-adsorbed coating or thick hydrogel of type-I collagen. Cells and their actin stress fibers oriented perpendicular to the direction of cyclic stretch on collagen-coated sheets, but oriented parallel to the stretch direction on collagen gels. There was significant alignment parallel to the direction of a steady increase in stretch for cells on collagen gels, while cells on collagen-coated sheets did not align in any direction. The extent of alignment was dependent on both strain rate and duration. Stretch-induced alignment on collagen gels was blocked by the myosin light-chain kinase inhibitor ML7, but not by the Rho-kinase inhibitor Y27632. We propose that active orientation of the actin cytoskeleton perpendicular and parallel to direction of stretch on stiff and soft substrates, respectively, are responses that tend to maintain intracellular tension at an optimal level. Further, our results indicate that cells can align along directions of matrix stress without collagen fibril alignment, indicating that matrix stress can directly regulate cell morphology.

Fabrication of nanowire channels with unidirectional alignment and controlled length by a simple, gas-blowing-assisted, selective-transfer-printing technique.

PubMed

Kim, Yong-Kwan; Kang, Pil Soo; Kim, Dae-Il; Shin, Gunchul; Kim, Gyu Tae; Ha, Jeong Sook

2009-03-01

A printing-based lithographic technique for the patterning of V(2)O(5) nanowire channels with unidirectional orientation and controlled length is introduced. The simple, directional blowing of a patterned polymer stamp with N(2) gas, inked with randomly distributed V(2)O(5) nanowires, induces alignment of the nanowires perpendicular to the long axis of the line patterns. Subsequent stamping on the amine-terminated surface results in the selective transfer of the aligned nanowires with a controlled length corresponding to the width of the relief region of the polymer stamp. By employing such a gas-blowing-assisted, selective-transfer-printing technique, two kinds of device structures consisting of nanowire channels and two metal electrodes with top contact, whereby the nanowires were aligned either parallel (parallel device) or perpendicular (serial device) to the current flow in the conduction channel, are fabricated. The electrical properties demonstrate a noticeable difference between the two devices, with a large hysteresis in the parallel device but none in the serial device. Systematic analysis of the hysteresis and the electrical stability account for the observed hysteresis in terms of the proton diffusion in the water layer of the V(2)O(5) nanowires, induced by the application of an external bias voltage higher than a certain threshold voltage.

Automated assembly of VECSEL components

NASA Astrophysics Data System (ADS)

Brecher, C.; Pyschny, N.; Haag, S.; Mueller, T.

2013-02-01

Due to the architectural advantage of an external cavity architecture that enables the integration of additional elements into the cavity (e.g. for mode control, frequency conversion, wavelength tuning or passive mode-locking) VECSELs are a rapidly developing laser technology. Nevertheless they often have to compete with direct (edge) emitting laser diodes which can have significant cost advantages thanks to their rather simple structure and production processes. One way to compensate the economical disadvantages of VECSELs is to optimize each component in terms of quality and costs and to apply more efficient (batch) production processes. In this context, the paper presents recent process developments for the automated assembly of VECSELs using a new type of desktop assembly station with an ultra-precise micromanipulator. The core concept is to create a dedicated process development environment from which implemented processes can be transferred fluently to production equipment. By now two types of processes have been put into operation on the desktop assembly station: 1.) passive alignment of the pump optics implementing a camera-based alignment process, where the pump spot geometry and position on the semiconductor chip is analyzed and evaluated; 2.) active alignment of the end mirror based on output power measurements and optimization algorithms. In addition to the core concept and corresponding hardware and software developments, detailed results of both processes are presented explaining measurement setups as well as alignment strategies and results.

Homogeneous alignment of liquid crystalline dendrimers confined in a slit-pore. A simulation study.

PubMed

Workineh, Zerihun G; Vanakaras, Alexandros G

2016-03-23

In this work we present results from isobaric-isothermal (NPT) Monte Carlo simulation studies of model liquid crystalline dendrimer (LCDr) systems confined in a slit-pore made of two parallel flat walls. The dendrimers are modelled as a collection of spherical and ellipsoidal particles corresponding to the junction points of the dendritic core and to the mesogenic units respectively. Assuming planar uniform (unidirectional) soft anchoring of the mesogenic units on the substrates we investigate the conformational and alignment properties of the LCDr system at different thermodynamic state points. Tractable coarse grained force fields have been used from our previous work. At low pressures the interior of the pore is almost empty, since almost all LCDrs are anchored to the substrates forming two-dimensional smectic-like structures with the mesogens aligned along the aligning direction of the substrates. As the pressure grows the LCDrs occupy the whole pore. However, even at low temperatures, the smectic organization does not transmit in the interior of the pore and is preserved for distances of 2-3 mesogenic diameters from the walls. For this reason, the global orientational order decreases with increasing pressure (density). In the vicinity (2-3 mesogenic diameters) of the pore walls, mesogenic units preserve the smectic structure whose layers are separated by layers of spherical beads. In this region individual LCDrs possess a rod like shape.

Homogeneous alignment of liquid crystalline dendrimers confined in a slit-pore. A simulation study

NASA Astrophysics Data System (ADS)

Workineh, Zerihun G.; Vanakaras, Alexandros G.

2016-03-01

In this work we present results from isobaric-isothermal (NPT) Monte Carlo simulation studies of model liquid crystalline dendrimer (LCDr) systems confined in a slit-pore made of two parallel flat walls. The dendrimers are modelled as a collection of spherical and ellipsoidal particles corresponding to the junction points of the dendritic core and to the mesogenic units respectively. Assuming planar uniform (unidirectional) soft anchoring of the mesogenic units on the substrates we investigate the conformational and alignment properties of the LCDr system at different thermodynamic state points. Tractable coarse grained force fields have been used from our previous work. At low pressures the interior of the pore is almost empty, since almost all LCDrs are anchored to the substrates forming two-dimensional smectic-like structures with the mesogens aligned along the aligning direction of the substrates. As the pressure grows the LCDrs occupy the whole pore. However, even at low temperatures, the smectic organization does not transmit in the interior of the pore and is preserved for distances of 2-3 mesogenic diameters from the walls. For this reason, the global orientational order decreases with increasing pressure (density). In the vicinity (2-3 mesogenic diameters) of the pore walls, mesogenic units preserve the smectic structure whose layers are separated by layers of spherical beads. In this region individual LCDrs possess a rod like shape.

Roll-to-Roll Continuous Manufacturing Multifunctional Nanocomposites by Electric-Field-Assisted "Z" Direction Alignment of Graphite Flakes in Poly(dimethylsiloxane).

PubMed

Guo, Yuanhao; Chen, Yuwei; Wang, Enmin; Cakmak, Miko

2017-01-11

A roll-to-roll continuous process was developed to manufacture large-scale multifunctional poly(dimethylsiloxane) (PDMS) films embedded with thickness direction ("Z" direction) aligned graphite nanoparticles by application of electric field. The kinetics of particle "Z" alignment and chain formation was studied by tracking the real-time change of optical light transmission through film thickness direction. Benefiting from the anisotropic structure of aligned particle chains, the electrical and thermal properties of the nanocomposites were dramatically enhanced through the thickness direction as compared to those of the nanocomposites containing the same particle loading without electrical field alignment. With 5 vol % graphite loading, 250 times higher electrical conductivity, 43 times higher dielectric permittivity, and 1.5 times higher thermal conductivity was achieved in the film thickness direction after the particles were aligned under electrical field. Moreover, the aligned nanocomposites with merely 2 vol % graphite particles exhibit even higher electric conductivity and dielectric permittivity than those of the nonaligned nanocomposites at random percolation threshold (10 vol % particles), as the "electric-field-directed" percolation threshold concentration is substantially decreased using this process. As the graphite loading increases to 20 vol %, the aligned nanocomposites exhibit thermal conductivity as high as 6.05 W/m·K, which is 35 times the thermal conductivity of pure matrix. This roll-to-roll electric field continuous process provides a simple, low-cost, and commercially viable method to manufacture multifunctional nanocomposites for applications as embedded capacitor, electromagnetic (EM) shielding, and thermal interface materials.

Compositions for directed alignment of conjugated polymers

DOEpatents

Kim, Jinsang; Kim, Bong-Gi; Jeong, Eun Jeong

2016-04-19

Conjugated polymers (CPs) achieve directed alignment along an applied flow field and a dichroic ratio of as high as 16.67 in emission from well-aligned thin films and fully realized anisotropic optoelectronic properties of CPs in field-effect transistor (FET).

Alignment of Tractograms As Graph Matching.

PubMed

Olivetti, Emanuele; Sharmin, Nusrat; Avesani, Paolo

2016-01-01

The white matter pathways of the brain can be reconstructed as 3D polylines, called streamlines, through the analysis of diffusion magnetic resonance imaging (dMRI) data. The whole set of streamlines is called tractogram and represents the structural connectome of the brain. In multiple applications, like group-analysis, segmentation, or atlasing, tractograms of different subjects need to be aligned. Typically, this is done with registration methods, that transform the tractograms in order to increase their similarity. In contrast with transformation-based registration methods, in this work we propose the concept of tractogram correspondence, whose aim is to find which streamline of one tractogram corresponds to which streamline in another tractogram, i.e., a map from one tractogram to another. As a further contribution, we propose to use the relational information of each streamline, i.e., its distances from the other streamlines in its own tractogram, as the building block to define the optimal correspondence. We provide an operational procedure to find the optimal correspondence through a combinatorial optimization problem and we discuss its similarity to the graph matching problem. In this work, we propose to represent tractograms as graphs and we adopt a recent inexact sub-graph matching algorithm to approximate the solution of the tractogram correspondence problem. On tractograms generated from the Human Connectome Project dataset, we report experimental evidence that tractogram correspondence, implemented as graph matching, provides much better alignment than affine registration and comparable if not better results than non-linear registration of volumes.

Apparatus for monitoring X-ray beam alignment

DOEpatents

Steinmeyer, Peter A.

1991-10-08

A self-contained, hand-held apparatus is provided for minitoring alignment of an X-ray beam in an instrument employing an X-ray source. The apparatus includes a transducer assembly containing a photoresistor for providing a range of electrical signals responsive to a range of X-ray beam intensities from the X-ray beam being aligned. A circuit, powered by a 7.5 VDC power supply and containing an audio frequency pulse generator whose frequency varies with the resistance of the photoresistor, is provided for generating a range of audible sounds. A portion of the audible range corresponds to low X-ray beam intensity. Another portion of the audible range corresponds to high X-ray beam intensity. The transducer assembly may include an a photoresistor, a thin layer of X-ray fluorescent material, and a filter layer transparent to X-rays but opaque to visible light. X-rays from the beam undergoing alignment penetrate the filter layer and excite the layer of fluorescent material. The light emitted from the fluorescent material alters the resistance of the photoresistor which is in the electrical circuit including the audio pulse generator and a speaker. In employing the apparatus, the X-ray beam is aligned to a complete alignment by adjusting the X-ray beam to produce an audible sound of the maximum frequency.

Apparatus for monitoring X-ray beam alignment

DOEpatents

Steinmeyer, P.A.

1991-10-08

A self-contained, hand-held apparatus is provided for monitoring alignment of an X-ray beam in an instrument employing an X-ray source. The apparatus includes a transducer assembly containing a photoresistor for providing a range of electrical signals responsive to a range of X-ray beam intensities from the X-ray beam being aligned. A circuit, powered by a 7.5 VDC power supply and containing an audio frequency pulse generator whose frequency varies with the resistance of the photoresistor, is provided for generating a range of audible sounds. A portion of the audible range corresponds to low X-ray beam intensity. Another portion of the audible range corresponds to high X-ray beam intensity. The transducer assembly may include an a photoresistor, a thin layer of X-ray fluorescent material, and a filter layer transparent to X-rays but opaque to visible light. X-rays from the beam undergoing alignment penetrate the filter layer and excite the layer of fluorescent material. The light emitted from the fluorescent material alters the resistance of the photoresistor which is in the electrical circuit including the audio pulse generator and a speaker. In employing the apparatus, the X-ray beam is aligned to a complete alignment by adjusting the X-ray beam to produce an audible sound of the maximum frequency. 2 figures.

Nuclear reactor alignment plate configuration

DOEpatents

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

2014-01-28

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

Diffractive optics for precision alignment of Euclid space telescope optics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Asfour, Jean-Michel; Weidner, Frank; Bodendorf, Christof; Bode, Andreas; Poleshchuk, Alexander G.; Nasyrov, Ruslan K.; Grupp, Frank; Bender, Ralf

2017-09-01

We present a method for precise alignment of lens elements using specific Computer Generated Hologram (CGH) with an integrated Fizeau reference flat surface and a Fizeau interferometer. The method is used for aligning the so called Camera Lens Assembly for ESAs Euclid telescope. Each lens has a corresponding annular area on the diffractive optics, which is used to control the position of each lens. The lenses are subsequently positioned using individual annular rings of the CGH. The overall alignment accuracy is below 1 µm, the alignment sensitivity is in the range of 0.1 µm. The achieved alignment accuracy of the lenses relative to each other is mainly depending on the stability in time of the alignment tower. Error budgets when using computer generated holograms and physical limitations are explained. Calibration measurements of the alignment system and the typically reached alignment accuracies will be shown and discussed.

Photovoltaic module and interlocked stack of photovoltaic modules

DOEpatents

Wares, Brian S.

2014-09-02

One embodiment relates to an arrangement of photovoltaic modules configured for transportation. The arrangement includes a plurality of photovoltaic modules, each photovoltaic module including a frame. A plurality of individual male alignment features and a plurality of individual female alignment features are included on each frame. Adjacent photovoltaic modules are interlocked by multiple individual male alignment features on a first module of the adjacent photovoltaic modules fitting into and being surrounded by corresponding individual female alignment features on a second module of the adjacent photovoltaic modules. Other embodiments, features and aspects are also disclosed.

A goal bias in action: The boundaries adults perceive in events align with sites of actor intent.

PubMed

Levine, Dani; Hirsh-Pasek, Kathy; Pace, Amy; Michnick Golinkoff, Roberta

2017-06-01

We live in a dynamic world comprised of continuous events. Remembering our past and predicting future events, however, requires that we segment these ongoing streams of information in a consistent manner. How is this segmentation achieved? This research examines whether the boundaries adults perceive in events, such as the Olympic figure skating routine used in these studies, align with the beginnings (sources) and endings (goals) of human goal-directed actions. Study 1 showed that a group of experts, given an explicit task with unlimited time to rewatch the event, identified the same subevents as one another, but with greater agreement as to the timing of goals than sources. In Study 2, experts, novices familiarized with the figure skating sequence, and unfamiliarized novices performed an online event segmentation task, marking boundaries as the video progressed in real time. The online boundaries of all groups corresponded with the sources and goals offered by Study 1's experts, with greater alignment of goals than sources. Additionally, expertise, but not mere perceptual familiarity, boosted the alignment of sources and goals. Finally, Study 3, which presented novices with the video played in reverse, indicated, unexpectedly, that even when spatiotemporal cues were disrupted, viewers' perceived event boundaries still aligned with their perception of the actors' intended sources and goals. This research extends the goal bias to event segmentation, and suggests that our spontaneous sensitivity toward goals may allow us to transform even relatively complex and unfamiliar event streams into structured and meaningful representations. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Anisotropic forces from spatially constrained focal adhesions mediate contact guidance directed cell migration

PubMed Central

Ray, Arja; Lee, Oscar; Win, Zaw; Edwards, Rachel M.; Alford, Patrick W.; Kim, Deok-Ho; Provenzano, Paolo P.

2017-01-01

Directed migration by contact guidance is a poorly understood yet vital phenomenon, particularly for carcinoma cell invasion on aligned collagen fibres. We demonstrate that for single cells, aligned architectures providing contact guidance cues induce constrained focal adhesion maturation and associated F-actin alignment, consequently orchestrating anisotropic traction stresses that drive cell orientation and directional migration. Consistent with this understanding, relaxing spatial constraints to adhesion maturation either through reduction in substrate alignment density or reduction in adhesion size diminishes the contact guidance response. While such interactions allow single mesenchymal-like cells to spontaneously ‘sense' and follow topographic alignment, intercellular interactions within epithelial clusters temper anisotropic cell–substratum forces, resulting in substantially lower directional response. Overall, these results point to the control of contact guidance by a balance of cell–substratum and cell–cell interactions, modulated by cell phenotype-specific cytoskeletal arrangements. Thus, our findings elucidate how phenotypically diverse cells perceive ECM alignment at the molecular level. PMID:28401884

Surface-Constrained Volumetric Brain Registration Using Harmonic Mappings

PubMed Central

Joshi, Anand A.; Shattuck, David W.; Thompson, Paul M.; Leahy, Richard M.

2015-01-01

In order to compare anatomical and functional brain imaging data across subjects, the images must first be registered to a common coordinate system in which anatomical features are aligned. Intensity-based volume registration methods can align subcortical structures well, but the variability in sulcal folding patterns typically results in misalignment of the cortical surface. Conversely, surface-based registration using sulcal features can produce excellent cortical alignment but the mapping between brains is restricted to the cortical surface. Here we describe a method for volumetric registration that also produces an accurate one-to-one point correspondence between cortical surfaces. This is achieved by first parameterizing and aligning the cortical surfaces using sulcal landmarks. We then use a constrained harmonic mapping to extend this surface correspondence to the entire cortical volume. Finally, this mapping is refined using an intensity-based warp. We demonstrate the utility of the method by applying it to T1-weighted magnetic resonance images (MRI). We evaluate the performance of our proposed method relative to existing methods that use only intensity information; for this comparison we compute the inter-subject alignment of expert-labeled sub-cortical structures after registration. PMID:18092736

A novel progesterone receptor membrane component (PGRMC) in the human and swine parasite Taenia solium: implications to the host-parasite relationship.

PubMed

Aguilar-Díaz, Hugo; Nava-Castro, Karen E; Escobedo, Galileo; Domínguez-Ramírez, Lenin; García-Varela, Martín; Del Río-Araiza, Víctor H; Palacios-Arreola, Margarita I; Morales-Montor, Jorge

2018-03-09

We have previously reported that progesterone (P 4 ) has a direct in vitro effect on the scolex evagination and growth of Taenia solium cysticerci. Here, we explored the hypothesis that the P 4 direct effect on T. solium might be mediated by a novel steroid-binding parasite protein. By way of using immunofluorescent confocal microscopy, flow cytometry analysis, double-dimension electrophoresis analysis, and sequencing the corresponding protein spot, we detected a novel PGRMC in T. solium. Molecular modeling studies accompanied by computer docking using the sequenced protein, together with phylogenetic analysis and sequence alignment clearly demonstrated that T. solium PGRMC is from parasite origin. Our results show that P 4 in vitro increases parasite evagination and scolex size. Using immunofluorescent confocal microscopy, we detected that parasite cells showed expression of a P 4 -binding like protein exclusively located at the cysticercus subtegumental tissue. Presence of the P 4 -binding protein in cyst cells was also confirmed by flow cytometry. Double-dimension electrophoresis analysis, followed by sequencing the corresponding protein spot, revealed a protein that was previously reported in the T. solium genome belonging to a membrane-associated progesterone receptor component (PGRMC). Molecular modeling studies accompanied by computer docking using the sequenced protein showed that PGRMC is potentially able to bind steroid hormones such as progesterone, estradiol, testosterone and dihydrodrotestosterone with different affinities. Phylogenetic analysis and sequence alignment clearly demonstrated that T. solium PGRMC is related to a steroid-binding protein of Echinoccocus granulosus, both of them being nested within a cluster including similar proteins present in platyhelminths such as Schistocephalus solidus and Schistosoma haematobium. Progesterone may directly act upon T. solium cysticerci probably by binding to PGRMC. This research has implications in the field of host-parasite co-evolution as well as the sex-associated susceptibility to this infection. In a more practical matter, present results may contribute to the molecular design of new drugs with anti-parasite actions.

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.

Individually addressable vertically aligned carbon nanofiber-based electrochemical probes

NASA Astrophysics Data System (ADS)

Guillorn, M. A.; McKnight, T. E.; Melechko, A.; Merkulov, V. I.; Britt, P. F.; Austin, D. W.; Lowndes, D. H.; Simpson, M. L.

2002-03-01

In this paper we present the fabrication and initial testing results of high aspect ratio vertically aligned carbon nanofiber (VACNF)-based electrochemical probes. Electron beam lithography was used to define the catalytic growth sites of the VACNFs. Following catalyst deposition, VACNF were grown using a plasma enhanced chemical vapor deposition process. Photolithography was performed to realize interconnect structures. These probes were passivated with a thin layer of SiO2, which was then removed from the tips of the VACNF, rendering them electrochemically active. We have investigated the functionality of completed devices using cyclic voltammetry (CV) of ruthenium hexammine trichloride, a highly reversible, outer sphere redox system. The faradaic current obtained during CV potential sweeps shows clear oxidation and reduction peaks at magnitudes that correspond well with the geometry of these nanoscale electrochemical probes. Due to the size and the site-specific directed synthesis of the VACNFs, these probes are ideally suited for characterizing electrochemical phenomena with an unprecedented degree of spatial resolution.

Aligned carbon nanotube/zinc oxide nanowire hybrids as high performance electrodes for supercapacitor applications

NASA Astrophysics Data System (ADS)

Al-Asadi, Ahmed S.; Henley, Luke Alexander; Wasala, Milinda; Muchharla, Baleeswaraiah; Perea-Lopez, Nestor; Carozo, Victor; Lin, Zhong; Terrones, Mauricio; Mondal, Kanchan; Kordas, Krisztian; Talapatra, Saikat

2017-03-01

Carbon nanotube/metal oxide based hybrids are envisioned as high performance electrochemical energy storage electrodes since these systems can provide improved performances utilizing an electric double layer coupled with fast faradaic pseudocapacitive charge storage mechanisms. In this work, we show that high performance supercapacitor electrodes with a specific capacitance of ˜192 F/g along with a maximum energy density of ˜3.8 W h/kg and a power density of ˜ 28 kW/kg can be achieved by synthesizing zinc oxide nanowires (ZnO NWs) directly on top of aligned multi-walled carbon nanotubes (MWCNTs). In comparison to pristine MWCNTs, these constitute a 12-fold of increase in specific capacitance as well as corresponding power and energy density values. These electrodes also possess high cycling stability and were able to retain ˜99% of their specific capacitance value over 2000 charging discharging cycles. These findings indicate potential use of a MWCNT/ZnO NW hybrid material for future electrochemical energy storage applications.

Analysis of turbulent heat and momentum transfer in a transitionally rough turbulent boundary layer

NASA Astrophysics Data System (ADS)

Doosttalab, Ali; Dharmarathne, Suranga; Tutkun, Murat; Adrian, Ronald; Castillo, Luciano

2016-11-01

A zero-pressure-gradient (ZPG) turbulent boundary layer over a transitionally rough surface is studied using direct numerical simulation (DNS). The rough surface is modeled as 24-grit sandpaper which corresponds to k+ 11 , where k+ is roughness height. Reynolds number based on momentum thickness is approximately 2400. The walls are isothermal and turbulent flow Prandtl number is 0.71. We simulate temperature as passive scalar. We compute the inner product of net turbulent force (d (u1ui) / dxi) and net turbulent heat flux (d (ui θ / dxi)) in order to investigate (i) the correlation between these vectorial quantities, (II) size of the projection of these fields on each other and (IIi) alignment of momentum and hear flux. The inner product in rough case results in larger projection and better alignment. In addition, our study on the vortices shows that surface roughness promotes production of vortical structures which affects the thermal transport near the wall.

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.

Projected power iteration for network alignment

NASA Astrophysics Data System (ADS)

Onaran, Efe; Villar, Soledad

2017-08-01

The network alignment problem asks for the best correspondence between two given graphs, so that the largest possible number of edges are matched. This problem appears in many scientific problems (like the study of protein-protein interactions) and it is very closely related to the quadratic assignment problem which has graph isomorphism, traveling salesman and minimum bisection problems as particular cases. The graph matching problem is NP-hard in general. However, under some restrictive models for the graphs, algorithms can approximate the alignment efficiently. In that spirit the recent work by Feizi and collaborators introduce EigenAlign, a fast spectral method with convergence guarantees for Erd-s-Renyí graphs. In this work we propose the algorithm Projected Power Alignment, which is a projected power iteration version of EigenAlign. We numerically show it improves the recovery rates of EigenAlign and we describe the theory that may be used to provide performance guarantees for Projected Power Alignment.

Superposition and alignment of labeled point clouds.

PubMed

Fober, Thomas; Glinca, Serghei; Klebe, Gerhard; Hüllermeier, Eyke

2011-01-01

Geometric objects are often represented approximately in terms of a finite set of points in three-dimensional euclidean space. In this paper, we extend this representation to what we call labeled point clouds. A labeled point cloud is a finite set of points, where each point is not only associated with a position in three-dimensional space, but also with a discrete class label that represents a specific property. This type of model is especially suitable for modeling biomolecules such as proteins and protein binding sites, where a label may represent an atom type or a physico-chemical property. Proceeding from this representation, we address the question of how to compare two labeled points clouds in terms of their similarity. Using fuzzy modeling techniques, we develop a suitable similarity measure as well as an efficient evolutionary algorithm to compute it. Moreover, we consider the problem of establishing an alignment of the structures in the sense of a one-to-one correspondence between their basic constituents. From a biological point of view, alignments of this kind are of great interest, since mutually corresponding molecular constituents offer important information about evolution and heredity, and can also serve as a means to explain a degree of similarity. In this paper, we therefore develop a method for computing pairwise or multiple alignments of labeled point clouds. To this end, we proceed from an optimal superposition of the corresponding point clouds and construct an alignment which is as much as possible in agreement with the neighborhood structure established by this superposition. We apply our methods to the structural analysis of protein binding sites.

Seismic Anisotropy Beneath the Eastern Flank of the Rio Grande Rift

NASA Astrophysics Data System (ADS)

Benton, N. W.; Pulliam, J.

2015-12-01

Shear wave splitting was measured across the eastern flank of the Rio Grande Rift (RGR) to investigate mechanisms of upper mantle anisotropy. Earthquakes recorded at epicentral distances of 90°-130° from EarthScope Transportable Array (TA) and SIEDCAR (SC) broadband seismic stations were examined comprehensively, via the Matlab program "Splitlab", to determine whether SKS and SKKS phases indicated anisotropic properties. Splitlab allows waveforms to be rotated, filtered, and windowed interactively and splitting measurements are made on a user-specified waveform segment via three independent methods simultaneously. To improve signal-to-noise and improve reliability, we stacked the error surfaces that resulted from grid searches in the measurements for each station location. Fast polarization directions near the Rio Grande Rift tend to be sub-parallel to the RGR but then change to angles that are consistent with North America's average plate motion, to the east. The surface erosional depression of the Pecos Valley coincides with fast polarization directions that are aligned in a more northerly direction than their neighbors, whereas the topographic high to the east coincides with an easterly change of the fast axis.The area above a mantle high velocity anomaly discovered separately via seismic tomography which may indicate thickened lithosphere, corresponds to unusually large delay times and fast polarization directions that are more closely aligned to a north-south orientation. The area of southeastern New Mexico that falls between the mantle fast anomaly and the Great Plains craton displays dramatically smaller delay times, as well as changes in fast axis directions toward the northeast. Changes in fast axis directions may indicate flow around the mantle anomaly; small delay times could indicate vertical or attenuated flow.

Dense depth maps from correspondences derived from perceived motion

NASA Astrophysics Data System (ADS)

Kirby, Richard; Whitaker, Ross

2017-01-01

Many computer vision applications require finding corresponding points between images and using the corresponding points to estimate disparity. Today's correspondence finding algorithms primarily use image features or pixel intensities common between image pairs. Some 3-D computer vision applications, however, do not produce the desired results using correspondences derived from image features or pixel intensities. Two examples are the multimodal camera rig and the center region of a coaxial camera rig. We present an image correspondence finding technique that aligns pairs of image sequences using optical flow fields. The optical flow fields provide information about the structure and motion of the scene, which are not available in still images but can be used in image alignment. We apply the technique to a dual focal length stereo camera rig consisting of a visible light-infrared camera pair and to a coaxial camera rig. We test our method on real image sequences and compare our results with the state-of-the-art multimodal and structure from motion (SfM) algorithms. Our method produces more accurate depth and scene velocity reconstruction estimates than the state-of-the-art multimodal and SfM algorithms.

First Near-infrared Imaging Polarimetry of Young Stellar Objects in the Circinus Molecular Cloud

NASA Astrophysics Data System (ADS)

Kwon, Jungmi; Nakagawa, Takao; Tamura, Motohide; Hough, James H.; Choi, Minho; Kandori, Ryo; Nagata, Tetsuya; Kang, Miju

2018-02-01

We present the results of near-infrared (NIR) linear imaging polarimetry in the J, H, and K s bands of the low-mass star cluster-forming region in the Circinus Molecular Cloud Complex. Using aperture polarimetry of point-like sources, positive detection of 314, 421, and 164 sources in the J, H, and K s bands, respectively, was determined from among 749 sources whose photometric magnitudes were measured. For the source classification of the 133 point-like sources whose polarization could be measured in all 3 bands, a color–color diagram was used. While most of the NIR polarizations of point-like sources are well-aligned and can be explained by dichroic polarization produced by aligned interstellar dust grains in the cloud, 123 highly polarized sources have also been identified with some criteria. The projected direction on the sky of the magnetic field in the Cir-MMS region is indicated by the mean polarization position angles (70°) of the point-like sources in the observed region, corresponding to approximately 1.6× 1.6 pc2. In addition, the magnetic field direction is compared with the outflow orientations associated with Infrared Astronomy Satellite sources, in which two sources were found to be aligned with each other and one source was not. We also show prominent polarization nebulosities over the Cir-MMS region for the first time. Our polarization data have revealed one clear infrared reflection nebula (IRN) and several candidate IRNe in the Cir-MMS field. In addition, the illuminating sources of the IRNe are identified with near- and mid-infrared sources.

Direction of balance and perception of the upright are perceptually dissociable

PubMed Central

Panic, Alexander Sacha; DiZio, Paul; Lackner, James R.

2015-01-01

We examined whether the direction of balance rather than an otolith reference determines the perceived upright. Participants seated in a device that rotated around the roll axis used a joystick to control its motion. The direction of balance of the device, the location where it would not be accelerated to either side, could be offset from the gravitational vertical, a technique introduced by Riccio, Martin, and Stoffregen (J Exp Psychol Hum Percept Perform 18: 624–644, 1992). Participants used the joystick to align themselves in different trials with the gravitational vertical, the direction of balance, the upright, or the direction that minimized oscillations. They pressed the joystick trigger whenever they thought they were at the instructed orientation. Achieved angles for the “align with gravity” and “align with the upright” conditions were not different from each other and were significantly displaced past the gravitational vertical opposite from the direction of balance. Mean indicated angles for align with gravity and align with the upright coincided with the gravitational vertical. Both mean achieved and indicated angles for the “minimize oscillations” and “align with the direction of balance” conditions were significantly deviated toward the gravitational vertical. Three control experiments requiring self-settings to instructed orientations only, perceptual judgments only, and perceptual judgments during passive exposure to dynamic roll profiles confirmed that perception of the upright is determined by gravity, not by the direction of balance. PMID:25761954

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.

Plasmonic nanoparticle chain in a light field: a resonant optical sail.

PubMed

Albaladejo, Silvia; Sáenz, Juan José; Marqués, Manuel I

2011-11-09

Optical trapping and driving of small objects has become a topic of increasing interest in multidisciplinary sciences. We propose to use a chain made of metallic nanoparticles as a resonant light sail, attached by one end point to a transparent object and propelling it by the use of electromagnetic radiation. Driving forces exerted on the chain are theoretically studied as a function of radiation's wavelength and chain's alignments with respect to the direction of radiation. Interestingly, there is a window in the frequency spectrum in which null-torque equilibrium configuration, with minimum geometric cross section, corresponds to a maximum in the driving force.

Single crystalline growth of a soluble organic semiconductor in a parallel aligned liquid crystal solvent using rubbing-treated polyimide films

NASA Astrophysics Data System (ADS)

Matsuzaki, Tomoya; Shibata, Yosei; Takeda, Risa; Ishinabe, Takahiro; Fujikake, Hideo

2017-01-01

For directional control of organic single crystals, we propose a crystal growth method using liquid crystal as the solvent. In this study, we examined the formation of 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT) single crystals using a parallel aligned liquid crystal (LC) cell and rubbing-treated polyimide films in order to clarify the effects of LC alignment on anisotropic C8-BTBT crystal growth. Based on the results, we found that the crystal growth direction of C8-BTBT single crystals was related to the direction of the aligned LC molecules because of rubbing treatment. Moreover, by optical evaluation, we found that the C8-BTBT single crystals have a aligned molecular structure.

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

PubMed

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

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

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

PubMed

Fröhlich, K U

1994-04-01

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

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction

PubMed Central

Cocco, Simona; Monasson, Remi; Weigt, Martin

2013-01-01

Various approaches have explored the covariation of residues in multiple-sequence alignments of homologous proteins to extract functional and structural information. Among those are principal component analysis (PCA), which identifies the most correlated groups of residues, and direct coupling analysis (DCA), a global inference method based on the maximum entropy principle, which aims at predicting residue-residue contacts. In this paper, inspired by the statistical physics of disordered systems, we introduce the Hopfield-Potts model to naturally interpolate between these two approaches. The Hopfield-Potts model allows us to identify relevant ‘patterns’ of residues from the knowledge of the eigenmodes and eigenvalues of the residue-residue correlation matrix. We show how the computation of such statistical patterns makes it possible to accurately predict residue-residue contacts with a much smaller number of parameters than DCA. This dimensional reduction allows us to avoid overfitting and to extract contact information from multiple-sequence alignments of reduced size. In addition, we show that low-eigenvalue correlation modes, discarded by PCA, are important to recover structural information: the corresponding patterns are highly localized, that is, they are concentrated in few sites, which we find to be in close contact in the three-dimensional protein fold. PMID:23990764

The beaming of subhalo accretion

NASA Astrophysics Data System (ADS)

Libeskind, Noam I.

2016-10-01

We examine the infall pattern of subhaloes onto hosts in the context of the large-scale structure. We find that the infall pattern is essentially driven by the shear tensor of the ambient velocity field. Dark matter subhaloes are preferentially accreted along the principal axis of the shear tensor which corresponds to the direction of weakest collapse. We examine the dependence of this preferential infall on subhalo mass, host halo mass and redshift. Although strongest for the most massive hosts and the most massive subhaloes at high redshift, the preferential infall of subhaloes is effectively universal in the sense that its always aligned with the axis of weakest collapse of the velocity shear tensor. It is the same shear tensor that dictates the structure of the cosmic web and hence the shear field emerges as the key factor that governs the local anisotropic pattern of structure formation. Since the small (sub-Mpc) scale is strongly correlated with the mid-range (~ 10 Mpc) scale - a scale accessible by current surveys of peculiar velocities - it follows that findings presented here open a new window into the relation between the observed large scale structure unveiled by current surveys of peculiar velocities and the preferential infall direction of the Local Group. This may shed light on the unexpected alignments of dwarf galaxies seen in the Local Group.

A convenient alignment approach for x-ray imaging experiments based on laser positioning devices

PubMed Central

Zhang, Da; Donovan, Molly; Wu, Xizeng; Liu, Hong

2008-01-01

This study presents a two-laser alignment approach for facilitating the precise alignment of various imaging and measuring components with respect to the x-ray beam. The first laser constantly pointed to the output window of the source, in a direction parallel to the path along which the components are placed. The second laser beam, originating from the opposite direction, was calibrated to coincide with the first laser beam. Thus, a visible indicator of the direction of the incident x-ray beam was established, and the various components could then be aligned conveniently and accurately with its help. PMID:19070224

A Novel Marker Based Method to Teeth Alignment in MRI

NASA Astrophysics Data System (ADS)

Luukinen, Jean-Marc; Aalto, Daniel; Malinen, Jarmo; Niikuni, Naoko; Saunavaara, Jani; Jääsaari, Päivi; Ojalammi, Antti; Parkkola, Riitta; Soukka, Tero; Happonen, Risto-Pekka

2018-04-01

Magnetic resonance imaging (MRI) can precisely capture the anatomy of the vocal tract. However, the crowns of teeth are not visible in standard MRI scans. In this study, a marker-based teeth alignment method is presented and evaluated. Ten patients undergoing orthognathic surgery were enrolled. Supraglottal airways were imaged preoperatively using structural MRI. MRI visible markers were developed, and they were attached to maxillary teeth and corresponding locations on the dental casts. Repeated measurements of intermarker distances in MRI and in a replica model was compared using linear regression analysis. Dental cast MRI and corresponding caliper measurements did not differ significantly. In contrast, the marker locations in vivo differed somewhat from the dental cast measurements likely due to marker placement inaccuracies. The markers were clearly visible in MRI and allowed for dental models to be aligned to head and neck MRI scans.

Highly Enhanced Gas Adsorption Properties in Vertically Aligned MoS2 Layers.

PubMed

Cho, Soo-Yeon; Kim, Seon Joon; Lee, Youhan; Kim, Jong-Seon; Jung, Woo-Bin; Yoo, Hae-Wook; Kim, Jihan; Jung, Hee-Tae

2015-09-22

In this work, we demonstrate that gas adsorption is significantly higher in edge sites of vertically aligned MoS2 compared to that of the conventional basal plane exposed MoS2 films. To compare the effect of the alignment of MoS2 on the gas adsorption properties, we synthesized three distinct MoS2 films with different alignment directions ((1) horizontally aligned MoS2 (basal plane exposed), (2) mixture of horizontally aligned MoS2 and vertically aligned layers (basal and edge exposed), and (3) vertically aligned MoS2 (edge exposed)) by using rapid sulfurization method of CVD process. Vertically aligned MoS2 film shows about 5-fold enhanced sensitivity to NO2 gas molecules compared to horizontally aligned MoS2 film. Vertically aligned MoS2 has superior resistance variation compared to horizontally aligned MoS2 even with same surface area exposed to identical concentration of gas molecules. We found that electrical response to target gas molecules correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. Density functional theory (DFT) calculations corroborate the experimental results as stronger NO2 binding energies are computed for multiple configurations near the edge sites of MoS2, which verifies that electrical response to target gas molecules (NO2) correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. We believe that this observation extends to other 2D TMD materials as well as MoS2 and can be applied to significantly enhance the gas sensor performance in these materials.

Rice crop growth monitoring using ENVISAT-1/ASAR AP mode

NASA Astrophysics Data System (ADS)

Konishi, Tomohisa; Suga, Yuzo; Omatu, Shigeru; Takeuchi, Shoji; Asonuma, Kazuyoshi

2007-10-01

Hiroshima Institute of Technology (HIT) is operating the direct down-links of microwave and optical earth observation satellite data in Japan. This study focuses on the validation for rice crop monitoring using microwave remotely sensed image data acquired by ENIVISAT-1 referring to ground truth data such as height of rice crop, vegetation cover rate and leaf area index in the test sites of Hiroshima district, the western part of Japan. ENVISAT-1/ASAR data has the capabilities for the monitoring of the rice crop growing cycle by using alternating cross polarization mode images. However, ASAR data is influenced by several parameters such as land cover structure, direction and alignment of rice crop fields in the test sites. In this study, the validation was carried out to be combined with microwave image data and ground truth data regarding rice crop fields to investigate the above parameters. Multi-temporal, multi-direction (descending and ascending) and multi-angle ASAR alternating cross polarization mode images were used to investigate during the rice crop growing cycle. On the other hand, LANDSAT-7/ETM+ data were used to detect land cover structure, direction and alignment of rice crop fields corresponding to the backscatter of ASAR. Finally, the extraction of rice planted area was attempted by using multi-temporal ASAR AP mode data such as VV/VH and HH/HV. As the result of this study, it is clear that the estimated rice planted area coincides with the existing statistical data for area of the rice crop field. In addition, HH/HV is more effective than VV/VH in the rice planted area extraction.

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

Dual Systems for Spatial Updating in Immediate and Retrieved Environments: Evidence from Bias Analysis.

PubMed

Liu, Chuanjun; Xiao, Chengli

2018-01-01

The spatial updating and memory systems are employed during updating in both the immediate and retrieved environments. However, these dual systems seem to work differently, as the difference of pointing latency and absolute error between the two systems vary across environments. To verify this issue, the present study employed the bias analysis of signed errors based on the hypothesis that the transformed representation will bias toward the original one. Participants learned a spatial layout and then either stayed in the learning location or were transferred to a neighboring room directly or after being disoriented. After that, they performed spatial judgments from perspectives aligned with the learning direction, aligned with the direction they faced during the test, or a novel direction misaligned with the two above-mentioned directions. The patterns of signed error bias were consistent across environments. Responses for memory aligned perspectives were unbiased, whereas responses for sensorimotor aligned perspectives were biased away from the memory aligned perspective, and responses for misaligned perspectives were biased toward sensorimotor aligned perspectives. These findings indicate that the spatial updating system is consistently independent of the spatial memory system regardless of the environments, but the updating system becomes less accessible as the environment changes from immediate to a retrieved one.

Dual Systems for Spatial Updating in Immediate and Retrieved Environments: Evidence from Bias Analysis

PubMed Central

Liu, Chuanjun; Xiao, Chengli

2018-01-01

The spatial updating and memory systems are employed during updating in both the immediate and retrieved environments. However, these dual systems seem to work differently, as the difference of pointing latency and absolute error between the two systems vary across environments. To verify this issue, the present study employed the bias analysis of signed errors based on the hypothesis that the transformed representation will bias toward the original one. Participants learned a spatial layout and then either stayed in the learning location or were transferred to a neighboring room directly or after being disoriented. After that, they performed spatial judgments from perspectives aligned with the learning direction, aligned with the direction they faced during the test, or a novel direction misaligned with the two above-mentioned directions. The patterns of signed error bias were consistent across environments. Responses for memory aligned perspectives were unbiased, whereas responses for sensorimotor aligned perspectives were biased away from the memory aligned perspective, and responses for misaligned perspectives were biased toward sensorimotor aligned perspectives. These findings indicate that the spatial updating system is consistently independent of the spatial memory system regardless of the environments, but the updating system becomes less accessible as the environment changes from immediate to a retrieved one. PMID:29467698

An efficient direct method for image registration of flat objects

NASA Astrophysics Data System (ADS)

Nikolaev, Dmitry; Tihonkih, Dmitrii; Makovetskii, Artyom; Voronin, Sergei

2017-09-01

Image alignment of rigid surfaces is a rapidly developing area of research and has many practical applications. Alignment methods can be roughly divided into two types: feature-based methods and direct methods. Known SURF and SIFT algorithms are examples of the feature-based methods. Direct methods refer to those that exploit the pixel intensities without resorting to image features and image-based deformations are general direct method to align images of deformable objects in 3D space. Nevertheless, it is not good for the registration of images of 3D rigid objects since the underlying structure cannot be directly evaluated. In the article, we propose a model that is suitable for image alignment of rigid flat objects under various illumination models. The brightness consistency assumptions used for reconstruction of optimal geometrical transformation. Computer simulation results are provided to illustrate the performance of the proposed algorithm for computing of an accordance between pixels of two images.

Relative properties of smooth terminating bands

NASA Astrophysics Data System (ADS)

Afanasjev, A. V.; Ragnarsson, I.

1998-01-01

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

Multianode Photomultiplier Tube Alignment for the MINERvA Experiment at Fermilab

NASA Astrophysics Data System (ADS)

Bruno, Jorge

2006-10-01

The MINERvA experiment (Main INjector ExpeRiment vA) at FNAL will study the neutrino-nucleon and neutrino-nucleus interaction. The light collection from the detector will be done via optic fibers using Hamamatsu H8804 64-channel photomultiplier tubes (PMT). Each PMT channel needs to be precisely aligned with the corresponding optic fiber. The MINERvA PMT optical boxes contain precision machined optic ``cookies'' which capture the 8x8 array of optic fibers. Each PMT-cookie pair needs to be aligned as precisely as possible. This contribution will describe the alignment setup and procedure implemented at James Madison University.

Rotationally inelastic collisions of He and Ar with NaK: Theory and Experiment

NASA Astrophysics Data System (ADS)

Richter, K.; Price, T. J.; Jones, J.; Faust, C.; Hickman, A. P.; Huennekens, J.; Malenda, R. F.; Ross, A. J.; Harker, H.; Crozet, P.; Forrey, R. C.

2015-05-01

Rotationally inelastic collisions of NaK A1Σ+ molecules with He and Ar are studied. At Lehigh, we use pump-probe polarization labeling (PL) and laser-induced fluorescence (LIF) spectroscopy. At Lyon, Fourier transform (FT)-resolved LIF spectra are recorded. In both cases, the pump laser excites a particular ro-vibrational level A1Σ+ (v , J). We observe strong direct lines corresponding to transitions from the (v , J) level pumped, and weak satellite lines corresponding to transitions from collisionally-populated levels (v ,J' = J + ΔJ). The ratios of satellite to direct line intensities in LIF and PL yield population and orientation transfer information. A strong propensity for ΔJ = even transitions is observed for both He and Ar perturbers. In the FT fluorescence experiment we also observe v-changing collisions. Ab initio potential surface and scattering calculations are underway for collisions in the A1Σ+ and X1Σ+ states. For He-NaK we have calculated potential surfaces using GAMESS and carried out coupled channel scattering calculations of transfer of population, orientation, and alignment. Calculations of v-changing collision cross sections are also in progress. Work supported by NSF, XSEDE and CNRS (PICS).

3D reconstruction of highly fragmented bone fractures

NASA Astrophysics Data System (ADS)

Willis, Andrew; Anderson, Donald; Thomas, Thad; Brown, Thomas; Marsh, J. Lawrence

2007-03-01

A system for the semi-automatic reconstruction of highly fragmented bone fractures, developed to aid in treatment planning, is presented. The system aligns bone fragment surfaces derived from segmentation of volumetric CT scan data. Each fragment surface is partitioned into intact- and fracture-surfaces, corresponding more or less to cortical and cancellous bone, respectively. A user then interactively selects fracture-surface patches in pairs that coarsely correspond. A final optimization step is performed automatically to solve the N-body rigid alignment problem. The work represents the first example of a 3D bone fracture reconstruction system and addresses two new problems unique to the reconstruction of fractured bones: (1) non-stationary noise inherent in surfaces generated from a difficult segmentation problem and (2) the possibility that a single fracture surface on a fragment may correspond to many other fragments.

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.

Strong polarization-dependent terahertz modulation of aligned Ag nanowires on Si substrate.

PubMed

Lee, Gyuseok; Maeng, Inhee; Kang, Chul; Oh, Myoung-Kyu; Kee, Chul-Sik

2018-05-14

Optically tunable, strong polarization-dependent transmission of terahertz pulses through aligned Ag nanowires on a Si substrate is demonstrated. Terahertz pulses primarily pass through the Ag nanowires and the transmittance is weakly dependent on the angle between the direction of polarization of the terahertz pulse and the direction of nanowire alignment. However, the transmission of a terahertz pulse through optically excited materials strongly depends on the polarization direction. The extinction ratio increases as the power of the pumping laser increases. The enhanced polarization dependency is explained by the redistribution of photocarriers, which accelerates the sintering effect along the direction of alignment of the Ag nanowires. The photocarrier redistribution effect is examined by the enhancement of terahertz emission from the sample. Oblique metal nanowires on Si could be utilized for designing optically tunable terahertz polarization modulators.

Thermal Conductivity of Polyimide/Carbon Nanofiller Blends

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

Global Regularity for the Fractional Euler Alignment System

NASA Astrophysics Data System (ADS)

Do, Tam; Kiselev, Alexander; Ryzhik, Lenya; Tan, Changhui

2018-04-01

We study a pressureless Euler system with a non-linear density-dependent alignment term, originating in the Cucker-Smale swarming models. The alignment term is dissipative in the sense that it tends to equilibrate the velocities. Its density dependence is natural: the alignment rate increases in the areas of high density due to species discomfort. The diffusive term has the order of a fractional Laplacian {(-partial _{xx})^{α/2}, α \\in (0, 1)}. The corresponding Burgers equation with a linear dissipation of this type develops shocks in a finite time. We show that the alignment nonlinearity enhances the dissipation, and the solutions are globally regular for all {α \\in (0, 1)}. To the best of our knowledge, this is the first example of such regularization due to the non-local nonlinear modulation of dissipation.

Direct numerical simulation of particle alignment in viscoelastic fluids

NASA Astrophysics Data System (ADS)

Hulsen, Martien; Jaensson, Nick; Anderson, Patrick

2016-11-01

Rigid particles suspended in viscoelastic fluids under shear can align in string-like structures in flow direction. To unravel this phenomenon, we present 3D direct numerical simulations of the alignment of two and three rigid, non-Brownian particles in a shear flow of a viscoelastic fluid. The equations are solved on moving, boundary-fitted meshes, which are locally refined to accurately describe the polymer stresses around and in between the particles. A small minimal gap size between the particles is introduced. The Giesekus model is used and the effect of the Weissenberg number, shear thinning and solvent viscosity is investigated. Alignment of two and three particles is observed. Morphology plots have been created for various combinations of fluid parameters. Alignment is mainly governed by the value of the elasticity parameter S, defined as half of the ratio between the first normal stress difference and shear stress of the suspending fluid. Alignment appears to occur above a critical value of S, which decreases with increasing shear thinning. This result, together with simulations of a shear-thinning Carreau fluid, leads us to the conclusion that normal stress differences are essential for particle alignment to occur, but it is also strongly promoted by shear thinning.

Oxygen Vacancy Linear Clustering in a Perovskite Oxide

DOE PAGES

Eom, Kitae; Choi, Euiyoung; Choi, Minsu; ...

2017-07-14

Oxygen vacancies have been implicitly assumed isolated ones, and understanding oxide materials possibly containing oxygen vacancies remains elusive within the scheme of the isolated vacancies, although the oxygen vacancies have been playing a decisive role in oxide materials. We report the presence of oxygen vacancy linear clusters and their orientation along a specific crystallographic direction in SrTiO 3, a representative of a perovskite oxide. The presence of the linear clusters and associated electron localization was revealed by an electronic structure represented in the increase in the Ti 2+ valence state or corresponding Ti 3d 2 electronic configuration along with divacancymore » cluster model analysis and transport measurement. The orientation of the linear clusters along the [001] direction in perovskite SrTiO 3 was verified by further X-ray diffuse scattering analysis. And because SrTiO 3 is an archetypical perovskite oxide, the vacancy linear clustering with the specific aligned direction and electron localization can be extended to a wide variety of the perovskite oxides.« less

Oxygen Vacancy Linear Clustering in a Perovskite Oxide

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

Eom, Kitae; Choi, Euiyoung; Choi, Minsu

Oxygen vacancies have been implicitly assumed isolated ones, and understanding oxide materials possibly containing oxygen vacancies remains elusive within the scheme of the isolated vacancies, although the oxygen vacancies have been playing a decisive role in oxide materials. We report the presence of oxygen vacancy linear clusters and their orientation along a specific crystallographic direction in SrTiO 3, a representative of a perovskite oxide. The presence of the linear clusters and associated electron localization was revealed by an electronic structure represented in the increase in the Ti 2+ valence state or corresponding Ti 3d 2 electronic configuration along with divacancymore » cluster model analysis and transport measurement. The orientation of the linear clusters along the [001] direction in perovskite SrTiO 3 was verified by further X-ray diffuse scattering analysis. And because SrTiO 3 is an archetypical perovskite oxide, the vacancy linear clustering with the specific aligned direction and electron localization can be extended to a wide variety of the perovskite oxides.« less

Assessment of Anisotropic Semiconductor Nanorod and Nanoplatelet Heterostructures with Polarized Emission for Liquid Crystal Display Technology.

PubMed

Cunningham, Patrick D; Souza, João B; Fedin, Igor; She, Chunxing; Lee, Byeongdu; Talapin, Dmitri V

2016-06-28

Semiconductor nanorods can emit linear-polarized light at efficiencies over 80%. Polarization of light in these systems, confirmed through single-rod spectroscopy, can be explained on the basis of the anisotropy of the transition dipole moment and dielectric confinement effects. Here we report emission polarization in macroscopic semiconductor-polymer composite films containing CdSe/CdS nanorods and colloidal CdSe nanoplatelets. Anisotropic nanocrystals dispersed in polymer films of poly butyl-co-isobutyl methacrylate (PBiBMA) can be stretched mechanically in order to obtain unidirectionally aligned arrays. A high degree of alignment, corresponding to an orientation factor of 0.87, was achieved and large areas demonstrated polarized emission, with the contrast ratio I∥/I⊥ = 5.6, making these films viable candidates for use in liquid crystal display (LCD) devices. To some surprise, we observed significant optical anisotropy and emission polarization for 2D CdSe nanoplatelets with the electronic structure of quantum wells. The aligned nanorod arrays serve as optical funnels, absorbing unpolarized light and re-emitting light from deep-green to red with quantum efficiencies over 90% and high degree of linear polarization. Our results conclusively demonstrate the benefits of anisotropic nanostructures for LCD backlighting. The polymer films with aligned CdSe/CdS dot-in-rod and rod-in-rod nanostructures show more than 2-fold enhancement of brightness compared to the emitter layers with randomly oriented nanostructures. This effect can be explained as the combination of linearly polarized luminescence and directional emission from individual nanostructures.

Aligning Classroom Instruction with Workplace Skills: Equipping CTE Students with the Math Skills Necessary for Entry-Level Carpentry

ERIC Educational Resources Information Center

Mohr, Cory

2008-01-01

With approximately 2,500 students dropping out of U.S. high schools every day, there exists a need to align classroom instruction with corresponding "real world" applications. In order to keep students' motivation high and help ensure high levels of validity in instruction, core curriculum instructors and career and technical education (CTE)…

System and method for detecting components of a mixture including tooth elements for alignment

DOEpatents

Sommer, Gregory Jon; Schaff, Ulrich Y.

2016-11-22

Examples are described including assay platforms having tooth elements. An impinging element may sequentially engage tooth elements on the assay platform to sequentially align corresponding detection regions with a detection unit. In this manner, multiple measurements may be made of detection regions on the assay platform without necessarily requiring the starting and stopping of a motor.

Analogical processes in children's understanding of spatial representations.

PubMed

Yuan, Lei; Uttal, David; Gentner, Dedre

2017-06-01

We propose that map reading can be construed as a form of analogical mapping. We tested 2 predictions that follow from this claim: First, young children's patterns of performance in map reading tasks should parallel those found in analogical mapping tasks; and, second, children will benefit from guided alignment instructions that help them see the relational correspondences between the map and the space. In 4 experiments, 3-year-olds completed a map reading task in which they were asked to find hidden objects in a miniature room, using a corresponding map. We manipulated the availability of guided alignment (showing children the analogical mapping between maps and spaces; Experiments 1, 2, and 3a), the format of guided alignment (gesture or relational language; Experiment 2), and the iconicity of maps (Experiments 3a and 3b). We found that (a) young children's difficulties in map reading follow from known patterns of analogical development-for example, focusing on object similarity over relational similarity; and (b) guided alignment based on analogical reasoning led to substantially better performance. Results also indicated that children's map reading performance was affected by the format of guided alignment, the iconicity of the maps, and the order of tasks. The results bear on the developmental mechanisms underlying young children's learning of spatial representations and also suggest ways to support this learning. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

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

PubMed Central

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

2017-01-01

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

Assessment of ERTS-1 imagery as a tool for regional geological analysis in New York State. [Lake Ontario

NASA Technical Reports Server (NTRS)

Isachsen, Y. W. (Principal Investigator); Fakundiny, R. H.; Forster, S. W.

1974-01-01

The author has identified the following significant results. Linear anomalies dominate the new geological information derived from ERTS-1 imagery, total lengths now exceeding 26,500 km. Maxima on rose diagrams for ERTS-1 anomalies correspond well with those for mapped faults and topographic lineaments. Multi-scale analysis of linears shows that single topographic linears at 1:2,500,000 may become dashed linears at 1:1,000,000 aligned zones of shorter parallel, en echelon, or conjugate linears at 1:5000,000, and shorter linears lacking any conspicuous zonal alignment at 1:250,000. Field work in the Catskills suggests that the prominent new NNE lineaments may be surface manifestations of dip slip faulting in the basement, and that it may become possible to map major joint sets over extensive plateau regions directly on the imagery. Most circular features found were explained away by U-2 airfoto analysis but several remain as anomalies. Visible glacial features include individual drumlins, drumlinoids, eskers, ice-marginal drainage channels, glacial lake shorelines, sand plains, and end moraines.

Probing interfacial energetics and charge transfer kinetics in semiconductor nanocomposites: New insights into heterostructured TiO 2/BiVO 4 photoanodes

DOE PAGES

Hess, Lucas H.; Cooper, Jason K.; Loiudice, Anna; ...

2017-02-28

Heterostructured nanocomposites offer promise for creating systems exhibiting functional properties that exceed those of the isolated components. For solar energy conversion, such combinations of semiconducting nanomaterials can be used to direct charge transfer along pathways that reduce recombination and promote efficient charge extraction. However, interfacial energetics and associated kinetic pathways often differ significantly from predictions derived from the characteristics of pure component materials, particularly at the nanoscale. Here, the emergent properties of TiO 2/BiVO 4 nanocomposite photoanodes are explored using a combination of X-ray and optical spectroscopies, together with photoelectrochemical (PEC) characterization. Application of these methods to both the puremore » components and the fully assembled nanocomposites reveals unpredicted interfacial energetic alignment, which promotes ultrafast injection of electrons from BiVO 4 into TiO 2. Physical charge separation yields extremely long-lived photoexcited states and correspondingly enhanced photoelectrochemical functionality. This work highlights the importance of probing emergent interfacial energetic alignment and kinetic processes for understanding mechanisms of solar energy conversion in complex nanocomposites.« less

Human Corneal Limbal-Epithelial Cell Response to Varying Silk Film Geometric Topography In Vitro

PubMed Central

Lawrence, Brian D.; Pan, Zhi; Liu, Aihong; Kaplan, David L.; Rosenblatt, Mark I.

2012-01-01

Silk fibroin films are a promising class of biomaterials that have a number of advantages for use in ophthalmic applications due to their transparent nature, mechanical properties and minimal inflammatory response upon implantation. Freestanding silk films with parallel line and concentric ring topographies were generated for in vitro characterization of human corneal limbal-epithelial (HCLE) cell response upon differing geometric patterned surfaces. Results indicated that silk film topography significantly affected initial HCLE culture substrate attachment, cellular alignment, cell-to-cell contact formation, actin cytoskeleton alignment, and focal adhesion (FA) localization. Most notably, parallel line patterned surfaces displayed a 36%–54% increase on average in initial cell attachment, which corresponded to an over 2-fold increase in FA localization when compared to other silk film surfaces and controls. In addition, distinct localization of FA formation was observed along the edges for all patterned silk film topographies. In conclusion, silk film feature topography appears to help direct corneal epithelial cell response and cytoskeleton development, especially in regards to FA distribution, in vitro. PMID:22705042

Anisotropic thermal property of magnetically oriented carbon nanotube polymer composites

NASA Astrophysics Data System (ADS)

Li, Bin; Dong, Shuai; Wang, Caiping; Wang, Xiaojie; Fang, Jun

2016-04-01

This paper proposes a method for preparing multi-walled carbon nanotubea/polydimethylsiloxane (MWCNTs/PDMS) composites with enhanced thermal properties by using a high magnetic field (up to 10T). The MWCNT are oriented magnetically inside a silicone by in-situ polymerization method. The anisotropic structure would be expected to produce directional thermal conductivity. This study will provide a new approach to the development of anisotropic thermal-conductive polymer composites. Systematic studies with the preparation of silicone/graphene composites corresponding to their thermal and mechanical properties are carried out under various conditions: intensity of magnetic field, time, temperature, fillings. The effect of MWCNT/graphene content and preparation procedures on thermal conductivity of composites is investigated. Dynamic mechanical analysis (DMA) is used to reveal the mechanical properties of the composites in terms of the filling contents and magnetic field strength. The scanning electron microscope (SEM) is used to observe the micro-structure of the MWCNT composites. The alignment of MWCNTs in PDMS matrix is also studied by Raman spectroscopy. The thermal conductivity measurements show that the magnetically aligned CNT-composites feature high anisotropy in thermal conductivity.

Fabrication and Characterization of Woodpile Structures for Direct Laser Acceleration

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

McGuinness, C.; Colby, E.; England, R.J.

2010-08-26

An eight and nine layer three dimensional photonic crystal with a defect designed specifically for accelerator applications has been fabricated. The structures were fabricated using a combination of nanofabrication techniques, including low pressure chemical vapor deposition, optical lithography, and chemical mechanical polishing. Limits imposed by the optical lithography set the minimum feature size to 400 nm, corresponding to a structure with a bandgap centered at 4.26 {micro}m. Reflection spectroscopy reveal a peak in reflectivity about the predicted region, and good agreement with simulation is shown. The eight and nine layer structures will be aligned and bonded together to form themore » complete seventeen layer woodpile accelerator structure.« less

FPFH-based graph matching for 3D point cloud registration

NASA Astrophysics Data System (ADS)

Zhao, Jiapeng; Li, Chen; Tian, Lihua; Zhu, Jihua

2018-04-01

Correspondence detection is a vital step in point cloud registration and it can help getting a reliable initial alignment. In this paper, we put forward an advanced point feature-based graph matching algorithm to solve the initial alignment problem of rigid 3D point cloud registration with partial overlap. Specifically, Fast Point Feature Histograms are used to determine the initial possible correspondences firstly. Next, a new objective function is provided to make the graph matching more suitable for partially overlapping point cloud. The objective function is optimized by the simulated annealing algorithm for final group of correct correspondences. Finally, we present a novel set partitioning method which can transform the NP-hard optimization problem into a O(n3)-solvable one. Experiments on the Stanford and UWA public data sets indicates that our method can obtain better result in terms of both accuracy and time cost compared with other point cloud registration methods.

A molecular design principle of lyotropic liquid-crystalline conjugated polymers with directed alignment capability for plastic electronics

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

Kim, Bong-Gi; Jeong, Eun Jeong; Chung, Jong Won

Conjugated polymers with a one-dimensional p-orbital overlap exhibit optoelectronic anisotropy. Their unique anisotropic properties can be fully realized in device applications only when the conjugated chains are aligned. Here, we report a molecular design principle of conjugated polymers to achieve concentration-regulated chain planarization, self-assembly, liquid-crystal-like good mobility and non-interdigitated side chains. As a consequence of these intra- and intermolecular attributes, chain alignment along an applied flow field occurs. This liquid-crystalline conjugated polymer was realized by incorporating intramolecular sulphur–fluorine interactions and bulky side chains linked to a tetrahedral carbon having a large form factor. By optimizing the polymer concentration and themore » flow field, we could achieve a high dichroic ratio of 16.67 in emission from conducting conjugated polymer films. Two-dimensional grazing-incidence X-ray diffraction was performed to analyse a well-defined conjugated polymer alignment. Thin-film transistors built on highly aligned conjugated polymer films showed more than three orders of magnitude faster carrier mobility along the conjugated polymer alignment direction than the perpendicular direction.« less

Improving ontology matching with propagation strategy and user feedback

NASA Astrophysics Data System (ADS)

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

2015-07-01

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

Rim-drive cable-aligned heliostat collector system

DOEpatents

Dolan, J.E.; Sands, T.D.

1982-09-30

Disclosed is a heliostat collector apparatus comprising at least one heliostat suspended from a plurality of longitudinally extending linkage means. An enclosure structure is disposed adjacent the heliostat and provides a means for allowing the heliostat to be substantially protected from weathering. A first drive means is operatively connected to the heliostat to effect steering thereof in at least one of first and second predetermined directions. Finally, a frame member is adapted for supporting the heliostat at an inner portion thereof. The frame includes a plurality of outer expandable portions. Each one of the expandable portions is adapted to slidably engage a corresponding one of the plurality of linkage means. The expandable portions are further adapted to allow the heliostat to be slidably moved along the linkage means in directions away from and towards the enclosure structure and to substantially reduce stress acting on the heliostat during steering.

Rim-drive cable-aligned heliostat collector system

DOEpatents

Dolan, James E.; Sands, Timothy D.

1984-01-01

Disclosed is a heliostat collector apparatus comprising at least one heliostat suspended from a plurality of longitudinally extending linkage means. An enclosure structure is disposed adjacent the heliostat and provides a means for allowing the heliostat to be substantially protected from weathering. A first drive means is operatively connected to the heliostat to effect steering thereof in at least one of first and second predetermined directions. Finally, a frame member is adapted for supporting the heliostat at an inner portion thereof. The frame includes a plurality of outer expandable portions. Each one of the expandable portions is adapted to slidably engage a corresponding one of the plurality of linkage means. The expandable portions are further adapted to allow the heliostat to be slidably moved along the linkage means in directions away from and towards the enclosure structure and to substantially reduce stress acting on the heliostat during steering.

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

Sharma, Rabindar K.; Reddy, G. B.

In this work, we have successfully developed plasma assisted paste sublimation route to deposit vertically aligned MoO{sub 3} nanoflakes (NFs) on nickel coated glass substrate in oxygen plasma ambience with the assistant of Ni thin layer as a catalyst. In our case, sublimation source (Mo strip surface) is resistively heated by flowing current across it. The structural, morphological, and optical properties of NFs have been investigated systematically using x-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) with selected area electron diffraction (SAED), High resolution transmission electron microscopy (HRTEM), micro-Raman spectroscopy, and Photoluminescence (PL) spectroscopy. Studies reveal thatmore » the presence of oxygen plasma and the nickel thin layer are very essential for the growth of vertically aligned NFs. The observed results divulge that α-MoO{sub 3} NFs are deposited uniformly on large scale with very high aspect (height/thickness) ratio more than 30 and well aligned along [0 k 0] crystallographic direction where k is even (2, 4, 6). Raman spectrum shows a significant size effect on the vibrational property of MoO{sub 3} nanoflakes. The PL spectrum of MoO{sub 3} NFs was recorded at room temperature and four prominent peaks at 365 nm, 395 nm, 452 nm, and 465 nm corresponding to UV-visible region were observed. In this paper, a three step growth strategy for the formation of MoO{sub 3} NFs has been proposed in detail.« less

Position measurement of the direct drive motor of Large Aperture Telescope

NASA Astrophysics Data System (ADS)

Li, Ying; Wang, Daxing

2010-07-01

Along with the development of space and astronomy science, production of large aperture telescope and super large aperture telescope will definitely become the trend. It's one of methods to solve precise drive of large aperture telescope using direct drive technology unified designed of electricity and magnetism structure. A direct drive precise rotary table with diameter of 2.5 meters researched and produced by us is a typical mechanical & electrical integration design. This paper mainly introduces position measurement control system of direct drive motor. In design of this motor, position measurement control system requires having high resolution, and precisely aligning the position of rotor shaft and making measurement, meanwhile transferring position information to position reversing information corresponding to needed motor pole number. This system has chosen high precision metal band coder and absolute type coder, processing information of coders, and has sent 32-bit RISC CPU making software processing, and gained high resolution composite coder. The paper gives relevant laboratory test results at the end, indicating the position measurement can apply to large aperture telescope control system. This project is subsidized by Chinese National Natural Science Funds (10833004).

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

NASA Technical Reports Server (NTRS)

Jennings, Donald

2013-01-01

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

Fabrication of high temperature superconductors

DOEpatents

Balachandran, Uthamalingam; Dorris, Stephen E.; Ma, Beihai; Li, Meiya

2003-06-17

A method of forming a biaxially aligned superconductor on a non-biaxially aligned substrate substantially chemically inert to the biaxially aligned superconductor comprising is disclosed. A non-biaxially aligned substrate chemically inert to the superconductor is provided and a biaxially aligned superconductor material is deposited directly on the non-biaxially aligned substrate. A method forming a plume of superconductor material and contacting the plume and the non-biaxially aligned substrate at an angle greater than 0.degree. and less than 90.degree. to deposit a biaxially aligned superconductor on the non-biaxially aligned substrate is also disclosed. Various superconductors and substrates are illustrated.

Generation of arbitrary vector beams with liquid crystal polarization converters and vector-photoaligned q-plates

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

Chen, Peng; Ji, Wei; Wei, Bing-Yan

Arbitrary vector beams (VBs) are realized by the designed polarization converters and corresponding vector-photoaligned q-plates. The polarization converter is a specific twisted nematic cell with one substrate homogeneously aligned and the other space-variantly aligned. By combining a polarization-sensitive alignment agent with a dynamic micro-lithography system, various categories of liquid crystal polarization converters are demonstrated. Besides, traditional radially/azimuthally polarized light, high-order and multi-ringed VBs, and a VB array with different orders are generated. The obtained converters are further utilized as polarization masks to implement vector-photoaligning. The technique facilitates both the volume duplication of these converters and the generation of another promisingmore » optical element, the q-plate, which is suitable for the generation of VBs for coherent lasers. The combination of proposed polarization converters and correspondingly fabricated q-plates would drastically enhance the capability of polarization control and may bring more possibilities for the design of photonic devices.« less

Alignment of ICNP® 2.0 ontology and a proposed INCP® Brazilian ontology.

PubMed

Carvalho, Carina Maris Gaspar; Cubas, Marcia Regina; Malucelli, Andreia; Nóbrega, Maria Miriam Lima da

2014-01-01

to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology. document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence, their names, and their sibling, parent, and child classes. there were 2,682 concepts present in the ICNP® 2.0 Ontology that were missing in the Brazilian Ontology; 717 concepts present in the Brazilian Ontology were missing in the ICNP® 2.0 Ontology; and there were 215 pairs of matching concepts. it is believed that the correspondences identified in this study might contribute to the interoperability between the representations of nursing practice elements in ICNP®, thus allowing the standardization of nursing records based on this classification system.

Directionally Antagonistic Graphene Oxide-Polyurethane Hybrid Aerogel as a Sound Absorber.

PubMed

Oh, Jung-Hwan; Kim, Jieun; Lee, Hyeongrae; Kang, Yeonjune; Oh, Il-Kwon

2018-06-21

Innovative sound absorbers, the design of which is based on carbon nanotubes and graphene derivatives, could be used to make more efficient sound absorbing materials because of their excellent intrinsic mechanical and chemical properties. However, controlling the directional alignments of low-dimensional carbon nanomaterials, such as restacking, alignment, and dispersion, has been a challenging problem when developing sound absorbing forms. Herein, we present the directionally antagonistic graphene oxide-polyurethane hybrid aerogel we developed as a sound absorber, the physical properties of which differ according to the alignment of the microscopic graphene oxide sheets. This porous graphene sound absorber has a microporous hierarchical cellular structure with adjustable stiffness and improved sound absorption performance, thereby overcoming the restrictions of both geometric and function-orientated functions. Furthermore, by controlling the inner cell size and aligned structure of graphene oxide layers in this study, we achieved remarkable improvement of the sound absorption performance at low frequency. This improvement is attributed to multiple scattering of incident and reflection waves on the aligned porous surfaces, and air-viscous resistance damping inside interconnected structures between the urethane foam and the graphene oxide network. Two anisotropic sound absorbers based on the directionally antagonistic graphene oxide-polyurethane hybrid aerogels were fabricated. They show remarkable differences owing to the opposite alignment of graphene oxide layers inside the polyurethane foam and are expected to be appropriate for the engineering design of sound absorbers in consideration of the wave direction.

Postural orientation and standing postural alignment in ambulant children with bilateral cerebral palsy.

PubMed

Domagalska-Szopa, Małgorzata; Szopa, Andrzej

2017-11-01

Standing postural alignment in children with cerebral palsy is usually altered by central postural control disorders. The primary aim of this study is to describe body alignment in a quiet standing position in ambulatory children with bilateral cerebral palsy compared with children with typical development. Fifty-eight children with bilateral cerebral palsy (aged 7-13years) and 45 age-matched children with typical development underwent a surface topography examination based on Moiré topography and were classified according to their sagittal postural profiles. The following eight grouping variables were extracted using a data reduction technique: angle of trunk inclination, pelvic tilt, and lordosis, the difference between kyphosis and lordosis, angle of vertebral lateral curvature, shoulder inclination, and shoulder and pelvic rotation. According to the cluster analysis results, 25% of the participants were classified into Cluster 1, 9% into Cluster 2, 49% in Cluster 3, and 17% in Cluster 4. Three different postural patterns emerged in accordance with the sagittal postural profiles in children with bilateral cerebral palsy and were defined as follows: 1) a lordotic postural pattern corresponding to forward-leaning posture; 2) a swayback postural pattern corresponding to backward-leaning posture; and 3) a balanced postural pattern corresponding to balanced posture. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

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

2011-06-02

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

Investigation of the growth of directionally solidified eutectics with potential as electron emitters

NASA Technical Reports Server (NTRS)

Chapman, A. T.; Cochran, J. K.

1976-01-01

The construction of a solar furnace was completed and it was tested after a preliminary alignment of the heliostat mirrors. After final alignment, the solar furnace is used for directional solidification experiments designed to simulate space conditions.

Understanding Interfacial Alignment in Solution Coated Conjugated Polymer Thin Films

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

Qu, Ge; Zhao, Xikang; Newbloom, Gregory M.

Domain alignment in conjugated polymer thin films can significantly enhance charge carrier mobility. However, the alignment mechanism during meniscus-guided solution coating remains unclear. Furthermore, interfacial alignment has been rarely studied despite its direct relevance and critical importance to charge transport. In this study, we uncover a significantly higher degree of alignment at the top interface of solution coated thin films, using a donor–acceptor conjugated polymer, poly(diketopyrrolopyrrole-co-thiopheneco- thieno[3,2- b]thiophene-co-thiophene) (DPP2T-TT), as the model system. At the molecular level, we observe in-plane π–π stacking anisotropy of up to 4.8 near the top interface with the polymer backbone aligned parallel to the coatingmore » direction. The bulk of the film is only weakly aligned with the backbone oriented transverse to coating. At the mesoscale, we observe a well-defined fibril-like morphology at the top interface with the fibril long axis pointing toward the coating direction. Significantly smaller fibrils with poor orientational order are found on the bottom interface, weakly aligned orthogonal to the fibrils on the top interface. The high degree of alignment at the top interface leads to a charge transport anisotropy of up to 5.4 compared to an anisotropy close to 1 on the bottom interface. We attribute the formation of distinct interfacial morphology to the skin-layer formation associated with high Peclet number, which promotes crystallization on the top interface while suppressing it in the bulk. As a result, we further infer that the interfacial fibril alignment is driven by the extensional flow on the top interface arisen from increasing solvent evaporation rate closer to the meniscus front.« less

Understanding Interfacial Alignment in Solution Coated Conjugated Polymer Thin Films

DOE PAGES

Qu, Ge; Zhao, Xikang; Newbloom, Gregory M.; ...

2017-08-01

Domain alignment in conjugated polymer thin films can significantly enhance charge carrier mobility. However, the alignment mechanism during meniscus-guided solution coating remains unclear. Furthermore, interfacial alignment has been rarely studied despite its direct relevance and critical importance to charge transport. In this study, we uncover a significantly higher degree of alignment at the top interface of solution coated thin films, using a donor–acceptor conjugated polymer, poly(diketopyrrolopyrrole-co-thiopheneco- thieno[3,2- b]thiophene-co-thiophene) (DPP2T-TT), as the model system. At the molecular level, we observe in-plane π–π stacking anisotropy of up to 4.8 near the top interface with the polymer backbone aligned parallel to the coatingmore » direction. The bulk of the film is only weakly aligned with the backbone oriented transverse to coating. At the mesoscale, we observe a well-defined fibril-like morphology at the top interface with the fibril long axis pointing toward the coating direction. Significantly smaller fibrils with poor orientational order are found on the bottom interface, weakly aligned orthogonal to the fibrils on the top interface. The high degree of alignment at the top interface leads to a charge transport anisotropy of up to 5.4 compared to an anisotropy close to 1 on the bottom interface. We attribute the formation of distinct interfacial morphology to the skin-layer formation associated with high Peclet number, which promotes crystallization on the top interface while suppressing it in the bulk. As a result, we further infer that the interfacial fibril alignment is driven by the extensional flow on the top interface arisen from increasing solvent evaporation rate closer to the meniscus front.« less

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics

PubMed Central

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

2015-01-01

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

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

PubMed

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

2015-01-01

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

Lamellar boundary alignment of DS-processed TiAl-W alloys by a solidification procedure

NASA Astrophysics Data System (ADS)

Jung, In-Soo; Oh, Myung-Hoon; Park, No-Jin; Kumar, K. Sharvan; Wee, Dang-Moon

2007-12-01

In this study, a β solidification procedure was used to align the lamellae in a Ti-47Al-2W (at.%) alloy parallel to the growth direction. The Bridgman technique and the floating zone process were used for directional solidification. The mechanical properties of the directionally solidified alloy were evaluated in tension at room temperature and at 800°C. At a growth rate of 30 mm/h (with the floating zone approach), the lamellae were well aligned parallel to the growth direction. The aligned lamellae yielded excellent room temperature tensile ductility. The tensile yield strength at 800°C was similar to that at room temperature. The orientation of the γ lamellar laths in the directionally solidified ingots, which were manufactured by means of a floating zone process, was identified with the aid of electron backscattered diffraction analysis. On the basis of this analysis, the preferred growth direction of the bcc-β dendrites that formed at high temperatures close to the melting point was inferred to be [001]β at a growth rate of 30 mm/h and [111]β at a growth rate of 90 mm/h.

Massively-Parallel Architectures for Automatic Recognition of Visual Speech Signals

DTIC Science & Technology

1988-10-12

Secusrity Clamifieation, Nlassively-Parallel Architectures for Automa ic Recognitio of Visua, Speech Signals 12. PERSONAL AUTHOR(S) Terrence J...characteristics of speech from tJhe, visual speech signals. Neural networks have been trained on a database of vowels. The rqw images of faces , aligned and...images of faces , aligned and preprocessed, were used as input to these network which were trained to estimate the corresponding envelope of the

Multilevel, Multicomponent Microarchitectures of Vertically-Aligned Carbon Nanotubes for Diverse Applications

DTIC Science & Technology

2011-01-31

Oxide from Synthesis to Proper- ties and to Novel Devices. J. Mater. Chem. 2007, 17, 711– 720. 29. Wang, Z. L. The New Field of Nanopiezotronics...regard, wehave reportedpreviously thepreparation of multicomponent micropatterns of VA- MWNTs interposed with nanoparticles ,17 nonaligned CNTs,18 or VA...aligned arrays on growth substrates, which enabled us to fabricate the CNT nanoelectrode *Address correspondence to lqu@bit.edu.cn, liming.dai

Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches.

PubMed

Lovell, Peter V; Huizinga, Nicole A; Getachew, Abel; Mees, Brianna; Friedrich, Samantha R; Wirthlin, Morgan; Mello, Claudio V

2018-05-18

Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of cDNA collections with expressed sequence tags (ESTs) and microarrays has allowed for extensive molecular characterizations of circuitry underlying vocal learning and production. However, poor database curation can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate ~ 35% of the oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches. We found that: (1) 5475 out of 43,084 oligos (a) failed to align to the zebra finch genome, (b) aligned to multiple loci, or (c) aligned to Chr_un only, and thus need to be flagged until a better genome assembly is available, or (d) reflect cloning artifacts; (2) Out of 9635 valid oligos examined further, 3120 were incorrectly named, including 1533 with no known orthologs; and (3) 2635 oligos required name update. The resulting curated dataset provides a reference for correcting gene identification errors in previous finch microarrays studies, and avoiding such errors in future studies.

Rotationally inelastic collisions of He and Ar with NaK: Theory and Experiment

NASA Astrophysics Data System (ADS)

Richter, K.; Price, T.; Jones, J.; Faust, C.; Hickman, A. P.; Huennekens, J.; Malenda, R. F.; Ross, A. J.; Crozet, P.

2014-05-01

Rotationally inelastic collisions of NaK (A1Σ+) molecules with He and Ar have been studied. At Lehigh, we use a pump-probe scheme (the probe is scanned over transitions to the 31 Π state) with either polarization labeling (PL) or laser-induced fluorescence (LIF) spectroscopy. At Lyon, one-laser excitation is used with Fourier Transform (FT) fluorescence spectroscopy. In both cases, the pump laser excites a particular ro-vibrational level A1Σ+ (v , J). We observe strong direct lines corresponding to transitions from the (v , J) level pumped, and weak satellite lines corresponding to transitions from collisionally-populated levels (v ,J' = J + ΔJ). The ratios of satellite to direct line intensities in LIF and PL yield information about population and orientation transfer. A strong propensity for ΔJ = even transitions is observed for both He and Ar perturbers. In the FT fluorescence experiment we also observe v changing collisions. Theoretical calculations are also underway for collisions in both the A1Σ+ and X1Σ+ states. For He-NaK we have calculated potential surfaces using GAMESS and carried out coupled channel scattering calculations of transfer of population, orientation, and alignment. Work supported by NSF, XSEDE and CNRS (PICS).

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

Estimation of relative effectiveness of phylogenetic programs by machine learning.

PubMed

Krivozubov, Mikhail; Goebels, Florian; Spirin, Sergei

2014-04-01

Reconstruction of phylogeny of a protein family from a sequence alignment can produce results of different quality. Our goal is to predict the quality of phylogeny reconstruction basing on features that can be extracted from the input alignment. We used Fitch-Margoliash (FM) method of phylogeny reconstruction and random forest as a predictor. For training and testing the predictor, alignments of orthologous series (OS) were used, for which the result of phylogeny reconstruction can be evaluated by comparison with trees of corresponding organisms. Our results show that the quality of phylogeny reconstruction can be predicted with more than 80% precision. Also, we tried to predict which phylogeny reconstruction method, FM or UPGMA, is better for a particular alignment. With the used set of features, among alignments for which the obtained predictor predicts a better performance of UPGMA, 56% really give a better result with UPGMA. Taking into account that in our testing set only for 34% alignments UPGMA performs better, this result shows a principal possibility to predict the better phylogeny reconstruction method basing on features of a sequence alignment.

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

NASA Astrophysics Data System (ADS)

Reid, Katharine L.

2018-03-01

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

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.

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

PubMed

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

2011-01-01

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

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

Automated Stitching of Microtubule Centerlines across Serial Electron Tomograms

PubMed Central

Weber, Britta; Tranfield, Erin M.; Höög, Johanna L.; Baum, Daniel; Antony, Claude; Hyman, Tony; Verbavatz, Jean-Marc; Prohaska, Steffen

2014-01-01

Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts' opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort. PMID:25438148

Automated stitching of microtubule centerlines across serial electron tomograms.

PubMed

Weber, Britta; Tranfield, Erin M; Höög, Johanna L; Baum, Daniel; Antony, Claude; Hyman, Tony; Verbavatz, Jean-Marc; Prohaska, Steffen

2014-01-01

Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts' opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort.

Quantitative regulation of bone-mimetic, oriented collagen/apatite matrix structure depends on the degree of osteoblast alignment on oriented collagen substrates.

PubMed

Matsugaki, Aira; Isobe, Yoshihiro; Saku, Taro; Nakano, Takayoshi

2015-02-01

Bone tissue has a specific anisotropic morphology derived from collagen fiber alignment and the related apatite crystal orientation as a bone quality index. However, the precise mechanism of cellular regulation of the crystallographic orientation of apatite has not been clarified. In this study, anisotropic construction of cell-produced mineralized matrix in vitro was established by initiating organized cellular alignment and subsequent oriented bone-like matrix (collagen/apatite) production. The oriented collagen substrates with three anisotropic levels were prepared by a hydrodynamic method. Primary osteoblasts were cultured on the fabricated substrates until mineralized matrix formation is confirmed. Osteoblast alignment was successfully regulated by the level of substrate collagen orientation, with preferential alignment along the direction of the collagen fibers. Notably, both fibrous orientation of newly synthesized collagen matrix and c-axis of produced apatite crystals showed preferential orientation along the cell direction. Because the degree of anisotropy of the deposited apatite crystals showed dependency on the directional distribution of osteoblasts cultured on the oriented collagen substrates, the cell orientation determines the crystallographic anisotropy of produced apatite crystals. To the best of our knowledge, this is the first report demonstrating that bone tissue anisotropy, even the alignment of apatite crystals, is controllable by varying the degree of osteoblast alignment via regulating the level of substrate orientation. © 2014 Wiley Periodicals, Inc.

Simple turbulence models and their application to boundary layer separation

NASA Technical Reports Server (NTRS)

Wadcock, A. J.

1980-01-01

Measurements in the boundary layer and wake of a stalled airfoil are presented in two coordinate systems, one aligned with the airfoil chord, the other being conventional boundary layer coordinates. The NACA 4412 airfoil is studied at a single angle of attack corresponding to maximum lift, the Reynolds number based on chord being 1.5 x 10 to the 6th power. Turbulent boundary layer separation occurred at the 85 percent chord position. The two-dimensionality of the flow was documented and the momentum integral equation studied to illustrate the importance of turbulence contributions as separation is approached. The assumptions of simple eddy-viscosity and mixing-length turbulence models are checked directly against experiment. Curvature effects are found to be important as separation is approached.

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

Statistical inference of protein structural alignments using information and compression.

PubMed

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

2017-04-01

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

Laser-assisted simultaneous transfer and patterning of vertically aligned carbon nanotube arrays on polymer substrates for flexible devices.

PubMed

In, Jung Bin; Lee, Daeho; Fornasiero, Francesco; Noy, Aleksandr; Grigoropoulos, Costas P

2012-09-25

We demonstrate a laser-assisted dry transfer technique for assembling patterns of vertically aligned carbon nanotube arrays on a flexible polymeric substrate. A laser beam is applied to the interface of a nanotube array and a polycarbonate sheet in contact with one another. The absorbed laser heat promotes nanotube adhesion to the polymer in the irradiated regions and enables selective pattern transfer. A combination of the thermal transfer mechanism with rapid direct writing capability of focused laser beam irradiation allows us to achieve simultaneous material transfer and direct micropatterning in a single processing step. Furthermore, we demonstrate that malleability of the nanotube arrays transferred onto a flexible substrate enables post-transfer tailoring of electric conductance by collapsing the aligned nanotubes in different directions. This work suggests that the laser-assisted transfer technique provides an efficient route to using vertically aligned nanotubes as conductive elements in flexible device applications.

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.

Neurogenic differentiation of human umbilical cord mesenchymal stem cells on aligned electrospun polypyrrole/polylactide composite nanofibers with electrical stimulation

NASA Astrophysics Data System (ADS)

Zhou, Junfeng; Cheng, Liang; Sun, Xiaodan; Wang, Xiumei; Jin, Shouhong; Li, Junxiang; Wu, Qiong

2016-09-01

Adult central nervous system (CNS) tissue has a limited capacity to recover after trauma or disease. Recent medical cell therapy using polymeric biomaterialloaded stem cells with the capability of differentiation to specific neural population has directed focuses toward the recovery of CNS. Fibers that can provide topographical, biochemical and electrical cues would be attractive for directing the differentiation of stem cells into electro-responsive cells such as neuronal cells. Here we report on the fabrication of an electrospun polypyrrole/polylactide composite nanofiber film that direct or determine the fate of mesenchymal stem cells (MSCs), via combination of aligned surface topography, and electrical stimulation (ES). The surface morphology, mechanical properties and electric properties of the film were characterized. Comparing with that on random surface film, expression of neurofilament-lowest and nestin of human umbilical cord mesenchymal stemcells (huMSCs) cultured on film with aligned surface topography and ES were obviously enhanced. These results suggest that aligned topography combining with ES facilitates the neurogenic differentiation of huMSCs and the aligned conductive film can act as a potential nerve scaffold.

Scalable Direct Writing of Lanthanide-Doped KMnF3 Perovskite Nanowires into Aligned Arrays with Polarized Up-Conversion Emission.

PubMed

Shi, Shuo; Sun, Ling-Dong; Xue, Ying-Xian; Dong, Hao; Wu, Ke; Guo, Shi-Chen; Wu, Bo-Tao; Yan, Chun-Hua

2018-05-09

The use of one-dimensional nano- and microstructured semiconductor and lanthanide materials is attractive for polarized-light-emission studies. Up-conversion emission from single-nanorod or anisotropic nanoparticles with a degree of polarization has also been discussed. However, microscale arrays of nanoparticles, especially well-aligned one-dimensional nanostructures as well as their up-conversion polarization characterization, have not been investigated yet. Herein, we present a novel and facile paradigm for preparing highly aligned arrays of lanthanide-doped KMnF 3 (KMnF 3 :Ln) perovskite nanowires, which are good candidates for polarized up-conversion emission studies. These perovskite nanowires, with a width of 10 nm and length of a few micrometers, are formed through the oriented attachment of KMnF 3 :Ln nanocubes along the [001] direction. By the employment of KMnF 3 :Ln nanowire gel as nanoink, a direct-writing method is developed to obtain diverse types of aligned patterns from the nanoscale to the wafer scale. Up-conversion emissions from the highly aligned nanowire arrays are polarized along the array direction with a polarization degree up to 60%. Taking advantage of microscopic nanowire arrays, these polarized up-conversion emissions should offer potential applications in light or information transportation.

Epitaxially grown collagen fibrils reveal diversity in contact guidance behavior among cancer cells.

PubMed

Wang, Juan; Petefish, Joseph W; Hillier, Andrew C; Schneider, Ian C

2015-01-01

Invasion of cancer cells into the surrounding tissue is an important step during cancer progression and is driven by cell migration. Cell migration can be random, but often it is directed by various cues such as aligned fibers composed of extracellular matrix (ECM), a process called contact guidance. During contact guidance, aligned fibers bias migration along the long axis of the fibers. These aligned fibers of ECM are commonly composed of type I collagen, an abundant structural protein around tumors. In this paper, we epitaxially grew several different patterns of organized type I collagen on mica and compared the morphology and contact guidance behavior of two invasive breast cancer cell lines (MDA-MB-231 and MTLn3 cells). Others have shown that these cells randomly migrate in qualitatively different ways. MDA-MB-231 cells exert large traction forces, tightly adhere to the ECM, and migrate with spindle-shaped morphology and thus adopt a mesenchymal mode of migration. MTLn3 cells exert small traction forces, loosely adhere to the ECM, and migrate with a more rounded morphology and thus adopt an amoeboid mode of migration. As the degree of alignment of type I collagen fibrils increases, cells become more elongated and engage in more directed contact guidance. MDA-MB-231 cells perceive the directional signal of highly aligned type I collagen fibrils with high fidelity, elongating to large extents and migrating directionally. Interestingly, behavior in MTLn3 cells differs. While highly aligned type I collagen fibril patterns facilitate spreading and random migration of MTLn3 cells, they do not support elongation or directed migration. Thus, different contact guidance cues bias cell migration differently and the fidelity of contact guidance is cell type dependent, suggesting that ECM alignment is a permissive cue for contact guidance, but requires a cell to have certain properties to interpret that cue.

Injectable Anisotropic Nanocomposite Hydrogels Direct in Situ Growth and Alignment of Myotubes

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

De France, Kevin J.; Yager, Kevin G.; Chan, Katelyn J. W.

Here, while injectable in situ cross-linking hydrogels have attracted increasing attention as minimally invasive tissue scaffolds and controlled delivery systems, their inherently disorganized and isotropic network structure limits their utility in engineering oriented biological tissues. Traditional methods to prepare anisotropic hydrogels are not easily translatable to injectable systems given the need for external equipment to direct anisotropic gel fabrication and/or the required use of temperatures or solvents incompatible with biological systems. Herein, we report a new class of injectable nanocomposite hydrogels based on hydrazone cross-linked poly(oligoethylene glycol methacrylate) and magnetically aligned cellulose nanocrystals (CNCs) capable of encapsulating skeletal muscle myoblastsmore » and promoting their differentiation into highly oriented myotubes in situ. CNC alignment occurs on the same time scale as network gelation and remains fixed after the removal of the magnetic field, enabling concurrent CNC orientation and hydrogel injection. The aligned hydrogels show mechanical and swelling profiles that can be rationally modulated by the degree of CNC alignment and can direct myotube alignment both in two- and three-dimensions following coinjection of the myoblasts with the gel precursor components. As such, these hydrogels represent a critical advancement in anisotropic biomimetic scaffolds that can be generated noninvasively in vivo following simple injection.« less

Injectable Anisotropic Nanocomposite Hydrogels Direct in Situ Growth and Alignment of Myotubes

DOE PAGES

De France, Kevin J.; Yager, Kevin G.; Chan, Katelyn J. W.; ...

2017-09-28

Here, while injectable in situ cross-linking hydrogels have attracted increasing attention as minimally invasive tissue scaffolds and controlled delivery systems, their inherently disorganized and isotropic network structure limits their utility in engineering oriented biological tissues. Traditional methods to prepare anisotropic hydrogels are not easily translatable to injectable systems given the need for external equipment to direct anisotropic gel fabrication and/or the required use of temperatures or solvents incompatible with biological systems. Herein, we report a new class of injectable nanocomposite hydrogels based on hydrazone cross-linked poly(oligoethylene glycol methacrylate) and magnetically aligned cellulose nanocrystals (CNCs) capable of encapsulating skeletal muscle myoblastsmore » and promoting their differentiation into highly oriented myotubes in situ. CNC alignment occurs on the same time scale as network gelation and remains fixed after the removal of the magnetic field, enabling concurrent CNC orientation and hydrogel injection. The aligned hydrogels show mechanical and swelling profiles that can be rationally modulated by the degree of CNC alignment and can direct myotube alignment both in two- and three-dimensions following coinjection of the myoblasts with the gel precursor components. As such, these hydrogels represent a critical advancement in anisotropic biomimetic scaffolds that can be generated noninvasively in vivo following simple injection.« less

Sample holder with optical features

DOEpatents

Milas, Mirko; Zhu, Yimei; Rameau, Jonathan David

2013-07-30

A sample holder for holding a sample to be observed for research purposes, particularly in a transmission electron microscope (TEM), generally includes an external alignment part for directing a light beam in a predetermined beam direction, a sample holder body in optical communication with the external alignment part and a sample support member disposed at a distal end of the sample holder body opposite the external alignment part for holding a sample to be analyzed. The sample holder body defines an internal conduit for the light beam and the sample support member includes a light beam positioner for directing the light beam between the sample holder body and the sample held by the sample support member.

Transmission electron microscope sample holder with optical features

DOEpatents

Milas, Mirko [Port Jefferson, NY; Zhu, Yimei [Stony Brook, NY; Rameau, Jonathan David [Coram, NY

2012-03-27

A sample holder for holding a sample to be observed for research purposes, particularly in a transmission electron microscope (TEM), generally includes an external alignment part for directing a light beam in a predetermined beam direction, a sample holder body in optical communication with the external alignment part and a sample support member disposed at a distal end of the sample holder body opposite the external alignment part for holding a sample to be analyzed. The sample holder body defines an internal conduit for the light beam and the sample support member includes a light beam positioner for directing the light beam between the sample holder body and the sample held by the sample support member.

An automatic approach for 3D registration of CT scans

NASA Astrophysics Data System (ADS)

Hu, Yang; Saber, Eli; Dianat, Sohail; Vantaram, Sreenath Rao; Abhyankar, Vishwas

2012-03-01

CT (Computed tomography) is a widely employed imaging modality in the medical field. Normally, a volume of CT scans is prescribed by a doctor when a specific region of the body (typically neck to groin) is suspected of being abnormal. The doctors are required to make professional diagnoses based upon the obtained datasets. In this paper, we propose an automatic registration algorithm that helps healthcare personnel to automatically align corresponding scans from 'Study' to 'Atlas'. The proposed algorithm is capable of aligning both 'Atlas' and 'Study' into the same resolution through 3D interpolation. After retrieving the scanned slice volume in the 'Study' and the corresponding volume in the original 'Atlas' dataset, a 3D cross correlation method is used to identify and register various body parts.

Spectroscopic characterizations of a mixed surfactant mesophase and its application in materials synthesis

NASA Astrophysics Data System (ADS)

Liu, Limin

A viscous lyotropic crystalline mesophase containing bis (2-ethylhexyl) sodium sulfosuccinate (AOT), alpha-phosphatidylcholine (lecithin), with comparable volume fractions of isooctane and water was characterized by Fourier-transform 31P and 1H nuclear magnetic resonance (NMR) spectroscopy. Shear alignment on the reverse hexagonal mesophase was reflected through both 31P NMR and 1H NMR spectra. A complicated 31P spectrum was observed as a result of superposition of chemical shifts according to the distribution of crystalline domains prior to shear. The initially disordered samples with polydomain structures became macroscopically aligned after Couette shear and the alignment retained for a long period of time. 31P NMR chemical shift anisotropy characteristics were used to elucidate orientation of the hexagonal phase. Interestingly, 1H NMR of the water, methyl and methylene groups exhibited spectral changes upon shear alignment closely corresponding with that of 31P NMR spectra. A reverse hexagonal to lamellar phase transition was manifested as an expanding of the expressed 31P NMR chemical shift anisotropy and an apparent reversal of the powder pattern with increasing water content and/or temperature. Correspondingly, 1H NMR spectra also experienced a spectral pattern transition as the water content or temperature was increased. These observations complement the findings of mesophase alignment obtained using small angle neutron scattering (SANS) and imply that 31P and 1H NMR spectroscopy can be used as probes to define microstructure and monitor orientation changes in this binary surfactant system. This is especially beneficial if these mesophases are used as templates for materials synthesis. The mesophase retains its alignment for extended periods allowing materials synthesis to be decoupled from the application of shear. Highly aligned string-like silica nanostructures were obtained through templated synthesis in the columnar hexagonal structure of the viscous lyotropic crystalline mesophase. A two-step procedure was used to first shear-align the surfactant mesophase, and then conduct synthesis under quiescent conditions in the mesophase. Polystyrene was post-grafted to the silica surface without disturbing its nanostring morphology. The coupling of materials synthesis in surfactant mesophases with processing techniques (e.g. extrusion) may result in functional materials, such as new catalyst support and membrane nanoarchitectures.

3D Modeling of Forbidden Line Emission in the Binary Wind Interaction Region of Eta Carinae

NASA Technical Reports Server (NTRS)

Madura, Thomas; Gull, T. R.; Owocki, S.; Okazaki, A. T.; Russell, C. M. P.

2010-01-01

We present recent work using three-dimensional (3D) Smoothed Particle Hydrodynamics (SPH) simulations to model the high ([Fe III], [Ar III], [Ne III] and [S III]) and low ([Fe II], [Ni II]) ionization forbidden emission lines observed in Eta Carinae using the HST/STIS. These structures are interpreted as the time-averaged, outer extensions of the primary wind and the wind-wind interaction region directly excited by the FUV of the hot companion star of this massive binary system. We discuss how analyzing the results of the 3D SPH simulations and synthetic slit spectra and comparing them to the spectra obtained with the HST/STIS helps us determine the absolute orientation of the binary orbit and helps remove the degeneracy inherent to models based solely on the observed RXTE X-ray light curve. A key point of this work is that spatially resolved observations like those with HST/STIS and comparison to 3D models are necessary to determine the alignment or misalignment of the orbital angular momentum axis with the Homunculus, or correspondingly, the alignment of the orbital plane with the Homunculus skirt.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

Coherent Pattern Prediction in Swarms of Delay-Coupled Agents

NASA Astrophysics Data System (ADS)

Mier-Y-Teran-Romero, Luis; Forgoston, Eric; Scwartz, Ira

2013-03-01

We consider a general swarm model of self-propelling particles interacting through a pairwise potential in the presence of a fixed communication time delay. Previous work has shown that swarms with communication time delays and noise may display pattern transitions that depend on the size of the coupling amplitude. We extend these results by completely unfolding the bifurcation structure of the mean field approximation. Our analysis reveals a direct correspondence between the different dynamical behaviors found in different regions of the coupling-time delay plane with the different classes of simulated coherent swarm patterns. We derive the spatio-temporal scales of the swarm structures, and also demonstrate how the complicated interplay of coupling strength, time delay, noise intensity, and choice of initial conditions can affect the swarm. In addition, when adding noise to the system, we find that for sufficiently large values of the coupling strength and/or the time delay, there is a noise intensity threshold that forces a transition of the swarm from a misaligned state into an aligned state. We show that this alignment transition exhibits hysteresis when the noise intensity is taken to be time dependent. Office of Naval Research, NIH (LMR and IBS) and NRL (EF)

Shear-Wave Splitting and Crustal Anisotropy in the Shillong-Mikir Plateau of Northeast India

NASA Astrophysics Data System (ADS)

Bora, Dipok K.; Hazarika, Devajit; Paul, Arpita; Borah, Kajaljyoti; Borgohain, Jayanta Madhab

2018-01-01

Seismic anisotropy of crust beneath the Shillong-Mikir Plateau and the surrounding regions of northeast India have been investigated with the help of splitting analysis of S-wave of local earthquakes. We estimate a total 83 pairs of splitting parameters ( Φ and δt) from 67 local shallow focus earthquakes (depth ≤ 32 km) recorded by the 10 broadband seismological stations operated in the study region. The results show delay times ranging from 0.02 to 0.2 s, which correspond to anisotropy up to 4%, suggesting significant strength of anisotropy in the study region. Fast polarization direction ( Φ) in the Shillong Plateau shows mostly NW-SE trend in the western part and NE-SW trend in the northern part. Φs near Kopili fault (KF) follows NW-SE trend. Φ at most of the stations in the study region is consistent with the local stress orientation, suggesting that the anisotropy is mainly caused by preferentially aligned cracks responding to the stress field. On the other hand, anisotropy observed near the KF is due to aligned macroscopic fracture related to strike-slip movement in the fault zone.

Novel electrospun gas diffusion layers for polymer electrolyte membrane fuel cells: Part II. In operando synchrotron imaging for microscale liquid water transport characterization

NASA Astrophysics Data System (ADS)

Chevalier, S.; Ge, N.; Lee, J.; George, M. G.; Liu, H.; Shrestha, P.; Muirhead, D.; Lavielle, N.; Hatton, B. D.; Bazylak, A.

2017-06-01

This is the second paper in a two-part series in which we investigate the impact of the gas diffusion layer structure on the liquid water distribution in an operating polymer electrolyte membrane (PEM) fuel cell through the procedures of design, fabrication, and testing of novel hydrophobic electrospun gas diffusion layers (eGDLs). In this work, fibre diameters and alignment in eGDLs are precisely controlled, and concurrent synchrotron X-ray radiography and electrochemical impedance spectroscopy (EIS) are used to evaluate the influence of the controlled eGDL parameters on the liquid water distribution and on membrane liquid water content. For eGDLs with small fibre diameters (150-200 nm) and correspondingly smaller pore sizes, reduced liquid water accumulation under the flow field ribs is observed. However, more liquid water is pinned onto the eGDL - at the interface with flow field channels. Orienting fibre alignment perpendicular to the flow field channel direction leads to improved eGDL-catalyst layer contact and prevents rib-channel membrane deformation. On the other hand, eGDLs facilitate significant membrane dry-out, even under highly humidified operating conditions at high current densities.

Identification the geothermal system using 1-D audio-magnetotelluric inversion in Lamongan volcano field, East Java, Indonesia

NASA Astrophysics Data System (ADS)

Ilham, N.; Niasari, S. W.

2018-04-01

Tiris village, Probolinggo, East Java, is one of geothermal potential areas in Indonesia. This area is located in a valley flank of Mount Lamongan and Argopuro volcanic complex. This research aimed to identify a geothermal system at Tiris area, particularly the fluid pathways. The geothermal potential can be seen from the presence of warm springs with temperature ranging 35-45°C. The warm spring locations are aligned in the same orientation with major fault structure in the area. The fault structure shows dominant northwest-southeast orientation. We used audio-magnetotelluric data in the frequency range of 10 Hz until 92 kHz. The total magnetotelluric sites are 6. From the data analysis, most of the data orientation were 2-D with geo-electrical direction north-south. We used 1-D inversion using Newton algorithm. The 1-D inversion resulted in low resistive anomaly that corresponds to Lamongan lavas. Additionally, the depth of the resistor are different between the area to the west (i.e. 75 m) and to the east (i.e. 25 m). This indicates that there is a fault around the aligned maar (e.g. Ranu Air).

Alignment with the Common Core State Standards: easyCBM K-3 Word Reading. Technical Report #1303

ERIC Educational Resources Information Center

Sáez, Leilani; Irvin, P. Shawn; Alonzo, Julie; Tindal, Gerald

2013-01-01

Five hundred and seventeen words from the easyCBM Word Reading assessment (n = 57 kindergarten, 117 first grade, 172 second grade, and 171 third grade) were examined by 15 teachers for their correspondence with the Common Core State Standards in English Language Arts. In particular, the degree of correspondence between Standard 3 ("Phonics…

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

PubMed

Quinn, Terrance; Sinkala, Zachariah

2014-01-01

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

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

PubMed

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

2016-08-26

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

Precision aligned split V-block

DOEpatents

George, Irwin S.

1984-01-01

A precision aligned split V-block for holding a workpiece during a milling operation having an expandable frame for allowing various sized workpieces to be accommodated, is easily secured directly to the mill table and having key lugs in one base of the split V-block that assures constant alignment.

Torsional ARC Effectively Expands the Visual Field in Hemianopia

PubMed Central

Satgunam, PremNandhini; Peli, Eli

2012-01-01

Purpose Exotropia in congenital homonymous hemianopia has been reported to provide field expansion that is more useful when accompanied with harmonios anomalous retinal correspondence (HARC). Torsional strabismus with HARC provides a similar functional advantage. In a subject with hemianopia demonstrating a field expansion consistent with torsion we documented torsional strabismus and torsional HARC. Methods Monocular visual fields under binocular fixation conditions were plotted using a custom dichoptic visual field perimeter (DVF). The DVF was also modified to measure perceived visual directions under dissociated and associated conditions across the central 50° diameter field. The field expansion and retinal correspondence of a subject with torsional strabismus (along with exotropia and right hypertropia) with congenital homonymous hemianopia was compared to that of another exotropic subject with acquired homonymous hemianopia without torsion and to a control subject with minimal phoria. Torsional rotations of the eyes were calculated from fundus photographs and perimetry. Results Torsional ARC documented in the subject with congenital homonymous hemianopia provided a functional binocular field expansion up to 18°. Normal retinal correspondence was mapped for the full 50° visual field in the control subject and for the seeing field of the acquired homonymous hemianopia subject, limiting the functional field expansion benefit. Conclusions Torsional strabismus with ARC, when occurring with homonymous hemianopia provides useful field expansion in the lower and upper fields. Dichoptic perimetry permits documentation of ocular alignment (lateral, vertical and torsional) and perceived visual direction under binocular and monocular viewing conditions. Evaluating patients with congenital or early strabismus for HARC is useful when considering surgical correction, particularly in the presence of congenital homonymous hemianopia. PMID:22885782

Systems Thinking and the Leadership Conundrum in Health Care

ERIC Educational Resources Information Center

Marchildon, Gregory P.; Fletcher, Amber J.

2016-01-01

The ability to think in terms of a system is critical to achieving common direction, alignment, and commitment in highly distributed health systems. In Canada, provincial and territorial ministries of health provide leadership on the direction of health reform while leadership to align system levels is determined by a far more distributed group of…

Polyethylene damage and deformation on fixed-bearing, non-conforming unicondylar knee replacements corresponding to progressive changes in alignment and fixation.

PubMed

Harman, Melinda K; Schmitt, Sabine; Rössing, Sven; Banks, Scott A; Sharf, Hans-Peter; Viceconti, Marco; Hodge, W Andrew

2010-07-01

Deviations from nominal alignment of unicondylar knee replacements impact knee biomechanics, including the load and stress distribution at the articular contact surfaces. This study characterizes relationships between the biomechanical environment, distinguished by progressive changes in alignment and fixation, and articular damage and deformation in a consecutive series of retrieved unicondylar knee replacements. Twenty seven fixed-bearing, non-conforming unicondylar knee replacements of one design were retrieved after 2 to 13 years of in vivo function. The in vivo biomechanical environment was characterized by grading component migration measured from full-length radiographs and grading component fixation based on intraoperative manual palpation. Articular damage patterns and linear deformation on the polyethylene inserts were measured using optical photogrammetry and contact point digitization. Articular damage patterns and surface deformation on the explanted polyethylene inserts corresponded to progressive changes in component alignment and fixation. Component migration produced higher deformation rates, whereas loosening contributed to larger damage areas but lower deformation rates. Migration and loosening of the femoral component, but not the tibial component, were factors contributing to large regions of abrasion concentrated on the articular periphery. Classifying component migration and fixation at revision proved useful for distinguishing common biomechanical conditions associated with the varied polyethylene damage patterns and linear deformation for this fixed-bearing, non-conforming design. Pre-clinical evaluations of unicondylar knee replacements that are capable of reproducing variations in clinical alignment and predicting the observed wear mechanisms are necessary to better understand the impact of knee biomechanics and design on unicondylar knee replacement longevity. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Permanent bending and alignment of ZnO nanowires.

PubMed

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

2011-05-06

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

Fabrication and design of bioactive agent coated, highly-aligned electrospun matrices for nerve tissue engineering: Preparation, characterization and application

NASA Astrophysics Data System (ADS)

Lee, Sang Jin; Heo, Min; Lee, Donghyun; Heo, Dong Nyoung; Lim, Ho-Nam; Kwon, Il Keun

2017-12-01

In this study, we designed highly-aligned thermoplastic polycarbonate urethane (PCU) fibrous scaffolds coated with bioactive compounds, such as Poly-L-Lysine (PLL) and Poly-L-Ornithine (PLO), to enhance cellular adhesion and directivity. These products were characterized by scanning electron microscope (SEM) analysis which demonstrated that highly aligned fiber strands were formed without beads when coated onto a mandrel rotating at 1800 rpm. During in vitro cell test, PLO-coated, aligned PCU scaffolds were found to have significantly higher proliferation rates than PLL coated and bare PCU scaffolds. Interestingly, dental pulp stem cells (DPSCs) were observed to stretch along the longitudinal axis parallel to the cell direction on highly aligned scaffolds. These results clearly confirm that our strategy may suggest a useful paradigm by inducing neural tissue repair as a means to remodeling and healing of tissue for restorative procedures in neural tissue engineering.

Alignment mechanism of carbon nanofibers produced by plasma-enhanced chemical-vapor deposition

NASA Astrophysics Data System (ADS)

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

2001-10-01

We report experimental evidence showing a direct correlation between the alignment of carbon nanofibers (CNFs) prepared by plasma-enhanced chemical-vapor deposition and the location of the catalyst particle during CNF growth. In particular, we find that CNFs that have a catalyst particle at the tip (i.e., growth proceeds from the tip) align along the electric-field lines, whereas CNFs with the particle at the base (i.e., growth proceeds from the base) grow in random orientations. We propose a model that explains the alignment process as a result of a feedback mechanism associated with a nonuniform stress (part tensile, part compressive) that is created across the interface of the catalyst particle with the CNF due to electrostatic forces. Furthermore, we propose that the alignment seen recently in some dense CNF films is due to a crowding effect and is not directly the result of electrostatic forces.

Magnetic Alignment in Carps: Evidence from the Czech Christmas Fish Market

PubMed Central

Hart, Vlastimil; Kušta, Tomáš; Němec, Pavel; Bláhová, Veronika; Ježek, Miloš; Nováková, Petra; Begall, Sabine; Červený, Jaroslav; Hanzal, Vladimír; Malkemper, Erich Pascal; Štípek, Kamil; Vole, Christiane; Burda, Hynek

2012-01-01

While magnetoreception in birds has been studied intensively, the literature on magnetoreception in bony fish, and particularly in non-migratory fish, is quite scarce. We examined alignment of common carps (Cyprinus carpio) at traditional Christmas sale in the Czech Republic. The sample comprised measurements of the directional bearings in 14,537 individual fish, distributed among 80 large circular plastic tubs, at 25 localities in the Czech Republic, during 817 sampling sessions, on seven subsequent days in December 2011. We found that carps displayed a statistically highly significant spontaneous preference to align their bodies along the North-South axis. In the absence of any other common orientation cues which could explain this directional preference, we attribute the alignment of the fish to the geomagnetic field lines. It is apparent that the display of magnetic alignment is a simple experimental paradigm of great heuristic potential. PMID:23227241

Evolution of Texture from a Single Crystal Ti-6Al-4V Substrate During Electron Beam Directed Energy Deposition

NASA Astrophysics Data System (ADS)

Butler, Todd M.; Brice, Craig A.; Tayon, Wesley A.; Semiatin, S. Lee; Pilchak, Adam L.

2017-10-01

Additive manufacturing of Ti-6Al-4V commonly produces 〈001〉 β -fiber textures aligned with the build direction. We have performed wire-feed electron beam directed energy deposition on the {112} β plane of a single prior β-grain. The build initially grew epitaxially from the substrate with the preferred 〈001〉 growth direction significantly angled away from the build direction. However, continued layer deposition drove the formation of a 〈001〉 β -fiber texture aligned with the build direction and the direction of the strongest thermal gradient.

Sensor assembly method using silicon interposer with trenches for three-dimensional binocular range sensors

NASA Astrophysics Data System (ADS)

Nakajima, Kazuhiro; Yamamoto, Yuji; Arima, Yutaka

2018-04-01

To easily assemble a three-dimensional binocular range sensor, we devised an alignment method for two image sensors using a silicon interposer with trenches. The trenches were formed using deep reactive ion etching (RIE) equipment. We produced a three-dimensional (3D) range sensor using the method and experimentally confirmed that sufficient alignment accuracy was realized. It was confirmed that the alignment accuracy of the two image sensors when using the proposed method is more than twice that of the alignment assembly method on a conventional board. In addition, as a result of evaluating the deterioration of the detection performance caused by the alignment accuracy, it was confirmed that the vertical deviation between the corresponding pixels in the two image sensors is substantially proportional to the decrease in detection performance. Therefore, we confirmed that the proposed method can realize more than twice the detection performance of the conventional method. Through these evaluations, the effectiveness of the 3D binocular range sensor aligned by the silicon interposer with the trenches was confirmed.

Hydrostatic self-aligning axial/torsional mechanism

DOEpatents

O'Connor, Daniel G.; Gerth, Howard L.

1990-01-01

The present invention is directed to a self-aligning axial/torsional loading mechanism for testing the strength of brittle materials which are sensitive to bending moments. Disposed inside said self-aligning loading mechanism is a frictionless hydrostatic ball joint with a flexure ring to accommodate torsional loads through said ball joint.

CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways.

PubMed

Abaka, Gamze; Bıyıkoğlu, Türker; Erten, Cesim

2013-07-01

Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism. We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. Open source codes, executable binary, useful scripts, all the experimental data and the results are freely available as part of the Supplementary Material at http://code.google.com/p/campways/. Supplementary data are available at Bioinformatics online.

Radio-Optical Alignments in a Low Radio Luminosity Sample

NASA Technical Reports Server (NTRS)

Lacy, Mark; Ridgway, Susan E.; Wold, Margrethe; Lilje, Per B.; Rawlings, Steve

1999-01-01

We present an optically-based study of the alignment between the radio axes and the optical major axes of eight z approximately 0.7 radio galaxies in a 7C sample. The radio galaxies in this sample are approximately 20-times less radio luminous than 3C galaxies at the same redshift, and are significantly less radio-luminous than any other well-defined samples studied to date. Using Nordic Optical Telescope images taken in good seeing conditions at rest-frame wavelengths just longward of the 4000A break, we find a statistically significant alignment effect in the 7C sample. Furthermore, in two cases where the aligned components are well separated from the host we have been able to confirm spectroscopically that they are indeed at the same redshift as the radio galaxy. However, a quantitative analysis of the alignment in this sample and in a corresponding 3C sample from HST (Hubble Space Telescope) archival data indicates that the percentage of aligned flux may be lower and of smaller spatial scale in the 7C sample. Our study suggests that alignments on the 50-kpc scale are probably closely related to the radio luminosity, whereas those on the 15 kpc scale are not. We discuss these results in the context of popular models for the alignment effect.

Using automatic alignment to analyze endangered language data: Testing the viability of untrained alignment

PubMed Central

DiCanio, Christian; Nam, Hosung; Whalen, Douglas H.; Timothy Bunnell, H.; Amith, Jonathan D.; García, Rey Castillo

2013-01-01

While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones. PMID:23967953

Using automatic alignment to analyze endangered language data: testing the viability of untrained alignment.

PubMed

DiCanio, Christian; Nam, Hosung; Whalen, Douglas H; Bunnell, H Timothy; Amith, Jonathan D; García, Rey Castillo

2013-09-01

While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones.

The identification of complete domains within protein sequences using accurate E-values for semi-global alignment

PubMed Central

Kann, Maricel G.; Sheetlin, Sergey L.; Park, Yonil; Bryant, Stephen H.; Spouge, John L.

2007-01-01

The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the corresponding protein sequence. Ideally, complete domains are aligned to protein subsequences, in a ‘semi-global alignment’. Local alignment, which aligns pieces of domains to subsequences, is common in high-throughput annotation applications, however. It is a mature technique, with the heuristics and accurate E-values required for screening large databases and evaluating the screening results. Hidden Markov models (HMMs) provide an alternative theoretical framework for semi-global alignment, but their use is limited because they lack heuristic acceleration and accurate E-values. Our new tool, GLOBAL, overcomes some limitations of previous semi-global HMMs: it has accurate E-values and the possibility of the heuristic acceleration required for high-throughput applications. Moreover, according to a standard of truth based on protein structure, two semi-global HMM alignment tools (GLOBAL and HMMer) had comparable performance in identifying complete domains, but distinctly outperformed two tools based on local alignment. When searching for complete protein domains, therefore, GLOBAL avoids disadvantages commonly associated with HMMs, yet maintains their superior retrieval performance. PMID:17596268

Micro-miniature gas chromatograph column disposed in silicon wafers

DOEpatents

Yu, Conrad M.

2000-01-01

A micro-miniature gas chromatograph column is fabricated by forming matching halves of a circular cross-section spiral microcapillary in two silicon wafers and then bonding the two wafers together using visual or physical alignment methods. Heating wires are deposited on the outside surfaces of each wafer in a spiral or serpentine pattern large enough in area to cover the whole microcapillary area inside the joined wafers. The visual alignment method includes etching through an alignment window in one wafer and a precision-matching alignment target in the other wafer. The two wafers are then bonded together using the window and target. The physical alignment methods include etching through vertical alignment holes in both wafers and then using pins or posts through corresponding vertical alignment holes to force precision alignment during bonding. The pins or posts may be withdrawn after curing of the bond. Once the wafers are bonded together, a solid phase of very pure silicone is injected in a solution of very pure chloroform into one end of the microcapillary. The chloroform lowers the viscosity of the silicone enough that a high pressure hypodermic needle with a thumbscrew plunger can force the solution into the whole length of the spiral microcapillary. The chloroform is then evaporated out slowly to leave the silicone behind in a deposit.

New powerful statistics for alignment-free sequence comparison under a pattern transfer model.

PubMed

Liu, Xuemei; Wan, Lin; Li, Jing; Reinert, Gesine; Waterman, Michael S; Sun, Fengzhu

2011-09-07

Alignment-free sequence comparison is widely used for comparing gene regulatory regions and for identifying horizontally transferred genes. Recent studies on the power of a widely used alignment-free comparison statistic D2 and its variants D*2 and D(s)2 showed that their power approximates a limit smaller than 1 as the sequence length tends to infinity under a pattern transfer model. We develop new alignment-free statistics based on D2, D*2 and D(s)2 by comparing local sequence pairs and then summing over all the local sequence pairs of certain length. We show that the new statistics are much more powerful than the corresponding statistics and the power tends to 1 as the sequence length tends to infinity under the pattern transfer model. Copyright © 2011 Elsevier Ltd. All rights reserved.

New Powerful Statistics for Alignment-free Sequence Comparison Under a Pattern Transfer Model

PubMed Central

Liu, Xuemei; Wan, Lin; Li, Jing; Reinert, Gesine; Waterman, Michael S.; Sun, Fengzhu

2011-01-01

Alignment-free sequence comparison is widely used for comparing gene regulatory regions and for identifying horizontally transferred genes. Recent studies on the power of a widely used alignment-free comparison statistic D2 and its variants D2∗ and D2s showed that their power approximates a limit smaller than 1 as the sequence length tends to infinity under a pattern transfer model. We develop new alignment-free statistics based on D2, D2∗ and D2s by comparing local sequence pairs and then summing over all the local sequence pairs of certain length. We show that the new statistics are much more powerful than the corresponding statistics and the power tends to 1 as the sequence length tends to infinity under the pattern transfer model. PMID:21723298

Direct measurement of clinical mammographic x-ray spectra using a CdTe spectrometer.

PubMed

Santos, Josilene C; Tomal, Alessandra; Furquim, Tânia A; Fausto, Agnes M F; Nogueira, Maria S; Costa, Paulo R

2017-07-01

To introduce and evaluate a method developed for the direct measurement of mammographic x-ray spectra using a CdTe spectrometer. The assembly of a positioning system and the design of a simple and customized alignment device for this application is described. A positioning system was developed to easily and accurately locate the CdTe detector in the x-ray beam. Additionally, an alignment device to line up the detector with the central axis of the radiation beam was designed. Direct x-ray spectra measurements were performed in two different clinical mammography units and the measured x-ray spectra were compared with computer-generated spectra. In addition, the spectrometer misalignment effect was evaluated by comparing the measured spectra when this device is aligned relatively to when it is misaligned. The positioning and alignment of the spectrometer have allowed the measurements of direct mammographic x-ray spectra in agreement with computer-generated spectra. The most accurate x-ray spectral shape, related with the minimal HVL value, and high photon fluence for measured spectra was found with the spectrometer aligned according to the proposed method. The HVL values derived from both simulated and measured x-ray spectra differ at most 1.3 and 4.5% for two mammography devices evaluated in this study. The experimental method developed in this work allows simple positioning and alignment of a spectrometer for x-ray spectra measurements given the geometrical constraints and maintenance of the original configurations of mammography machines. © 2017 American Association of Physicists in Medicine.

Roll to Roll Electric Field "Z" Alignment of Nanoparticles from Polymer Solutions for Manufacturing Multifunctional Capacitor Films.

PubMed

Guo, Yuanhao; Batra, Saurabh; Chen, Yuwei; Wang, Enmin; Cakmak, Miko

2016-07-20

A roll to roll continuous processing method is developed for vertical alignment ("Z" alignment) of barium titanate (BaTiO3) nanoparticle columns in polystyrene (PS)/toluene solutions. This is accomplished by applying an electric field to a two-layer solution film cast on a carrier: one is the top sacrificial layer contacting the electrode and the second is the polymer solution dispersed with BaTiO3 particles. Flexible Teflon coated mesh is utilized as the top electrode that allows the evaporation of solvent through the openings. The kinetics of particle alignment and chain buckling is studied by the custom-built instrument measuring the real time optical light transmission during electric field application and drying steps. The nanoparticles dispersed in the composite bottom layer form chains due to dipole-dipole interaction under an applied electric field. In relatively weak electric fields, the particle chain axis tilts away from electric field direction due to bending caused by the shrinkage of the film during drying. The use of strong electric fields leads to maintenance of alignment of particle chains parallel to the electric field direction overcoming the compression effect. At the end of the process, the surface features of the top porous electrodes are imprinted at the top of the top sacrificial layer. By removing this layer a smooth surface film is obtained. The nanocomposite films with "Z" direction alignment of BaTiO3 particles show substantially increased dielectric permittivity in the thickness direction for enhancing the performance of capacitors.

Understanding band alignments in semiconductor heterostructures: Composition dependence and type-I-type-II transition of natural band offsets in nonpolar zinc-blende AlxGa1 -xN /AlyGa1 -yN composites

NASA Astrophysics Data System (ADS)

Landmann, M.; Rauls, E.; Schmidt, W. G.

2017-04-01

The composition dependence of the natural band alignment at nonpolar AlxGa1 -xN /AlyGa1 -yN heterojunctions is investigated via hybrid functional based density functional theory. Accurate band-gap data are provided using Heyd-Scuseria-Ernzerhof (HSE) type hybrid functionals with a composition dependent exact-exchange contribution. The unstrained band alignment between zincblende (zb) AlxGa1 -xN semiconductor alloys is studied within the entire ternary composition range utilizing the Branch-point technique to align the energy levels related to the bulklike direct Γv→Γc and indirect, pseudodirect, respectively, Γv→Xc type transitions in zb-AlxGa1 -xN . While the zb-GaN/AlxGa1 -xN band edges consistently show a type-I alignment, the relative position of fundamental band edges changes to a type-II alignment in the Al-rich composition ranges of zb-AlxGa1 -xN /AlN and zb-AlxGa1 -xN /AlyGa1 -yN systems. The presence of a direct-indirect band-gap transition at xc=0.63 in zb-AlxGa1 -xN semiconductor alloys gives rise to a notably different composition dependence of band discontinuities in the direct and indirect energy-gap ranges. Below the critical direct-indirect Al/Ga-crossover concentration, the band offsets show a close to linear dependence on the alloy composition. In contrast, notable bowing characteristics of all band discontinuities are observed above the critical crossover composition.

Direct determination of resonance energy transfer in photolyase: structural alignment for the functional state.

PubMed

Tan, Chuang; Guo, Lijun; Ai, Yuejie; Li, Jiang; Wang, Lijuan; Sancar, Aziz; Luo, Yi; Zhong, Dongping

2014-11-13

Photoantenna is essential to energy transduction in photoinduced biological machinery. A photoenzyme, photolyase, has a light-harvesting pigment of methenyltetrahydrofolate (MTHF) that transfers its excitation energy to the catalytic flavin cofactor FADH¯ to enhance DNA-repair efficiency. Here we report our systematic characterization and direct determination of the ultrafast dynamics of resonance energy transfer from excited MTHF to three flavin redox states in E. coli photolyase by capturing the intermediates formed through the energy transfer and thus excluding the electron-transfer quenching pathway. We observed 170 ps for excitation energy transferring to the fully reduced hydroquinone FADH¯, 20 ps to the fully oxidized FAD, and 18 ps to the neutral semiquinone FADH(•), and the corresponding orientation factors (κ(2)) were determined to be 2.84, 1.53 and 1.26, respectively, perfectly matching with our calculated theoretical values. Thus, under physiological conditions and over the course of evolution, photolyase has adopted the optimized orientation of its photopigment to efficiently convert solar energy for repair of damaged DNA.

Improvement of the optimum pH of Aspergillus niger xylanase towards an alkaline pH by site-directed mutagenesis.

PubMed

Li, Fei; Xie, Jingcong; Zhang, Xuesong; Zhao, Linguo

2015-01-01

In an attempt to shift the optimal pH of the xylanase B (XynB) from Aspergillus niger towards alkalinity, target mutation sites were selected by alignment between Aspergillus niger xylanase B and other xylanases that have alkalophilic pH optima that highlight charged residues in the eight-residues-longer loop in the alkalophilic xylanase. Multiple engineered XynB mutants were created by site-directed mutagenesis with substitutions Q164K and Q164K+D117N. The variant XynB-117 had the highest optimum pH (at 5.5), which corresponded to a basic 0.5 pH unit shift when compared with the wild-type enzyme. However, the optimal pH of the XynB- 164 mutation was not changed, similar to the wild type. These results suggest that the residues at positions 164 and 117 in the eight-residues-longer loop and the cleft's edge are important in determining the pH optima of XynB from Aspergillus niger.

HIGH FREQUENCY POWER TRANSMISSION LINE FOR CYCLOTRONS AND THE LIKE

DOEpatents

Armstrong, W.J.

1954-04-20

High-frequency power transmission systems, particularly a stacked capacitance alternating power current transmission line wherein maximum utilization of the effective conductios skin of the line conductors is achieved while enabling a low impedance to be obtained are reported. The transmission line consists of a number of flat metal strips with interleaved dielectric strips. The metal dielectric strips are coiled spirally with the axis of the spiral extending along the length of the strips, and the alternating metal strips at the output end have outwardly extending aligned lugs which are directly strapped together and connected to the respective terminals on the load. At the input end of the transmission line, similarly, the alternate metal strips are directly strapped together and connected to an altereating current source. With the arrangement described each metal strip conducts on both sides, so that the metal strips are designed to have a thickness corresponding to twice the depth of the "skin effect" conducting lamina of each conductor at the source frequency.

Measuring antimatter gravity with muonium

DOE PAGES

Kaplan, Daniel M.; Kirch, Klaus; Mancini, Derrick; ...

2015-05-29

The gravitational acceleration of antimatter, ¯g, has never been directly measured and could bear importantly on our understanding of gravity, the possible existence of a fifth force, and the nature and early history of the universe. Only two avenues for such a measurement appear to be feasible: antihydrogen and muonium. The muonium measurement requires a novel, monoenergetic, low-velocity, horizontal muonium beam directed at an atom interferometer. The precision three-grating interferometer can be produced in silicon nitride or ultrananocrystalline diamond using state-of-the-art nanofabrication. The required precision alignment and calibration at the picometer level also appear to be feasible. With 100 nmmore » grating pitch, a 10% measurement of ¯g can be made using some months of surface-muon beam time, and a 1% or better measurement with a correspondingly larger exposure. This could constitute the first gravitational measurement of leptonic matter, of 2nd-generation matter and, possibly, the first measurement of the gravitational acceleration of antimatter.« less

Transcript mapping for handwritten English documents

NASA Astrophysics Data System (ADS)

Jose, Damien; Bharadwaj, Anurag; Govindaraju, Venu

2008-01-01

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

Seamless, axially aligned, fiber tubes, meshes, microbundles and gradient biomaterial constructs

PubMed Central

Elia, Roberto; Firpo, Matthew A.; Kaplan, David L.; Peattie, Robert A.

2012-01-01

A new electrospinning apparatus was developed to generate nanofibrous materials with improved organizational control. The system functions by oscillating the deposition signal (ODS) of multiple collectors, allowing significantly improved nanofiber control by manipulating the electric field which drives the electrospinning process. Other electrospinning techniques designed to impart deposited fiber organizational control, such as rotating mandrels or parallel collector systems, do not generate seamless constructs with high quality alignment in sizes large enough for medical devices. In contrast, the ODS collection system produces deposited fiber networks with highly pure alignment in a variety of forms and sizes, including flat (8 × 8 cm2), tubular (1.3 cm diameter), or rope-like microbundle (45 μm diameter) samples. Additionally, the mechanism of our technique allows for scale-up beyond these dimensions. The ODS collection system produced 81.6 % of fibers aligned within 5° of the axial direction, nearly a four-fold improvement over the rotating mandrel technique. The meshes produced from the 9 % (w/v) fibroin/PEO blend demonstrated significant mechanical anisotropy due to the fiber alignment. In 37 °C PBS, aligned samples produced an ultimate tensile strength of 16.47 ± 1.18 MPa, a Young's modulus of 37.33 MPa, and a yield strength of 7.79 ± 1.13 MPa. The material was 300 % stiffer when extended in the direction of fiber alignment and required 20 times the amount of force to be deformed, compared to aligned meshes extended perpendicular to the fiber direction. The ODS technique could be applied to any electrospinnable polymer to overcome the more limited uniformity and induced mechanical strain of rotating mandrel techniques, and greatly surpasses the limited length of standard parallel collector techniques. PMID:22890517

Ionospheric electron heating, optical emissions, and striations induced by powerful HF radio waves at high latitudes: Aspect angle dependence

NASA Astrophysics Data System (ADS)

Rietveld, M. T.; Kosch, M. J.; Blagoveshchenskaya, N. F.; Kornienko, V. A.; Leyser, T. B.; Yeoman, T. K.

2003-04-01

In recent years, large electron temperature increases of 300% (3000 K above background) caused by powerful HF-radio wave injection have been observed during nighttime using the EISCAT incoherent scatter radar near Tromsø in northern Norway. In a case study we examine the spatial structure of the modified region. The electron heating is accompanied by ion heating of about 100 degrees and magnetic field-aligned measurements show ion outflows increasing with height up to 300 m s-1 at 582 km. The electron density decreases by up to 20%. When the radar antenna was scanned between three elevations from near field-aligned to vertical, the strongest heating effects were always obtained in the field-aligned position. When the HF-pump beam was scanned between the same three positions, the heating was still almost always strongest in the field-aligned direction. Simultaneous images of the 630 nm O(1D) line in the radio-induced aurora showed that the enhancement caused by the HF radio waves also remained localized near the field-aligned position. Coherent HF radar backscatter also appeared strongest when the pump beam was pointed field-aligned. These results are similar to some Langmuir turbulence phenomena which also show a strong preference for excitation by HF rays launched in the field-aligned direction. The correlation of the position of largest temperature enhancement with the position of the radio-induced aurora suggests that a common mechanism, upper-hybrid wave turbulence, is responsible for both effects. Why the strongest heating effects occur for HF rays directed along the magnetic field is still unclear, but self-focusing on field-aligned striations is a candidate mechanism, and possibly ionospheric tilts may be important.

Customization and design of directed self-assembly using hybrid prepatterns

NASA Astrophysics Data System (ADS)

Cheng, Joy; Doerk, Gregory S.; Rettner, Charles T.; Singh, Gurpreet; Tjio, Melia; Truong, Hoa; Arellano, Noel; Balakrishnan, Srinivasan; Brink, Markus; Tsai, Hsinyu; Liu, Chi-Chun; Guillorn, Michael; Sanders, Daniel P.

2015-03-01

Diminishing error tolerance renders the customization of patterns created through directed self-assembly (DSA) extremely challenging at tighter pitch. A self-aligned customization scheme can be achieved using a hybrid prepattern comprising both organic and inorganic regions that serves as a guiding prepattern to direct the self-assembly of the block copolymers as well as a cut mask pattern for the DSA arrays aligned to it. In this paper, chemoepitaxy-based self-aligned customization is demonstrated using two types of organic-inorganic prepatterns. CHEETAH prepattern for "CHemoepitaxy Etch Trim using a self-Aligned Hardmask" of preferential hydrogen silsesquioxane (HSQ, inorganic resist), non-preferential organic underlayer is fabricated using electron beam lithography. Customized trench or hole arrays can be achieved through co-transfer of DSA-formed arrays and CHEETAH prepattern. Herein, we also introduce a tone-reversed version called reverse-CHEETAH (or rCHEETAH) in which customized line segments can be achieved through co-transfer of DSA-formed arrays formed on a prepattern wherein the inorganic HSQ regions are nonpreferential and the organic regions are PMMA preferential. Examples of two-dimensional self-aligned customization including 25nm pitch fin structures and an 8-bar "IBM" illustrate the versatility of this customization scheme using rCHEETAH.

Interplanetary magnetic field dependency of stable Sun-aligned polar cap arcs

NASA Technical Reports Server (NTRS)

Valladares, C. E.; Carlson, H. C., Jr.; Fukui, K.

1994-01-01

This is the first analysis, using a statistically significant data set, of the morphological dependence of the presence, orientation, and motion of stable sun-aligned polar cap arcs upon the vector interplanetary magnetic field (IMF). For the one winter season analyzed we had 1392 all-sky 630.0-nm images of 2-min resolution containing a total of 150 polar cap arcs, all with corresponding values of the IMF as measured by International Monitoring Platform (IMP) 8 or International Sun Earth Explorer (ISEE) 2. After demonstrating an unbiased data set with smooth normal distributions of events versus the dimensions of time, space, and IMF component, we examine IMF dependencies of the properties of the optical arcs. A well-defined dependence for B(sub z) is found for the presence/absence of stable Sun-aligned polar cap arcs. Consistent with previous statistical studies, the probability of observing polar cap aurora steadily increases for larger positive values of B(sub z), and linearly decreases when B(sub z) becomes more negative. The probability of observing Sun-aligned arcs within the polar cap is determined to vary sharply as a function of the arc location; arcs were observed 40% of the time on the dawnside and only 10% on the duskside. This implies an overall probability of at least 40% for the whole polar cap. 20% of the arcs were observed during 'southward IMF conditions,' but in fact under closer inspection were found to have been formed under northward IMF conditions; these 'residual' positive B(sub z) arcs ha d a delayed residence time in the polar cap of about what would be expected after a north to south transition of B(sub z). A firm dependence on B(sub y) is also found for both the orientation and the dawn-dusk direction of motion of the arcs. All the arcs are Sun-aligned to a first approximation, but present deviations from this orientation, depending primarily upon the location of the arc in corrected geomagnetic (CG) coordinates. The arcs populating the 06-12 and the 12-18 quadrants of the CG coordinate system point toward the cusp. The B(sub y) dependency of the arc alignment is consistent with a cusp displacement in local time according to the sign of B(sub y). We found that the arc direction of motion depended both on B(sub y) and the arc location within the polar cap. For a given value of B(sub y) two well-defined regions (or cells) exist. Within each cell the arcs move in the same direction toward the boundary between the cells. The arcs located in the duskside move dawnward; those in the dawnside move duskward. The relative size of these dusk and dawn regions (or cells) are controlled by the magnitude of B(sub y). This persistent dusk-dawn motion fo the polar cap arcs is interpreted in terms of newly open flux tubes entering the polar cap and exerting a displacement of the convective cells and the polar cap arcs that are embedded within them.

Directly measuring of thermal pulse transfer in one-dimensional highly aligned carbon nanotubes

PubMed Central

Zhang, Guang; Liu, Changhong; Fan, Shoushan

2013-01-01

Using a simple and precise instrument system, we directly measured the thermo-physical properties of one-dimensional highly aligned carbon nanotubes (CNTs). A kind of CNT-based macroscopic materials named super aligned carbon nanotube (SACNT) buckypapers was measured in our experiment. We defined a new one-dimensional parameter, the “thermal transfer speed” to characterize the thermal damping mechanisms in the SACNT buckypapers. Our results indicated that the SACNT buckypapers with different densities have obviously different thermal transfer speeds. Furthermore, we found that the thermal transfer speed of high-density SACNT buckypapers may have an obvious damping factor along the CNTs aligned direction. The anisotropic thermal diffusivities of SACNT buckypapers could be calculated by the thermal transfer speeds. The thermal diffusivities obviously increase as the buckypaper-density increases. For parallel SACNT buckypapers, the thermal diffusivity could be as high as 562.2 ± 55.4 mm2/s. The thermal conductivities of these SACNT buckypapers were also calculated by the equation k = Cpαρ. PMID:23989589

Directly measuring of thermal pulse transfer in one-dimensional highly aligned carbon nanotubes.

PubMed

Zhang, Guang; Liu, Changhong; Fan, Shoushan

2013-01-01

Using a simple and precise instrument system, we directly measured the thermo-physical properties of one-dimensional highly aligned carbon nanotubes (CNTs). A kind of CNT-based macroscopic materials named super aligned carbon nanotube (SACNT) buckypapers was measured in our experiment. We defined a new one-dimensional parameter, the "thermal transfer speed" to characterize the thermal damping mechanisms in the SACNT buckypapers. Our results indicated that the SACNT buckypapers with different densities have obviously different thermal transfer speeds. Furthermore, we found that the thermal transfer speed of high-density SACNT buckypapers may have an obvious damping factor along the CNTs aligned direction. The anisotropic thermal diffusivities of SACNT buckypapers could be calculated by the thermal transfer speeds. The thermal diffusivities obviously increase as the buckypaper-density increases. For parallel SACNT buckypapers, the thermal diffusivity could be as high as 562.2 ± 55.4 mm(2)/s. The thermal conductivities of these SACNT buckypapers were also calculated by the equation k = Cpαρ.

Automatic alignment of double optical paths in excimer laser amplifier

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

Carbon nanotube-based sensor and method for detection of crack growth in a structure

NASA Technical Reports Server (NTRS)

Smits, Jan M. (Inventor); Moore, Thomas C. (Inventor); Kite, Marlen T. (Inventor); Wincheski, Russell A. (Inventor); Ingram, JoAnne L. (Inventor); Watkins, Anthony N. (Inventor); Williams, Phillip A. (Inventor)

2007-01-01

A sensor has a plurality of carbon nanotube (CNT)-based conductors operatively positioned on a substrate. The conductors are arranged side-by-side, such as in a substantially parallel relationship to one another. At least one pair of spaced-apart electrodes is coupled to opposing ends of the conductors. A portion of each of the conductors spanning between each pair of electrodes comprises a plurality of carbon nanotubes arranged end-to-end and substantially aligned along an axis. Because a direct correlation exists between the resistance of a carbon nanotube and its strain, changes experienced by the portion of the structure to which the sensor is coupled induce a corresponding change in the electrical properties of the conductors, thereby enabling detection of crack growth in the structure.

Impending flop for brand antiretrovirals in the emerging markets?

PubMed

Daniele, Dionisio; Daniela, Messeri

2008-01-01

Forecasts from Country choices, South-South partnerships and Clinton Foundation-UNITAID coalition show that present policies for brand ARVs are at the risk of flop in emerging South markets such as India, China, Thailand and Brazil.The dynamics explored in this article highlight the risks the originator companies are running in the emerging markets, along with their interest in direct agreements with the generic industry for the manufacturing and marketing of ARVs.Resulting information here would suggest the brand enterprises:To look for fast registration of their ARVs by regulatory authorities in all countries enlisted for differential pricing.To secure all formulations differentiated prices.To align with the Clinton-UNITAID prices for the corresponding generics.To pursue flexible negotiations with the generic companies to secure both counterparts long-term advantages.

Direct induction of molecular alignment in liquid crystal polymer network film by photopolymerization

NASA Astrophysics Data System (ADS)

Hisano, K.; Aizawa, M.; Ishizu, M.; Kurata, Y.; Shishido, A.

2016-09-01

Liquid crystal (LC) is the promising material for the fabrication of high-performance soft, flexible devices. The fascinating and useful properties arise from their cooperative effect that inherently allows the macroscopic integration and control of molecular alignment through various external stimuli. To date, light-matter interaction is the most attractive stimuli and researchers developed photoalignment through photochemical or photophysical reactions triggered by linearly polarized light. Here we show the new choice based on molecular diffusion by photopolymerization. We found that photopolymerization of a LC monomer and a crosslinker through a photomask enables to direct molecular alignment in the resultant LC polymer network film. The key generating the molecular alignment is molecular diffusion due to the difference of chemical potentials between irradiated and unirradiated regions. This concept is applicable to various shapes of photomask and two-dimensional molecular alignments can be fabricated depending on the spatial design of photomask. By virtue of the inherent versatility of molecular diffusion in materials, the process would shed light on the fabrication of various high-performance flexible materials with molecular alignment having controlled patterns.

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.

Microelectrode array-induced neuronal alignment directs neurite outgrowth: analysis using a fast Fourier transform (FFT).

PubMed

Radotić, Viktorija; Braeken, Dries; Kovačić, Damir

2017-12-01

Many studies have shown that the topography of the substrate on which neurons are cultured can promote neuronal adhesion and guide neurite outgrowth in the same direction as the underlying topography. To investigate this effect, isotropic substrate-complementary metal-oxide-semiconductor (CMOS) chips were used as one example of microelectrode arrays (MEAs) for directing neurite growth of spiral ganglion neurons. Neurons were isolated from 5 to 7-day-old rat pups, cultured 1 day in vitro (DIV) and 4 DIV, and then fixed with 4% paraformaldehyde. For analysis of neurite alignment and orientation, fast Fourier transformation (FFT) was used. Results revealed that on the micro-patterned surface of a CMOS chip, neurons orient their neurites along three directional axes at 30, 90, and 150° and that neurites aligned in straight lines between adjacent pillars and mostly followed a single direction while occasionally branching perpendicularly. We conclude that the CMOS substrate guides neurites towards electrodes by means of their structured pillar organization and can produce electrical stimulation of aligned neurons as well as monitoring their neural activities once neurites are in the vicinity of electrodes. These findings are of particular interest for neural tissue engineering with the ultimate goal of developing a new generation of MEA essential for improved electrical stimulation of auditory neurons.

MEMS packaging with etching and thinning of lid wafer to form lids and expose device wafer bond pads

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

Chanchani, Rajen; Nordquist, Christopher; Olsson, Roy H

In wafer-level packaging of microelectromechanical (MEMS) devices a lid wafer is bonded to a MEMS wafer in a predermined aligned relationship. Portions of the lid wafer are removed to separate the lid wafer into lid portions that respectively correspond in alignment with MEMS devices on the MEMS wafer, and to expose areas of the MEMS wafer that respectively contain sets of bond pads respectively coupled to the MEMS devices.

Thermal Conductivity of Polyimide/Carbon Nanofiller Blends

NASA Technical Reports Server (NTRS)

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

2007-01-01

In efforts to improve the thermal conductivity (TC) of Ultem(TM) 1000, it was compounded with three carbon based nano-fillers. Multiwalled carbon nanotubes (MWCNT), vapor grown carbon nanofibers (CNF) and expanded graphite (EG) were investigated. Ribbons were extruded to form samples in which the nano-fillers were aligned. Samples were also fabricated by compression molding in which the nano-fillers were randomly oriented. The thermal properties were evaluated by DSC and TGA, and the mechanical properties of the aligned samples were determined by tensile testing. The degree of dispersion and alignment of the nanoparticles were investigated with high-resolution scanning electron microscopy. The thermal conductivity of the samples was measured in both the direction of alignment as well as perpendicular to that direction using the Nanoflash technique. The results of this study will be presented.

Ion-beam-spurted dimethyl-sulfate-doped PEDOT:PSS composite-layer-aligning liquid crystal with low residual direct-current voltage

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

Liu, Yang; Lee, Ju Hwan; Seo, Dae-Shik, E-mail: dsseo@yonsei.ac.kr

2016-09-05

Thin ion-beam (IB)-spurted dimethyl sulfate/poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (DMS/PEDOT:PSS) layers with improved electro-optic performance are presented for aligning liquid crystals. IB spurting is effective for enhancing the conductivity of such layers, as well as the anchoring energy of the liquid crystals sandwiched between them. Compared with a commercial twisted-nematic cell assembled with polyimide alignment layers, the same cell assembled with 3.0-keV IB-spurted DMS/PEDOT:PSS alignment layers shows a 38% faster switching and a 93% lower residual direct current. The improved electro-optic performance here is likely due to the enhanced electric field effect and the charge-releasing ability of thin IB-spurted DMS/PEDOT:PSS layers.

Thermal Conductivity of Polyimide/Nanofiller Blends

NASA Technical Reports Server (NTRS)

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

2006-01-01

In efforts to improve the thermal conductivity of Ultem(TM) 1000, it was compounded with three carbon based nano-fillers. Multiwalled carbon nanotubes (MWCNT), vapor grown carbon nanofibers (CNF) and expanded graphite (EG) were investigated. Ribbons were extruded to form samples in which the nano-fillers were aligned. Samples were also fabricated by compression molding in which the nano-fillers were randomly oriented. The thermal properties were evaluated by DSC and TGA, and the mechanical properties of the aligned samples were determined by tensile testing. The degree of dispersion and alignment of the nanoparticles were investigated with high-resolution scanning electron microscopy. The thermal conductivity of the samples was measured in both the direction of alignment as well as perpendicular to that direction using the Nanoflash technique. The results of this study will be presented.

Enabling complex nanoscale pattern customization using directed self-assembly.

PubMed

Doerk, Gregory S; Cheng, Joy Y; Singh, Gurpreet; Rettner, Charles T; Pitera, Jed W; Balakrishnan, Srinivasan; Arellano, Noel; Sanders, Daniel P

2014-12-16

Block copolymer directed self-assembly is an attractive method to fabricate highly uniform nanoscale features for various technological applications, but the dense periodicity of block copolymer features limits the complexity of the resulting patterns and their potential utility. Therefore, customizability of nanoscale patterns has been a long-standing goal for using directed self-assembly in device fabrication. Here we show that a hybrid organic/inorganic chemical pattern serves as a guiding pattern for self-assembly as well as a self-aligned mask for pattern customization through cotransfer of aligned block copolymer features and an inorganic prepattern. As informed by a phenomenological model, deliberate process engineering is implemented to maintain global alignment of block copolymer features over arbitrarily shaped, 'masking' features incorporated into the chemical patterns. These hybrid chemical patterns with embedded customization information enable deterministic, complex two-dimensional nanoscale pattern customization through directed self-assembly.

Cancer-associated fibroblasts promote directional cancer cell migration by aligning fibronectin.

PubMed

Erdogan, Begum; Ao, Mingfang; White, Lauren M; Means, Anna L; Brewer, Bryson M; Yang, Lijie; Washington, M Kay; Shi, Chanjuan; Franco, Omar E; Weaver, Alissa M; Hayward, Simon W; Li, Deyu; Webb, Donna J

2017-11-06

Cancer-associated fibroblasts (CAFs) are major components of the carcinoma microenvironment that promote tumor progression. However, the mechanisms by which CAFs regulate cancer cell migration are poorly understood. In this study, we show that fibronectin (Fn) assembled by CAFs mediates CAF-cancer cell association and directional migration. Compared with normal fibroblasts, CAFs produce an Fn-rich extracellular matrix with anisotropic fiber orientation, which guides the cancer cells to migrate directionally. CAFs align the Fn matrix by increasing nonmuscle myosin II- and platelet-derived growth factor receptor α-mediated contractility and traction forces, which are transduced to Fn through α5β1 integrin. We further show that prostate cancer cells use αv integrin to migrate efficiently and directionally on CAF-derived matrices. We demonstrate that aligned Fn is a prominent feature of invasion sites in human prostatic and pancreatic carcinoma samples. Collectively, we present a new mechanism by which CAFs organize the Fn matrix and promote directional cancer cell migration. © 2017 Erdogan et al.

Cancer-associated fibroblasts promote directional cancer cell migration by aligning fibronectin

PubMed Central

Ao, Mingfang; White, Lauren M.; Means, Anna L.; Yang, Lijie; Washington, M. Kay; Franco, Omar E.; Li, Deyu; Webb, Donna J.

2017-01-01

Cancer-associated fibroblasts (CAFs) are major components of the carcinoma microenvironment that promote tumor progression. However, the mechanisms by which CAFs regulate cancer cell migration are poorly understood. In this study, we show that fibronectin (Fn) assembled by CAFs mediates CAF–cancer cell association and directional migration. Compared with normal fibroblasts, CAFs produce an Fn-rich extracellular matrix with anisotropic fiber orientation, which guides the cancer cells to migrate directionally. CAFs align the Fn matrix by increasing nonmuscle myosin II- and platelet-derived growth factor receptor α–mediated contractility and traction forces, which are transduced to Fn through α5β1 integrin. We further show that prostate cancer cells use αv integrin to migrate efficiently and directionally on CAF-derived matrices. We demonstrate that aligned Fn is a prominent feature of invasion sites in human prostatic and pancreatic carcinoma samples. Collectively, we present a new mechanism by which CAFs organize the Fn matrix and promote directional cancer cell migration. PMID:29021221

Functional Geometry Alignment and Localization of Brain Areas.

PubMed

Langs, Georg; Golland, Polina; Tie, Yanmei; Rigolo, Laura; Golby, Alexandra J

2010-01-01

Matching functional brain regions across individuals is a challenging task, largely due to the variability in their location and extent. It is particularly difficult, but highly relevant, for patients with pathologies such as brain tumors, which can cause substantial reorganization of functional systems. In such cases spatial registration based on anatomical data is only of limited value if the goal is to establish correspondences of functional areas among different individuals, or to localize potentially displaced active regions. Rather than rely on spatial alignment, we propose to perform registration in an alternative space whose geometry is governed by the functional interaction patterns in the brain. We first embed each brain into a functional map that reflects connectivity patterns during a fMRI experiment. The resulting functional maps are then registered, and the obtained correspondences are propagated back to the two brains. In application to a language fMRI experiment, our preliminary results suggest that the proposed method yields improved functional correspondences across subjects. This advantage is pronounced for subjects with tumors that affect the language areas and thus cause spatial reorganization of the functional regions.

Alignment method for solar collector arrays

DOEpatents

Driver, Jr., Richard B

2012-10-23

The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

Cortex-based inter-subject analysis of iEEG and fMRI data sets: application to sustained task-related BOLD and gamma responses.

PubMed

Esposito, Fabrizio; Singer, Neomi; Podlipsky, Ilana; Fried, Itzhak; Hendler, Talma; Goebel, Rainer

2013-02-01

Linking regional metabolic changes with fluctuations in the local electromagnetic fields directly on the surface of the human cerebral cortex is of tremendous importance for a better understanding of detailed brain processes. Functional magnetic resonance imaging (fMRI) and intra-cranial electro-encephalography (iEEG) measure two technically unrelated but spatially and temporally complementary sets of functional descriptions of human brain activity. In order to allow fine-grained spatio-temporal human brain mapping at the population-level, an effective comparative framework for the cortex-based inter-subject analysis of iEEG and fMRI data sets is needed. We combined fMRI and iEEG recordings of the same patients with epilepsy during alternated intervals of passive movie viewing and music listening to explore the degree of local spatial correspondence and temporal coupling between blood oxygen level dependent (BOLD) fMRI changes and iEEG spectral power modulations across the cortical surface after cortex-based inter-subject alignment. To this purpose, we applied a simple model of the iEEG activity spread around each electrode location and the cortex-based inter-subject alignment procedure to transform discrete iEEG measurements into cortically distributed group patterns by establishing a fine anatomic correspondence of many iEEG cortical sites across multiple subjects. Our results demonstrate the feasibility of a multi-modal inter-subject cortex-based distributed analysis for combining iEEG and fMRI data sets acquired from multiple subjects with the same experimental paradigm but with different iEEG electrode coverage. The proposed iEEG-fMRI framework allows for improved group statistics in a common anatomical space and preserves the dynamic link between the temporal features of the two modalities. Copyright © 2012 Elsevier Inc. All rights reserved.

Coevolution of a multilayer node-aligned network whose layers represent different social relations.

PubMed

Bahulkar, Ashwin; Szymanski, Boleslaw K; Chan, Kevin; Lizardo, Omar

2017-01-01

We examine the coevolution of three-layer node-aligned network of university students. The first layer is defined by nominations based on perceived prominence collected from repeated surveys during the first four semesters; the second is a behavioral layer representing actual students' interactions based on records of mobile calls and text messages; while the third is a behavioral layer representing potential face-to-face interactions suggested by bluetooth collocations. We address four interrelated questions. First, we ask whether the formation or dissolution of a link in one of the layers precedes or succeeds the formation or dissolution of the corresponding link in another layer (temporal dependencies). Second, we explore the causes of observed temporal dependencies between the layers. For those temporal dependencies that are confirmed, we measure the predictive capability of such dependencies. Third, we observe the progress towards nominations and the stages that lead to them. Finally, we examine whether the differences in dissolution rates of symmetric (undirected) versus asymmetric (directed) links co-exist in all layers. We find strong patterns of reciprocal temporal dependencies between the layers. In particular, the creation of an edge in either behavioral layer generally precedes the formation of a corresponding edge in the nomination layer. Conversely, the decay of a link in the nomination layer generally precedes a decline in the intensity of communication and collocation. Finally, nodes connected by asymmetric nomination edges have lower overall communication and collocation volumes and more asymmetric communication flows than the nodes linked by symmetric edges. We find that creation and dissolution of cognitively salient contacts have temporal dependencies with communication and collocation behavior.

Game Times and Higher Winning Percentages of West Coast Teams of the National Football League Correspond With Reduced Prevalence of Regular Season Injury.

PubMed

Brager, Allison J; Mistovich, R Justin

2017-02-01

Brager, AJ and Mistovich, RJ. Game times and higher winning percentages of west coast teams of the National Football League correspond with reduced prevalence of regular season injury. J Strength Cond Res 31(2): 462-467, 2017-West coast teams of the National Football League are more statistically likely to win home night games against east coast opponents. The alignment of game times with daily rhythms of alertness is thought to contribute to this advantage. This study aims to determine whether rates of turnovers and injuries during the regular season, putative measures of mental and physical fatigue, impact winning percentages. Regular season schedules and rates of turnovers for each of the 32 teams were obtained from Pro-Football-Reference. We developed our own metric of injury risk for each position obtained from depth charts and regular season schedules. This metric compared cumulative weeks on injury reserve with cumulative time zone travel. West coast teams traveled 4 times as often as east coast teams. However, teams traveling eastward won twice as many games. There was no relationship between the extent and direction of travel and number of turnovers. Losing teams had more turnovers. The offensive and defensive lines in Central Time (CT) were placed on injury reserve 4 times as often as offensive and defensive lines in Pacific Time (PT). Injury prevalence in CT vs. PT was most prominent midseason. Plotting midseason game time relative to biological time revealed that PT teams play games closer to endogenous peaks in alertness, whereas CT teams play games closer to endogenous troughs in alertness. Overall, closer alignment of game time with the endogenous "alerting" signal may protect west coast teams from fatigue-related injuries and suggests for modified strength and conditioning programs.

Crystal alignments in the Fast ice of arctic Alaska

NASA Astrophysics Data System (ADS)

Weeks, W. F.; Gow, A. J.

1980-02-01

Field observations at 60 sites located in the fast or near-fast ice along a 1200-km stretch of the north coast of Alaska between the Bering Strait and Barter Island have shown that the great majority of the ice samples (95%) exhibit striking c axis alignments within the horizontal plane. In all cases the degree of preferred orientation increased with depth in the ice. Representative standard deviations around a mean direction in the horizontal plane are commonly less than ±10° for samples collected near the bottom of the ice. At a given site the mean c axis direction ?0 may vary as much as 20° with vertical location in the ice sheet. The c axis allignments in the nearshore region generally parallel the coast, with strong alignments occurring in the lagoon systems between the barrier islands and the coast and seaward of the barrier islands. In passes between islands and in entrances such as the opening to Kotzebue Sound the alignment is parallel to the channel. Only limited observations are available farther seaward over the inner (10- to 50-m isobaths) and outer (50-m isobath to shelf break) shelf regions. These indicate NE-SW and E-W alignments, respectively, in the Beaufort Sea north of Prudhoe Bay. The general patterns of the alignments support the correlation between the preferred c axis direction and the current direction at the ice/water interface suggested by Weeks and Gow (1978). A comparison between c axis alignments and instantaneous current measurements made at 42 locations shows that the most frequent current direction coincides with ?0. At the one site where we were able to determine the current direction (52°T) over a longer period (7 hours), the agreement with ?0. (48°T) was excellent. Similarly, if only ?0. values determined in the nearshore region are considered, the most frequent deviation is 10° or less between ?0. and the trend of the adjacent shoreline, which is presumably parallel to the prevailing longshore currents. The c axis alignments are believed to be the result of geometric selection, with the most favored orientation being that in which the current flows normal to the (0001) plates of ice that comprise the dendritic sea ice/seawater interface. The instantaneous current observations suggest SW nearshore currents along the Chukchi coast between SW of Point Lay and SW of the Rogers-Post Monument. In the vicinity of Barrow all currents measured along the Chukchi coast were toward the NE. Current directions along the Beaufort coast in the nearshore region were generally parallel to the coast, with 45% of the observations indicating currents toward the E and 55% currents toward the W.

Thermal Conductivity of Ultem(TradeMark)/Carbon Nanofiller Blends

NASA Technical Reports Server (NTRS)

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

2006-01-01

In an effort to improve polymer thermal conductivity (TC), Ultem(TradeMark) 1000 was compounded with nano-fillers of carbon allotropes. Ultem(TradeMark) 1000 was selected since it is both solution and melt processable. As-received and modified multiwalled carbon nanotubes (MWCNTs), vapor grown carbon nanofibers (CNF) and expanded graphite (EG) were investigated. MWCNTs were modified by functionalizing the surface through oxidization with concentrated acids, mixing with an alkyl bromide, and addition of alkyl and phosphorus compounds after initial treatment with n-butyl lithium. Functionalization was performed to improve the TC compatibility between the resin and MWCNTs. It was postulated that this may provide an improved interface between the MWCNT and the polymer which would result in enhanced TC. The nano-fillers were mixed with Ultem(TradeMark) 1000 in the melt and in solution at concentrations ranging from 5 to 40 wt%. Ribbons were extruded from the blends to form samples where the nano-fillers were aligned to some degree in the extrusion direction. Samples were also fabricated by compression molding resulting in random orientation of the nano-fillers. Thermal properties of the samples were evaluated by Differential Scanning Calorimetry (DSC) and Thermal Gravimetric Analyzer (TGA). Tensile properties of aligned samples were determined at room temperature. The specimens were cut from the ribbons in the extrusion direction; hence the nano-fillers are somewhat aligned in the direction of stress. Typically it was observed that melt mixed samples exhibited superior mechanical properties compared to solution mixed samples. As expected, increased filler loading led to increased modulus and decreased elongation with respect to the neat polymer. The degree of dispersion and alignment of the nano-fillers was determined by high-resolution scanning electron microscopy (HRSEM). HRSEM of the ribbons revealed that the MWCNTs and CNFs were predominantly aligned in the flow direction. The TC of the samples was measured using a Nanoflash(TradeMark) instrument. Since the MWCNTs and CNF are anisotropic, the TC was expected to be different in the longitudinal (parallel to the nanotube and fiber axis) and transverse (perpendicular to the nanotube and fiber axis) directions. The extruded ribbons provided samples for transverse TC measurements. However, to determine the TC in the longitudinal direction, the ribbons needed to be stacked and molded under 1.7 MPa and 270 C. Samples were then obtained by cutting the molded block with a diamond saw. The largest TC improvement was achieved for aligned samples when the measurement was performed in the direction of MWCNT and CNF alignment (i.e. longitudinal axis). Unaligned samples also showed a significant improvement in TC and may be potentially useful in applications when it is not possible to align the nano-filler. The results of this study will be presented.

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

PubMed

Neuwald, Andrew F

2009-08-01

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

Omni-Directional Viewing-Angle Switching through Control of the Beam Divergence Angle in a Liquid Crystal Panel

NASA Astrophysics Data System (ADS)

Baek, Jong-In; Kim, Ki-Han; Kim, Jae Chang; Yoon, Tae-Hoon

2010-01-01

This paper proposes a method of omni-directional viewing-angle switching by controlling the beam diverging angle (BDA) in a liquid crystal (LC) panel. The LCs aligned randomly by in-cell polymer structures diffuse the collimated backlight for the bright state of the wide viewing-angle mode. We align the LCs homogeneously by applying an in-plane field for the narrow viewing-angle mode. By doing this the scattering is significantly reduced so that the small BDA is maintained as it passes through the LC layer. The dark state can be obtained by aligning the LCs homeotropically with a vertical electric field. We demonstrated experimentally the omni-directional switching of the viewing-angle, without an additional panel or backlighting system.

Tool for Inspecting Alignment of Twinaxial Connectors

NASA Technical Reports Server (NTRS)

Smith, Christopher R.

2008-01-01

A proposed tool would be used to inspect alignments of mating twinaxial-connector assemblies on interconnecting wiring harnesses. More specifically, the tool would be used to inspect the alignment of each contact pin of each connector on one assembly with the corresponding socket in the corresponding connector on the other assembly. It is necessary to inspect the alignment because if mating of the assemblies is attempted when any pin/socket pair is misaligned beyond tolerance, the connection will not be completed and the dielectric material in the socket will be damaged (see Figure 1). Although the basic principle of the tool is applicable to almost any type of mating connector assemblies, the specific geometry of the tool must match the pin-and-socket geometry of the specific mating assemblies to be inspected. In the original application for which the tool was conceived, each of the mating assemblies contains eight twinaxial connectors; the pin diameter is 0.014 in. (.0.35 mm), and the maximum allowable pin/socket misalignment is 0.007 in. (.0.18 mm). Incomplete connections can result in loss of flight data within the functional path to the space shuttle crew cockpit displays. The tool (see Figure 2) would consist mainly of a transparent disk with alignment clocking tabs that can be fitted onto either connector assembly. Sets of circles or equivalent reference markings are affixed to the face of the tool, located at the desired positions of the mating contact pairs. An inspector would simply fit the tool onto a connector assembly, engaging the clocking tabs until the tool fits tightly. The inspector would then align one set of circles positioning a line of sight perpendicular to one contact within the connector assembly. Mis alignments would be evidenced by the tip of a pin contact straying past the inner edge of the circle. Socket contact misalignments would be evidenced by a crescent-shaped portion of the white dielectric appearing within the circle. The tool could include a variable magnifier plus an illuminator that could be configured so as not to cast shadows.

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

PubMed

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

2017-01-21

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

An alignment method for mammographic X-ray spectroscopy under clinical conditions.

PubMed

Miyajima, S; Imagawa, K; Matsumoto, M

2002-09-01

This paper describes an alignment method for mammographic X-ray spectroscopy under clinical conditions. A pinhole, a fluorescent screen, a laser device and the case for a detector are used for alignment of the focal spot, a collimator and a detector. The method determines the line between the focal spot and the point of interest in an X-ray field radiographically. The method allows alignment for both central axis and off-axis directions.

Alignment by Maximization of Mutual Information

DTIC Science & Technology

1995-06-01

Davi Geiger, David Chapman, Jose Robles, Tao Alter, Misha Bolotski, Jonathan Connel, Karen Sarachik, Maja Mataric , Ian Horswill, Colin Angle...the same pose. These images are very different and are in fact anti-correlated: bright pixels in the left image correspond to dark pixels in the right...image; dark pixels in the left image correspond to bright pixels in the right image. No variant of correlation could match these images together

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.

Markov random field based automatic image alignment for electron tomography.

PubMed

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

2008-03-01

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

Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference.

PubMed

Swain, Timothy D

2018-01-01

The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA. Copyright © 2017 Elsevier Inc. All rights reserved.

Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)☆

PubMed Central

Parson, Walther; Strobl, Christina; Huber, Gabriela; Zimmermann, Bettina; Gomes, Sibylle M.; Souto, Luis; Fendt, Liane; Delport, Rhena; Langit, Reina; Wootton, Sharon; Lagacé, Robert; Irwin, Jodi

2013-01-01

Insights into the human mitochondrial phylogeny have been primarily achieved by sequencing full mitochondrial genomes (mtGenomes). In forensic genetics (partial) mtGenome information can be used to assign haplotypes to their phylogenetic backgrounds, which may, in turn, have characteristic geographic distributions that would offer useful information in a forensic case. In addition and perhaps even more relevant in the forensic context, haplogroup-specific patterns of mutations form the basis for quality control of mtDNA sequences. The current method for establishing (partial) mtDNA haplotypes is Sanger-type sequencing (STS), which is laborious, time-consuming, and expensive. With the emergence of Next Generation Sequencing (NGS) technologies, the body of available mtDNA data can potentially be extended much more quickly and cost-efficiently. Customized chemistries, laboratory workflows and data analysis packages could support the community and increase the utility of mtDNA analysis in forensics. We have evaluated the performance of mtGenome sequencing using the Personal Genome Machine (PGM) and compared the resulting haplotypes directly with conventional Sanger-type sequencing. A total of 64 mtGenomes (>1 million bases) were established that yielded high concordance with the corresponding STS haplotypes (<0.02% differences). About two-thirds of the differences were observed in or around homopolymeric sequence stretches. In addition, the sequence alignment algorithm employed to align NGS reads played a significant role in the analysis of the data and the resulting mtDNA haplotypes. Further development of alignment software would be desirable to facilitate the application of NGS in mtDNA forensic genetics. PMID:23948325

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

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

Zemla, A; Lang, D; Kostova, T

2010-11-29

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

The anatomy of a freezing lead

NASA Astrophysics Data System (ADS)

Gow, Anthony J.; Meese, Debra A.; Perovich, Donald K.; Tucker, Walter B.

1990-10-01

Winter leads are regions of intense ice growth with resultant large fluxes of heat to the atmosphere and salt to the ocean. They constitute a major source of new ice in the Arctic basin. During the 1988 drift phase of the Coordinated Eastern Arctic Experiment we were afforded a unique opportunity to conduct a detailed, long-term study of a freezing lead. Measurements were made from September 17 to November 18, during which time the ice grew from open water to a thickness of 0.56 m. Cores were removed from the lead ice on a routine basis and analyzed for ice temperature, salinity, density, and structure. From these measurements the derived quantities of brine volume, porosity, heat flux to the atmosphere, and salt flux to the ocean were computed. In addition to this 2-month time series study of ice cores, the spatial variation in lead ice properties was investigated on September 30. Thin-section studies of ice structure indicated that the upper 0.05-0.15 m of the ice sheet was granular and that the lower portion was columnar. Typically, a portion of the granular layer was snow ice. Once the transition from granular to columnar ice had occurred, granular ice did not reappear. As the ice grew thicker the c axes of the ice crystals became aligned within the horizontal plane. This alignment direction corresponded closely with the inferred direction of the current at the ice/water interface. Vertical temperature profiles in the ice were approximately linear. Salinity profiles were usually C-shaped with bulk salinities ranging from 9 to 6‰, before stabilizing at 6‰ for ice thicker than 0.35 m. Core data were used to compute the flux of heat to the atmosphere and the flux of salt to the ocean for seven time intervals during the experiment. Heat fluxes ranged from 89 to 29 W/m2 with an average of 50 W m-2, roughly 3 times the corresponding value from multiyear ice. The flux of salt from the lead ice to the ocean varied from 0.51 to 0.06 kg m-2 d-1, averaging 0.21 kg m-2 d-1.

Physics of self-aligned assembly at room temperature

NASA Astrophysics Data System (ADS)

Dubey, V.; Beyne, E.; Derakhshandeh, J.; De Wolf, I.

2018-01-01

Self-aligned assembly, making use of capillary forces, is considered as an alternative to active alignment during thermo-compression bonding of Si chips in the 3D heterogeneous integration process. Various process parameters affect the alignment accuracy of the chip over the patterned binding site on a substrate/carrier wafer. This paper discusses the chip motion due to wetting and capillary force using a transient coupled physics model for the two regimes (that is, wetting regime and damped oscillatory regime) in the temporal domain. Using the transient model, the effect of the volume of the liquid and the placement accuracy of the chip on the alignment force is studied. The capillary time (that is, the time it takes for the chip to reach its mean position) for the chip is directly proportional to the placement offset and inversely proportional to the viscosity. The time constant of the harmonic oscillations is directly proportional to the gap between the chips due to the volume of the fluid. The predicted behavior from transient simulations is next experimentally validated and it is confirmed that the liquid volume and the initial placement affect the final alignment accuracy of the top chip on the bottom substrate. With statistical experimental data, we demonstrate an alignment accuracy reaching <1 μm.

Neural-network-directed alignment of optical systems using the laser-beam spatial filter as an example

NASA Technical Reports Server (NTRS)

Decker, Arthur J.; Krasowski, Michael J.; Weiland, Kenneth E.

1993-01-01

This report describes an effort at NASA Lewis Research Center to use artificial neural networks to automate the alignment and control of optical measurement systems. Specifically, it addresses the use of commercially available neural network software and hardware to direct alignments of the common laser-beam-smoothing spatial filter. The report presents a general approach for designing alignment records and combining these into training sets to teach optical alignment functions to neural networks and discusses the use of these training sets to train several types of neural networks. Neural network configurations used include the adaptive resonance network, the back-propagation-trained network, and the counter-propagation network. This work shows that neural networks can be used to produce robust sequencers. These sequencers can learn by example to execute the step-by-step procedures of optical alignment and also can learn adaptively to correct for environmentally induced misalignment. The long-range objective is to use neural networks to automate the alignment and operation of optical measurement systems in remote, harsh, or dangerous aerospace environments. This work also shows that when neural networks are trained by a human operator, training sets should be recorded, training should be executed, and testing should be done in a manner that does not depend on intellectual judgments of the human operator.

Enhanced piezoresponse of highly aligned electrospun poly(vinylidene fluoride) nanofibers

NASA Astrophysics Data System (ADS)

Kang, Sung Bum; Won, Sang Hyuk; Im, Min Ji; Kim, Chan Ul; Park, Won Il; Baik, Jeong Min; Choi, Kyoung Jin

2017-09-01

Well-ordered nanostructure arrays with controlled densities can potentially improve material properties; however, their fabrication typically involves the use of complicated processing techniques. In this work, we demonstrate a uniaxial alignment procedure for fabricating poly(vinylidene fluoride) (PVDF) electrospun nanofibers (NFs) by introducing collectors with additional steps. The mechanism of the observed NF alignment, which occurs due to the concentration of lateral electric field lines around collector steps, has been elucidated via finite-difference time-domain simulations. The membranes composed of well-aligned PVDF NFs are characterized by a higher content of the PVDF β-phase, as compared to those manufactured from randomly orientated fibers. The piezoelectric energy harvester, which was fabricated by transferring well-aligned PVDF NFs onto flexible substrates with Ag electrodes attached to both sides, exhibited a 2-fold increase in the output voltage and a 3-fold increase in the output current as compared to the corresponding values obtained for the device manufactured from randomly oriented NFs. The enhanced piezoresponse observed for the aligned PVDF NFs is due to their higher β-phase content, denser structure, smaller effective radius of curvature during bending, greater applied strain, and higher fraction of contributing NFs.

Kernel Manifold Alignment for Domain Adaptation.

PubMed

Tuia, Devis; Camps-Valls, Gustau

2016-01-01

The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors' knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational efficiency, and discuss the generalization performance of KEMA under Rademacher principles of stability. Aligning multimodal data with KEMA reports outstanding benefits when used as a data pre-conditioner step in the standard data analysis processing chain. KEMA exhibits very good performance over competing methods in synthetic controlled examples, visual object recognition and recognition of facial expressions tasks. KEMA is especially well-suited to deal with high-dimensional problems, such as images and videos, and under complicated distortions, twists and warpings of the data manifolds. A fully functional toolbox is available at https://github.com/dtuia/KEMA.git.

Formation of wormlike aggregates of fluorocarbon-hydrocarbon hybrid surfactant by Langmuir-Blodgett transfer and alignment of gold nanoparticles.

PubMed

Kondo, Yukishige; Fukuoka, Hiroshi; Nakano, Shuichi; Hayashi, Kohei; Tsukagoshi, Tatsuya; Matsumoto, Mutsuyoshi; Yoshino, Norio

2007-05-22

A novel anionic fluorocarbon-hydrocarbon hybrid surfactant (SS-Hyb-Na+) with a disulfide group has been synthesized from 11-bromo-1-undecanal and perfluorohexylethyl iodide via three steps. The Langmuir-Blodgett (LB) transfer of the 1:100 (mol/mol) mixed monolayer of SS-Hyb-Na+ and stearyl alcohol (C18OH) formed on an aqueous solution containing a cationic polymer, poly(diallyldimethylammonium chloride) (PDDA+Cl-) onto a hydrophobic silicon wafer yields the formation of wormlike aggregates consisting of SS-Hyb-/PDDA+ polyion complexes. It is found that the aggregates align along the withdrawal direction of the wafer substrate. When the wafer on which the wormlike aggregates exist is immersed into the dispersion of gold nanoparticles (Au NPs) prepared by the citrate reduction method, Au NPs align along the wormlike structures. Even though the surface of the wafer is placed either vertical or parallel to the monolayer compression direction during the LB transfer, the one-dimensional (1D) array of Au NPs is observed along the withdrawal direction of the wafer. This indicates that the wormlike aggregates of SS-Hyb-/PDDA+ complexes are aligned during the LB transfer, and the aligned aggregates behave as a scaffold in the 1D array of Au NPs.

The alignment between phenotypic plasticity, the major axis of genetic variation and the response to selection.

PubMed

Lind, Martin I; Yarlett, Kylie; Reger, Julia; Carter, Mauricio J; Beckerman, Andrew P

2015-10-07

Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing genetic variation in the direction favoured by selection and reflected in plasticity. We evaluated this theory in the freshwater crustacean Daphnia pulex, facing predation risk from two contrasting size-selective predators. We estimated plasticity in several life-history traits, the G matrix of these traits, the selection gradients on reproduction and survival, and the predicted responses to selection. Using these data, we tested whether the genetic lines of least resistance and the predicted response to selection aligned with plasticity. We found predator environment-specific G matrices, but shared genetic architecture across environments resulted in more constraint in the G matrix than in the plasticity of the traits, sometimes preventing alignment of the two. However, as the importance of survival selection increased, the difference between environments in their predicted response to selection increased and resulted in closer alignment between the plasticity and the predicted selection response. Therefore, plasticity may indeed aid adaptation to new environments. © 2015 The Authors.

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

PubMed Central

2012-01-01

Background Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. Results The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Conclusions Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family. PMID:22793672

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

PubMed

Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl

2012-07-13

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

Electrospun fibrinogen-PLA nanofibres for vascular tissue engineering.

PubMed

Gugutkov, D; Gustavsson, J; Cantini, M; Salmeron-Sánchez, M; Altankov, G

2017-10-01

Here we report on the development of a new type of hybrid fibrinogen-polylactic acid (FBG-PLA) nanofibres (NFs) with improved stiffness, combining the good mechanical properties of PLA with the excellent cell recognition properties of native FBG. We were particularly interested in the dorsal and ventral cell response to the nanofibres' organization (random or aligned), using human umbilical endothelial cells (HUVECs) as a model system. Upon ventral contact with random NFs, the cells developed a stellate-like morphology with multiple projections. The well-developed focal adhesion complexes suggested a successful cellular interaction. However, time-lapse analysis shows significantly lowered cell movements, resulting in the cells traversing a relatively short distance in multiple directions. Conversely, an elongated cell shape and significantly increased cell mobility were observed in aligned NFs. To follow the dorsal cell response, artificial wounds were created on confluent cell layers previously grown on glass slides and covered with either random or aligned NFs. Time-lapse analysis showed significantly faster wound coverage (within 12 h) of HUVECs on aligned samples vs. almost absent directional migration on random ones. However, nitric oxide (NO) release shows that endothelial cells possess lowered functionality on aligned NFs compared to random ones, where significantly higher NO production was found. Collectively, our studies show that randomly organized NFs could support the endothelization of implants while aligned NFs would rather direct cell locomotion for guided neovascularization. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Anisotropic, lightweight, strong, and super thermally insulating nanowood with naturally aligned nanocellulose

PubMed Central

Li, Tian; Song, Jianwei; Zhao, Xinpeng; Yang, Zhi; Pastel, Glenn; Xu, Shaomao; Jia, Chao; Dai, Jiaqi; Chen, Chaoji; Gong, Amy; Jiang, Feng; Yao, Yonggang; Fan, Tianzhu; Yang, Bao; Wågberg, Lars; Yang, Ronggui; Hu, Liangbing

2018-01-01

There has been a growing interest in thermal management materials due to the prevailing energy challenges and unfulfilled needs for thermal insulation applications. We demonstrate the exceptional thermal management capabilities of a large-scale, hierarchal alignment of cellulose nanofibrils directly fabricated from wood, hereafter referred to as nanowood. Nanowood exhibits anisotropic thermal properties with an extremely low thermal conductivity of 0.03 W/m·K in the transverse direction (perpendicular to the nanofibrils) and approximately two times higher thermal conductivity of 0.06 W/m·K in the axial direction due to the hierarchically aligned nanofibrils within the highly porous backbone. The anisotropy of the thermal conductivity enables efficient thermal dissipation along the axial direction, thereby preventing local overheating on the illuminated side while yielding improved thermal insulation along the backside that cannot be obtained with isotropic thermal insulators. The nanowood also shows a low emissivity of <5% over the solar spectrum with the ability to effectively reflect solar thermal energy. Moreover, the nanowood is lightweight yet strong, owing to the effective bonding between the aligned cellulose nanofibrils with a high compressive strength of 13 MPa in the axial direction and 20 MPa in the transverse direction at 75% strain, which exceeds other thermal insulation materials, such as silica and polymer aerogels, Styrofoam, and wool. The excellent thermal management, abundance, biodegradability, high mechanical strength, low mass density, and manufacturing scalability of the nanowood make this material highly attractive for practical thermal insulation applications. PMID:29536048

Orientational alignment in cavity quantum electrodynamics

NASA Astrophysics Data System (ADS)

Keeling, Jonathan; Kirton, Peter G.

2018-05-01

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

Differential rotation in solar-like stars from global simulations

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

Guerrero, G.; Kosovichev, A. G.; Smolarkiewicz, P. K.

2013-12-20

To explore the physics of large-scale flows in solar-like stars, we perform three-dimensional anelastic simulations of rotating convection for global models with stratification resembling the solar interior. The numerical method is based on an implicit large-eddy simulation approach designed to capture effects from non-resolved small scales. We obtain two regimes of differential rotation, with equatorial zonal flows accelerated either in the direction of rotation (solar-like) or in the opposite direction (anti-solar). While the models with the solar-like differential rotation tend to produce multiple cells of meridional circulation, the models with anti-solar differential rotation result in only one or two meridionalmore » cells. Our simulations indicate that the rotation and large-scale flow patterns critically depend on the ratio between buoyancy and Coriolis forces. By including a sub-adiabatic layer at the bottom of the domain, corresponding to the stratification of a radiative zone, we reproduce a layer of strong radial shear similar to the solar tachocline. Similarly, enhanced super-adiabaticity at the top results in a near-surface shear layer located mainly at lower latitudes. The models reveal a latitudinal entropy gradient localized at the base of the convection zone and in the stable region, which, however, does not propagate across the convection zone. In consequence, baroclinicity effects remain small, and the rotation isocontours align in cylinders along the rotation axis. Our results confirm the alignment of large convective cells along the rotation axis in the deep convection zone and suggest that such 'banana-cell' pattern can be hidden beneath the supergranulation layer.« less

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.

Induction and quantification of collagen fiber alignment in a three-dimensional hydroxyapatite-collagen composite scaffold.

PubMed

Banglmaier, Richard F; Sander, Edward A; VandeVord, Pamela J

2015-04-01

Hydroxyapatite-collagen composite scaffolds are designed to serve as a regenerative load bearing replacement that mimics bone. However, the material properties of these scaffolds are at least an order of magnitude less than that of bone and subject to fail under physiological loading conditions. These scaffolds compositionally resemble bone but they do not possess important structural attributes such as an ordered arrangement of collagen fibers, which is a correlate to the mechanical properties in bone. Furthermore, it is unclear how much ordering of structure is satisfactory to mimic bone. Therefore, quantitative methods are needed to characterize collagen fiber alignment in these scaffolds for better correlation between the scaffold structure and the mechanical properties. A combination of extrusion and compaction was used to induce collagen fiber alignment in composite scaffolds. Collagen fiber alignment, due to extrusion and compaction, was quantified from polarized light microscopy images with a Fourier transform image processing algorithm. The Fourier transform method was capable of resolving the degree of collagen alignment from polarized light images. Anisotropy indices of the image planes ranged from 0.08 to 0.45. Increases in the degree of fiber alignment induced solely by extrusion (0.08-0.25) or compaction (0.25-0.44) were not as great as those by the combination of extrusion and compaction (0.35-0.45). Additional measures of randomness and fiber direction corroborate these anisotropy findings. This increased degree of collagen fiber alignment was induced in a preferred direction that is consistent with the extrusion direction and parallel with the compacted plane. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Techniques for Type I Collagen Organization

NASA Astrophysics Data System (ADS)

Anderson-Jackson, LaTecia Diamond

Tissue Engineering is a process in which cells, engineering, and material methods are used in amalgamation to improve biological functions. The purpose of tissue engineering is to develop alternative solutions to treat or cure tissues and organs that have been severely altered or damaged by diseases, congenital defects, trauma, or cancer. One of the most common and most promising biological materials for tissue engineering to develop scaffolds is Type I collagen. A major challenge in biomedical research is aligning Type I collagen to mimic biological structures, such as ligaments, tendons, bones, and other hierarchal aligned structures within the human body. The intent of this research is to examine possible techniques for organizing Type I collagen and to assess which of the techniques is effective for potential biological applications. The techniques used in this research to organize collagen are soft lithography with solution-assisted sonication embossing, directional freezing, and direct poling. The final concentration used for both soft lithography with solution-assisted sonication embossing and direct poling was 1 mg/ml, whereas for directional freezing the final concentration varied between 4mg/ml, 2mg/ml, and 1 mg/ml. These techniques were characterized using the Atomic Force Microscope (AFM) and Helium Ion Microscope (HIM). In this study, we have found that out of the three techniques, the soft lithography and directional freezing techniques have been successful in organizing collagen in a particular pattern, but not alignment. We concluded alignment may be dependent on the pH of collagen and the amount of acetic acid used in collagen solution. However, experiments are still being conducted to optimize all three techniques to align collagen in a unidirectional arrangement.

Band Alignment and Controllable Electron Migration between Rutile and Anatase TiO2

PubMed Central

Mi, Yang; Weng, Yuxiang

2015-01-01

TiO2 is the most promising semiconductor for photocatalytic splitting of water for hydrogen and degradation of pollutants. The highly photocatalytic active form is its mixed phase of two polymorphs anatase and rutile rather than their pristine compositions. Such a synergetic effect is understood by the staggered band alignment favorable to spatial charge separation. However, electron migration in either direction between the two phases has been reported, the reason of which is still unknown. We determined the band alignment by a novel method, i.e., transient infrared absorption-excitation energy scanning spectra, showing their conduction bands being aligned, thus the electron migration direction is controlled by dynamical factors, such as varying the particle size of anatase, putting electron or hole scavengers on either the surface of anatase or rutile phases, or both. A quantitative criterion capable of predicting the migration direction under various conditions including particle size and surface chemical reactions is proposed, the predictions have been verified experimentally in several typical cases. This would give rise to a great potential in designing more effective titania photocatalysts. PMID:26169699

Theoretical studies on lattice-oriented growth of single-walled carbon nanotubes on sapphire

NASA Astrophysics Data System (ADS)

Li, Zhengwei; Meng, Xianhong; Xiao, Jianliang

2017-09-01

Due to their excellent mechanical and electrical properties, single-walled carbon nanotubes (SWNTs) can find broad applications in many areas, such as field-effect transistors, logic circuits, sensors and flexible electronics. High-density, horizontally aligned arrays of SWNTs are essential for high performance electronics. Many experimental studies have demonstrated that chemical vapor deposition growth of nanotubes on crystalline substrates such as sapphire offers a promising route to achieve such dense, perfectly aligned arrays. In this work, a theoretical study is performed to quantitatively understand the van der Waals interactions between SWNTs and sapphire substrates. The energetically preferred alignment directions of SWNTs on A-, R- and M-planes and the random alignment on the C-plane predicted by this study are all in good agreement with experiments. It is also shown that smaller SWNTs have better alignment than larger SWNTs due to their stronger interaction with sapphire substrate. The strong vdW interactions along preferred alignment directions can be intuitively explained by the nanoscale ‘grooves’ formed by atomic lattice structures on the surface of sapphire. This study provides important insights to the controlled growth of nanotubes and potentially other nanomaterials.

Beam alignment based on two-dimensional power spectral density of a near-field image.

PubMed

Wang, Shenzhen; Yuan, Qiang; Zeng, Fa; Zhang, Xin; Zhao, Junpu; Li, Kehong; Zhang, Xiaolu; Xue, Qiao; Yang, Ying; Dai, Wanjun; Zhou, Wei; Wang, Yuanchen; Zheng, Kuixing; Su, Jingqin; Hu, Dongxia; Zhu, Qihua

2017-10-30

Beam alignment is crucial to high-power laser facilities and is used to adjust the laser beams quickly and accurately to meet stringent requirements of pointing and centering. In this paper, a novel alignment method is presented, which employs data processing of the two-dimensional power spectral density (2D-PSD) for a near-field image and resolves the beam pointing error relative to the spatial filter pinhole directly. Combining this with a near-field fiducial mark, the operation of beam alignment is achieved. It is experimentally demonstrated that this scheme realizes a far-field alignment precision of approximately 3% of the pinhole size. This scheme adopts only one near-field camera to construct the alignment system, which provides a simple, efficient, and low-cost way to align lasers.

Coherent radar estimates of high latitude field-aligned currents: the importance of conductance gradients

NASA Astrophysics Data System (ADS)

Kosch, M.; Nielsen, E.

Two bi-static VHF radar systems STARE and SABRE have been employed to estimate ionospheric electric field distributions in the geomagnetic latitude range 61 1 - 69 3 degrees over Scandinavia corresponding to the global Region 2 current system 173 days of data from all four radars have been analysed during the period 1982 to 1986 The average magnetic field-aligned currents have been computed as a function of the Kp and Ae indices using an empirical model of ionospheric Pedersen and Hall conductance taking into account conductance gradients The divergence of horizontal Pedersen currents and Hall conductance gradients have approximately the same importance for generating the Region 2 field-aligned currents Pedersen conductance gradients have a significant modifying effect A case study of field-aligned currents has been performed using the STARE radar system to obtain the instantaneous ionospheric electric field distribution in the vicinity of an auroral arc The instantaneous Hall conductance was estimated from the Scandinavian Magnetometer Array This study clearly shows that even for quiet steady state geomagnetic conditions conductance gradients are important modifiers of magnetic field-aligned currents

Summarizing Audiovisual Contents of a Video Program

NASA Astrophysics Data System (ADS)

Gong, Yihong

2003-12-01

In this paper, we focus on video programs that are intended to disseminate information and knowledge such as news, documentaries, seminars, etc, and present an audiovisual summarization system that summarizes the audio and visual contents of the given video separately, and then integrating the two summaries with a partial alignment. The audio summary is created by selecting spoken sentences that best present the main content of the audio speech while the visual summary is created by eliminating duplicates/redundancies and preserving visually rich contents in the image stream. The alignment operation aims to synchronize each spoken sentence in the audio summary with its corresponding speaker's face and to preserve the rich content in the visual summary. A Bipartite Graph-based audiovisual alignment algorithm is developed to efficiently find the best alignment solution that satisfies these alignment requirements. With the proposed system, we strive to produce a video summary that: (1) provides a natural visual and audio content overview, and (2) maximizes the coverage for both audio and visual contents of the original video without having to sacrifice either of them.

Pattern and polarization measurements of integrated-circuit spiral antennas at 10-μm wavelength

NASA Astrophysics Data System (ADS)

MacDonald, Michael E.; Grossman, Erich N.

1996-12-01

Radiation patterns are presented for planar equiangular spiral antennas at wavelengths of approximately 10 micrometers . These antennas are fabricated using integrated-circuit processes on silicon substrates and are coupled through dielectric lenses. Patterns are presented over a full 2D scan for orthogonal linear polarizations, and for left- circular (LCP) and right-circular (RCP) polarizations. The antennas respond preferentially to left-circularly polarized radiation, as expected for the left-handed sense of the spiral arms. Cross-polarization ratios as large as 10 dB in circular polarization are obtained, corresponding to an axial ratio of 1.2. No difference in response between horizontally and vertically polarized radiation is observed, as expected for circularly polarized antennas. Directivities as large as 14 dB in left-circular polarization have been obtained. The cross-polarized directivity is considerably lower than the co-polarized directivity. All patterns are approximately circularly symmetric about the (theta) equals 0 axis. The cross-polarization ratio and pattern symmetry strongly depend on the alignment of the antenna and detector response is antenna coupled, even at radiation wavelength of the same order of magnitude as the resolution limit of the optical lithography used to define the antenna geometry.

Thermal feature extraction of servers in a datacenter using thermal image registration

NASA Astrophysics Data System (ADS)

Liu, Hang; Ran, Jian; Xie, Ting; Gao, Shan

2017-09-01

Thermal cameras provide fine-grained thermal information that enhances monitoring and enables automatic thermal management in large datacenters. Recent approaches employing mobile robots or thermal camera networks can already identify the physical locations of hot spots. Other distribution information used to optimize datacenter management can also be obtained automatically using pattern recognition technology. However, most of the features extracted from thermal images, such as shape and gradient, may be affected by changes in the position and direction of the thermal camera. This paper presents a method for extracting the thermal features of a hot spot or a server in a container datacenter. First, thermal and visual images are registered based on textural characteristics extracted from images acquired in datacenters. Then, the thermal distribution of each server is standardized. The features of a hot spot or server extracted from the standard distribution can reduce the impact of camera position and direction. The results of experiments show that image registration is efficient for aligning the corresponding visual and thermal images in the datacenter, and the standardization procedure reduces the impacts of camera position and direction on hot spot or server features.

Slit-Slat Collimator Equipped Gamma Camera for Whole-Mouse SPECT-CT Imaging

NASA Astrophysics Data System (ADS)

Cao, Liji; Peter, Jörg

2012-06-01

A slit-slat collimator is developed for a gamma camera intended for small-animal imaging (mice). The tungsten housing of a roof-shaped collimator forms a slit opening, and the slats are made of lead foils separated by sparse polyurethane material. Alignment of the collimator with the camera's pixelated crystal is performed by adjusting a micrometer screw while monitoring a Co-57 point source for maximum signal intensity. For SPECT, the collimator forms a cylindrical field-of-view enabling whole mouse imaging with transaxial magnification and constant on-axis sensitivity over the entire axial direction. As the gamma camera is part of a multimodal imaging system incorporating also x-ray CT, five parameters corresponding to the geometric displacements of the collimator as well as to the mechanical co-alignment between the gamma camera and the CT subsystem are estimated by means of bimodal calibration sources. To illustrate the performance of the slit-slat collimator and to compare its performance to a single pinhole collimator, a Derenzo phantom study is performed. Transaxial resolution along the entire long axis is comparable to a pinhole collimator of same pinhole diameter. Axial resolution of the slit-slat collimator is comparable to that of a parallel beam collimator. Additionally, data from an in-vivo mouse study are presented.

Alignment nature of ZnO nanowires grown on polished and nanoscale etched lithium niobate surface through self-seeding thermal evaporation method

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

Mohanan, Ajay Achath; Parthiban, R.; Ramakrishnan, N., E-mail: ramakrishnan@monash.edu

Highlights: • ZnO nanowires were grown directly on LiNbO{sub 3} surface for the first time by thermal evaporation. • Self-alignment of the nanowires due to step bunching of LiNbO{sub 3} surface is observed. • Increased roughness in surface defects promoted well-aligned growth of nanowires. • Well-aligned growth was then replicated in 50 nm deep trenches on the surface. • Study opens novel pathway for patterned growth of ZnO nanowires on LiNbO{sub 3} surface. - Abstract: High aspect ratio catalyst-free ZnO nanowires were directly synthesized on lithium niobate substrate for the first time through thermal evaporation method without the use ofmore » a buffer layer or the conventional pre-deposited ZnO seed layer. As-grown ZnO nanowires exhibited a crisscross aligned growth pattern due to step bunching of the polished lithium niobate surface during the nanowire growth process. On the contrary, scratches on the surface and edges of the substrate produced well-aligned ZnO nanowires in these defect regions due to high surface roughness. Thus, the crisscross aligned nature of high aspect ratio nanowire growth on the lithium niobate surface can be changed to well-aligned growth through controlled etching of the surface, which is further verified through reactive-ion etching of lithium niobate. The investigations and discussion in the present work will provide novel pathway for self-seeded patterned growth of well-aligned ZnO nanowires on lithium niobate based micro devices.« less

Theory of electrical conductivity and dielectric permittivity of highly aligned graphene-based nanocomposites.

PubMed

Xia, Xiaodong; Hao, Jia; Wang, Yang; Zhong, Zheng; Weng, George J

2017-05-24

Highly aligned graphene-based nanocomposites are of great interest due to their excellent electrical properties along the aligned direction. Graphene fillers in these composites are not necessarily perfectly aligned, but their orientations are highly confined to a certain angle, [Formula: see text] with 90° giving rise to the randomly oriented state and 0° to the perfectly aligned one. Recent experiments have shown that electrical conductivity and dielectric permittivity of highly aligned graphene-polymer nanocomposites are strongly dependent on this distribution angle, but at present no theory seems to exist to address this issue. In this work we present a new effective-medium theory that is derived from the underlying physical process including the effects of graphene orientation, filler loading, aspect ratio, percolation threshold, interfacial tunneling, and Maxwell-Wagner-Sillars polarization, to determine these two properties. The theory is formulated in the context of preferred orientational average. We highlight this new theory with an application to rGO/epoxy nanocomposites, and demonstrate that the calculated in-plane and out-of-plane conductivity and permittivity are in agreement with the experimental data as the range of graphene orientations changes from the randomly oriented to the highly aligned state. We also show that the percolation thresholds of highly aligned graphene nanocomposites are in general different along the planar and the normal directions, but they converge into a single one when the statistical distribution of graphene fillers is spherically symmetric.

Measurement of large parallel and perpendicular electric fields on electron spatial scales in the terrestrial bow shock.

PubMed

Bale, S D; Mozer, F S

2007-05-18

Large parallel (

Large-Scale Direct-Writing of Aligned Nanofibers for Flexible Electronics.

PubMed

Ye, Dong; Ding, Yajiang; Duan, Yongqing; Su, Jiangtao; Yin, Zhouping; Huang, Yong An

2018-05-01

Nanofibers/nanowires usually exhibit exceptionally low flexural rigidities and remarkable tolerance against mechanical bending, showing superior advantages in flexible electronics applications. Electrospinning is regarded as a powerful process for this 1D nanostructure; however, it can only be able to produce chaotic fibers that are incompatible with the well-patterned microstructures in flexible electronics. Electro-hydrodynamic (EHD) direct-writing technology enables large-scale deposition of highly aligned nanofibers in an additive, noncontact, real-time adjustment, and individual control manner on rigid or flexible, planar or curved substrates, making it rather attractive in the fabrication of flexible electronics. In this Review, the ground-breaking research progress in the field of EHD direct-writing technology is summarized, including a brief chronology of EHD direct-writing techniques, basic principles and alignment strategies, and applications in flexible electronics. Finally, future prospects are suggested to advance flexible electronics based on orderly arranged EHD direct-written fibers. This technology overcomes the limitations of the resolution of fabrication and viscosity of ink of conventional inkjet printing, and represents major advances in manufacturing of flexible electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electro-optic characteristics of 4-domain vertical alignment nematic liquid crystal display with interdigital electrode

NASA Astrophysics Data System (ADS)

Hong, S. H.; Jeong, Y. H.; Kim, H. Y.; Cho, H. M.; Lee, W. G.; Lee, S. H.

2000-06-01

We have fabricated a vertically aligned 4-domain nematic liquid crystal display cell with thin film transistor. Unlike the conventional method constructing 4-domain, i.e., protrusion and surrounding electrode which needs additional processes, in this study the pixel design forming 4-domain with interdigital electrodes is suggested. In the device, one pixel is divided into two parts. One part has a horizontal electric field in the vertical direction and the other part has a horizontal one in the horizontal direction. Such fields in the horizontal and vertical direction drive the liquid crystal director to tilt down in four directions. In this article, the electro-optic characteristics of cells with 2 and 4 domain have been studied. The device with 4 domain shows faster response time than normal twisted-nematic and in-plane switching cells, wide viewing angle with optical compensation film, and more stable color characteristics than 2-domain vertical alignment cell with similar structure.

Single-walled carbon nanotubes/polymer composite electrodes patterned directly from solution.

PubMed

Chang, Jingbo; Najeeb, Choolakadavil Khalid; Lee, Jae-Hyeok; Kim, Jae-Ho

2011-06-07

This work describes a simple technique for direct patterning of single-walled carbon nanotube (SWNT)/poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT-PSS) composite electrodes in a large area on a substrate based on the solution transfer process by microcontact printing using poly(dimethylsiloxane) (PDMS) stamps. Various shapes of SWNT/PEDOT-PSS composite patterns, such as line, circle, and square, can be easily fabricated with high pattern fidelity and structural integrity. The single parallel line pattern device exhibits high electrical conductivity (0.75 × 10(5) S/m) and electronic stability because of alignment of nanotubes and big-size SWNT bundles (∼5 nm). The electromechanical study reveals that the composite patterns show ∼1% resistance change along SWNT alignment direction and ∼5% resistance change along vertical alignment direction after 200 bend cycles. Our approach provides a facile, low-cost method to pattern transparent conductive SWNT/polymer composite electrodes and demonstrates a novel platform for future integration of conducting SWNT/polymer composite patterns for optoelectronic applications.

[The clinical value of cartilaginous surface and corresponding osseous contour of patellofemoral joint].

PubMed

Zhang, Jian-Bing; Chen, Bai-Cheng; Zhang, Jing; Wang, Zhi-Qiang; Yan, Chang-Bao

2010-11-15

to investigate if the cartilaginous surface and corresponding osseous contour of the patellofemoral joint match in the axial plane for providing theoretical basis with evaluating alignment of patellofemoral joint and designing the part of patellofemoral joint in knee prosthesis. from January 2009 to March 2010, 9 human cadaver knees were prepared, which chandra of patellofemoral joint didn't degenerate. Each specimen was sectioned in the axial plane at 20° to 30° knee flax. The cross-sections revealed characteristics in the bony anatomy and corresponding articular surface geometry of the patellofemoral joint in the axial plane. Evaluating parameters included osseous patella congruence angle (OPCA), chondral patella congruence angle (CPCA), patella chondral convex point parameter (PCCPP), patella subchondral osseous convex point parameter (PSOCPP), the parameters of the deepest (chondral or osseous) point of the intercondylar sulcus. After that, the osseous and cartilaginous contours and subchondral osseous contours of the patella in the axial plane were analyzed through MRI data of 11 patients who didn't degenerate in patellofemoral joint cartilage. Parameters as same as cadaver knees were compared. data from specimens of OPCA was (-4.5 ± 1.1)°, CPCA was (0.5 ± 0.8)°, PCCPP was 1.13 ± 0.11, PSOCPP was 1.67 ± 0.14, PCDPIS was 1.35 ± 0.28, PODPIS was 1.38 ± 0.33. Date from MRI of OPCA was (-3.8 ± 1.4)°, CPCA was (0.7 ± 1.0)°, PCCPP was 1.05 ± 0.21, PSOCPP was 1.73 ± 0.18, PCDPIS was 1.41 ± 0.21, PODPIS was 1.37 ± 0.27. The patella exhibited significant differences in the bony vs. chondral anatomy (P < 0.05), but the intercondylar sulcus nearly match in the bony vs. chondral anatomy. the cartilaginous surface and corresponding osseous contour of the patella don't match in the patellofemoral joint axial plane, but that of the trochlea nearly matches. This is very important for accurately evaluating alignment of patellofemoral joint because the normal osseous alignment of patellofemoral joint don't represent the normal alignment and helpful for designing the part of patellofemoral joint in knee prosthesis.

Hydrophilic Channel Alignment of Perfluoronated Sulfonic-Acid Ionomers for Vanadium Redox Flow Batteries.

PubMed

So, Soonyong; Cha, Min Suc; Jo, Sang-Woo; Kim, Tae-Ho; Lee, Jang Yong; Hong, Young Taik

2018-06-13

It is known that uniaxially drawn perfluoronated sulfonic-acid ionomers (PFSAs) show diffusion anisotropy because of the aligned water channels along the deformation direction. We apply the uniaxially stretched membranes to vanadium redox flow batteries (VRFBs) to suppress the permeation of active species, vanadium ions through the transverse directions. The aligned water channels render much lower vanadium permeability, resulting in higher Coulombic efficiency (>98%) and longer self-discharge time (>250 h). Similar to vanadium ions, proton conduction through the membranes also decreases as the stretching ratio increases, but the thinned membranes show the enhanced voltage and energy efficiencies over the range of current density, 50-100 mA/cm 2 . Hydrophilic channel alignment of PFSAs is also beneficial for long-term cycling of VRFBs in terms of capacity retention and cell performances. This simple pretreatment of membranes offers an effective and facile way to overcome high vanadium permeability of PFSAs for VRFBs.

Highly efficient growth of vertically aligned carbon nanotubes on Fe-Ni based metal alloy foils for supercapacitors

NASA Astrophysics Data System (ADS)

Amalina Raja Seman, Raja Noor; Asyadi Azam, Mohd; Ambri Mohamed, Mohd

2016-12-01

Supercapacitors are highly promising energy devices with superior charge storage performance and a long lifecycle. Construction of the supercapacitor cell, especially electrode fabrication, is critical to ensure good performance in applications. This work demonstrates direct growth of vertically aligned carbon nanotubes (CNTs) on Fe-Ni based metal alloy foils, namely SUS 310S, Inconel 600 and YEF 50, and their use in symmetric vertically aligned CNT supercapacitor electrodes. Alumina and cobalt thin film catalysts were deposited onto the foils, and then CNT growth was performed using alcohol catalytic chemical vapour deposition. By this method, vertically aligned CNTs were successfully grown and used directly as a binder-free supercapacitor electrode to deliver excellent electrochemical performance. The device showed relatively good specific capacitance, a superior rate capability and excellent cycle stability, maintaining about 96% capacitance up to 1000 cycles.

Anisotropic Mechanical Properties of Magnetically Aligned Fibrin Gels Measured by Magnetic Resonance Elastography

PubMed Central

Namani, Ravi; Wood, Matthew D.; Sakiyama-Elbert, Shelly E.; Bayly, Philip V.

2009-01-01

The anisotropic mechanical properties of magnetically aligned fibrin gels were measured by magnetic resonance elastography (MRE) and by a standard mechanical test: unconfined compression. Soft anisotropic biomaterials are notoriously difficult to characterize, especially in vivo. MRE is well-suited for efficient, non-invasive, and nondestructive assessment of shear modulus. Direction-dependent differences in shear modulus were found to be statistically significant for gels polymerized at magnetic fields of 11.7T and 4.7T compared to control gels. Mechanical anisotropy was greater in the gels polymerized at the higher magnetic field. These observations were consistent with results from unconfined compression tests. Analysis of confocal microscopy images of gels showed measurable alignment of fibrils in gels polymerized at 11.7T. This study provides direct, quantitative measurements of the anisotropy in mechanical properties that accompanies fibril alignment in fibrin gels. PMID:19656516

Photodetection and Photoswitch Based On Polarized Optical Response of Macroscopically Aligned Carbon Nanotubes.

PubMed

Zhang, Ling; Wu, Yang; Deng, Lei; Zhou, Yi; Liu, Changhong; Fan, Shoushan

2016-10-12

Light polarization is extensively applied in optical detection, industry processing and telecommunication. Although aligned carbon nanotube naturally suppresses the transmittance of light polarized parallel to its axial direction, there is little application regarding the photodetection of carbon nanotube based on this anisotropic interaction with linearly polarized light. Here, we report a photodetection device realized by aligned carbon nanotube. Because of the different absorption behavior of polarized light with respect to polarization angles, such device delivers an explicit response to specific light wavelength regardless of its intensity. Furthermore, combining both experimental and mathematical analysis, we found that the light absorption of different wavelength causes characteristic thermoelectric voltage generation, which makes aligned carbon nanotube promising in optical detection. This work can also be utilized directly in developing new types of photoswitch that features a broad spectrum application from near-ultraviolet to intermediate infrared with easy integration into practical electric devices, for instance, a "wavelength lock".

Method and apparatus for aligning a solar concentrator using two lasers

DOEpatents

Diver Jr., Richard Boyer

2003-07-22

A method and apparatus are provided for aligning the facets of a solar concentrator. A first laser directs a first laser beam onto a selected facet of the concentrator such that a target board positioned adjacent to the first laser at approximately one focal length behind the focal point of the concentrator is illuminated by the beam after reflection thereof off of the selected facet. A second laser, located adjacent to the vertex of the optical axis of the concentrator, is used to direct a second laser beam onto the target board at a target point thereon. By adjusting the selected facet to cause the first beam to illuminate the target point on the target board produced by the second beam, the selected facet can be brought into alignment with the target point. These steps are repeated for other selected facets of the concentrator, as necessary, to provide overall alignment of the concentrator.

A new network representation of the metabolism to detect chemical transformation modules.

PubMed

Sorokina, Maria; Medigue, Claudine; Vallenet, David

2015-11-14

Metabolism is generally modeled by directed networks where nodes represent reactions and/or metabolites. In order to explore metabolic pathway conservation and divergence among organisms, previous studies were based on graph alignment to find similar pathways. Few years ago, the concept of chemical transformation modules, also called reaction modules, was introduced and correspond to sequences of chemical transformations which are conserved in metabolism. We propose here a novel graph representation of the metabolic network where reactions sharing a same chemical transformation type are grouped in Reaction Molecular Signatures (RMS). RMS were automatically computed for all reactions and encode changes in atoms and bonds. A reaction network containing all available metabolic knowledge was then reduced by an aggregation of reaction nodes and edges to obtain a RMS network. Paths in this network were explored and a substantial number of conserved chemical transformation modules was detected. Furthermore, this graph-based formalism allows us to define several path scores reflecting different biological conservation meanings. These scores are significantly higher for paths corresponding to known metabolic pathways and were used conjointly to build association rules that should predict metabolic pathway types like biosynthesis or degradation. This representation of metabolism in a RMS network offers new insights to capture relevant metabolic contexts. Furthermore, along with genomic context methods, it should improve the detection of gene clusters corresponding to new metabolic pathways.

Self-aligned spatial filtering using laser optical tweezers.

PubMed

Birkbeck, Aaron L; Zlatanovic, Sanja; Esener, Sadik C

2006-09-01

We present an optical spatial filtering device that has been integrated into a microfluidic system and whose motion and alignment is controlled using a laser optical tweezer. The lithographically patterned micro-optical spatial filter device filters out higher frequency additive noise components by automatically aligning itself in three dimensions to the focus of the laser beam. This self-alignment capability is achieved through the attachment of a refractive optical element directly over the circular aperture or pinhole of the spatial filter. A discussion of two different spatial filter designs is presented along with experimental results that demonstrate the effectiveness of the self-aligned micro-optic spatial filter.

Formation of Highly Aligned Collagen Nanofibers by Continuous Cyclic Stretch of a Collagen Hydrogel Sheet.

PubMed

Nam, Eunryel; Lee, Won Chul; Takeuchi, Shoji

2016-07-01

A collagen sheet with highly aligned collagen fibers is fabricated by continuous cyclic stretch. The rearrangement of the collagen fibers depends on the different process parameters of the cyclic stretch, including magnitude, frequency, and period of stretch. The collagen fibers are aligned perpendicularly to the direction of the stretch. Corneal stromal cells and smooth muscle cells cultivated on the highly aligned collagen sheet show alignment along the collagen fibers without the stretch during culture. Thus, the sheet can be a suitable scaffold for use in regenerative medicine. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A practical strategy for the accurate measurement of residual dipolar couplings in strongly aligned small molecules

NASA Astrophysics Data System (ADS)

Liu, Yizhou; Cohen, Ryan D.; Martin, Gary E.; Williamson, R. Thomas

2018-06-01

Accurate measurement of residual dipolar couplings (RDCs) requires an appropriate degree of alignment in order to optimize data quality. An overly weak alignment yields very small anisotropic data that are susceptible to measurement errors, whereas an overly strong alignment introduces extensive anisotropic effects that severely degrade spectral quality. The ideal alignment amplitude also depends on the specific pulse sequence used for the coupling measurement. In this work, we introduce a practical strategy for the accurate measurement of one-bond 13C-1H RDCs up to a range of ca. -300 to +300 Hz, corresponding to an alignment that is an order of magnitude stronger than typically employed for small molecule structural elucidation. This strong alignment was generated in the mesophase of the commercially available poly-γ-(benzyl-L-glutamate) polymer. The total coupling was measured by the simple and well-studied heteronuclear two-dimensional J-resolved experiment, which performs well in the presence of strong anisotropic effects. In order to unequivocally determine the sign of the total coupling and resolve ambiguities in assigning total couplings in the CH2 group, coupling measurements were conducted at an isotropic condition plus two anisotropic conditions of different alignment amplitudes. Most RDCs could be readily extracted from these measurements whereas more complicated spectral effects resulting from strong homonuclear coupling could be interpreted either theoretically or by simulation. Importantly, measurement of these very large RDCs actually offers significantly improved data quality and utility for the structure determination of small organic molecules.

Increased dermal collagen bundle alignment in systemic sclerosis is associated with a cell migration signature and role of Arhgdib in directed fibroblast migration on aligned ECMs

PubMed Central

Lafyatis, Robert; Burkly, Linda C.

2017-01-01

Systemic sclerosis (SSc) is a devastating disease affecting the skin and internal organs. Dermal fibrosis manifests early and Modified Rodnan Skin Scores (MRSS) correlate with disease progression. Transcriptomics of SSc skin biopsies suggest the role of the in vivo microenvironment in maintaining the pathological myofibroblasts. Therefore, defining the structural changes in dermal collagen in SSc patients could inform our understanding of fibrosis pathogenesis. Here, we report a method for quantitative whole-slide image analysis of dermal collagen from SSc patients, and our findings of more aligned dermal collagen bundles in diffuse cutaneous SSc (dcSSc) patients. Using the bleomycin-induced mouse model of SSc, we identified a distinct high dermal collagen bundle alignment gene signature, characterized by a concerted upregulation in cell migration, adhesion, and guidance pathways, and downregulation of spindle, replication, and cytokinesis pathways. Furthermore, increased bundle alignment induced a cell migration gene signature in fibroblasts in vitro, and these cells demonstrated increased directed migration on aligned ECM fibers that is dependent on expression of Arhgdib (Rho GDP-dissociation inhibitor 2). Our results indicate that increased cell migration is a cellular response to the increased collagen bundle alignment featured in fibrotic skin. Moreover, many of the cell migration genes identified in our study are shared with human SSc skin and may be new targets for therapeutic intervention. PMID:28662216

SU-D-BRF-03: Improvement of TomoTherapy Megavoltage Topogram Image Quality for Automatic Registration During Patient Localization

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

Scholey, J; White, B; Qi, S

2014-06-01

Purpose: To improve the quality of mega-voltage orthogonal scout images (MV topograms) for a fast and low-dose alternative technique for patient localization on the TomoTherapy HiART system. Methods: Digitally reconstructed radiographs (DRR) of anthropomorphic head and pelvis phantoms were synthesized from kVCT under TomoTherapy geometry (kV-DRR). Lateral (LAT) and anterior-posterior (AP) aligned topograms were acquired with couch speeds of 1cm/s, 2cm/s, and 3cm/s. The phantoms were rigidly translated in all spatial directions with known offsets in increments of 5mm, 10mm, and 15mm to simulate daily positioning errors. The contrast of the MV topograms was automatically adjusted based on the imagemore » intensity characteristics. A low-pass fast Fourier transform filter removed high-frequency noise and a Weiner filter reduced stochastic noise caused by scattered radiation to the detector array. An intensity-based image registration algorithm was used to register the MV topograms to a corresponding kV-DRR by minimizing the mean square error between corresponding pixel intensities. The registration accuracy was assessed by comparing the normalized cross correlation coefficients (NCC) between the registered topograms and the kV-DRR. The applied phantom offsets were determined by registering the MV topograms with the kV-DRR and recovering the spatial translation of the MV topograms. Results: The automatic registration technique provided millimeter accuracy and was robust for the deformed MV topograms for three tested couch speeds. The lowest average NCC for all AP and LAT MV topograms was 0.96 for the head phantom and 0.93 for the pelvis phantom. The offsets were recovered to within 1.6mm and 6.5mm for the processed and the original MV topograms respectively. Conclusion: Automatic registration of the processed MV topograms to a corresponding kV-DRR recovered simulated daily positioning errors that were accurate to the order of a millimeter. These results suggest the clinical use of MV topograms as a promising alternative to MVCT patient alignment.« less

A continuous process to align electrospun nanofibers into parallel and crossed arrays

NASA Astrophysics Data System (ADS)

Laudenslager, Michael J.; Sigmund, Wolfgang M.

2013-04-01

Electrical, optical, and mechanical properties of nanofibers are strongly affected by their orientation. Electrospinning is a nanofiber processing technique that typically produces nonwoven meshes of randomly oriented fibers. While several alignment techniques exist, they are only able to produce either a very thin layer of aligned fibers or larger quantities of fibers with less control over their alignment and orientation. The technique presented herein fills the gap between these two methods allowing one to produce thick meshes of highly oriented nanofibers. In addition, this technique is not limited to collection of fibers along a single axis. Modifications to the basic setup allow collection of crossed fibers without stopping and repositioning the apparatus. The technique works for a range of fiber sizes. In this study, fiber diameters ranged from 100 nm to 1 micron. This allows a few fibers at a time to rapidly deposit in alternating directions creating an almost woven structure. These aligned nanofibers have the potential to improve the performance of energy storage and thermoelectric devices and hold great promise for directed cell growth applications.

Monitoring of the alignment in developing tissue-engineered constructs by elastic scattering spectroscopy

NASA Astrophysics Data System (ADS)

Kostyuk, Oksana P.; Brown, Robert A.

2004-07-01

Elastic light scattering spectroscopy was applied to monitor the development of alignment in fibroblast-populated collagen gels. Gels were seeded with human dermal fibroblasts in rectangular moulds so uniaxial tension was generated in the central zone of the gels due to cell contraction. There was a gradual transition from a disorganized matrix with round cells to highly organized cell/collagen matrix, aligned in the direction of the principal strain developed during gel contraction (observed with light microscopy under phase contrast). Spectra of the backscattered light (320 - 850 nm) were acquired via an optical probe with 2.75-mm source-detector separation, positioned perpendicularly to the gel surface, at 0, 17, 24, 41, 47, 65 and 72h. Spectra were registered for light propagating along, perpendicular and at intermediate angles relative to the cell/collagen matrix alignment, at 45° intervals. Backscatter was isotropic for non-contracted gels. However, as gels contracted, anisotropy of backscatter gradually increased. This was characterized by an 'anisotropy factor,' AF (500 nm), calculated as the ratio of backscatter intensities at 90° and 0° positions of the probe, at 500 nm. AF (500nm) increased from 1.2 +/- 0.1 at 0h up to 2.6 +/- 0.4 at 72h of contraction, with more backscatter detected perpendicular to the cell/collagen matrix alignment than in parallel direction. Thus, backscatter anisotropy allows determination of the direction of the preferential alignment and quantitative monitoring of its development during gel contraction. It is possible to use measurements of this type to quantify a proportion of oriented fibrils in the gel using modeling.

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.

Interpolation schemes for peptide rearrangements.

PubMed

Bauer, Marianne S; Strodel, Birgit; Fejer, Szilard N; Koslover, Elena F; Wales, David J

2010-02-07

A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures. We also demonstrate the superiority of natural coordinate methods in conjunction with internal alignment. Checking the potential energy of the interpolated structures can act as a criterion for the choice of the interpolation coordinate system, which reduces failures and connection times significantly.

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.

The irreversibility line of magnetically grain-aligned Hg-1212 sample - Evidences of flux line lattice melting

NASA Astrophysics Data System (ADS)

de Andrade, R., Jr.; Lanfredi, A. J. C.; Ortiz, W. A.; Leite, E. R.

1997-08-01

The irreversibility line (IL) of a magnetically grain-aligned HgBa2CaCu2O6+δ (Hg-1212) sample was determined from magnetization measurements, with the magnetic fieldH parallel to the samplec-axis. The grain-aligned sample was made by mixing powdered polycrystalline samples with epoxy resin, cured under 94 KOe at room temperature. For fields below 10 kOe the Il is well fitted by a model of flux line lattice melting due to thermal fluctuations. For higher fields the IL behavior changes to an exponential growth of Hirr with 1/T. This change is related to a corresponding alteration in the character of the vortex fluctuations leading to the melting of the flux line lattice.

Crust-mantle mechanical coupling in Eastern Mediterranean and Eastern Turkey

PubMed Central

Sinan Özeren, M.

2012-01-01

Present-day crust-mantle coupling in the Eastern Mediterranean and eastern Turkey is studied using the Global Positioning System (GPS) and seismic anisotropy data. The general trend of the shear wave fast-splitting directions in NE Turkey and Lesser Caucaus align well with the geodetic velocities in an absolute plate motion frame of reference pointing to an effective coupling in this part of the region of weak surface deformation. Farther south, underneath the Bitlis Suture, however, there are significant Pn delays with E-W anisotropy axes indicating significant lateral escape. Meanwhile, the GPS reveals very little surface deformation. This mismatch possibly suggests a decoupling along the suture. In the Aegean, the shear wave anisotropy and the Pn anisotropy directions agree with the extensional component of the right-lateral shear strains except under the Crete Basin and other parts of the southern Aegean Sea. This extensional direction matches perfectly also with the southward pulling force vectors across the Hellenic trench; however, the maximum right-lateral shear directions obtained from the GPS data in the Aegean do not match either of these anisotropies. Seismic anisotropy from Rayleigh waves sampled at 15 s, corresponding to the lower crust, match the maximum right-lateral maximum shear directions from the GPS indicating decoupling between the crust and the mantle. This decoupling most likely results from the lateral variations of the gravitational potential energies and the slab-pull forces. PMID:22592788

Crust-mantle mechanical coupling in Eastern Mediterranean and eastern Turkey.

PubMed

Özeren, M Sinan

2012-05-29

Present-day crust-mantle coupling in the Eastern Mediterranean and eastern Turkey is studied using the Global Positioning System (GPS) and seismic anisotropy data. The general trend of the shear wave fast-splitting directions in NE Turkey and Lesser Caucaus align well with the geodetic velocities in an absolute plate motion frame of reference pointing to an effective coupling in this part of the region of weak surface deformation. Farther south, underneath the Bitlis Suture, however, there are significant Pn delays with E-W anisotropy axes indicating significant lateral escape. Meanwhile, the GPS reveals very little surface deformation. This mismatch possibly suggests a decoupling along the suture. In the Aegean, the shear wave anisotropy and the Pn anisotropy directions agree with the extensional component of the right-lateral shear strains except under the Crete Basin and other parts of the southern Aegean Sea. This extensional direction matches perfectly also with the southward pulling force vectors across the Hellenic trench; however, the maximum right-lateral shear directions obtained from the GPS data in the Aegean do not match either of these anisotropies. Seismic anisotropy from Rayleigh waves sampled at 15 s, corresponding to the lower crust, match the maximum right-lateral maximum shear directions from the GPS indicating decoupling between the crust and the mantle. This decoupling most likely results from the lateral variations of the gravitational potential energies and the slab-pull forces.

Controlled alignment of carbon nanofibers in a large-scale synthesis process

NASA Astrophysics Data System (ADS)

Merkulov, Vladimir I.; Melechko, A. V.; Guillorn, M. A.; Simpson, M. L.; Lowndes, D. H.; Whealton, J. H.; Raridon, R. J.

2002-06-01

Controlled alignment of catalytically grown carbon nanofibers (CNFs) at a variable angle to the substrate during a plasma-enhanced chemical vapor deposition process is achieved. The CNF alignment is controlled by the direction of the electric field lines during the synthesis process. Off normal CNF orientations are achieved by positioning the sample in the vicinity of geometrical features of the sample holder, where bending of the electric field lines occurs. The controlled growth of kinked CNFs that consist of two parts aligned at different angles to the substrate normal also is demonstrated.

Spatial Distributions of Young Stars

NASA Astrophysics Data System (ADS)

Kraus, Adam L.; Hillenbrand, Lynne A.

2008-10-01

We analyze the spatial distribution of young stars in Taurus-Auriga and Upper Sco, as determined from the two-point correlation function (i.e., the mean surface density of neighbors). The corresponding power-law fits allow us to determine the fractal dimensions of each association's spatial distribution, measure the stellar velocity dispersions, and distinguish between the bound binary population and chance alignments of members. We find that the fractal dimension of Taurus is D ~ 1.05, consistent with its filamentary structure. The fractal dimension of Upper Sco may be even shallower (D ~ 0.7), but this fit is uncertain due to the limited area and possible spatially variable incompleteness. We also find that random stellar motions have erased all primordial structure on scales of lsim0.07° in Taurus and lsim1.7° in Upper Sco; given ages of ~1 and ~5 Myr, the corresponding internal velocity dispersions are ~0.2 and ~1.0 km s-1, respectively. Finally, we find that binaries can be distinguished from chance alignments at separations of lsim120'' (17,000 AU) in Taurus and lsim75'' (11,000 AU) in Upper Sco. The binary populations in these associations that we previously studied, spanning separations of 3''-30'', is dominated by binary systems. However, the few lowest mass pairs (Mprim <~ 0.3 M⊙) might be chance alignments.

The speech focus position effect on jaw-finger coordination in a pointing task.

PubMed

Rochet-Capellan, Amélie; Laboissière, Rafael; Galván, Arturo; Schwartz, Jean-Luc

2008-12-01

This article investigates jaw-finger coordination in a task involving pointing to a target while naming it with a CVCV (e.g., /papa/) versus CVCV (e.g., /papa/) word. According to the authors' working hypothesis, the pointing apex (gesture extremum) would be synchronized with the apex of the jaw-opening gesture corresponding to the stressed syllable. Jaw and finger motions were recorded using Optotrak (Northern Digital, Waterloo, Ontario, Canada). The effects of stress position on jaw-finger coordination were tested across different target positions (near vs. far) and different consonants in the target word (/t/ vs. /p/). Twenty native Portuguese Brazilian speakers participated in the experiment (all conditions). Jaw response starts earlier, and finger-target alignment period is longer for CVCV words than for CVCV ones. The apex of the jaw-opening gesture for the stressed syllable appears synchronized with the onset of the finger-target alignment period (corresponding to the pointing apex) for CVCV words and with the offset of that period for CVCV words. For both stress conditions, the stressed syllable occurs within the finger-target alignment period because of tight finger-jaw coordination. This result is interpreted as evidence for an anchoring of the speech deictic site (part of speech that shows) in the pointing gesture.

Automatic lung nodule matching for the follow-up in temporal chest CT scans

NASA Astrophysics Data System (ADS)

Hong, Helen; Lee, Jeongjin; Shin, Yeong Gil

2006-03-01

We propose a fast and robust registration method for matching lung nodules of temporal chest CT scans. Our method is composed of four stages. First, the lungs are extracted from chest CT scans by the automatic segmentation method. Second, the gross translational mismatch is corrected by the optimal cube registration. This initial registration does not require extracting any anatomical landmarks. Third, initial alignment is step by step refined by the iterative surface registration. To evaluate the distance measure between surface boundary points, a 3D distance map is generated by the narrow-band distance propagation, which drives fast and robust convergence to the optimal location. Fourth, nodule correspondences are established by the pairs with the smallest Euclidean distances. The results of pulmonary nodule alignment of twenty patients are reported on a per-center-of mass point basis using the average Euclidean distance (AED) error between corresponding nodules of initial and follow-up scans. The average AED error of twenty patients is significantly reduced to 4.7mm from 30.0mm by our registration. Experimental results show that our registration method aligns the lung nodules much faster than the conventional ones using a distance measure. Accurate and fast result of our method would be more useful for the radiologist's evaluation of pulmonary nodules on chest CT scans.

Heparin/collagen encapsulating nerve growth factor multilayers coated aligned PLLA nanofibrous scaffolds for nerve tissue engineering.

PubMed

Zhang, Kuihua; Huang, Dianwu; Yan, Zhiyong; Wang, Chunyang

2017-07-01

Biomimicing topological structure of natural nerve tissue to direct axon growth and controlling sustained release of moderate neurotrophic factors are extremely propitious to the functional recovery of damaged nervous systems. In this study, the heparin/collagen encapsulating nerve growth factor (NGF) multilayers were coated onto the aligned poly-L-lactide (PLLA) nanofibrous scaffolds via a layer-by-layer (LbL) self-assembly technique to combine biomolecular signals, and physical guidance cues for peripheral nerve regeneration. Scanning electronic microscopy (SEM) revealed that the surface of aligned PLLA nanofibrous scaffolds coated with heparin/collagen multilayers became rougher and appeared some net-like filaments and protuberances in comparison with PLLA nanofibrous scaffolds. The heparin/collagen multilayers did not destroy the alignment of nanofibers. X-ray photoelectron spectroscopy and water contact angles displayed that heparin and collagen were successfully coated onto the aligned PLLA nanofibrous scaffolds and improved its hydrophilicity. Three-dimensional (3 D) confocal microscopy images further demonstrated that collagen, heparin, and NGF were not only coated onto the surface of aligned PLLA nanofibrous scaffolds but also permeated into the inner of scaffolds. Moreover, NGF presented a sustained release for 2 weeks from aligned nanofibrous scaffolds coated with 5.5 bilayers or above and remained good bioactivity. The heparin/collagen encapsulating NGF multilayers coated aligned nanofibrous scaffolds, in particular 5.5 bilayers or above, was more beneficial to Schwann cells (SCs) proliferation and PC12 cells differentiation as well as the SC cytoskeleton and neurite growth along the direction of nanofibrous alignment compared to the aligned PLLA nanofibrous scaffolds. This novel scaffolds combining sustained release of bioactive NGF and aligned nanofibrous topography presented an excellent potential in peripheral nerve regeneration. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1900-1910, 2017. © 2017 Wiley Periodicals, Inc.

REDIdb: the RNA editing database.

PubMed

Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

2007-01-01

The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

Aspect-object alignment with Integer Linear Programming in opinion mining.

PubMed

Zhao, Yanyan; Qin, Bing; Liu, Ting; Yang, Wei

2015-01-01

Target extraction is an important task in opinion mining. In this task, a complete target consists of an aspect and its corresponding object. However, previous work has always simply regarded the aspect as the target itself and has ignored the important "object" element. Thus, these studies have addressed incomplete targets, which are of limited use for practical applications. This paper proposes a novel and important sentiment analysis task, termed aspect-object alignment, to solve the "object neglect" problem. The objective of this task is to obtain the correct corresponding object for each aspect. We design a two-step framework for this task. We first provide an aspect-object alignment classifier that incorporates three sets of features, namely, the basic, relational, and special target features. However, the objects that are assigned to aspects in a sentence often contradict each other and possess many complicated features that are difficult to incorporate into a classifier. To resolve these conflicts, we impose two types of constraints in the second step: intra-sentence constraints and inter-sentence constraints. These constraints are encoded as linear formulations, and Integer Linear Programming (ILP) is used as an inference procedure to obtain a final global decision that is consistent with the constraints. Experiments on a corpus in the camera domain demonstrate that the three feature sets used in the aspect-object alignment classifier are effective in improving its performance. Moreover, the classifier with ILP inference performs better than the classifier without it, thereby illustrating that the two types of constraints that we impose are beneficial.

DNATagger, colors for codons.

PubMed

Scherer, N M; Basso, D M

2008-09-16

DNATagger is a web-based tool for coloring and editing DNA, RNA and protein sequences and alignments. It is dedicated to the visualization of protein coding sequences and also protein sequence alignments to facilitate the comprehension of evolutionary processes in sequence analysis. The distinctive feature of DNATagger is the use of codons as informative units for coloring DNA and RNA sequences. The codons are colored according to their corresponding amino acids. It is the first program that colors codons in DNA sequences without being affected by "out-of-frame" gaps of alignments. It can handle single gaps and gaps inside the triplets. The program also provides the possibility to edit the alignments and change color patterns and translation tables. DNATagger is a JavaScript application, following the W3C guidelines, designed to work on standards-compliant web browsers. It therefore requires no installation and is platform independent. The web-based DNATagger is available as free and open source software at http://www.inf.ufrgs.br/~dmbasso/dnatagger/.

Hydrodynamic Equations for Flocking Models without Velocity Alignment

NASA Astrophysics Data System (ADS)

Peruani, Fernando

2017-10-01

The spontaneous emergence of collective motion patterns is usually associated with the presence of a velocity alignment mechanism that mediates the interactions among the moving individuals. Despite of this widespread view, it has been shown recently that several flocking behaviors can emerge in the absence of velocity alignment and as a result of short-range, position-based, attractive forces that act inside a vision cone. Here, we derive the corresponding hydrodynamic equations of a microscopic position-based flocking model, reviewing and extending previous reported results. In particular, we show that three distinct macroscopic collective behaviors can be observed: i) the coarsening of aggregates with no orientational order, ii) the emergence of static, elongated nematic bands, and iii) the formation of moving, locally polar structures, which we call worms. The derived hydrodynamic equations indicate that active particles interacting via position-based interactions belong to a distinct class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems.

High-throughput electrical measurement and microfluidic sorting of semiconductor nanowires.

PubMed

Akin, Cevat; Feldman, Leonard C; Durand, Corentin; Hus, Saban M; Li, An-Ping; Hui, Ho Yee; Filler, Michael A; Yi, Jingang; Shan, Jerry W

2016-05-24

Existing nanowire electrical characterization tools not only are expensive and require sophisticated facilities, but are far too slow to enable statistical characterization of highly variable samples. They are also generally not compatible with further sorting and processing of nanowires. Here, we demonstrate a high-throughput, solution-based electro-orientation-spectroscopy (EOS) method, which is capable of automated electrical characterization of individual nanowires by direct optical visualization of their alignment behavior under spatially uniform electric fields of different frequencies. We demonstrate that EOS can quantitatively characterize the electrical conductivities of nanowires over a 6-order-of-magnitude range (10(-5) to 10 S m(-1), corresponding to typical carrier densities of 10(10)-10(16) cm(-3)), with different fluids used to suspend the nanowires. By implementing EOS in a simple microfluidic device, continuous electrical characterization is achieved, and the sorting of nanowires is demonstrated as a proof-of-concept. With measurement speeds two orders of magnitude faster than direct-contact methods, the automated EOS instrument enables for the first time the statistical characterization of highly variable 1D nanomaterials.

Electric Field Control of Interfacial Ferromagnetism in CaMnO3/CaRuO3 Heterostructures

NASA Astrophysics Data System (ADS)

Grutter, A. J.; Kirby, B. J.; Gray, M. T.; Flint, C. L.; Alaan, U. S.; Suzuki, Y.; Borchers, J. A.

2015-07-01

New mechanisms for achieving direct electric field control of ferromagnetism are highly desirable in the development of functional magnetic interfaces. To that end, we have probed the electric field dependence of the emergent ferromagnetic layer at CaRuO3/CaMnO3 interfaces in bilayers fabricated on SrTiO3. Using polarized neutron reflectometry, we are able to detect the ferromagnetic signal arising from a single atomic monolayer of CaMnO3, manifested as a spin asymmetry in the reflectivity. We find that the application of an electric field of 600 kV /m across the bilayer induces a significant increase in this spin asymmetry. Modeling of the reflectivity suggests that this increase corresponds to a transition from canted antiferromagnetism to full ferromagnetic alignment of the Mn4 + ions at the interface. This increase from 1 μB to 2.5 - 3.0 μB per Mn is indicative of a strong magnetoelectric coupling effect, and such direct electric field control of the magnetization at an interface has significant potential for spintronic applications.

27 T ultra-high static magnetic field changes orientation and morphology of mitotic spindles in human cells

PubMed Central

Zhang, Lei; Hou, Yubin; Li, Zhiyuan; Ji, Xinmiao; Wang, Ze; Wang, Huizhen; Tian, Xiaofei; Yu, Fazhi; Yang, Zhenye; Pi, Li; Mitchison, Timothy J; Lu, Qingyou; Zhang, Xin

2017-01-01

Purified microtubules have been shown to align along the static magnetic field (SMF) in vitro because of their diamagnetic anisotropy. However, whether mitotic spindle in mammalian cells can be aligned by magnetic field has not been experimentally proved. In particular, the biological effects of SMF of above 20 T (Tesla) on mammalian cells have never been reported. Here we found that in both CNE-2Z and RPE1 human cells spindle orients in 27 T SMF. The direction of spindle alignment depended on the extent to which chromosomes were aligned to form a planar metaphase plate. Our results show that the magnetic torque acts on both microtubules and chromosomes, and the preferred direction of spindle alignment relative to the field depends more on chromosome alignment than microtubules. In addition, spindle morphology was also perturbed by 27 T SMF. This is the first reported study that investigated the mammalian cellular responses to ultra-high magnetic field of above 20 T. Our study not only found that ultra-high magnetic field can change the orientation and morphology of mitotic spindles, but also provided a tool to probe the role of spindle orientation and perturbation in developmental and cancer biology. DOI: http://dx.doi.org/10.7554/eLife.22911.001 PMID:28244368

us9805_dni

Science.gov Websites

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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.

Modeling of Sensor Placement Strategy for Shape Sensing and Structural Health Monitoring of a Wing-Shaped Sandwich Panel Using Inverse Finite Element Method.

PubMed

Kefal, Adnan; Yildiz, Mehmet

2017-11-30

This paper investigated the effect of sensor density and alignment for three-dimensional shape sensing of an airplane-wing-shaped thick panel subjected to three different loading conditions, i.e., bending, torsion, and membrane loads. For shape sensing analysis of the panel, the Inverse Finite Element Method (iFEM) was used together with the Refined Zigzag Theory (RZT), in order to enable accurate predictions for transverse deflection and through-the-thickness variation of interfacial displacements. In this study, the iFEM-RZT algorithm is implemented by utilizing a novel three-node C°-continuous inverse-shell element, known as i3-RZT. The discrete strain data is generated numerically through performing a high-fidelity finite element analysis on the wing-shaped panel. This numerical strain data represents experimental strain readings obtained from surface patched strain gauges or embedded fiber Bragg grating (FBG) sensors. Three different sensor placement configurations with varying density and alignment of strain data were examined and their corresponding displacement contours were compared with those of reference solutions. The results indicate that a sparse distribution of FBG sensors (uniaxial strain measurements), aligned in only the longitudinal direction, is sufficient for predicting accurate full-field membrane and bending responses (deformed shapes) of the panel, including a true zigzag representation of interfacial displacements. On the other hand, a sparse deployment of strain rosettes (triaxial strain measurements) is essentially enough to produce torsion shapes that are as accurate as those of predicted by a dense sensor placement configuration. Hence, the potential applicability and practical aspects of i3-RZT/iFEM methodology is proven for three-dimensional shape-sensing of future aerospace structures.

Utilization of cone-beam CT for offline evaluation of target volume coverage during prostate image-guided radiotherapy based on bony anatomy alignment.

PubMed

Paluska, Petr; Hanus, Josef; Sefrova, Jana; Rouskova, Lucie; Grepl, Jakub; Jansa, Jan; Kasaova, Linda; Hodek, Miroslav; Zouhar, Milan; Vosmik, Milan; Petera, Jiri

2012-01-01

To assess target volume coverage during prostate image-guided radiotherapy based on bony anatomy alignment and to assess possibility of safety margin reduction. Implementation of IGRT should influence safety margins. Utilization of cone-beam CT provides current 3D anatomic information directly in irradiation position. Such information enables reconstruction of the actual dose distribution. Seventeen prostate patients were treated with daily bony anatomy image-guidance. Cone-beam CT (CBCT) scans were acquired once a week immediately after bony anatomy alignment. After the prostate, seminal vesicles, rectum and bladder were contoured, the delivered dose distribution was reconstructed. Target dose coverage was evaluated by the proportion of the CTV encompassed by the 95% isodose. Original plans employed a 1 cm safety margin. Alternative plans assuming a smaller 7 mm margin between CTV and PTV were evaluated in the same way. Rectal and bladder volumes were compared with the initial ones. Rectal and bladder volumes irradiated with doses higher than 75 Gy, 70 Gy, 60 Gy, 50 Gy and 40 Gy were analyzed. In 12% of reconstructed plans the prostate coverage was not sufficient. The prostate underdosage was observed in 5 patients. Coverage of seminal vesicles was not satisfactory in 3% of plans. Most of the target underdosage corresponded to excessive rectal or bladder filling. Evaluation of alternative plans assuming a smaller 7 mm margin revealed 22% and 11% of plans where prostate and seminal vesicles coverage, respectively, was compromised. These were distributed over 8 and 7 patients, respectively. Sufficient dose coverage of target volumes was not achieved for all patients. Reducing of safety margin is not acceptable. Initial rectal and bladder volumes cannot be considered representative for subsequent treatment.

Inflight alignment of payload inertial reference from Shuttle navigation system

NASA Astrophysics Data System (ADS)

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

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

Analysis of Preferred Directions in Phase Space for Tidal Measurements at Europa

NASA Astrophysics Data System (ADS)

Boone, D.; Scheeres, D. J.

2012-12-01

The NASA Jupiter Europa Orbiter mission requires a circular, near-polar orbit to measure Europa's Love numbers, geophysical coefficients which give insight into whether a liquid ocean exists. This type of orbit about planetary satellites is known to be unstable. The effects of Jupiter's tidal gravity are seen in changes in Europa's gravity field and surface deformation, which are sensed through doppler tracking over time and altimetry measurements respectively. These two measurement types separately determine the h and k Love numbers, a combination of which bounds how thick the ice shell of Europa is and whether liquid water is present. This work shows how the properties of an unstable periodic orbit about Europa generate preferred measurement directions in position and velocity phase space for the orbit determination process. We generate an error covariance over seven days for the orbiter state and science parameters using a periodic orbit and then disperse the orbit initial conditions in a Monte Carlo simulation according to this covariance. The dispersed orbits are shown to have a bias toward longer lifetimes and we discuss this as an effect of the stable and unstable manifolds of the periodic orbit. Using an epoch formulation of a square-root information filter, measurements aligned with the unstable manifold mapped back in time add more information to the orbit determination process than measurements aligned with the stable manifold. This corresponds to a contraction in the uncertainty of the estimate of the desired parameters, including the Love numbers. We demonstrate this mapping mathematically using a representation of the State Transition Matrix involving its eigenvectors and eigenvalues. Then using the properties of left and right eigenvectors, we show how measurements in the orbit determination process are mapped in time leading to a concentration of information at epoch. We present examples of measurements taken on different time schedules to show the effect of preferred phase space directions in the estimation process. Manifold coordinate decomposition is applied to the orbit initial conditions as well as measurement partials in the filter to show the alignment of each with the stable and unstable manifolds of the periodic orbit. The connection between orbit lifetime and regions of increased information density in phase space is made using the properties of these manifolds. Low altitude, near-polar periodic orbits with these characteristics are discussed along with the estimation results for the Love numbers, orbiter state, and orbit lifetime. Different measurement schedules and the resulting estimation performance are presented along with an analysis of information content for single measurements with respect to manifold alignment. These results allow more sensitive estimation of the tidal Love numbers and may allow measurements to be taken less frequently or compensate for corrupted data arcs. Other measurement types will be mapped in the same way using the State Transition matrix and have increased information density at epoch if aligned with the unstable manifold. In the same way, these results are applicable to planetary satellite orbiters about Enceladus or Dione since they share the governing equations of motion and properties of unstable periodic orbits.

Closing the Expectations Gap 2013. 50-State Progress Report on the Alignment of State K-12 Policies and Practice with the Demands of College and Careers

ERIC Educational Resources Information Center

Achieve, Inc., 2013

2013-01-01

This eighth annual report has taken a directional change from prior years where the primary aim was preparing students to graduate from high school. The new focus is on the K-12 alignment where, at the direction of 48 states, the National Governors Association, and the Council of Chief State School Officers, the Common Core State Standards were…

Cell-cell interactions mediate cytoskeleton organization and collective endothelial cell chemotaxis.

PubMed

Shamloo, Amir

2014-09-01

This study investigates the role of cell-cell and cell-ligand interactions in cytoskeleton organization of endothelial cells (ECs) and their directional migration within a microfluidic device. The migration of ECs in response to a biochemical factor was studied. Mathematical analysis of the cell migration pathways and cellular cytoskeleton revealed that directional migration, migration persistence length, migration speed, and cytoskeletal stress fiber alignment can be mediated by the level of cell contacts as well as the presence or absence of a biochemical polarizing factor. It was shown that in the presence of a biochemical polarizing factor, higher cell density and more frequent cell contacts has a reinforcing effect on collective cell chemotaxis. In contrast, in the absence of a polarizing factor, high cell density can decrease or suppress the ability of the cells to migrate. Also, the correlation of actin stress fiber organization and alignment with directional migration of ECs was investigated. It was shown that in the presence of a biochemical polarizing factor, stress fibers within the cytoskeleton of ECs can be significantly aligned parallel to the gradient direction when the cells have higher level of contacts. The results also show that the organization and alignment of actin stress fibers is mediated by cell adhesion junctions during collective cell migration and introduce cell-cell interactions as a key factor during collective cell chemotaxis. © 2014 Wiley Periodicals, Inc.

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

PubMed Central

Burian, Agata; Uyttewaal, Magalie

2013-01-01

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

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

PubMed

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

2018-06-01

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

A Robust Method to Generate Mechanically Anisotropic Vascular Smooth Muscle Cell Sheets for Vascular Tissue Engineering.

PubMed

Backman, Daniel E; LeSavage, Bauer L; Shah, Shivem B; Wong, Joyce Y

2017-06-01

In arterial tissue engineering, mimicking native structure and mechanical properties is essential because compliance mismatch can lead to graft failure and further disease. With bottom-up tissue engineering approaches, designing tissue components with proper microscale mechanical properties is crucial to achieve the necessary macroscale properties in the final implant. This study develops a thermoresponsive cell culture platform for growing aligned vascular smooth muscle cell (VSMC) sheets by photografting N-isopropylacrylamide (NIPAAm) onto micropatterned poly(dimethysiloxane) (PDMS). The grafting process is experimentally and computationally optimized to produce PNIPAAm-PDMS substrates optimal for VSMC attachment. To allow long-term VSMC sheet culture and increase the rate of VSMC sheet formation, PNIPAAm-PDMS surfaces were further modified with 3-aminopropyltriethoxysilane yielding a robust, thermoresponsive cell culture platform for culturing VSMC sheets. VSMC cell sheets cultured on patterned thermoresponsive substrates exhibit cellular and collagen alignment in the direction of the micropattern. Mechanical characterization of patterned, single-layer VSMC sheets reveals increased stiffness in the aligned direction compared to the perpendicular direction whereas nonpatterned cell sheets exhibit no directional dependence. Structural and mechanical anisotropy of aligned, single-layer VSMC sheets makes this platform an attractive microstructural building block for engineering a vascular graft to match the in vivo mechanical properties of native arterial tissue. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

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

2013-12-01

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

Multiple network alignment via multiMAGNA+.

PubMed

Vijayan, Vipin; Milenkovic, Tijana

2017-08-21

Network alignment (NA) aims to find a node mapping that identifies topologically or functionally similar network regions between molecular networks of different species. Analogous to genomic sequence alignment, NA can be used to transfer biological knowledge from well- to poorly-studied species between aligned network regions. Pairwise NA (PNA) finds similar regions between two networks while multiple NA (MNA) can align more than two networks. We focus on MNA. Existing MNA methods aim to maximize total similarity over all aligned nodes (node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Directly optimizing edge conservation during alignment construction in addition to node conservation may result in superior alignments. Thus, we present a novel MNA method called multiMAGNA++ that can achieve this. Indeed, multiMAGNA++ outperforms or is on par with existing MNA methods, while often completing faster than existing methods. That is, multiMAGNA++ scales well to larger network data and can be parallelized effectively. During method evaluation, we also introduce new MNA quality measures to allow for more fair MNA method comparison compared to the existing alignment quality measures. MultiMAGNA++ code is available on the method's web page at http://nd.edu/~cone/multiMAGNA++/.

Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity

PubMed Central

Sun, Meng; Bloom, Alexander B.; Zaman, Muhammad H.

2015-01-01

Metastatic cancers aggressively reorganize collagen in their microenvironment. For example, radially orientated collagen fibers have been observed surrounding tumor cell clusters in vivo. The degree of fiber alignment, as a consequence of this remodeling, has often been difficult to quantify. In this paper, we present an easy to implement algorithm for accurate detection of collagen fiber orientation in a rapid pixel-wise manner. This algorithm quantifies the alignment of both computer generated and actual collagen fiber networks of varying degrees of alignment within 5°°. We also present an alternative easy method to calculate the alignment index directly from the standard deviation of fiber orientation. Using this quantitative method for determining collagen alignment, we demonstrate that the number of collagen fiber intersections has a negative correlation with the degree of fiber alignment. This decrease in intersections of aligned fibers could explain why cells move more rapidly along aligned fibers than unaligned fibers, as previously reported. Overall, our paper provides an easier, more quantitative and quicker way to quantify fiber orientation and alignment, and presents a platform in studying effects of matrix and cellular properties on fiber alignment in complex 3D environments. PMID:26158674

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.

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

Webb, Aaron P.; Carlson, Charles T.; Honan, Michael

A plurality of masks is attached to the underside of a mask frame. This attachment is made such that each mask can independently move relative to the mask frame in three directions. This relative movement allows each mask to adjust its position to align with respective alignment pins disposed on a working surface. In one embodiment, each mask is attached to the mask frame using fasteners, where the fasteners have a shaft with a diameter smaller than the diameter of the mounting hole disposed on the mask. A bias element may be used to allow relative movement between the maskmore » and the mask frame in the vertical direction. Each mask may also have kinematic features to mate with the respective alignment pins on the working surface.« less

Solvent-vapor-assisted dewetting of prepatterned thin polymer films: control of morphology, order, and pattern miniaturization.

PubMed

Bhandaru, Nandini; Goohpattader, Partho Sarathi; Faruqui, Danish; Mukherjee, Rabibrata; Sharma, Ashutosh

2015-03-17

Ultrathin (<100 nm) unstable polymer films exposed to a solvent vapor dewet by the growth of surface instability, the wavelength (λ) of which depends on the film thickness (h(f)). While the dewetting of a flat polymer thin film results in random structures, we show that the dewetting of a prepatterned film results in myriad ordered mesoscale morphologies under specific conditions. Such a film undergoes rupture over the thinnest parts when the initial local thickness of these zones (h(rm)) is lower than a limiting thickness h(lim) ≈ 10 nm. Additionally, the width of the pattern grooves (l(s)) must be wider than λ(s) corresponding to a flat film having a thickness of h(rm) for pattern-directed dewetting to take place over surface-tension-induced flattening. We first present an experimentally obtained morphology phase diagram that captures the conditions where a transition from surface-tension-induced flattening to pattern-directed-rupture takes place. Subsequently, we show the versatility of this technique in achieving a variety of aligned mesopatterns starting from a prepatterned film with simple grating geometry. The morphology of the evolving patterns depends on several parameters such as the initial film thickness (h(f)), prepattern amplitude (h(st)), duration of solvent vapor exposure (SVE), and wettability of the stamp used for patterning. Periodic rupture of the film at regular intervals imposes directionality on the evolving patterns, resulting in isolated long threads/cylindrical ridges of polymers, which subsequently disintegrate into an aligned array of droplets due to Rayleigh-Plateau instability under specific conditions. Other patterns such as a double periodic array of droplets and an array of holes are also possible to obtain. The evolution can be interrupted at any intermediate stage by terminating the solvent vapor annealing, allowing the creation of pattern morphology on demand. The created patterns are significantly miniaturized in size as compared to features obtained from dewetting a flat film with the same hf.

Correlation of ICME Magnetic Fields at Radially Aligned Spacecraft

NASA Astrophysics Data System (ADS)

Good, S. W.; Forsyth, R. J.; Eastwood, J. P.; Möstl, C.

2018-03-01

The magnetic field structures of two interplanetary coronal mass ejections (ICMEs), each observed by a pair of spacecraft close to radial alignment, have been analysed. The ICMEs were observed in situ by MESSENGER and STEREO-B in November 2010 and November 2011, while the spacecraft were separated by more than 0.6 AU in heliocentric distance, less than 4° in heliographic longitude, and less than 7° in heliographic latitude. Both ICMEs took approximately two days to travel between the spacecraft. The ICME magnetic field profiles observed at MESSENGER have been mapped to the heliocentric distance of STEREO-B and compared directly to the profiles observed by STEREO-B. Figures that result from this mapping allow for easy qualitative assessment of similarity in the profiles. Macroscale features in the profiles that varied on timescales of one hour, and which corresponded to the underlying flux rope structure of the ICMEs, were well correlated in the solar east-west and north-south directed components, with Pearson's correlation coefficients of approximately 0.85 and 0.95, respectively; microscale features with timescales of one minute were uncorrelated. Overall correlation values in the profiles of one ICME were increased when an apparent change in the flux rope axis direction between the observing spacecraft was taken into account. The high degree of similarity seen in the magnetic field profiles may be interpreted in two ways. If the spacecraft sampled the same region of each ICME ( i.e. if the spacecraft angular separations are neglected), the similarity indicates that there was little evolution in the underlying structure of the sampled region during propagation. Alternatively, if the spacecraft observed different, nearby regions within the ICMEs, it indicates that there was spatial homogeneity across those different regions. The field structure similarity observed in these ICMEs points to the value of placing in situ space weather monitors well upstream of the Earth.

Exciton Fine-Structure Splitting in Self-Assembled Lateral InAs/GaAs Quantum-Dot Molecular Structures.

PubMed

Fillipov, Stanislav; Puttisong, Yuttapoom; Huang, Yuqing; Buyanova, Irina A; Suraprapapich, Suwaree; Tu, Charles W; Chen, Weimin M

2015-06-23

Fine-structure splitting (FSS) of excitons in semiconductor nanostructures is a key parameter that has significant implications in photon entanglement and polarization conversion between electron spins and photons, relevant to quantum information technology and spintronics. Here, we investigate exciton FSS in self-organized lateral InAs/GaAs quantum-dot molecular structures (QMSs) including laterally aligned double quantum dots (DQDs), quantum-dot clusters (QCs), and quantum rings (QRs), by employing polarization-resolved microphotoluminescence (μPL) spectroscopy. We find a clear trend in FSS between the studied QMSs depending on their geometric arrangements, from a large FSS in the DQDs to a smaller FSS in the QCs and QRs. This trend is accompanied by a corresponding difference in the optical polarization directions of the excitons between these QMSs, namely, the bright-exciton lines are linearly polarized preferably along or perpendicular to the [11̅0] crystallographic axis in the DQDs that also defines the alignment direction of the two constituting QDs, whereas in the QCs and QRs, the polarization directions are randomly oriented. We attribute the observed trend in the FSS to a significant reduction of the asymmetry in the lateral confinement potential of the excitons in the QRs and QCs as compared with the DQDs, as a result of a compensation between the effects of lateral shape anisotropy and piezoelectric field. Our work demonstrates that FSS strongly depends on the geometric arrangements of the QMSs, which effectively tune the degree of the compensation effects and are capable of reducing FSS even in a strained QD system to a limit similar to strain-free QDs. This approach provides a pathway in obtaining high-symmetry quantum emitters desirable for realizing photon entanglement and spintronic devices based on such nanostructures, utilizing an uninterrupted epitaxial growth procedure without special requirements for lattice-matched materials combinations, specific substrate orientations, and nanolithography.

Amperometric Detection in Microchip Electrophoresis Devices: Effect of Electrode Material and Alignment on Analytical Performance

PubMed Central

Fischer, David J.; Hulvey, Matthew K.; Regel, Anne R.; Lunte, Susan M.

2012-01-01

The fabrication and evaluation of different electrode materials and electrode alignments for microchip electrophoresis with electrochemical (EC) detection is described. The influences of electrode material, both metal and carbon-based, on sensitivity and limits of detection (LOD) were examined. In addition, the effects of working electrode alignment on analytical performance (in terms of peak shape, resolution, sensitivity, and LOD) were directly compared. Using dopamine (DA), norepinephrine (NE), and catechol (CAT) as test analytes, it was found that pyrolyzed photoresist electrodes with end-channel alignment yielded the lowest limit of detection (35 nM for DA). In addition to being easier to implement, end-channel alignment also offered better analytical performance than off-channel alignment for the detection of all three analytes. In-channel electrode alignment resulted in a 3.6-fold reduction in peak skew and reduced peak tailing by a factor of 2.1 for catechol in comparison to end-channel alignment. PMID:19802847

Energy level alignment in TiO2/metal sulfide/polymer interfaces for solar cell applications.

PubMed

Lindblad, Rebecka; Cappel, Ute B; O'Mahony, Flannan T F; Siegbahn, Hans; Johansson, Erik M J; Haque, Saif A; Rensmo, Håkan

2014-08-28

Semiconductor sensitized solar cell interfaces have been studied with photoelectron spectroscopy to understand the interfacial electronic structures. In particular, the experimental energy level alignment has been determined for complete TiO2/metal sulfide/polymer interfaces. For the metal sulfides CdS, Sb2S3 and Bi2S3 deposited from single source metal xanthate precursors, it was shown that both driving forces for electron injection into TiO2 and hole transfer to the polymer decrease for narrower bandgaps. The energy level alignment results were used in the discussion of the function of solar cells with the same metal sulfides as light absorbers. For example Sb2S3 showed the most favourable energy level alignment with 0.3 eV driving force for electron injection and 0.4 eV driving force for hole transfer and also the most efficient solar cells due to high photocurrent generation. The energy level alignment of the TiO2/Bi2S3 interface on the other hand showed no driving force for electron injection to TiO2, and the performance of the corresponding solar cell was very low.

Development and preliminary evaluation of a new anatomically based prosthetic alignment method for below-knee prosthesis.

PubMed

Tafti, Nahid; Karimlou, Masoud; Mardani, Mohammad Ali; Jafarpisheh, Amir Salar; Aminian, Gholam Reza; Safari, Reza

2018-04-20

The objectives of current study were to a) assess similarities and relationships between anatomical landmark-based angles and distances of lower limbs in unilateral transtibial amputees and b) develop and evaluate a new anatomically based static prosthetic alignment method. First sub-study assessed the anthropometrical differences and relationships between the lower limbs in the photographs taken from amputees. Data were analysed via paired t-test and regression analysis. Results show no significant differences in frontal and transverse planes. In the sagittal plane, the anthropometric parameters of the amputated limb were significantly correlated to the corresponding variables of the sound limb. The results served as bases for the development of a new prosthetic alignment method. The method was evaluated on a single subject study. Prosthetic alignment carried out by an experienced prosthetist was compared with such alignment adjusted by an inexperienced prosthetist but with the use of the developed method. In sagittal and frontal planes, the socket angle was tuned with respect to the shin angle, and the position of the prosthetic foot was tuned in relation to the pelvic landmarks. Further study is needed to assess the proposed method on a larger sample of amputees and prosthetists.

Method for protein structure alignment

DOEpatents

Blankenbecler, Richard; Ohlsson, Mattias; Peterson, Carsten; Ringner, Markus

2005-02-22

This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

Multimodal Image Alignment via Linear Mapping between Feature Modalities.

PubMed

Jiang, Yanyun; Zheng, Yuanjie; Hou, Sujuan; Chang, Yuchou; Gee, James

2017-01-01

We propose a novel landmark matching based method for aligning multimodal images, which is accomplished uniquely by resolving a linear mapping between different feature modalities. This linear mapping results in a new measurement on similarity of images captured from different modalities. In addition, our method simultaneously solves this linear mapping and the landmark correspondences by minimizing a convex quadratic function. Our method can estimate complex image relationship between different modalities and nonlinear nonrigid spatial transformations even in the presence of heavy noise, as shown in our experiments carried out by using a variety of image modalities.

SU-E-J-33: Comparison Between Soft Tissue Alignment and Bony Alignment for Pancreatic Cancer Radiotherapy

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

Suh, Y; Crane, C; Krishnan, S

Purpose An IGRT modality for pancreatic cancer treatment with dose escalation at our institution is in-room daily CT imaging. The purpose of this study is to assess the difference between soft tissue alignment and bony alignment for pancreatic tumor localization. Methods Eighteen patients with pancreatic tumors who underwent IMRT treatment with an inspiration breath-hold technique between July 2012 and February 2015 are included in this study. Prior to each treatment, a CT scan was acquired. The CT image guidance started with auto-alignment to either the bony anatomy (vertebral bodies) or fiducials (for the six patients with the stent in/near themore » tumor) and then, when necessary, manual adjustments were made based on soft tissue alignment using clinical software (CT-Assisted Targeting system). The difference between soft tissue alignment and bony/fiducial alignment was evaluated. Results Of all 380 treatments, manual adjustment was made in 225 treatments, ranging from 11% (3 treatments out of 28) to 96% (27 treatments out of 28) per patient. The mean of the difference between soft tissue alignment and bony/fiducial alignment per patient ranged from −3.6 to 0.3 mm, −1.5 to 2.8 mm, and −3.3 to 3.4 mm in the AP, SI, and RL directions, respectively. The maximum difference over all treatments was −9.5, −14.6, and −14.6 mm in the AP, SI, and RL directions, respectively. Conclusion About 60% of the time, manual adjustment based on soft tissue alignment was required. The extent of manual adjustment was usually small but varied significantly from patient to patient. The ultimate goal of the IGRT modality using daily CT imaging is not to fully cover the target but to spare organs-at-risk as much as possible to avoid them moving into higher dose gradients than accepted in the treatment plan. To this end, manual adjustment based on soft tissue alignment is critically important.« less

Neurient: An Algorithm for Automatic Tracing of Confluent Neuronal Images to Determine Alignment

PubMed Central

Mitchel, J.A.; Martin, I.S.

2013-01-01

A goal of neural tissue engineering is the development and evaluation of materials that guide neuronal growth and alignment. However, the methods available to quantitatively evaluate the response of neurons to guidance materials are limited and/or expensive, and may require manual tracing to be performed by the researcher. We have developed an open source, automated Matlab-based algorithm, building on previously published methods, to trace and quantify alignment of fluorescent images of neurons in culture. The algorithm is divided into three phases, including computation of a lookup table which contains directional information for each image, location of a set of seed points which may lie along neurite centerlines, and tracing neurites starting with each seed point and indexing into the lookup table. This method was used to obtain quantitative alignment data for complex images of densely cultured neurons. Complete automation of tracing allows for unsupervised processing of large numbers of images. Following image processing with our algorithm, available metrics to quantify neurite alignment include angular histograms, percent of neurite segments in a given direction, and mean neurite angle. The alignment information obtained from traced images can be used to compare the response of neurons to a range of conditions. This tracing algorithm is freely available to the scientific community under the name Neurient, and its implementation in Matlab allows a wide range of researchers to use a standardized, open source method to quantitatively evaluate the alignment of dense neuronal cultures. PMID:23384629

Simultaneous velocity and concentration field measurements of passive-scalar mixing in a confined rectangular jet

NASA Astrophysics Data System (ADS)

Feng, Hua; Olsen, Michael G.; Hill, James C.; Fox, Rodney O.

2007-06-01

Simultaneous velocity and concentration fields in a confined liquid-phase rectangular jet with a Reynolds number based on the hydraulic diameter of 50,000 (or 10,000 based on the velocity difference between streams and the jet exit dimension) and a Schmidt number of 1,250 were obtained by means of a combined particle image velocimetry (PIV) and planar laser-induced fluorescence (PLIF) system. Data were collected at the jet exit and six further downstream locations. The velocity and concentration field data were analyzed for flow statistics such as turbulent fluxes, turbulent viscosity and diffusivity, and turbulent Schmidt number ( Sc T ). The streamwise turbulent flux was found to be larger than the transverse turbulent flux, and the mean concentration gradient was not aligned with the turbulent flux vector. The average Sc T was found to vary both in streamwise and in cross stream directions and had a mean value around 0.8, a value consistent with the literature. Spatial correlation fields of turbulent fluxes and concentration were then determined. The R u'ϕ' correlation was elliptical in shape with a major axis tilted downward with respect to the streamwise axis, whereas the R v'ϕ' correlation was an ellipse with a major axis aligned with the cross-stream direction. Negative regions of R u'ϕ' were observed in the outer streams, and these negatively correlated regions decayed with downstream distance and finally disappeared altogether. The R ϕ'ϕ' correlation field was found to be an ellipse with the major axis inclined at about 45° with respect to the streamwise direction. Linear stochastic estimation was used to interpret spatial correlation data and to determine conditional flow structures. It is believed that a vortex street formed near the splitter plate is responsible for the negatively correlated region observed in the R u'ϕ' spatial correlations of turbulent fluxes. A positive concentration fluctuation event was observed to correspond to a finger of nearly uniform concentration fluid reaching out into the outer stream, whereas a negative event corresponds to a pocket of nearly uniform fluid being entrained from the outer stream into the center jet region. Large-scale vortical structures were observed in the conditional velocity fields with an elliptical shape and a streamwise major axis. The growth of the structure size increased linearly initially but then grew more slowly as the flow transitioned toward channel flow.

Electromechanical modeling and experimental verification of a directly printed nanocomposite

NASA Astrophysics Data System (ADS)

Nafari, Alireza; Sodano, Henry A.

2018-03-01

Piezoelectric materials are currently among the most promising building blocks of sensing, actuating and energy harvesting systems. However, these materials are limited in applications due to difficulty in machining and casting it on to curve surfaces. To mitigate this issue, one method is through additive manufacturing (direct printing) of piezoelectric nanocomposite in which piezoelectric nanomaterials are embedded into a polymer matrix. Although significant progress has been recently made in this area, modeling the electromechanical response of a directly printed nanocomposite remains a challenge. Thus the objective of this study is to develop robust micromechanical and finite element models that allows the study of the electroelastic properties of a directly printed nanocomposite containing piezoelectric inclusions. Furthermore, the dependence of these properties on geometrical parameters such as aspect ratio and alignment of the active phase are investigated. The focus of this work is a demonstration of the effect gradual alignment of piezoelectric nanowires in a nanocomposite from randomly oriented to purely aligned improves the electroelastic properties of a directly printed nanocomposite. Finally, these models are verified through experimental measurement of electroelastic properties of the nanocomposites containing barium titanate nanowires in Polydimethylsiloxane (PDMS) polymer.

Enhanced pyroelectric and piezoelectric properties of PZT with aligned porosity for energy harvesting applications† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7ta00967d Click here for additional data file.

PubMed Central

Zhang, Yan; Xie, Mengying; Roscow, James; Bao, Yinxiang; Zhou, Kechao

2017-01-01

This paper demonstrates the significant benefits of exploiting highly aligned porosity in piezoelectric and pyroelectric materials for improved energy harvesting performance. Porous lead zirconate (PZT) ceramics with aligned pore channels and varying fractions of porosity were manufactured in a water-based suspension using freeze-casting. The aligned porous PZT ceramics were characterized in detail for both piezoelectric and pyroelectric properties and their energy harvesting performance figures of merit were assessed parallel and perpendicular to the freezing direction. As a result of the introduction of porosity into the ceramic microstructure, high piezoelectric and pyroelectric harvesting figures of merits were achieved for porous freeze-cast PZT compared to dense PZT due to the reduced permittivity and volume specific heat capacity. Experimental results were compared to parallel and series analytical models with good agreement and the PZT with porosity aligned parallel to the freezing direction exhibited the highest piezoelectric and pyroelectric harvesting response; this was a result of the enhanced interconnectivity of the ferroelectric material along the poling direction and reduced fraction of unpoled material that leads to a higher polarization. A complete thermal energy harvesting system, composed of a parallel-aligned PZT harvester element and an AC/DC converter, was successfully demonstrated by charging a storage capacitor. The maximum energy density generated by the 60 vol% porous parallel-connected PZT when subjected to thermal oscillations was 1653 μJ cm–3, which was 374% higher than that of the dense PZT with an energy density of 446 μJ cm–3. The results are beneficial for the design and manufacture of high performance porous pyroelectric and piezoelectric materials in devices for energy harvesting and sensor applications. PMID:28580142

Enhanced pyroelectric and piezoelectric properties of PZT with aligned porosity for energy harvesting applications.

PubMed

Zhang, Yan; Xie, Mengying; Roscow, James; Bao, Yinxiang; Zhou, Kechao; Zhang, Dou; Bowen, Chris R

2017-04-14

This paper demonstrates the significant benefits of exploiting highly aligned porosity in piezoelectric and pyroelectric materials for improved energy harvesting performance. Porous lead zirconate (PZT) ceramics with aligned pore channels and varying fractions of porosity were manufactured in a water-based suspension using freeze-casting. The aligned porous PZT ceramics were characterized in detail for both piezoelectric and pyroelectric properties and their energy harvesting performance figures of merit were assessed parallel and perpendicular to the freezing direction. As a result of the introduction of porosity into the ceramic microstructure, high piezoelectric and pyroelectric harvesting figures of merits were achieved for porous freeze-cast PZT compared to dense PZT due to the reduced permittivity and volume specific heat capacity. Experimental results were compared to parallel and series analytical models with good agreement and the PZT with porosity aligned parallel to the freezing direction exhibited the highest piezoelectric and pyroelectric harvesting response; this was a result of the enhanced interconnectivity of the ferroelectric material along the poling direction and reduced fraction of unpoled material that leads to a higher polarization. A complete thermal energy harvesting system, composed of a parallel-aligned PZT harvester element and an AC/DC converter, was successfully demonstrated by charging a storage capacitor. The maximum energy density generated by the 60 vol% porous parallel-connected PZT when subjected to thermal oscillations was 1653 μJ cm -3 , which was 374% higher than that of the dense PZT with an energy density of 446 μJ cm -3 . The results are beneficial for the design and manufacture of high performance porous pyroelectric and piezoelectric materials in devices for energy harvesting and sensor applications.

Epitaxial growth of aligned AlGalnN nanowires by metal-organic chemical vapor deposition

DOEpatents

Han, Jung; Su, Jie

2008-08-05

Highly ordered and aligned epitaxy of III-Nitride nanowires is demonstrated in this work. <1010> M-axis is identified as a preferential nanowire growth direction through a detailed study of GaN/AlN trunk/branch nanostructures by transmission electron microscopy. Crystallographic selectivity can be used to achieve spatial and orientational control of nanowire growth. Vertically aligned (Al)GaN nanowires are prepared on M-plane AlN substrates. Horizontally ordered nanowires, extending from the M-plane sidewalls of GaN hexagonal mesas or islands demonstrate new opportunities for self-aligned nanowire devices, interconnects, and networks.

An MHD simulation of By-dependent magnetospheric convection and field-aligned currents during northward IMF

NASA Technical Reports Server (NTRS)

Ogino, T.; Walker, R. J.; Ashour-Abdalla, M.; Dawson, J. M.

1985-01-01

A three-dimensional MHD simulation code is used to model the magnetospheric configuration when the IMF has both a northward B(z) component and a B(y) component in the east-west direction. Projections of the plasma pressure, the field-aligned velocity, the field-aligned vorticity, and the field-aligned current along the magnetic field lines into the northern ionosphere are shown and discussed. Cross-sectional patterns of these parameters are shown. The results demonstrate that the B(y) component of the IMF strongly influences the plasma sheet configuration and the magnetospheric convection pattern.

Performance management models for public health: Public Health Accreditation Board/Baldrige connections, alignment, and distinctions.

PubMed

Gorenflo, Grace G; Klater, David M; Mason, Marlene; Russo, Pamela; Rivera, Lillian

2014-01-01

The nationally known Malcolm Baldrige Award for Excellence ("Baldrige program") recognizes outstanding performance management and is specifically cited by the Public Health Accreditation Board (PHAB) as a potential framework for PHAB's requisite performance management system. The authors developed a crosswalk that identifies alignments between the 2 programs and is a highlight of the Quest for Exceptional Performance tool that is intended to help health departments capitalize on the connections between the 2 programs. To provide deeper insight into the most robust connections between the 2 programs. The authors developed a crosswalk by listing the PHAB measures, identifying corresponding Baldrige areas to address, and assigning a rating regarding the strength of the alignment. Subsequently, they generated a matrix with numerical scores reflecting the strength of the PHAB-Baldrige alignments that were then analyzed for frequency and strength of alignment by PHAB domain and by Baldrige category. The tool developers and 3 public health leaders with experience in the Baldrige program contributed to both the design and the analyses. The measures used reflected both the frequency and strength of alignments. Of the 123 alignments identified in the crosswalk, 39 were rated as high, 40 as medium, and 44 as low. The strongest connections were in the areas of performance management, quality improvement, strategic planning, workforce development, assessment and analysis, and customer service. While the areas with the most frequent and strongest connections provide the most useful basis for health departments pursuing Baldrige recognition or using Baldrige criteria as a framework for performance management, all alignments could be considered for both purposes.

Superemission in vertically-aligned single-wall carbon nanotubes

NASA Astrophysics Data System (ADS)

Khmelinskii, Igor; Makarov, Vladimir

2016-09-01

Presently we used two samples of vertically aligned single-wall carbon nanotubes (VA SWCNTs) with parallelepiped geometry, sized 0.02 cm × 0.2 cm × 1.0 cm and 0.2 cm × 0.2 cm × 1.0 cm. We report absorption and emission properties of the VA SWCNTs, including strong anisotropy in both their absorption and emission spectra. We found that the emission spectra extend from the middle-IR range to the near-IR range, with such extended spectra being reported for the first time. Pumping the VA SWCNTs in the direction normal to their axis, superemission (SE) was observed in the direction along their axis. The SE band maximum is located at 7206 ± 0.4 cm-1. The energy and the power density of the superemission were estimated, along with the diffraction-limited divergence. At the pumping energy of 3 mJ/pulse, the SE energy measured by the detector was 0.74 mJ/pulse, corresponding to the total SE energy of 1.48 mJ/pulse, with the energy density of 18.5 mJ cm-2/pulse and the SE power density of 1.2 × 105 W cm-2/pulse. We report that a bundle of VA SWCNTs is an emitter with a relatively small divergence, not exceeding 3.9 × 10-3 rad. We developed a theoretical approach to explain such absorption and emission spectra. The developed theory is based on the earlier proposed SSH theory, which we extended to include the exchange interactions between the closest SWCNT neighbors. The developed theoretical ideas were implemented in a homemade FORTRAN code. This code was successfully used to calculate and reproduce the experimental spectra and to determine the SWCNT species that originate the respective absorption bands, with acceptable agreement between theory and experiment.

Spontaneous high-gamma band activity reflects functional organization of auditory cortex in the awake macaque.

PubMed

Fukushima, Makoto; Saunders, Richard C; Leopold, David A; Mishkin, Mortimer; Averbeck, Bruno B

2012-06-07

In the absence of sensory stimuli, spontaneous activity in the brain has been shown to exhibit organization at multiple spatiotemporal scales. In the macaque auditory cortex, responses to acoustic stimuli are tonotopically organized within multiple, adjacent frequency maps aligned in a caudorostral direction on the supratemporal plane (STP) of the lateral sulcus. Here, we used chronic microelectrocorticography to investigate the correspondence between sensory maps and spontaneous neural fluctuations in the auditory cortex. We first mapped tonotopic organization across 96 electrodes spanning approximately two centimeters along the primary and higher auditory cortex. In separate sessions, we then observed that spontaneous activity at the same sites exhibited spatial covariation that reflected the tonotopic map of the STP. This observation demonstrates a close relationship between functional organization and spontaneous neural activity in the sensory cortex of the awake monkey. Copyright © 2012 Elsevier Inc. All rights reserved.

Spontaneous high-gamma band activity reflects functional organization of auditory cortex in the awake macaque

PubMed Central

Fukushima, Makoto; Saunders, Richard C.; Leopold, David A.; Mishkin, Mortimer; Averbeck, Bruno B.

2012-01-01

Summary In the absence of sensory stimuli, spontaneous activity in the brain has been shown to exhibit organization at multiple spatiotemporal scales. In the macaque auditory cortex, responses to acoustic stimuli are tonotopically organized within multiple, adjacent frequency maps aligned in a caudorostral direction on the supratemporal plane (STP) of the lateral sulcus. Here we used chronic micro-electrocorticography to investigate the correspondence between sensory maps and spontaneous neural fluctuations in the auditory cortex. We first mapped tonotopic organization across 96 electrodes spanning approximately two centimeters along the primary and higher auditory cortex. In separate sessions we then observed that spontaneous activity at the same sites exhibited spatial covariation that reflected the tonotopic map of the STP. This observation demonstrates a close relationship between functional organization and spontaneous neural activity in the sensory cortex of the awake monkey. PMID:22681693

Communication: Memory effects and active Brownian diffusion

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

Ghosh, Pulak K.; Li, Yunyun, E-mail: yunyunli@tongji.edu.cn; Marchegiani, Giampiero

A self-propelled artificial microswimmer is often modeled as a ballistic Brownian particle moving with constant speed aligned along one of its axis, but changing direction due to random collisions with the environment. Similarly to thermal noise, its angular randomization is described as a memoryless stochastic process. Here, we speculate that finite-time correlations in the orientational dynamics can affect the swimmer’s diffusivity. To this purpose, we propose and solve two alternative models. In the first one, we simply assume that the environmental fluctuations governing the swimmer’s propulsion are exponentially correlated in time, whereas in the second one, we account for possiblemore » damped fluctuations of the propulsion velocity around the swimmer’s axis. The corresponding swimmer’s diffusion constants are predicted to get, respectively, enhanced or suppressed upon increasing the model memory time. Possible consequences of this effect on the interpretation of the experimental data are discussed.« less

Ferromagnetic Switching of Knotted Vector Fields in Liquid Crystal Colloids.

PubMed

Zhang, Qiaoxuan; Ackerman, Paul J; Liu, Qingkun; Smalyukh, Ivan I

2015-08-28

We experimentally realize polydomain and monodomain chiral ferromagnetic liquid crystal colloids that exhibit solitonic and knotted vector field configurations. Formed by dispersions of ferromagnetic nanoplatelets in chiral nematic liquid crystals, these colloidal ferromagnets exhibit spontaneous long-range alignment of magnetic dipole moments of individual platelets, giving rise to a continuum of the magnetization field M(r). Competing effects of surface confinement and chirality prompt spontaneous formation and enable the optical generation of localized twisted solitonic structures with double-twist tubes and torus knots of M(r), which exhibit a strong sensitivity to the direction of weak magnetic fields ∼1  mT. Numerical modeling, implemented through free energy minimization to arrive at a field-dependent three-dimensional M(r), shows a good agreement with experiments and provides insights into the torus knot topology of observed field configurations and the corresponding physical underpinnings.

Communication: Memory effects and active Brownian diffusion

NASA Astrophysics Data System (ADS)

Ghosh, Pulak K.; Li, Yunyun; Marchegiani, Giampiero; Marchesoni, Fabio

2015-12-01

A self-propelled artificial microswimmer is often modeled as a ballistic Brownian particle moving with constant speed aligned along one of its axis, but changing direction due to random collisions with the environment. Similarly to thermal noise, its angular randomization is described as a memoryless stochastic process. Here, we speculate that finite-time correlations in the orientational dynamics can affect the swimmer's diffusivity. To this purpose, we propose and solve two alternative models. In the first one, we simply assume that the environmental fluctuations governing the swimmer's propulsion are exponentially correlated in time, whereas in the second one, we account for possible damped fluctuations of the propulsion velocity around the swimmer's axis. The corresponding swimmer's diffusion constants are predicted to get, respectively, enhanced or suppressed upon increasing the model memory time. Possible consequences of this effect on the interpretation of the experimental data are discussed.

Induction melter apparatus

DOEpatents

Roach, Jay A [Idaho Falls, ID; Richardson, John G [Idaho Falls, ID; Raivo, Brian D [Idaho Falls, ID; Soelberg, Nicholas R [Idaho Falls, ID

2008-06-17

Apparatus and methods of operation are provided for a cold-crucible-induction melter for vitrifying waste wherein a single induction power supply may be used to effect a selected thermal distribution by independently energizing at least two inductors. Also, a bottom drain assembly may be heated by an inductor and may include an electrically resistive heater. The bottom drain assembly may be cooled to solidify molten material passing therethrough to prevent discharge of molten material therefrom. Configurations are provided wherein the induction flux skin depth substantially corresponds with the central longitudinal axis of the crucible. Further, the drain tube may be positioned within the induction flux skin depth in relation to material within the crucible or may be substantially aligned with a direction of flow of molten material within the crucible. An improved head design including four shells forming thermal radiation shields and at least two gas-cooled plenums is also disclosed.

Operating an induction melter apparatus

DOEpatents

Roach, Jay A.; Richardson, John G.; Raivo, Brian D.; Soelberg, Nicholas R.

2006-01-31

Apparatus and methods of operation are provided for a cold-crucible-induction melter for vitrifying waste wherein a single induction power supply may be used to effect a selected thermal distribution by independently energizing at least two inductors. Also, a bottom drain assembly may be heated by an inductor and may include an electrically resistive heater. The bottom drain assembly may be cooled to solidify molten material passing therethrough to prevent discharge of molten material therefrom. Configurations are provided wherein the induction flux skin depth substantially corresponds with the central longitudinal axis of the crucible. Further, the drain tube may be positioned within the induction flux skin depth in relation to material within the crucible or may be substantially aligned with a direction of flow of molten material within the crucible. An improved head design including four shells forming thermal radiation shields and at least two gas-cooled plenums is also disclosed.

Making a difference: ethical consumption and the everyday.

PubMed

Adams, Matthew; Raisborough, Jayne

2010-06-01

Our everyday shopping practices are increasingly marketed as opportunities to 'make a difference' via our ethical consumption choices. In response to a growing body of work detailing the ways in which specific alignments of 'ethics' and 'consumption' are mediated, we explore how 'ethical' opportunities such as the consumption of Fairtrade products are recognized, experienced and taken-up in the everyday. The 'everyday' is approached here via a specially commissioned Mass Observation directive, a volunteer panel of correspondents in the UK. Our on-going thematic analysis of their autobiographical accounts aims to explore a complex unevenness in the ways 'ordinary' people experience and negotiate calls to enact their ethical agency through consumption. Situating ethical consumption, moral obligation and choice in the everyday is, we argue, important if we are to avoid both over-exaggerating the reflexive and self-conscious sensibilities involved in ethical consumption, and, adhering to a reductive understanding of ethical self-expression.

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.

Perceiving and Acting on Complex Affordances: How Children and Adults Bicycle Across Two Lanes of Opposing Traffic

PubMed Central

Grechkin, Timofey Y.; Chihak, Benjamin J.; Cremer, James F.; Kearney, Joseph K.; Plumert, Jodie M.

2014-01-01

This investigation examined how children and adults negotiate a challenging perceptual-motor problem with significant real-world implications – bicycling across two lanes of opposing traffic. Twelve- and 14-year-olds and adults rode a bicycling simulator through an immersive virtual environment. Participants crossed intersections with continuous cross traffic coming from opposing directions. Opportunities for crossing were divided into aligned (far gap opens with or before near gap) and rolling (far gap opens after near gap) gap pairs. Children and adults preferred rolling to aligned gap pairs, though this preference was stronger for adults than for children. Crossing aligned versus rolling gap pairs produced substantial differences in direction of travel, speed of crossing, and timing of entry into the near and far lanes. For both aligned and rolling gap pairs, children demonstrated less skill than adults in coordinating self and object movement. These findings have implications for understanding perception-action-cognition links and for understanding risk factors underlying car-bicycle collisions. PMID:22924952

Thermal Conductivity of Polymer/Nano-filler Blends

NASA Technical Reports Server (NTRS)

Ghose, Sayata; Watson, Kent A.; Delozier, Donovan M.; Working, Dennis C.; Connell, John W.; Smith, Joseph G.; Sun, Y. P.; Lin, Y.

2006-01-01

To improve the thermal conductivity of an ethylene vinyl acetate copolymer, Elvax 260 was compounded with three carbon based nano-fillers. Multiwalled carbon nanotubes (MWCNT), vapor grown carbon nanofibers (CNF) and expanded graphite (EG) were investigated. In an attempt to improve compatibility between the Elvax and nanofillers, MWCNTs and EGs were modified through non covalent and covalent attachment of alkyl groups. Ribbons were extruded to form samples in which the nanofillers were aligned, and samples were also fabricated by compression molding in which the nano-fillers were randomly oriented. The thermal properties were evaluated by DSC and TGA, and mechanical properties of the aligned samples were determined by tensile testing. The degree of dispersion and alignment of the nanoparticles were investigated using high-resolution scanning electron microscopy. Thermal conductivity measurements were performed using a Nanoflash technique. The thermal conductivity of the samples was measured in both the direction of alignment as well as perpendicular to that direction. The results of this study will be presented.

Pivots for pointing: visually-monitored pointing has higher arm elevations than pointing blindfolded.

PubMed

Wnuczko, Marta; Kennedy, John M

2011-10-01

Observers pointing to a target viewed directly may elevate their fingertip close to the line of sight. However, pointing blindfolded, after viewing the target, they may pivot lower, from the shoulder, aligning the arm with the target as if reaching to the target. Indeed, in Experiment 1 participants elevated their arms more in visually monitored than blindfolded pointing. In Experiment 2, pointing to a visible target they elevated a short pointer more than a long one, raising its tip to the line of sight. In Experiment 3, the Experimenter aligned the participant's arm with the target. Participants judged they were pointing below a visually monitored target. In Experiment 4, participants viewing another person pointing, eyes-open or eyes-closed, judged the target was aligned with the pointing arm. In Experiment 5, participants viewed their arm and the target via a mirror and posed their arm so that it was aligned with the target. Arm elevation was higher in pointing directly.

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.

Technical Note: A direct ray-tracing method to compute integral depth dose in pencil beam proton radiography with a multilayer ionization chamber.

PubMed

Farace, Paolo; Righetto, Roberto; Deffet, Sylvain; Meijers, Arturs; Vander Stappen, Francois

2016-12-01

To introduce a fast ray-tracing algorithm in pencil proton radiography (PR) with a multilayer ionization chamber (MLIC) for in vivo range error mapping. Pencil beam PR was obtained by delivering spots uniformly positioned in a square (45 × 45 mm 2 field-of-view) of 9 × 9 spots capable of crossing the phantoms (210 MeV). The exit beam was collected by a MLIC to sample the integral depth dose (IDD MLIC ). PRs of an electron-density and of a head phantom were acquired by moving the couch to obtain multiple 45 × 45 mm 2 frames. To map the corresponding range errors, the two-dimensional set of IDD MLIC was compared with (i) the integral depth dose computed by the treatment planning system (TPS) by both analytic (IDD TPS ) and Monte Carlo (IDD MC ) algorithms in a volume of water simulating the MLIC at the CT, and (ii) the integral depth dose directly computed by a simple ray-tracing algorithm (IDD direct ) through the same CT data. The exact spatial position of the spot pattern was numerically adjusted testing different in-plane positions and selecting the one that minimized the range differences between IDD direct and IDD MLIC . Range error mapping was feasible by both the TPS and the ray-tracing methods, but very sensitive to even small misalignments. In homogeneous regions, the range errors computed by the direct ray-tracing algorithm matched the results obtained by both the analytic and the Monte Carlo algorithms. In both phantoms, lateral heterogeneities were better modeled by the ray-tracing and the Monte Carlo algorithms than by the analytic TPS computation. Accordingly, when the pencil beam crossed lateral heterogeneities, the range errors mapped by the direct algorithm matched better the Monte Carlo maps than those obtained by the analytic algorithm. Finally, the simplicity of the ray-tracing algorithm allowed to implement a prototype procedure for automated spatial alignment. The ray-tracing algorithm can reliably replace the TPS method in MLIC PR for in vivo range verification and it can be a key component to develop software tools for spatial alignment and correction of CT calibration.

Spatio-temporal alignment of pedobarographic image sequences.

PubMed

Oliveira, Francisco P M; Sousa, Andreia; Santos, Rubim; Tavares, João Manuel R S

2011-07-01

This article presents a methodology to align plantar pressure image sequences simultaneously in time and space. The spatial position and orientation of a foot in a sequence are changed to match the foot represented in a second sequence. Simultaneously with the spatial alignment, the temporal scale of the first sequence is transformed with the aim of synchronizing the two input footsteps. Consequently, the spatial correspondence of the foot regions along the sequences as well as the temporal synchronizing is automatically attained, making the study easier and more straightforward. In terms of spatial alignment, the methodology can use one of four possible geometric transformation models: rigid, similarity, affine, or projective. In the temporal alignment, a polynomial transformation up to the 4th degree can be adopted in order to model linear and curved time behaviors. Suitable geometric and temporal transformations are found by minimizing the mean squared error (MSE) between the input sequences. The methodology was tested on a set of real image sequences acquired from a common pedobarographic device. When used in experimental cases generated by applying geometric and temporal control transformations, the methodology revealed high accuracy. In addition, the intra-subject alignment tests from real plantar pressure image sequences showed that the curved temporal models produced better MSE results (P < 0.001) than the linear temporal model. This article represents an important step forward in the alignment of pedobarographic image data, since previous methods can only be applied on static images.

Automatic initialization for 3D bone registration

NASA Astrophysics Data System (ADS)

Foroughi, Pezhman; Taylor, Russell H.; Fichtinger, Gabor

2008-03-01

In image-guided bone surgery, sample points collected from the surface of the bone are registered to the preoperative CT model using well-known registration methods such as Iterative Closest Point (ICP). These techniques are generally very sensitive to the initial alignment of the datasets. Poor initialization significantly increases the chances of getting trapped local minima. In order to reduce the risk of local minima, the registration is manually initialized by locating the sample points close to the corresponding points on the CT model. In this paper, we present an automatic initialization method that aligns the sample points collected from the surface of pelvis with CT model of the pelvis. The main idea is to exploit a mean shape of pelvis created from a large number of CT scans as the prior knowledge to guide the initial alignment. The mean shape is constant for all registrations and facilitates the inclusion of application-specific information into the registration process. The CT model is first aligned with the mean shape using the bilateral symmetry of the pelvis and the similarity of multiple projections. The surface points collected using ultrasound are then aligned with the pelvis mean shape. This will, in turn, lead to initial alignment of the sample points with the CT model. The experiments using a dry pelvis and two cadavers show that the method can align the randomly dislocated datasets close enough for successful registration. The standard ICP has been used for final registration of datasets.

Highly anisotropic magneto-transport and field orientation dependent oscillations in aligned carbon nanotube/epoxy composites

NASA Astrophysics Data System (ADS)

Wells, Brian; Kumar, Raj; Reynolds, C. Lewis; Peters, Kara; Bradford, Philip D.

2017-12-01

Carbon nanotubes (CNTs) have been widely investigated as additive materials for composites with potential applications in electronic devices due to their extremely large electrical conductivity and current density. Here, highly aligned CNT composite films were created using a sequential layering fabrication technique. The degree of CNT alignment leads to anisotropic resistance values which varies >400× in orthogonal directions. Similarly, the magnetoresistance (MR) of the CNT composite differs depending upon the relative direction of current and the applied magnetic field. A suppression of negative to positive MR crossover was also observed. More importantly, an overall positive magnetoresistance behavior with localized +/- oscillations was discovered at low fields which persists up to room temperature when the current (I) and in-plane magnetic field (B) were parallel to the axis of CNT (B∥I∥CNT), which is consistent with Aharonov-Bohm oscillations in our CNT/epoxy composites. When the current, applied magnetic field, and nanotube axis are aligned, the in-plane MR is positive instead of negative as observed for all other field, current, and tube orientations. Here, we provide in-depth analysis of the conduction mechanism and anisotropy in the magneto-transport properties of these aligned CNT-epoxy composites.

Laser-fiber coupling by means of a silicon micro-optical bench and a self-aligned soldering process

NASA Astrophysics Data System (ADS)

Schmidt, Jan P.; Cordes, A.; Mueller, Joerg; Burkhardt, Hans

1995-02-01

The alignment of laser diodes to monomode fibers has to meet extremely close tolerances for a low coupling loss. Typically < 0.5 micrometers in lateral and vertical direction and less than two degrees in angle deviation are allowed for a coupling loss below 2 dB. Presently such close tolerances can only be met by gluing or soldering both components on separate base plates and combining them via piezoactivated alignment monitoring the output of the circuit and then gluing them using UV-hardening epoxies. Such a procedure is not very economical and not useful for mass applications. This paper presents the principle and realization of a silicon micro-optical bench for laser-fiber-coupling, which avoids the above mentioned disadvantages. The micro-optical bench is realized using well controlled plasma etching processes to transfer the guiding patterns for the laser and the fiber into the silicon substrate, keeping geometry tolerances below +/- 0.5 micrometers in lateral and vertical direction. Mounting the laser diode by means of a self-aligned soldering process, an additional contribution to the precise alignment of the laser is further improved.

Walking Drosophila align with the e-vector of linearly polarized light through directed modulation of angular acceleration

PubMed Central

Velez, Mariel M.; Wernet, Mathias F.; Clark, Damon A.

2014-01-01

Understanding the mechanisms that link sensory stimuli to animal behavior is a central challenge in neuroscience. The quantitative description of behavioral responses to defined stimuli has led to a rich understanding of different behavioral strategies in many species. One important navigational cue perceived by many vertebrates and insects is the e-vector orientation of linearly polarized light. Drosophila manifests an innate orientation response to this cue (‘polarotaxis’), aligning its body axis with the e-vector field. We have established a population-based behavioral paradigm for the genetic dissection of neural circuits guiding polarotaxis to both celestial as well as reflected polarized stimuli. However, the behavioral mechanisms by which flies align with a linearly polarized stimulus remain unknown. Here, we present a detailed quantitative description of Drosophila polarotaxis, systematically measuring behavioral parameters that are modulated by the stimulus. We show that angular acceleration is modulated during alignment, and this single parameter may be sufficient for alignment. Furthermore, using monocular deprivation, we show that each eye is necessary for modulating turns in the ipsilateral direction. This analysis lays the foundation for understanding how neural circuits guide these important visual behaviors. PMID:24810784

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

Growth of Vertically Aligned ZnO Nanowire Arrays Using Bilayered Metal Catalysts

DTIC Science & Technology

2012-01-01

12] J. P. Liu, C. X. Guo, C. M. Li et al., “Carbon-decorated ZnO nanowire array: a novel platform for direct electrochemistry of enzymes and...cited. Vertically aligned, high-density ZnO nanowires (NWs) were grown for the first time on c-plane sapphire using binary alloys of Ni/Au or Cu/Au as...deleterious to the ZnO NW array growth. Significant improvement of the Au adhesion on the substrate was noted, opening the potential for direct

Perceptually aligning apical frequency regions leads to more binaural fusion of speech in a cochlear implant simulation.

PubMed

Staisloff, Hannah E; Lee, Daniel H; Aronoff, Justin M

2016-07-01

For bilateral cochlear implant users, the left and right arrays are typically not physically aligned, resulting in a degradation of binaural fusion, which can be detrimental to binaural abilities. Perceptually aligning the two arrays can be accomplished by disabling electrodes in one ear that do not have a perceptually corresponding electrode in the other side. However, disabling electrodes at the edges of the array will cause compression of the input frequency range into a smaller cochlear extent, which may result in reduced spectral resolution. An alternative approach to overcome this mismatch would be to only align one edge of the array. By aligning either only the apical or basal end of the arrays, fewer electrodes would be disabled, potentially causing less reduction in spectral resolution. The goal of this study was to determine the relative effect of aligning either the basal or apical end of the electrode with regards to binaural fusion. A vocoder was used to simulate cochlear implant listening conditions in normal hearing listeners. Speech signals were vocoded such that the two ears were either predominantly aligned at only the basal or apical end of the simulated arrays. The experiment was then repeated with a spectrally inverted vocoder to determine whether the detrimental effects on fusion were related to the spectral-temporal characteristics of the stimuli or the location in the cochlea where the misalignment occurred. In Experiment 1, aligning the basal portion of the simulated arrays led to significantly less binaural fusion than aligning the apical portions of the simulated array. However, when the input was spectrally inverted, aligning the apical portion of the simulated array led to significantly less binaural fusion than aligning the basal portions of the simulated arrays. These results suggest that, for speech, with its predominantly low frequency spectral-temporal modulations, it is more important to perceptually align the apical portion of the array to better preserve binaural fusion. By partially aligning these arrays, cochlear implant users could potentially increase their ability to fuse speech sounds presented to the two ears while maximizing spectral resolution. Copyright © 2016 Elsevier B.V. All rights reserved.

Note: A simple sample transfer alignment for ultra-high vacuum systems.

PubMed

Tamtögl, A; Carter, E A; Ward, D J; Avidor, N; Kole, P R; Jardine, A P; Allison, W

2016-06-01

The alignment of ultra-high-vacuum sample transfer systems can be problematic when there is no direct line of sight to assist the user. We present the design of a simple and cheap system which greatly simplifies the alignment of sample transfer devices. Our method is based on the adaptation of a commercial digital camera which provides live views from within the vacuum chamber. The images of the camera are further processed using an image recognition and processing code which determines any misalignments and reports them to the user. Installation has proven to be extremely useful in order to align the sample with respect to the transfer mechanism. Furthermore, the alignment software can be easily adapted for other systems.

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.

Measuring Alignments between Galaxies and the Cosmic Web at z ˜ 2-3 Using IGM Tomography

NASA Astrophysics Data System (ADS)

Krolewski, Alex; Lee, Khee-Gan; Lukić, Zarija; White, Martin

2017-03-01

Many galaxy formation models predict alignments between galaxy spin and the cosmic web (I.e., directions of filaments and sheets), leading to an intrinsic alignment between galaxies that creates a systematic error in weak-lensing measurements. These effects are often predicted to be stronger at high redshifts (z ≳ 1) that are inaccessible to massive galaxy surveys on foreseeable instrumentation, but IGM tomography of the Lyα forest from closely spaced quasars and galaxies is starting to measure the z ˜ 2-3 cosmic web with requisite fidelity. Using mock surveys from hydrodynamical simulations, we examine the utility of this technique, in conjunction with coeval galaxy samples, to measure alignment between galaxies and the cosmic web at z ˜ 2.5. We show that IGM tomography surveys with ≲5 h -1 Mpc sightline spacing can accurately recover the eigenvectors of the tidal tensor, which we use to define the directions of the cosmic web. For galaxy spins and shapes, we use a model parameterized by the alignment strength, {{Δ }}< \\cos θ > , with respect to the tidal tensor eigenvectors from the underlying density field, and also consider observational effects such as errors in the galaxy position angle, inclination, and redshift. Measurements using the upcoming ˜1 deg2 CLAMATO tomographic survey and 600 coeval zCOSMOS-Deep galaxies should place 3σ limits on extreme alignment models with {{Δ }}< \\cos θ > ˜ 0.1, but much larger surveys encompassing >10,000 galaxies, such as Subaru PFS, will be required to constrain models with {{Δ }}< \\cos θ > ˜ 0.03. These measurements will constrain models of galaxy-cosmic web alignment and test tidal torque theory at z ˜ 2, improving our understanding of the physics of intrinsic alignments.

Measuring Alignments between Galaxies and the Cosmic Web at z ~ 2–3 Using IGM Tomography

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

Krolewski, Alex; Lee, Khee-Gan; Luki?, Zarija

Many galaxy formation models predict alignments between galaxy spin and the cosmic web (i.e., directions of filaments and sheets), leading to an intrinsic alignment between galaxies that creates a systematic error in weak-lensing measurements. These effects are often predicted to be stronger at high redshifts (z ≳ 1) that are inaccessible to massive galaxy surveys on foreseeable instrumentation, but IGM tomography of the Lyα forest from closely spaced quasars and galaxies is starting to measure the z ~ 2-3 cosmic web with requisite fidelity. Using mock surveys from hydrodynamical simulations, we examine the utility of this technique, in conjunction withmore » coeval galaxy samples, to measure alignment between galaxies and the cosmic web at z ~ 2.5. We show that IGM tomography surveys with ≲ 5 h -1 Mpc sightline spacing can accurately recover the eigenvectors of the tidal tensor, which we use to define the directions of the cosmic web. For galaxy spins and shapes, we use a model parameterized by the alignment strength, Δ (cos θ), with respect to the tidal tensor eigenvectors from the underlying density field, and also consider observational effects such as errors in the galaxy position angle, inclination, and redshift. Measurements using the upcoming ~ 1 deg 2 CLAMATO tomographic survey and 600 coeval zCOSMOS-Deep galaxies should place 3σ limits on extreme alignment models with Δ (cos θ) ~ 0.1, but much larger surveys encompassing > 10,000 galaxies, such as Subaru PFS, will be required to constrain models with Δ (cos θ) ~ 0.3. These measurements will constrain models of galaxy-cosmic web alignment and test tidal torque theory at z ~ 2, improving our understanding of the physics of intrinsic alignments.« less

Measuring Alignments between Galaxies and the Cosmic Web at z ~ 2–3 Using IGM Tomography

DOE PAGES

Krolewski, Alex; Lee, Khee-Gan; Luki?, Zarija; ...

2017-02-28

Many galaxy formation models predict alignments between galaxy spin and the cosmic web (i.e., directions of filaments and sheets), leading to an intrinsic alignment between galaxies that creates a systematic error in weak-lensing measurements. These effects are often predicted to be stronger at high redshifts (z ≳ 1) that are inaccessible to massive galaxy surveys on foreseeable instrumentation, but IGM tomography of the Lyα forest from closely spaced quasars and galaxies is starting to measure the z ~ 2-3 cosmic web with requisite fidelity. Using mock surveys from hydrodynamical simulations, we examine the utility of this technique, in conjunction withmore » coeval galaxy samples, to measure alignment between galaxies and the cosmic web at z ~ 2.5. We show that IGM tomography surveys with ≲ 5 h -1 Mpc sightline spacing can accurately recover the eigenvectors of the tidal tensor, which we use to define the directions of the cosmic web. For galaxy spins and shapes, we use a model parameterized by the alignment strength, Δ (cos θ), with respect to the tidal tensor eigenvectors from the underlying density field, and also consider observational effects such as errors in the galaxy position angle, inclination, and redshift. Measurements using the upcoming ~ 1 deg 2 CLAMATO tomographic survey and 600 coeval zCOSMOS-Deep galaxies should place 3σ limits on extreme alignment models with Δ (cos θ) ~ 0.1, but much larger surveys encompassing > 10,000 galaxies, such as Subaru PFS, will be required to constrain models with Δ (cos θ) ~ 0.3. These measurements will constrain models of galaxy-cosmic web alignment and test tidal torque theory at z ~ 2, improving our understanding of the physics of intrinsic alignments.« less

Alignment hierarchies: engineering architecture from the nanometre to the micrometre scale.

PubMed

Kureshi, Alvena; Cheema, Umber; Alekseeva, Tijna; Cambrey, Alison; Brown, Robert

2010-12-06

Natural tissues are built of metabolites, soluble proteins and solid extracellular matrix components (largely fibrils) together with cells. These are configured in highly organized hierarchies of structure across length scales from nanometre to millimetre, with alignments that are dominated by anisotropies in their fibrillar matrix. If we are to successfully engineer tissues, these hierarchies need to be mimicked with an understanding of the interaction between them. In particular, the movement of different elements of the tissue (e.g. molecules, cells and bulk fluids) is controlled by matrix structures at distinct scales. We present three novel systems to introduce alignment of collagen fibrils, cells and growth factor gradients within a three-dimensional collagen scaffold using fluid flow, embossing and layering of construct. Importantly, these can be seen as different parts of the same hierarchy of three-dimensional structure, as they are all formed into dense collagen gels. Fluid flow aligns collagen fibrils at the nanoscale, embossed topographical features provide alignment cues at the microscale and introducing layered configuration to three-dimensional collagen scaffolds provides microscale- and mesoscale-aligned pathways for protein factor delivery as well as barriers to confine protein diffusion to specific spatial directions. These seemingly separate methods can be employed to increase complexity of simple extracellular matrix scaffolds, providing insight into new approaches to directly fabricate complex physical and chemical cues at different hierarchical scales, similar to those in natural tissues.

Mechanical Design, Simulation, and Testing of Self-Aligning Gaussian Telescope and Stand for ITER LFS Reflectometer Diagnostic

NASA Astrophysics Data System (ADS)

Broughton, Rachel; Gomez, Michael; Zolfaghari, Ali; Morris, Lewis

2016-10-01

A self-aligning Gaussian telescope has been designed to compensate for the effect of movement in the ITER vacuum vessel on the transmission line. The purpose of the setup is to couple microwaves into and out of the vessel across the vacuum windows while allowing for both slow movements of the vessel, due to thermal growth, and rapid movements, due to vibrations and disruptions. Additionally, a test stand has been designed specifically to hold this telescope in order to imitate these movements. Consequently, this will allow for the assessment of the efficacy in applying the self-aligning Gaussian telescope approach. The motions of the test stand, as well as the stress on the telescope mechanism, have been virtually simulated using ANSYS workbench. A prototype of this test stand and self-aligning telescope will be built using a combination of custom machined parts and ordered parts. The completed mechanism will be tested at the lab in four different ways: slow single- and multi-direction movements, rapid multi-direction movement, functional laser alignment and self-aligning tests, and natural frequency tests. Once the prototype successfully passes all requirements, it will be tested with microwaves in the LFSR transmission line test stand at General Atomics. This work is supported by US DOE Contract No. DE-AC02-09CH11466.

Inner Core Anisotropy in Attenuation

NASA Astrophysics Data System (ADS)

Yu, W.; Wen, L.

2004-12-01

It is now well established that the compressional velocity in the Earth's inner core varies in both direction and geographic location. The compressional waves travel faster along the polar directions than along the equatorial directions. Such polar-equatorial difference is interpreted as a result of inner core anisotropy in velocity (with a magnitude of about 3%) and such anisotropy appears to be stronger in the ``western hemisphere" (180oW -40oE) than in the ``eastern hemisphere" (40oE-180oE). Along the equatorial paths, the compressional velocity also exhibits a hemispheric pattern with the eastern hemisphere being about 1% higher than the western hemisphere. Possible explanations for the causes of the velocity in anisotropy and the hemispheric difference in velocity along the equatorial paths include different geometric inclusions of melt or different alignments of iron crystals which are known to be anisotropic in velocities. Here, we report an observation of ubiquitous correlation between small (large) amplitude and fast (slow) travel time of the PKIKP waves sampling the top 300 km of the inner core. We study this correlation by jointly analyzing the differential travel times and amplitude ratios of the PKiKP-PKIKP and the PKPbc-PKIKP phases recorded by the Global Seismographic Network (1990-2001), various regional seismic networks (BANJO, BLSP, FREESIA, GEOFON, GEOSCOPE, Kazakhstan, Kyrgyz, MEDNET, and OHP), and several PASSCAL Networks deployed in Alaska and Antarctica (XE: 1999-2001, XF: 1995-1996, and YI: 1998-1999). Our dataset consists of 310 PKiKP-PKIKP and 240 PKPbc-PKIKP phases, selected from a total of more than 16,000 observations. PKIKP waves exhibit relatively smaller amplitudes for those sampling the eastern hemisphere along the equatorial paths and even smaller amplitudes for those sampling the polar paths in the western hemisphere. One simple explanation for the velocity-attenuation relation is that the inner core is anisotropic in attenuation and the direction of high attenuation correlates with that of high P velocity. Different anisotropic behaviors in velocity and attenuation can be best explained by different alignments of iron crystals under the hypothesis that iron crystals are anisotropic in both velocity and attenuation and their axes of high P velocity correspond to those of high attenuation.

Using Multimedia Metadata to Improve Network Efficiency

DTIC Science & Technology

2012-09-01

the north-aligned bounding box. When compared using all angular variations for the direction-of-travel-aligned 3:4 aspect ratio bounding box, the...programs that run the experiment are written in Java . The experiment consists of two distinct programs that communicate via Java sockets (TCP). 1

'Fixed-axis' magnetic orientation by an amphibian: non-shoreward-directed compass orientation, misdirected homing or positioning a magnetite-based map detector in a consistent alignment relative to the magnetic field?

PubMed

Phillips, John B; Borland, S Chris; Freake, Michael J; Brassart, Jacques; Kirschvink, Joseph L

2002-12-01

Experiments were carried out to investigate the earlier prediction that prolonged exposure to long-wavelength (>500 nm) light would eliminate homing orientation by male Eastern red-spotted newts Notophthalmus viridescens. As in previous experiments, controls held in outdoor tanks under natural lighting conditions and tested in a visually uniform indoor arena under full-spectrum light were homeward oriented. As predicted, however, newts held under long-wavelength light and tested under either full-spectrum or long-wavelength light (>500 nm) failed to show consistent homeward orientation. The newts also did not orient with respect to the shore directions in the outdoor tanks in which they were held prior to testing. Unexpectedly, however, the newts exhibited bimodal orientation along a more-or-less 'fixed' north-northeast-south-southwest magnetic axis. The orientation exhibited by newts tested under full-spectrum light was indistinguishable from that of newts tested under long-wavelength light, although these two wavelength conditions have previously been shown to differentially affect both shoreward compass orientation and homing orientation. To investigate the possibility that the 'fixed-axis' response of the newts was mediated by a magnetoreception mechanism involving single-domain particles of magnetite, natural remanent magnetism (NRM) was measured from a subset of the newts. The distribution of NRM alignments with respect to the head-body axis of the newts was indistinguishable from random. Furthermore, there was no consistent relationship between the NRM of individual newts and their directional response in the overall sample. However, under full-spectrum, but not long-wavelength, light, the alignment of the NRM when the newts reached the 20 cm radius criterion circle in the indoor testing arena (estimated by adding the NRM alignment measured from each newt to its magnetic bearing) was non-randomly distributed. These findings are consistent with the earlier suggestion that homing newts use the light-dependent magnetic compass to align a magnetite-based 'map detector' when obtaining the precise measurements necessary to derive map information from the magnetic field. However, aligning the putative map detector does not explain the fixed-axis response of newts tested under long-wavelength light. Preliminary evidence suggests that, in the absence of reliable directional information from the magnetic compass (caused by the 90 degrees rotation of the response of the magnetic compass under long-wavelength light), newts may resort to a systematic sampling strategy to identify alignment(s) of the map detector that yields reliable magnetic field measurements.

Wellbore inertial directional surveying system

DOEpatents

Andreas, R.D.; Heck, G.M.; Kohler, S.M.; Watts, A.C.

1982-09-08

A wellbore inertial directional surveying system for providing a complete directional survey of an oil or gas well borehole to determine the displacement in all three directions of the borehole path relative to the well head at the surface. The information generated by the present invention is especially useful when numerous wells are drilled to different geographical targets from a single offshore platform. Accurate knowledge of the path of the borehole allows proper well spacing and provides assurance that target formations are reached. The tool is lowered down into a borehole on an electrical cable. A computer positioned on the surface communicates with the tool via the cable. The tool contains a sensor block which is supported on a single gimbal, the rotation axis of which is aligned with the cylinder axis of the tool and, correspondingly, the borehole. The gyroscope measurement of the sensor block rotation is used in a null-seeking servo loop which essentially prevents rotation of the sensor block about the gimbal axis. Angular rates of the sensor block about axes which are perpendicular to te gimbal axis are measured by gyroscopes in a manner similar to a strapped-down arrangement. Three accelerometers provide acceleration information as the tool is lowered within the borehole. The uphole computer derives position information based upon acceleration information and angular rate information. Kalman estimation techniques are used to compensate for system errors. 25 figures.

Wellbore inertial directional surveying system

DOEpatents

Andreas, Ronald D.; Heck, G. Michael; Kohler, Stewart M.; Watts, Alfred C.

1991-01-01

A wellbore inertial directional surveying system for providing a complete directional survey of an oil or gas well borehole to determine the displacement in all three directions of the borehole path relative to the well head at the surface. The information generated by the present invention is especially useful when numerous wells are drilled to different geographical targets from a single off-shore platform. Accurate knowledge of the path of the borehole allows proper well spacing and provides assurance that target formations are reached. The tool is lowered down into a borehole on the electrical cable. A computer positioned on the surface communicates with the tool via the cable. The tool contains a sensor block which is supported on a single gimbal, the rotation axis of which is aligned with the cylinder axis of the tool and, correspondingly, the borehole. The gyroscope measurement of the sensor block rotation is used in a null-seeking servo loop which essentially prevents rotation of the sensor block aboutthe gimbal axis. Angular rates of the sensor block about axes which are perpendicular to the gimbal axis are measured by gyroscopes in a manner similar to a strapped-down arrangement. Three accelerometers provide acceleration information as the tool is lowered within the borehole. The uphole computer derives position information based upon acceleration information and anular rate information. Kalman estimation techniques are used to compensate for system errors.

Flavor gauge models below the Fermi scale

DOE PAGES

Babu, K. S.; Friedland, A.; Machado, P. A. N.; ...

2017-12-18

The mass and weak interaction eigenstates for the quarks of the third generation are very well aligned, an empirical fact for which the Standard Model offers no explanation. We explore the possibility that this alignment is due to an additional gauge symmetry in the third generation. Specifically, we construct and analyze an explicit, renormalizable model with a gauge boson,more » $X$, corresponding to the $B-L$ symmetry of the third family. Having a relatively light (in the MeV to multi-GeV range), flavor-nonuniversal gauge boson results in a variety of constraints from different sources. By systematically analyzing 20 different constraints, we identify the most sensitive probes: kaon, $B^+$, $D^+$ and Upsilon decays, $$D-\\bar{D}^0$$ mixing, atomic parity violation, and neutrino scattering and oscillations. For the new gauge coupling $$g_X$$ in the range $$(10^{-2} - 10^{-4})$$ the model is shown to be consistent with the data. Possible ways of testing the model in $b$ physics, top and $Z$ decays, direct collider production and neutrino oscillation experiments, where one can observe nonstandard matter effects, are outlined. The choice of leptons to carry the new force is ambiguous, resulting in additional phenomenological implications, such as non-universality in semileptonic bottom decays. In conclusion, the proposed framework provides interesting connections between neutrino oscillations, flavor and collider physics.« less

Catalyst-free fabrication of novel ZnO/CuO core-Shell nanowires heterojunction: Controlled growth, structural and optoelectronic properties

NASA Astrophysics Data System (ADS)

Khan, Muhammad Arif; Wahab, Yussof; Muhammad, Rosnita; Tahir, Muhammad; Sakrani, Samsudi

2018-03-01

Development of controlled growth and vertically aligned ZnO/CuO core-shell heterojunction nanowires (NWs) with large area by a catalyst free vapor deposition and oxidation approach has been investigated. Structural characterization reveals successful fabrication of a core ZnO nanowire having single crystalline hexagonal wurtzite structure along [002] direction and CuO nanostructure shell with thickness (8-10 nm) having polycrystalline monoclinic structure. The optical property analysis suggests that the reflectance spectrum of ZnO/CuO heterostructure nanowires is decreased by 18% in the visible range, which correspondingly shows high absorption in this region as compared to pristine ZnO nanowires. The current-voltage (I-V) characteristics of core-shell heterojunction nanowires measured by conductive atomic force microscopy (C-AFM) shows excellent rectifying behavior, which indicates the characteristics of a good p-n junction. The high-resolution transmission electron microscopy (HRTEM) has confirmed the sharp junction interface between the core-shell heterojunction nanowire arrays. The valence band offset and conduction band offset at ZnO/CuO heterointerfaces are measured to be 2.4 ± 0.05 and 0.23 ± 0.005 eV respectively, using X-ray photoelectron spectroscopy (XPS) and a type-II band alignment structure is found. The results of this study contribute to the development of new advanced device heterostructures for solar energy conversion and optoelectronics applications.

Flavor gauge models below the Fermi scale

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

Babu, K. S.; Friedland, A.; Machado, P. A. N.

The mass and weak interaction eigenstates for the quarks of the third generation are very well aligned, an empirical fact for which the Standard Model offers no explanation. We explore the possibility that this alignment is due to an additional gauge symmetry in the third generation. Specifically, we construct and analyze an explicit, renormalizable model with a gauge boson,more » $X$, corresponding to the $B-L$ symmetry of the third family. Having a relatively light (in the MeV to multi-GeV range), flavor-nonuniversal gauge boson results in a variety of constraints from different sources. By systematically analyzing 20 different constraints, we identify the most sensitive probes: kaon, $B^+$, $D^+$ and Upsilon decays, $$D-\\bar{D}^0$$ mixing, atomic parity violation, and neutrino scattering and oscillations. For the new gauge coupling $$g_X$$ in the range $$(10^{-2} - 10^{-4})$$ the model is shown to be consistent with the data. Possible ways of testing the model in $b$ physics, top and $Z$ decays, direct collider production and neutrino oscillation experiments, where one can observe nonstandard matter effects, are outlined. The choice of leptons to carry the new force is ambiguous, resulting in additional phenomenological implications, such as non-universality in semileptonic bottom decays. In conclusion, the proposed framework provides interesting connections between neutrino oscillations, flavor and collider physics.« less

Kirkpatrick-Baez microscope for hard X-ray imaging of fast ignition experiments.

PubMed

Friesen, H; Tiedje, H F; Hey, D S; Mo, M Z; Beaudry, A; Fedosejevs, R; Tsui, Y Y; Mackinnon, A; McLean, H S; Patel, P K

2013-02-01

A Kirkpatrick-Baez X-ray microscope has been developed for use on the Titan laser facility at the Lawrence Livermore National Laboratory in Fast Ignition experiments. It was developed as a broadband alternative to narrow band Bragg crystal imagers for imaging Kα emission from tracer layers. A re-entrant design is employed which allows for alignment from outside the chamber. The mirrors are coated with Pt and operate at a grazing incident angle of 0.5° providing higher resolution than an equal brightness pinhole and sufficient bandwidth to image thermally shifted characteristic Kα emission from heated Cu tracer layers in Fast Ignition experiments. The superpolished substrates (<1 Å rms roughness) had a final visible wavelength roughness of 1.7 Å after coating, and exhibited a reflectivity corresponding to an X-ray wavelength roughness of 7 ± 1 Å. A unique feature of this design is that during experiments, the unfiltered direct signal along with the one-dimensional reflections are retained on the detector in order to enable a live indication of alignment and incident angle. The broad spectral window from 4 to 9 keV enables simultaneous observation of emission from several spectral regions of interest, which has been demonstrated to be particularly useful for cone-wire targets. An experimentally measured resolution of 15 μm has been obtained at the center of the field of view.

Structure of High Latitude Currents in Magnetosphere-Ionosphere Models

NASA Astrophysics Data System (ADS)

Wiltberger, M.; Rigler, E. J.; Merkin, V.; Lyon, J. G.

2017-03-01

Using three resolutions of the Lyon-Fedder-Mobarry global magnetosphere-ionosphere model (LFM) and the Weimer 2005 empirical model we examine the structure of the high latitude field-aligned current patterns. Each resolution was run for the entire Whole Heliosphere Interval which contained two high speed solar wind streams and modest interplanetary magnetic field strengths. Average states of the field-aligned current (FAC) patterns for 8 interplanetary magnetic field clock angle directions are computed using data from these runs. Generally speaking the patterns obtained agree well with results obtained from the Weimer 2005 computing using the solar wind and IMF conditions that correspond to each bin. As the simulation resolution increases the currents become more intense and narrow. A machine learning analysis of the FAC patterns shows that the ratio of Region 1 (R1) to Region 2 (R2) currents decreases as the simulation resolution increases. This brings the simulation results into better agreement with observational predictions and the Weimer 2005 model results. The increase in R2 current strengths also results in the cross polar cap potential (CPCP) pattern being concentrated in higher latitudes. Current-voltage relationships between the R1 and CPCP are quite similar at the higher resolution indicating the simulation is converging on a common solution. We conclude that LFM simulations are capable of reproducing the statistical features of FAC patterns.

Anisotropic thermal conductivity in epoxy-bonded magnetocaloric composites

NASA Astrophysics Data System (ADS)

Weise, Bruno; Sellschopp, Kai; Bierdel, Marius; Funk, Alexander; Bobeth, Manfred; Krautz, Maria; Waske, Anja

2016-09-01

Thermal management is one of the crucial issues in the development of magnetocaloric refrigeration technology for application. In order to ensure optimal exploitation of the materials "primary" properties, such as entropy change and temperature lift, thermal properties (and other "secondary" properties) play an important role. In magnetocaloric composites, which show an increased cycling stability in comparison to their bulk counterparts, thermal properties are strongly determined by the geometric arrangement of the corresponding components. In the first part of this paper, the inner structure of a polymer-bonded La(Fe, Co, Si)13-composite was studied by X-ray computed tomography. Based on this 3D data, a numerical study along all three spatial directions revealed anisotropic thermal conductivity of the composite: Due to the preparation process, the long-axis of the magnetocaloric particles is aligned along the xy plane which is why the in-plane thermal conductivity is larger than the thermal conductivity along the z-axis. Further, the study is expanded to a second aspect devoted to the influence of particle distribution and alignment within the polymer matrix. Based on an equivalent ellipsoids model to describe the inner structure of the composite, numerical simulation of the thermal conductivity in different particle arrangements and orientation distributions were performed. This paper evaluates the possibilities of microstructural design for inducing and adjusting anisotropic thermal conductivity in magnetocaloric composites.

Planform structure and heat transfer in turbulent free convection over horizontal surfaces

NASA Astrophysics Data System (ADS)

Theerthan, S. Ananda; Arakeri, Jaywant H.

2000-04-01

This paper deals with turbulent free convection in a horizontal fluid layer above a heated surface. Experiments have been carried out on a heated surface to obtain and analyze the planform structure and the heat transfer under different conditions. Water is the working fluid and the range of flux Rayleigh numbers (Ra) covered is 3×107-2×1010. The different conditions correspond to Rayleigh-Bénard convection, convection with either the top water surface open to atmosphere or covered with an insulating plate, and with an imposed external flow on the heated boundary. Without the external flow the planform is one of randomly oriented line plumes. At large Rayleigh number Ra and small aspect ratio (AR), these line plumes seem to align along the diagonal, presumably due to a large scale flow. The side views show inclined dyelines, again indicating a large scale flow. When the external flow is imposed, the line plumes clearly align in the direction of external flow. The nondimensional average plume spacing, Raλ1/3, varies between 40 and 90. The heat transfer rate, for all the experiments conducted, represented as RaδT-1/3, where δT is the conduction layer thickness, varies only between 0.1-0.2, showing that in turbulent convection the heat transfer rates are similar under the different conditions.

Individual Differences in the Alignment of Structural and Functional Markers of the V5/MT Complex in Primates

PubMed Central

Large, I.; Bridge, H.; Ahmed, B.; Clare, S.; Kolasinski, J.; Lam, W. W.; Miller, K. L.; Dyrby, T. B.; Parker, A. J.; Smith, J. E. T.; Daubney, G.; Sallet, J.; Bell, A. H.; Krug, K.

2016-01-01

Extrastriate visual area V5/MT in primates is defined both structurally by myeloarchitecture and functionally by distinct responses to visual motion. Myelination is directly identifiable from postmortem histology but also indirectly by image contrast with structural magnetic resonance imaging (sMRI). First, we compared the identification of V5/MT using both sMRI and histology in Rhesus macaques. A section-by-section comparison of histological slices with in vivo and postmortem sMRI for the same block of cortical tissue showed precise correspondence in localizing heavy myelination for V5/MT and neighboring MST. Thus, sMRI in macaques accurately locates histologically defined myelin within areas known to be motion selective. Second, we investigated the functionally homologous human motion complex (hMT+) using high-resolution in vivo imaging. Humans showed considerable intersubject variability in hMT+ location, when defined with myelin-weighted sMRI signals to reveal structure. When comparing sMRI markers to functional MRI in response to moving stimuli, a region of high myelin signal was generally located within the hMT+ complex. However, there were considerable differences in the alignment of structural and functional markers between individuals. Our results suggest that variation in area identification for hMT+ based on structural and functional markers reflects individual differences in human regional brain architecture. PMID:27371764

Structure of high latitude currents in global magnetospheric-ionospheric models

USGS Publications Warehouse

Wiltberger, M; Rigler, E. J.; Merkin, V; Lyon, J. G

2016-01-01

Using three resolutions of the Lyon-Fedder-Mobarry global magnetosphere-ionosphere model (LFM) and the Weimer 2005 empirical model we examine the structure of the high latitude field-aligned current patterns. Each resolution was run for the entire Whole Heliosphere Interval which contained two high speed solar wind streams and modest interplanetary magnetic field strengths. Average states of the field-aligned current (FAC) patterns for 8 interplanetary magnetic field clock angle directions are computed using data from these runs. Generally speaking the patterns obtained agree well with results obtained from the Weimer 2005 computing using the solar wind and IMF conditions that correspond to each bin. As the simulation resolution increases the currents become more intense and narrow. A machine learning analysis of the FAC patterns shows that the ratio of Region 1 (R1) to Region 2 (R2) currents decreases as the simulation resolution increases. This brings the simulation results into better agreement with observational predictions and the Weimer 2005 model results. The increase in R2 current strengths also results in the cross polar cap potential (CPCP) pattern being concentrated in higher latitudes. Current-voltage relationships between the R1 and CPCP are quite similar at the higher resolution indicating the simulation is converging on a common solution. We conclude that LFM simulations are capable of reproducing the statistical features of FAC patterns.

A rib-specific multimodal registration algorithm for fused unfolded rib visualization using PET/CT

NASA Astrophysics Data System (ADS)

Kaftan, Jens N.; Kopaczka, Marcin; Wimmer, Andreas; Platsch, Günther; Declerck, Jérôme

2014-03-01

Respiratory motion affects the alignment of PET and CT volumes from PET/CT examinations in a non-rigid manner. This becomes particularly apparent if reviewing fine anatomical structures such as ribs when assessing bone metastases, which frequently occur in many advanced cancers. To make this routine diagnostic task more efficient, a fused unfolded rib visualization for 18F-NaF PET/CT is presented. It allows to review the whole rib cage in a single image. This advanced visualization is enabled by a novel rib-specific registration algorithm that rigidly optimizes the local alignment of each individual rib in both modalities based on a matched filter response function. More specifically, rib centerlines are automatically extracted from CT and subsequently individually aligned to the corresponding bone-specific PET rib uptake pattern. The proposed method has been validated on 20 PET/CT scans acquired at different clinical sites. It has been demonstrated that the presented rib- specific registration method significantly improves the rib alignment without having to run complex deformable registration algorithms. At the same time, it guarantees that rib lesions are not further deformed, which may otherwise affect quantitative measurements such as SUVs. Considering clinically relevant distance thresholds, the centerline portion with good alignment compared to the ground truth improved from 60:6% to 86:7% after registration while approximately 98% can be still considered as acceptably aligned.

Optimal Alignment of Structures for Finite and Periodic Systems.

PubMed

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

2017-10-10

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

Numerical Upscaling of Solute Transport in Fractured Porous Media Based on Flow Aligned Blocks

NASA Astrophysics Data System (ADS)

Leube, P.; Nowak, W.; Sanchez-Vila, X.

2013-12-01

High-contrast or fractured-porous media (FPM) pose one of the largest unresolved challenges for simulating large hydrogeological systems. The high contrast in advective transport between fast conduits and low-permeability rock matrix, including complex mass transfer processes, leads to the typical complex characteristics of early bulk arrivals and long tailings. Adequate direct representation of FPM requires enormous numerical resolutions. For large scales, e.g. the catchment scale, and when allowing for uncertainty in the fracture network architecture or in matrix properties, computational costs quickly reach an intractable level. In such cases, multi-scale simulation techniques have become useful tools. They allow decreasing the complexity of models by aggregating and transferring their parameters to coarser scales and so drastically reduce the computational costs. However, these advantages come at a loss of detail and accuracy. In this work, we develop and test a new multi-scale or upscaled modeling approach based on block upscaling. The novelty is that individual blocks are defined by and aligned with the local flow coordinates. We choose a multi-rate mass transfer (MRMT) model to represent the remaining sub-block non-Fickian behavior within these blocks on the coarse scale. To make the scale transition simple and to save computational costs, we capture sub-block features by temporal moments (TM) of block-wise particle arrival times to be matched with the MRMT model. By predicting spatial mass distributions of injected tracers in a synthetic test scenario, our coarse-scale solution matches reasonably well with the corresponding fine-scale reference solution. For predicting higher TM-orders (such as arrival time and effective dispersion), the prediction accuracy steadily decreases. This is compensated to some extent by the MRMT model. If the MRMT model becomes too complex, it loses its effect. We also found that prediction accuracy is sensitive to the choice of the effective dispersion coefficients and on the block resolution. A key advantage of the flow-aligned blocks is that the small-scale velocity field is reproduced quite accurately on the block-scale through their flow alignment. Thus, the block-scale transverse dispersivities remain in the similar magnitude as local ones, and they do not have to represent macroscopic uncertainty. Also, the flow-aligned blocks minimize numerical dispersion when solving the large-scale transport problem.

An experimental approach in revisiting the magnetic orientation of cattle.

PubMed

Weijers, Debby; Hemerik, Lia; Heitkönig, Ignas M A

2018-01-01

In response to the increasing number of observational studies on an apparent south-north orientation in non-homing, non-migrating terrestrial mammals, we experimentally tested the alignment hypothesis using strong neodymium magnets on the resting orientation of individual cattle in Portugal. Contrary to the hypothesis, the 34 cows in the experiment showed no directional preference, neither with, nor without a strong neodymium magnet fixed to their collar. The concurrently performed 2,428 daytime observations-excluding the hottest part of the day-of 659 resting individual cattle did not show a south-north alignment when at rest either. The preferred compass orientation of these cows was on average 130 degrees from the magnetic north (i.e., south east). Cow compass orientation correlated significantly with sun direction, but not with wind direction. In as far as we can determine, this is the first experimental test on magnetic orientation in larger, non-homing, non-migrating mammals. These experimental and observational findings do not support previously published suggestions on the magnetic south-north alignment in these mammals.

Higher Order Lagrange Finite Elements In M3D

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

J. Chen; H.R. Strauss; S.C. Jardin

The M3D code has been using linear finite elements to represent multilevel MHD on 2-D poloidal planes. Triangular higher order elements, up to third order, are constructed here in order to provide M3D the capability to solve highly anisotropic transport problems. It is found that higher order elements are essential to resolve the thin transition layer characteristic of the anisotropic transport equation, particularly when the strong anisotropic direction is not aligned with one of the Cartesian coordinates. The transition layer is measured by the profile width, which is zero for infinite anisotropy. It is shown that only higher order schemesmore » have the ability to make this layer converge towards zero when the anisotropy gets stronger and stronger. Two cases are considered. One has the strong transport direction partially aligned with one of the element edges, the other doesn't have any alignment. Both cases have the strong transport direction misaligned with the grid line by some angles.« less

Convection of wall shear stress events in a turbulent boundary layer

NASA Astrophysics Data System (ADS)

Pabon, Rommel; Mills, David; Ukeiley, Lawrence; Sheplak, Mark

2017-11-01

The fluctuating wall shear stress is measured in a zero pressure gradient turbulent boundary layer of Reτ 1700 simultaneously with velocity measurements using either hot-wire anemometry or particle image velocimetry. These experiments elucidate the patterns of large scale structures in a single point measurement of the wall shear stress, as well as their convection velocity at the wall. The wall shear stress sensor is a CS-A05 one-dimensional capacitice floating element from Interdisciplinary Consulting Corp. It has a nominal bandwidth from DC to 5 kHz and a floating element size of 1 mm in the principal sensing direction (streamwise) and 0.2 mm in the cross direction (spanwise), allowing the large scales to be well resolved in the current experimental conditions. In addition, a two sensor array of CS-A05 aligned in the spanwise direction with streamwise separations O (δ) is utilized to capture the convection velocity of specific scales of the shear stress through a bandpass filter and peaks in the correlation. Thus, an average wall normal position for the corresponding convecting event can be inferred at least as high as the equivalent local streamwise velocity. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1315138.

Satellite-Tracking Millimeter-Wave Reflector Antenna System For Mobile Satellite-Tracking

NASA Technical Reports Server (NTRS)

Densmore, Arthur C. (Inventor); Jamnejad, Vahraz (Inventor); Woo, Kenneth E. (Inventor)

2001-01-01

A miniature dual-band two-way mobile satellite-tracking antenna system mounted on a movable vehicle includes a miniature parabolic reflector dish having an elliptical aperture with major and minor elliptical axes aligned horizontally and vertically, respectively, to maximize azimuthal directionality and minimize elevational directionality to an extent corresponding to expected pitch excursions of the movable ground vehicle. A feed-horn has a back end and an open front end facing the reflector dish and has vertical side walls opening out from the back end to the front end at a lesser horn angle and horizontal top and bottom walls opening out from the back end to the front end at a greater horn angle. An RF circuit couples two different signal bands between the feed-horn and the user. An antenna attitude controller maintains an antenna azimuth direction relative to the satellite by rotating it in azimuth in response to sensed yaw motions of the movable ground vehicle so as to compensate for the yaw motions to within a pointing error angle. The controller sinusoidally dithers the antenna through a small azimuth dither angle greater than the pointing error angle while sensing a signal from the satellite received at the reflector dish, and deduces the pointing angle error from dither-induced fluctuations in the received signal.

A satellite-tracking millimeter-wave reflector antenna system for mobile satellite-tracking

NASA Technical Reports Server (NTRS)

Densmore, Arthur C. (Inventor); Jamnejad, Vahraz (Inventor); Woo, Kenneth E. (Inventor)

1995-01-01

A miniature dual-band two-way mobile satellite tracking antenna system mounted on a movable ground vehicle includes a miniature parabolic reflector dish having an elliptical aperture with major and minor elliptical axes aligned horizontally and vertically, respectively, to maximize azimuthal directionality and minimize elevational directionality to an extent corresponding to expected pitch excursions of the movable ground vehicle. A feed-horn has a back end and an open front end facing the reflector dish and has vertical side walls opening out from the back end to the front end at a lesser horn angle and horizontal top and bottom walls opening out from the back end to the front end at a greater horn angle. An RF circuit couples two different signal bands between the feed-horn and the user. An antenna attitude controller maintains an antenna azimuth direction relative to the satellite by rotating it in azimuth in response to sensed yaw motions of the movable ground vehicle so as to compensate for the yaw motions to within a pointing error angle. The controller sinusoidally dithers the antenna through a small azimuth dither angle greater than the pointing error angle while sensing a signal from the satellite received at the reflector dish, and deduces the pointing angle error from dither-induced fluctuations in the received signal.

Note: O-ring stack system for electron gun alignment.

PubMed

Park, In-Yong; Cho, Boklae; Han, Cheolsu; Shin, Seungmin; Lee, Dongjun; Ahn, Sang Jung

2015-01-01

We present a reliable method for aligning an electron gun which consists of an electron source and lenses by controlling a stack of rubber O-rings in a vacuum condition. The beam direction angle is precisely tilted along two axes by adjusting the height difference of a stack of O-rings. In addition, the source position is shifted in each of three orthogonal directions. We show that the tilting angle and linear shift along the x and y axes as obtained from ten stacked O-rings are ±2.55° and ±2 mm, respectively. This study can easily be adapted to charged particle gun alignment and adjustments of the flange position in a vacuum, ensuring that its results can be useful with regard to electrical insulation between flanges with slight modifications.

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

PubMed Central

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

2016-01-01

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

Comminution process to produce wood particles of uniform size and shape with disrupted grain structure from veneer

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

Dooley, James H.; Lanning, David N.

Comminution process of wood veneer to produce wood particles, by feeding wood veneer in a direction of travel substantially normal to grain through a counter rotating pair of intermeshing arrays of cutting discs arrayed axially perpendicular to the direction of wood veneer travel, wherein the cutting discs have a uniform thickness (Td), to produce wood particles characterized by a length dimension (L) substantially equal to the Td and aligned substantially parallel to grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) aligned normal to W and L, wherein the W.times.H dimensions definemore » a pair of substantially parallel end surfaces with end checking between crosscut fibers.« less

Nanoimprinted ultrafine line and space nanogratings for liquid crystal alignment.

PubMed

Liu, Yan Jun; Loh, Wei Wei; Leong, Eunice Sok Ping; Kustandi, Tanu Suryadi; Sun, Xiao Wei; Teng, Jing Hua

2012-11-23

Ultrafine 50 nm line and space nanogratings were fabricated using nanoimprint lithography, and were further used as an alignment layer for liquid crystals. The surface morphologies of the nanogratings were characterized and their surface energies were estimated through the measurement of the contact angles for two different liquids. Experimental results show that the surface energies of the nanogratings are anisotropic: the surface free energy towards the direction parallel to the grating lines is higher than that in the direction perpendicular to the grating lines. Electro-optical characteristics were tested from a twisted nematic liquid crystal cell, which was assembled using two identical nanogratings. Experimental results show that such a kind of nanograting is promising as an alternative to the conventional rubbing process for liquid crystal alignment.

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

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.

Photopolymerized materials and patterning for improved performance of neural prosthetics

NASA Astrophysics Data System (ADS)

Tuft, Bradley William

Neural prosthetics are used to replace or substantially augment remaining motor and sensory functions of neural pathways that were lost or damaged due to physical trauma, disease, or genetics. However, due to poor spatial signal resolution, neural prostheses fail to recapitulate the intimate, precise interactions inherent to neural networks. Designing materials and interfaces that direct de novo nerve growth to spatially specific stimulating elements is, therefore, a promising method to enhance signal specificity and performance of prostheses such as the successful cochlear implant (CI) and the developing retinal implant. In this work, the spatial and temporal reaction control inherent to photopolymerization was used to develop methods to generate micro and nanopatterned materials that direct neurite growth from prosthesis relevant neurons. In particular, neurite growth and directionality has been investigated in response to physical, mechanical, and chemical cues on photopolymerized surfaces. Spiral ganglion neurons (SGNs) serve as the primary neuronal model as they are the principal target for CI stimulation. The objective of the research is to rationally design materials that spatially direct neurite growth and to translate fundamental understanding of nerve cell-material interactions into methods of nerve regeneration that improve neural prosthetic performance. A rapid, single-step photopolymerization method was developed to fabricate micro and nanopatterned physical cues on methacrylate surfaces by selectively blocking light with photomasks. Feature height is readily tuned by modulating parameters of the photopolymerizaiton including initiator concentration and species, light intensity, separation distance from the photomask, and radiation exposure time. Alignment of neural elements increases significantly with increasing feature amplitude and constant periodicity, as well as with decreasing periodicity and constant amplitude. SGN neurite alignment strongly correlates with the maximum feature slope. Neurite alignment is compared on unpatterned, unidirectional, and multidirectional photopolymerized micropatterns. The effect of substrate rigidity on neurite alignment to physical cues was determined by maintaining equivalent pattern microfeatures, afforded by the reaction control of photopolymerization, while concomitantly altering the composition of several copolymer platforms to tune matrix stiffness. For each platform, neurite alignment to unidirectional patterns increases with increasing substrate rigidity. Interestingly, SGN neurites respond to material stiffness cues that are orders of magnitude higher (GPa) than what is typically ascribed to neural environments (kPa). Finally, neurite behavior at bioactive borders of various adhesion modulating molecules was evaluated on micropatterned materials to determine which cues took precedence in establishing neurite directionality. At low microfeatures aspect ratios, neurites align to the pattern direction but are then caused to turn and repel from or turn and align to bioactive borders. Conversely, physical cues dominate neurite path-finding as pattern feature slope increases, i.e. aspect ratio of sloping photopolymerized features increases, causing neurites to readily cross bioactive borders. The photopolymerization method developed in this work to generate micro and nanopatterned materials serves as an additional surface engineering tool that enables investigation of cell-material interactions including directed de novo neurite growth. The results of this interdisciplinary effort contribute substantially to polymer neural regeneration technology and will lead to development of advanced biomaterials that improve neural prosthetic tissue integration and performance by spatially directing nerve growth.

John H. Dillon Medal Lecture: Magnetic Field Directed Self-Assembly of Block Copolymers and Surfactant Mesophases

NASA Astrophysics Data System (ADS)

Osuji, Chinedum

2015-03-01

Molecular self-assembly of block copolymers and small molecule surfactants gives rise to a rich phase behavior as a function of temperature, composition, and other variables. We consider the directed self-assembly of such soft mesophases using magnetic fields, principally through the use of in situ x-ray scattering studies. Field alignment is predicated on a sufficiently large product of magnetic anisotropy and grain size to produce magnetostatic interactions which are substantive relative to thermal forces. We examine the role of field strength on the phase behavior and alignment dynamics of a series of soft mesophases, outlining the possibility to readily create highly ordered functional materials over macroscopic length scales. We show that magnetic fields as large as 10 T have little discernable impact on the stability of block copolymer systems considered, with shifts in order-disorder transition temperatures of roughly 5 mK or smaller. Consequently, directed self-assembly in these systems proceeds by nucleation of randomly aligned grains which thereafter rotate into registry with the field. We highlight the tradeoff between decreasing mobility and increasing anisotropic field interaction that dictates alignment kinetics while transiting from a high temperature disordered state to an ordered system at lower temperatures. NSF support through DMR-0847534 is gratefully acknowledged.

Nanostructured pillars based on vertically aligned carbon nanotubes as the stationary phase in micro-CEC.

PubMed

Wu, Ren-Guei; Yang, Chung-Shi; Wang, Pen-Cheng; Tseng, Fan-Gang

2009-06-01

We present a micro-CEC chip carrying out a highly efficient separation of dsDNA fragments through vertically aligned multi-wall carbon nanotubes (MWCNTs) in a microchannel. The vertically aligned MWCNTs were grown directly in the microchannel to form straight nanopillar arrays as ordered and directional chromatographic supports. 1-Pyrenedodecanoic acid was employed for the surface modification of the MWCNTs' stationary phase to adsorb analytes by hydrophobic interactions. This device was used for separating dsDNA fragments of three different lengths (254, 360, and 572 bp), and fluorescence detection was employed to verify the electrokinetic transport in the MWCNT array. The micro-CEC separation of the three compounds was achieved in less than 300 s at a field strength of 66 V/cm due to superior laminar flow patterns and a lower flow resistance resulting from the vertically aligned MWCNTs being used as the stationary phase medium. In addition, a fivefold reduction of band broadening was obtained when the analyte was separated by the chromatographic MWCNT array channel instead of the CE channel. From all of the results, we suggest that an in situ grown and directional MWCNT array can potentially be useful for preparing more diversified forms of stationary phases for vertically efficient chip-based electrochromatography.

Regionally variant collagen alignment correlates with viscoelastic properties of the disc of the human temporomandibular joint.

PubMed

Gutman, Shawn; Kim, Daniel; Tarafder, Solaiman; Velez, Sergio; Jeong, Julia; Lee, Chang H

2018-02-01

To determine the regionally variant quality of collagen alignment in human TMJ discs and its statistical correlation with viscoelastic properties. For quantitative analysis of the quality of collagen alignment, horizontal sections of human TMJ discs with Pricrosirius Red staining were imaged under circularly polarized microscopy. Mean angle and angular deviation of collagen fibers in each region were analyzed using a well-established automated image-processing for angular gradient. Instantaneous and relaxation moduli of each disc region were measured under stress-relaxation test both in tensile and compression. Then Spearman correlation analysis was performed between the angular deviation and the moduli. To understand the effect of glycosaminoglycans on the correlation, TMJ disc samples were treated by chondroitinase ABC (C-ABC). Our imaging processing analysis showed the region-variant direction of collagen alignment, consistently with previous findings. Interestingly, the quality of collagen alignment, not only the directions, was significantly different in between the regions. The angular deviation of fiber alignment in the anterior and intermediate regions were significantly smaller than the posterior region. Medial and lateral regions showed significantly bigger angular deviation than all the other regions. The regionally variant angular deviation values showed statistically significant correlation with the tensile instantaneous modulus and the relaxation modulus, partially dependent on C-ABC treatment. Our findings suggest the region-variant degree of collagen fiber alignment is likely attributed to the heterogeneous viscoelastic properties of TMJ disc that may have significant implications in development of regenerative therapy for TMJ disc. Copyright © 2017 Elsevier Ltd. All rights reserved.

An automatic alignment system for measuring optical path of transmissometer based on light beam scanning

NASA Astrophysics Data System (ADS)

Zhou, Shudao; Ma, Zhongliang; Wang, Min; Peng, Shuling

2018-05-01

This paper proposes a novel alignment system based on the measurement of optical path using a light beam scanning mode in a transmissometer. The system controls both the probe beam and the receiving field of view while scanning in two vertical directions. The system then calculates the azimuth angle of the transmitter and the receiver to determine the precise alignment of the optical path. Experiments show that this method can determine the alignment angles in less than 10 min with errors smaller than 66 μrad in the azimuth. This system also features high collimation precision, process automation and simple installation.

In Situ alignment system for phase-shifting point-diffraction interferometry

DOEpatents

Goldberg, Kenneth Alan; Naulleau, Patrick P.

2000-01-01

A device and method to facilitate the gross alignment of patterned object- and image-plane masks in optical systems such as the phase-shifting point diffraction interferometer are provided. When an array of similar pinholes or discreet mask fields is used, confusion can occur over the alignment of the focused beams within the field. Adding to the mask pattern a circumscribed or inscribed set of symbols that are identifiable in situ facilitates the unambiguous gross alignment of the object- and/or image-plane masks. Alternatively, a system of markings can be encoded directly into the window shape to accomplish this same task.

X-ray microprobe of orbital alignment in strong-field ionized atoms.

PubMed

Young, L; Arms, D A; Dufresne, E M; Dunford, R W; Ederer, D L; Höhr, C; Kanter, E P; Krässig, B; Landahl, E C; Peterson, E R; Rudati, J; Santra, R; Southworth, S H

2006-08-25

We have developed a synchrotron-based, time-resolved x-ray microprobe to investigate optical strong-field processes at intermediate intensities (10(14) - 10(15) W/cm2). This quantum-state specific probe has enabled the direct observation of orbital alignment in the residual ion produced by strong-field ionization of krypton atoms via resonant, polarized x-ray absorption. We found strong alignment to persist for a period long compared to the spin-orbit coupling time scale (6.2 fs). The observed degree of alignment can be explained by models that incorporate spin-orbit coupling. The methodology is applicable to a wide range of problems.

Precision alignment device

DOEpatents

Jones, N.E.

1988-03-10

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

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.

Precision alignment device

DOEpatents

Jones, Nelson E.

1990-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

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

DOE PAGES

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

2014-01-01

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

Quantifying selective alignment of ensemble nitrogen-vacancy centers in (111) diamond

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

Tahara, Kosuke; Ozawa, Hayato; Iwasaki, Takayuki

2015-11-09

Selective alignment of nitrogen-vacancy (NV) centers in diamond is an important technique towards its applications. Quantification of the alignment ratio is necessary to design the optimized diamond samples. However, this is not a straightforward problem for dense ensemble of the NV centers. We estimate the alignment ratio of ensemble NV centers along the [111] direction in (111) diamond by optically detected magnetic resonance measurements. Diamond films deposited by N{sub 2} doped chemical vapor deposition have NV center densities over 1 × 10{sup 15 }cm{sup −3} and alignment ratios over 75%. Although spin coherence time (T{sub 2}) is limited to a few μs bymore » electron spins of nitrogen impurities, the combination of the selective alignment and the high density can be a possible way to optimize NV-containing diamond samples for the sensing applications.« less

Identification of true EST alignments for recognising transcribed regions.

PubMed

Ma, Chuang; Wang, Jia; Li, Lun; Duan, Mo-Jie; Zhou, Yan-Hong

2011-01-01

Transcribed regions can be determined by aligning Expressed Sequence Tags (ESTs) with genome sequences. The kernel of this strategy is to effectively distinguish true EST alignments from spurious ones. In this study, three measures including Direction Check, Identity Check and Terminal Check were introduced to more effectively eliminate spurious EST alignments. On the basis of these introduced measures and other widely used measures, a computational tool, named ESTCleanser, has been developed to identify true EST alignments for obtaining reliable transcribed regions. The performance of ESTCleanser has been evaluated on the well-annotated human ENCyclopedia of DNA Elements (ENCODE) regions using human ESTs in the dbEST database. The evaluation results show that the accuracy of ESTCleanser at exon and intron levels is more remarkably enhanced than that of UCSC-spliced EST alignments. This work would be helpful to EST-based researches on finding new genes, complementing genome annotation, recognising alternative splicing events and Single Nucleotide Polymorphisms (SNPs), etc.

Apparatus and methods for aligning holes through wheels and spacers and stacking the wheels and spacers to form a turbine rotor

DOEpatents

Berry, Robert Randolph; Palmer, Gene David; Wilson, Ian David

2000-01-01

A gas turbine rotor stacking fixture includes upstanding bolts for reception in aligned bolt holes in superposed aft disk, wheels and spacers and upstanding alignment rods received in openings of the disk, wheels and spacers during the rotor stacking assembly. The axially registering openings enable insertion of thin-walled tubes circumferentially about the rim of the rotor, with tight tolerances to the openings to provide supply and return steam for cooling buckets. The alignment rods have radial dimensions substantially less than their dimensions in a circumferential direction to allow for radial opening misalignment due to thermal expansion, tolerance stack-up and wheel-to-spacer mismatch due to rabbet mechanical growth. The circumferential dimension of the alignment rods affords tightly toleranced alignment of the openings through which the cooling tubes are installed.

Numerical simulation of large-scale field-aligned current generation from finite-amplitude magnetosonic waves

NASA Technical Reports Server (NTRS)

Yamauchi, M.

1994-01-01

A two-dimensional numerical simulation of finite-amplitude magnetohydrodynamic (MHD) magnetosonic waves is performed under a finite-velocity background convection condition. Isothermal cases are considered for simplicity. External dissipation is introduced by assuming that the field-aligned currents are generated in proportion to the accumulated charges. The simulation results are as follows: Paired field-aligned currents are found from the simulated waves. The flow directions of these field-aligned currents depend on the angle between the background convection and the wave normal, and hence two pairs of field-aligned currents are found from a bowed wave if we look at the overall structure. The majority of these field-aligned currents are closed within each pair rather than between two wings. These features are not observed under slow background convection. The result could be applied to the cusp current system and the substorm current system.

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

Alignment and calibration of the MgF2 biplate compensator for applications in rotating-compensator multichannel ellipsometry.

PubMed

Lee, J; Rovira, P I; An, I; Collins, R W

2001-08-01

Biplate compensators made from MgF2 are being used increasingly in rotating-element single-channel and multichannel ellipsometers. For the measurement of accurate ellipsometric spectra, the compensator must be carefully (i) aligned internally to ensure that the fast axes of the two plates are perpendicular and (ii) calibrated to determine the phase retardance delta versus photon energy E. We present alignment and calibration procedures for multichannel ellipsometer configurations with special attention directed to the precision, accuracy, and reproducibility in the determination of delta (E). Run-to-run variations in external compensator alignment, i.e., alignment with respect to the incident beam, can lead to irreproducibilities in delta of approximately 0.2 degrees . Errors in the ellipsometric measurement of a sample can be minimized by calibrating with an external compensator alignment that matches as closely as possible that used in the measurement.

Prediction of β-turns in proteins from multiple alignment using neural network

PubMed Central

Kaur, Harpreet; Raghava, Gajendra Pal Singh

2003-01-01

A neural network-based method has been developed for the prediction of β-turns in proteins by using multiple sequence alignment. Two feed-forward back-propagation networks with a single hidden layer are used where the first-sequence structure network is trained with the multiple sequence alignment in the form of PSI-BLAST–generated position-specific scoring matrices. The initial predictions from the first network and PSIPRED-predicted secondary structure are used as input to the second structure-structure network to refine the predictions obtained from the first net. A significant improvement in prediction accuracy has been achieved by using evolutionary information contained in the multiple sequence alignment. The final network yields an overall prediction accuracy of 75.5% when tested by sevenfold cross-validation on a set of 426 nonhomologous protein chains. The corresponding Qpred, Qobs, and Matthews correlation coefficient values are 49.8%, 72.3%, and 0.43, respectively, and are the best among all the previously published β-turn prediction methods. The Web server BetaTPred2 (http://www.imtech.res.in/raghava/betatpred2/) has been developed based on this approach. PMID:12592033

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

PubMed

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

2012-01-01

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

Optimization of Buckypaper-enhanced Multifunctional Thermoplastic Composites

PubMed Central

Li, Zhongrui; Liang, Zhiyong

2017-01-01

A series of flattened-nanotube reinforced thermoplastic composites are sizably fabricated as a function of buckypaper loading. The effects of the volume fraction, nanotube alignment and length on the tensile performance of the composites are factored into a general expression. The incorporation of self-reinforcing polyphenylene resin (Parmax) into a highly aligned buckypaper frame at an optimal weight ratio boosts the tensile strength and Young’s modulus of the buckypaper/Parmax composite to 1145 MPa and 150 GPa, respectively, far exceeding those of Parmax and aligned buckypaper individually. The composite also exhibits improved thermal (>65 W/m-K) and electrical (~700 S/cm) conductivities, as well as high thermoelectric power (22 μV/K) at room temperature. Meanwhile, the composite displays a heterogeneously complex structure. The hexyl groups of Parmax noncovalently interact with the honeycomb structure of the flattened nanotube through π-stacking and CH-π interaction, correspondingly improving the dispersity of polymer on the nanotube surface and the interfacial stress transferring while the high alignment degrees of nanotube facilitate phonon and charge transport in the composites. PMID:28205637

"Master-Slave" Biological Network Alignment

NASA Astrophysics Data System (ADS)

Ferraro, Nicola; Palopoli, Luigi; Panni, Simona; Rombo, Simona E.

Performing global alignment between protein-protein interaction (PPI) networks of different organisms is important to infer knowledge about conservation across species. Known methods that perform this task operate symmetrically, that is to say, they do not assign a distinct role to the input PPI networks. However, in most cases, the input networks are indeed distinguishable on the basis of how well the corresponding organism is biologically well-characterized. For well-characterized organisms the associated PPI network supposedly encode in a sound manner all the information about their proteins and associated interactions, which is far from being the case for not well characterized ones. Here the new idea is developed to devise a method for global alignment of PPI networks that in fact exploit differences in the characterization of organisms at hand. We assume that the PPI network (called Master) of the best characterized is used as a fingerprint to guide the alignment process to the second input network (called Slave), so that generated results preferably retain the structural characteristics of the Master (and using the Slave) network. We tested our method showing that the results it returns are biologically relevant.

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.

The Alignment effect of brightest cluster galaxies in the SDSS

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

Kim, R. S. J.; Annis, J.; Strauss, M. A.

2001-10-01

One of the most vital observational clues for unraveling the origin of Brightest Cluster Galaxies (BCG) is the observed alignment of the BCGs with their host cluster and its surroundings. We have examined the BCG-cluster alignment effect, using clusters of galaxies detected from the Sloan Digital Sky Survey (SDSS). We find that the BCGs are preferentially aligned with the principal axis of their hosts, to a much higher redshift (z >~ 0.3) than probed by previous studies (z <~ 0.1). The alignment effect strongly depends on the magnitude difference of the BCG and the second and third brightest cluster members:more » we find a strong alignment effect for the dominant BCGs, while less dominant BCGs do not show any departure from random alignment with respect to the cluster. We therefore claim that the alignment process originates from the same process that makes the BCG grow dominant, be it direct mergers in the early stage of cluster formation, or a later process that resembles the galactic cannibalism scenario. We do not find strong evidence for (or against) redshift evolution between 0« less

Critical Science Instrument Alignment of the James Webb Space Telescope (JWST) Integrated Science Instrument Module (ISIM)

NASA Technical Reports Server (NTRS)

Rohrbach, Scott O.; Kubalak, David A.; Gracey, Renee M.; Sabatke, Derek S.; Howard, Joseph M.; Telfer, Randal C.; Zielinski, Thomas P.

2016-01-01

This paper describes the critical instrument alignment terms associated with the six-degree of freedom alignment of each the Science Instrument (SI) in the James Webb Space Telescope (JWST), including focus, pupil shear, pupil clocking, and boresight. We present the test methods used during cryogenic-vacuum tests to directly measure the performance of each parameter, the requirements levied on each, and the impact of any violations of these requirements at the instrument and Observatory level.

A study of field-aligned currents observed at high and low altitudes in the nightside magnetosphere

NASA Technical Reports Server (NTRS)

Elphic, R. C.; Craven, J. D.; Frank, L. A.; Sugiura, M.

1988-01-01

Field-aligned current structures on auroral field lines observed at low and high altitudes using DE 1 and ISEE 2 magnetometer, and particle data observed when the spacecraft are in magnetic conjunction in the near-midnight magnetosphere, are investigated. To minimize latitudinal ambiguity, the plasma-sheet boundary layer observed with ISEE 2 and the discrete aurora at the poleward edge of the auroral oval with DE 1 are studied. The overall current observed at highest latitudes is flowing into the ionosphere, and is likely to be carried by ionospheric electrons flowing upward. There are, however, smaller-scale current structures within this region. The sense and magnitude of the field-aligned currents agree at the two sites. The ISEE 2 data suggests that the high-latitude downward current corresponds to the high-latitude boundary of the plasma-sheet boundary layer, and may be associated with the ion beams observed there.

An Automatic Registration Algorithm for 3D Maxillofacial Model

NASA Astrophysics Data System (ADS)

Qiu, Luwen; Zhou, Zhongwei; Guo, Jixiang; Lv, Jiancheng

2016-09-01

3D image registration aims at aligning two 3D data sets in a common coordinate system, which has been widely used in computer vision, pattern recognition and computer assisted surgery. One challenging problem in 3D registration is that point-wise correspondences between two point sets are often unknown apriori. In this work, we develop an automatic algorithm for 3D maxillofacial models registration including facial surface model and skull model. Our proposed registration algorithm can achieve a good alignment result between partial and whole maxillofacial model in spite of ambiguous matching, which has a potential application in the oral and maxillofacial reparative and reconstructive surgery. The proposed algorithm includes three steps: (1) 3D-SIFT features extraction and FPFH descriptors construction; (2) feature matching using SAC-IA; (3) coarse rigid alignment and refinement by ICP. Experiments on facial surfaces and mandible skull models demonstrate the efficiency and robustness of our algorithm.

Is Tutoring Teaching? Exploring Tutoring's Potential to Improve Mathematics Teacher Education

ERIC Educational Resources Information Center

Rasche, Alexander N.

2017-01-01

This study investigated the tutoring practices of mathematics tutors working in one university tutoring center and the corresponding rationale exhibited by the mathematics tutors. This study illustrates how the tutoring practices of mathematics tutors align with the Eight Mathematics Teaching Practices outlined in NCTM's recent publication…

From Curriculum to Workplace Requirements: Do They "Match"?

ERIC Educational Resources Information Center

Lomas, Gregor; Mills, Kelvin

2013-01-01

This paper examines correspondences and disjunctions within a national curriculum and between various aspects of its delivery, and how these align with the mathematical needs of the workplace. This is investigated in the context of the New Zealand school mathematics curriculum; the Numeracy Development Project; the senior school assessment regime,…

Millennial Expectations and Constructivist Methodologies: Their Corresponding Characteristics and Alignment

ERIC Educational Resources Information Center

Carter, Timothy L.

2008-01-01

In recent years, much emphasis has been placed on constructivist methodologies and their potential benefit for learners of various ages (Brandt & Perkins, 2000; Brooks, 1990). Although certain aspects of the constructivist paradigm have replaced several aspects of the behaviorist paradigm for a large contingency of stakeholders (particularly,…

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.

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.

YAHA: fast and flexible long-read alignment with optimal breakpoint detection.

PubMed

Faust, Gregory G; Hall, Ira M

2012-10-01

With improved short-read assembly algorithms and the recent development of long-read sequencers, split mapping will soon be the preferred method for structural variant (SV) detection. Yet, current alignment tools are not well suited for this. We present YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints. YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from http://faculty.virginia.edu/irahall/YAHA. imh4y@virginia.edu.

Single-Axis Accelerometer

NASA Technical Reports Server (NTRS)

Tucker, Dennis Stephen (Inventor); Capo-Lugo, Pedro A. (Inventor)

2016-01-01

A single-axis accelerometer includes a housing defining a sleeve. An object/mass is disposed in the sleeve for sliding movement therein in a direction aligned with the sleeve's longitudinal axis. A first piezoelectric strip, attached to a first side of the object and to the housing, is longitudinally aligned with the sleeve's longitudinal axis. The first piezoelectric strip includes a first strip of a piezoelectric material with carbon nanotubes substantially aligned along a length thereof. A second piezoelectric strip, attached to a second side of the object and to the housing, is longitudinally aligned with the sleeve's longitudinal axis. The second piezoelectric strip includes a second strip of the piezoelectric material with carbon nanotubes substantially aligned along a length thereof. A voltage sensor is electrically coupled to at least one of the first and second piezoelectric strips.

Progress in ETA-II magnetic field alignment using stretched wire and low energy electron beam techniques

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

Deadrick, F.J.; Griffith, L.V.

1990-08-17

Flux line alignment of the solenoidal focus magnets used on the ETA-II linear induction accelerator is a key element leading to a reduction of beam corkscrew motion. Two techniques have been used on the ETA-II accelerator to measure and establish magnet alignment. A low energy electron beam has been used to directly map magnetic field lines, and recent work has utilized a pulsed stretched wire technique to measure magnet tilts and offsets with respect to a reference axis. This paper reports on the techniques used in the ETA-II accelerator alignment, and presents results from those measurements which show that acceleratormore » is magnetically aligned to within {approximately}{plus minus}200 microns. 3 refs., 8 figs.« less

Nanofiber Orientation and Surface Functionalization Modulate Human Mesenchymal Stem Cell Behavior In Vitro

PubMed Central

Kolambkar, Yash M.; Bajin, Mehmet; Wojtowicz, Abigail; Hutmacher, Dietmar W.; García, Andrés J.

2014-01-01

Electrospun nanofiber meshes have emerged as a new generation of scaffold membranes possessing a number of features suitable for tissue regeneration. One of these features is the flexibility to modify their structure and composition to orchestrate specific cellular responses. In this study, we investigated the effects of nanofiber orientation and surface functionalization on human mesenchymal stem cell (hMSC) migration and osteogenic differentiation. We used an in vitro model to examine hMSC migration into a cell-free zone on nanofiber meshes and mitomycin C treatment to assess the contribution of proliferation to the observed migration. Poly (ɛ-caprolactone) meshes with oriented topography were created by electrospinning aligned nanofibers on a rotating mandrel, while randomly oriented controls were collected on a stationary collector. Both aligned and random meshes were coated with a triple-helical, type I collagen-mimetic peptide, containing the glycine-phenylalanine-hydroxyproline-glycine-glutamate-arginine (GFOGER) motif. Our results indicate that nanofiber GFOGER peptide functionalization and orientation modulate cellular behavior, individually, and in combination. GFOGER significantly enhanced the migration, proliferation, and osteogenic differentiation of hMSCs on nanofiber meshes. Aligned nanofiber meshes displayed increased cell migration along the direction of fiber orientation compared to random meshes; however, fiber alignment did not influence osteogenic differentiation. Compared to each other, GFOGER coating resulted in a higher proliferation-driven cell migration, whereas fiber orientation appeared to generate a larger direct migratory effect. This study demonstrates that peptide surface modification and topographical cues associated with fiber alignment can be used to direct cellular behavior on nanofiber mesh scaffolds, which may be exploited for tissue regeneration. PMID:24020454

Measurement of photoluminescence from a twisted-nematic liquid crystal/dye cell for an application in an energy-harvesting display

NASA Astrophysics Data System (ADS)

Ohta, Masamichi; Itaya, Shunsuke; Ozawa, Shintaro; Binti, M. Azmi; Dianah, Nada; Fujieda, Ichiro

2016-09-01

One can convert a Luminescent Solar Concentrator (LSC) to an energy-harvesting display by scanning a laser beam on it. By incorporating a guest-host system of liquid crystal (LC) and dye materials in an LSC, the power of photoluminescence (PL) utilized for either display or energy-harvesting can be adjusted to the changes in ambient lighting conditions. We have measured basic characteristics of an LC/dye cell with twisted-nematic (TN) alignment. These are absorption of the laser light, PL radiation pattern, contrast of luminance, spreading of the PL generated by a narrow laser beam, and their dependencies on the bias. The results are similar to those of the LC/dye cell with antiparallel (AP) alignment with the following exceptions. First, absorption by the TN cell depends on the bias for both polarization components of the excitation light, while the AP cell exhibits a bias dependency only for the component polarized along the alignment direction. Second, the PL from the TN cell is mostly polarized along the alignment direction on the exit side of the cell while the PL from the AP cell is mostly polarized along its alignment direction. These observations can be attributed to the fact that the polarization plane of a linearly polarized light rotates as it propagated the TN-LC layer. For both AP and TN cells, low-intensity PL is observed from the whole cell surfaces. This can degrade the contrast of a displayed image. Bias application to the cell suppresses this effect.

The Harang reversal and the interchange stability of the magnetotail

NASA Astrophysics Data System (ADS)

Ohtani, Shinichi; Gkioulidou, Matina; Wang, Chih-Ping; Wolf, Richard A.

2016-04-01

The present study addresses steady convection in the plasma sheet in terms of the interchange stability with special attention to the Harang reversal. The closure of the tail current with a field-aligned current (FAC) results from the divergence/convergence of the pressure gradient current. If the magnetotail is in a steady state, the associated change of local plasma pressure p has to balance with its advective change. Accordingly, for adiabatic transport, the flux tube entropy parameter pVγ increases and decreases along the convection path in regions corresponding to downward and upward FACs, respectively. This requirement, along with the condition for the interchange stability imposes an important constraint on the direction of convection especially in the regions of downward FACs. It is deduced that for the dusk cell, the convection in the downward R2 current has to be directed azimuthally duskward, which follows the sunward, possibly dawnward deflected, convection in the region of the premidnight upward R1 current. This duskward turn of convection takes place in the vicinity of the R1-R2 demarcation, and it presumably corresponds to the Harang reversal. For the dawn cell the convection in the postmidnight downward R1 current has to deflect dawnward, and then it proceeds sunward in the upward R2 current. The continuity of the associated ionospheric currents consistently reproduces the assumed FAC distribution. The proposed interrelationships between the convection and FACs are also verified with a quasi-steady plasma sheet configuration and convection reproduced by a modified Rice Convection Model with force balance.

Multilayer Microfluidic Devices Created From A Single Photomask

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

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

2013-08-28

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

Nanotopography guides and directs cell migration in amoeboid and epithelial cells

NASA Astrophysics Data System (ADS)

Lee, Rachel; Das, Satarupa; Hourwitz, Matthew; Sun, Xiaoyu; Parent, Carole; Fourkas, John; Losert, Wolfgang

Cell migration plays a critical role in development, angiogenesis, immune response, wound healing, and cancer metastasis. In many cases, cells also move in the context of a matrix of collagen fibers, and the alignment of these fibers can both affect the migration phenotype and guide cells. Here we show that both fast and slow migrating cells - amoeboid HL-60 and epithelial MCF10A - are affected in similar ways by micro/nanostructures with dimensions similar to those of collagen fibers. Cell alignment enhances the efficiency of migration by increasing directional persistence.

Integrated filter and detector array for spectral imaging

NASA Technical Reports Server (NTRS)

Labaw, Clayton C. (Inventor)

1992-01-01

A spectral imaging system having an integrated filter and photodetector array is disclosed. The filter has narrow transmission bands which vary in frequency along the photodetector array. The frequency variation of the transmission bands is matched to, and aligned with, the frequency variation of a received spectral image. The filter is deposited directly on the photodetector array by a low temperature deposition process. By depositing the filter directly on the photodetector array, permanent alignment is achieved for all temperatures, spectral crosstalk is substantially eliminated, and a high signal to noise ratio is achieved.

Effects of fiber motion on the acoustic behavior of an anisotropic, flexible fibrous material

NASA Technical Reports Server (NTRS)

Dahl, Milo D.; Rice, Edward J.; Groesbeck, Donald E.

1990-01-01

The acoustic behavior of a flexible fibrous material was studied experimentally. The material consisted of cylindrically shaped fibers arranged in a batting with the fibers primarily aligned parallel to the face of the batting. This type of material was considered anisotropic, with the acoustic propagation constant depending on whether the direction of sound propagation was parallel or normal to the fiber arrangement. Normal incidence sound absorption measurements were taken for both fiber orientations over the frequency range 140 to 1500 Hz and with bulk densities ranging from 4.6 to 67 kg/cu m. When the sound propagated in a direction normal to the fiber alignment, the measured sound absorption showed the occurrence of a strong resonance, which increased absorption above that attributed to viscous and thermal effects. When the sound propagated in a direction parallel to the fiber alignment, indications of strong resonances in the data were not present. The resonance in the data for fibers normal to the direction of sound propagation is attributed to fiber motion. An analytical model was developed for the acoustic behavior of the material displaying the same fiber motion characteristics shown in the measurements.

enoLOGOS: a versatile web tool for energy normalized sequence logos

PubMed Central

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

2005-01-01

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

Stiff, porous scaffolds from magnetized alumina particles aligned by magnetic freeze casting.

PubMed

Frank, Michael B; Naleway, Steven E; Haroush, Tsuk; Liu, Chin-Hung; Siu, Sze Hei; Ng, Jerry; Torres, Ivan; Ismail, Ali; Karandikar, Keyur; Porter, Michael M; Graeve, Olivia A; McKittrick, Joanna

2017-08-01

Bone consists of a hard mineral phase and a compliant biopolymer phase resulting in a composite material that is both lightweight and strong. Osteoporosis that degrades spongy bone preferentially over time leads to bone brittleness in the elderly. A porous ceramic material that can mimic spongy bone for a one-time implant provides a potential solution for the future needs of an aging population. Scaffolds made by magnetic freeze casting resemble the aligned porosity of spongy bone. A magnetic field applied throughout freezing induces particle chaining and alignment of lamellae structures between growing ice crystals. After freeze drying to extract the ice and sintering to strengthen the scaffold, cubes from the scaffold center are mechanically compressed along longitudinal (z-axis, ice growth direction) and transverse (y-axis, magnetic field direction) axes. The best alignment of lamellar walls in the scaffold center occurs when applying magnetic freeze casting with the largest particles (350nm) at an intermediate magnetic field strength (75mT), which also agrees with stiffness enhancement results in both z and y-axes. Magnetic moments of different sized magnetized alumina particles help determine the ideal magnetic field strength needed to induce alignment in the scaffold center rather than just at the poles. Copyright © 2017 Elsevier B.V. All rights reserved.

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

DOE PAGES

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

2016-03-30

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

Comminution process to produce engineered wood particles of uniform size and shape with disrupted grain structure from veneer

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

Dooley, James H; Lanning, David N

Comminution process of wood veneer to produce wood particles, by feeding wood veneer in a direction of travel substantially normal to grain through a counter rotating pair of intermeshing arrays of cutting discs arrayed axially perpendicular to the direction of veneer travel, wherein the cutting discs have a uniform thickness (Td), to produce wood particles characterized by a length dimension (L) substantially equal to the Td and aligned substantially parallel to grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) substantially equal to the veneer thickness (Tv) and aligned normal to Wmore » and L, wherein the W.times.H dimensions define a pair of substantially parallel end surfaces with end checking between crosscut fibers.« less

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

PubMed

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

2013-02-07

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

Microstructural Architecture, Microstructures, and Mechanical Properties for a Nickel-Base Superalloy Fabricated by Electron Beam Melting

NASA Astrophysics Data System (ADS)

Murr, L. E.; Martinez, E.; Gaytan, S. M.; Ramirez, D. A.; Machado, B. I.; Shindo, P. W.; Martinez, J. L.; Medina, F.; Wooten, J.; Ciscel, D.; Ackelid, U.; Wicker, R. B.

2011-11-01

Microstructures and a microstructural, columnar architecture as well as mechanical behavior of as-fabricated and processed INCONEL alloy 625 components produced by additive manufacturing using electron beam melting (EBM) of prealloyed precursor powder are examined in this study. As-fabricated and hot-isostatically pressed ("hipped") [at 1393 K (1120 °C)] cylinders examined by optical metallography (OM), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy-dispersive (X-ray) spectrometry (EDS), and X-ray diffraction (XRD) exhibited an initial EBM-developed γ″ (bct) Ni3Nb precipitate platelet columnar architecture within columnar [200] textured γ (fcc) Ni-Cr grains aligned in the cylinder axis, parallel to the EBM build direction. Upon annealing at 1393 K (1120 °C) (hot-isostatic press (HIP)), these precipitate columns dissolve and the columnar, γ, grains recrystallized forming generally equiaxed grains (with coherent {111} annealing twins), containing NbCr2 laves precipitates. Microindentation hardnesses decreased from 2.7 to 2.2 GPa following hot-isostatic pressing ("hipping"), and the corresponding engineering (0.2 pct) offset yield stress decreased from 0.41 to 0.33 GPa, while the UTS increased from 0.75 to 0.77 GPa. However, the corresponding elongation increased from 44 to 69 pct for the hipped components.

Klystron having electrostatic quadrupole focusing arrangement

DOEpatents

Maschke, Alfred W.

1983-08-30

A klystron includes a source for emitting at least one electron beam, and an accelerator for accelarating the beam in a given direction through a number of drift tube sections successively aligned relative to one another in the direction of the beam. A number of electrostatic quadrupole arrays are successively aligned relative to one another along at least one of the drift tube sections in the beam direction for focusing the electron beam. Each of the electrostatic quadrupole arrays forms a different quadrupole for each electron beam. Two or more electron beams can be maintained in parallel relationship by the quadrupole arrays, thereby enabling space charge limitations encountered with conventional single beam klystrons to be overcome.

Klystron having electrostatic quadrupole focusing arrangement

DOEpatents

Maschke, A.W.

1983-08-30

A klystron includes a source for emitting at least one electron beam, and an accelerator for accelerating the beam in a given direction through a number of drift tube sections successively aligned relative to one another in the direction of the beam. A number of electrostatic quadrupole arrays are successively aligned relative to one another along at least one of the drift tube sections in the beam direction for focusing the electron beam. Each of the electrostatic quadrupole arrays forms a different quadrupole for each electron beam. Two or more electron beams can be maintained in parallel relationship by the quadrupole arrays, thereby enabling space charge limitations encountered with conventional single beam klystrons to be overcome. 4 figs.

The Integration of It Governance, Information Security Leadership and Strategic Alignment in Healthcare: A Correlational Study

ERIC Educational Resources Information Center

Taft, Tiffany H.

2017-01-01

This dissertation is a study of the relationship between Information Technology Governance (ITG), information security leadership, and strategic alignment within a healthcare organization. Strong organizational leadership and adherence to the process are vital to the formulation and management of performance and implementation of key directives.…

Adult Basic Education: Aligning Adult Basic Education and Postsecondary Education

ERIC Educational Resources Information Center

Texas Higher Education Coordinating Board, 2008

2008-01-01

In 2007, the 80th Texas Legislature included a rider to the General Appropriations Act for the Texas Higher Education Coordinating Board. The rider directed the agency to coordinate with the Texas Education Agency to develop and implement plans to align adult basic education with postsecondary education. The Coordinating Board, in collaboration…

Exploiting both optical and electrical anisotropy in nanowire electrodes for higher transparency.

PubMed

Dong, Jianjin; Goldthorpe, Irene A

2018-01-26

Transparent electrodes such as indium tin oxide and random meshes of silver nanowires (AgNWs) have isotropic in-plane properties. However, we show that imparting some alignment to AgNWs can create anisotropic transparency and electrical conductivity characteristics that may benefit many applications. For example, liquid crystal displays and the touch sensors on top of them often only need to be transparent to one type of polarized light as well as predominantly conductive in only one direction. Herein, AgNWs are slightly preferentially aligned during their deposition by rod coating. Compared to randomly oriented AgNW films, the alignment boosts the transparency to perpendicularly polarized light, as well as achieves a higher transparency for a given sheet resistance in one direction compared to randomly oriented AgNWs films. These factors together increase the transparency of a 16 Ω/sq electrode by 7.3 percentage points. The alignment technique is cheap and scalable, compatible with roll-to-roll processes, and most importantly does not require extra processing steps, as rod coating is already a standard process for AgNW electrode fabrication.

Exploiting both optical and electrical anisotropy in nanowire electrodes for higher transparency

NASA Astrophysics Data System (ADS)

Dong, Jianjin; Goldthorpe, Irene A.

2018-01-01

Transparent electrodes such as indium tin oxide and random meshes of silver nanowires (AgNWs) have isotropic in-plane properties. However, we show that imparting some alignment to AgNWs can create anisotropic transparency and electrical conductivity characteristics that may benefit many applications. For example, liquid crystal displays and the touch sensors on top of them often only need to be transparent to one type of polarized light as well as predominantly conductive in only one direction. Herein, AgNWs are slightly preferentially aligned during their deposition by rod coating. Compared to randomly oriented AgNW films, the alignment boosts the transparency to perpendicularly polarized light, as well as achieves a higher transparency for a given sheet resistance in one direction compared to randomly oriented AgNWs films. These factors together increase the transparency of a 16 Ω/sq electrode by 7.3 percentage points. The alignment technique is cheap and scalable, compatible with roll-to-roll processes, and most importantly does not require extra processing steps, as rod coating is already a standard process for AgNW electrode fabrication.

Helicity-dependent single-walled carbon nanotube alignment on graphite for helical angle and handedness recognition

PubMed Central

Chen, Yabin; Shen, Ziyong; Xu, Ziwei; Hu, Yue; Xu, Haitao; Wang, Sheng; Guo, Xiaolei; Zhang, Yanfeng; Peng, Lianmao; Ding, Feng; Liu, Zhongfan; Zhang, Jin

2013-01-01

Aligned single-walled carbon nanotube arrays provide a great potential for the carbon-based nanodevices and circuit integration. Aligning single-walled carbon nanotubes with selected helicities and identifying their helical structures remain a daunting issue. The widely used gas-directed and surface-directed growth modes generally suffer the drawbacks of mixed and unknown helicities of the aligned single-walled carbon nanotubes. Here we develop a rational approach to anchor the single-walled carbon nanotubes on graphite surfaces, on which the orientation of each single-walled carbon nanotube sensitively depends on its helical angle and handedness. This approach can be exploited to conveniently measure both the helical angle and handedness of the single-walled carbon nanotube simultaneously at a low cost. In addition, by combining with the resonant Raman spectroscopy, the (n,m) index of anchored single-walled carbon nanotube can be further determined from the (d,θ) plot, and the assigned (n,m) values by this approach are validated by both the electronic transition energy Eii measurement and nanodevice application. PMID:23892334

Alignment of SWNTs by protein-ligand interaction of functionalized magnetic particles under low magnetic fields.

PubMed

Park, Tae Jung; Park, Jong Pil; Lee, Seok Jae; Jung, Dae-Hwan; Ko, Young Koan; Jung, Hee-Tae; Lee, Sang Yup

2011-05-01

Carbon nanotubes (CNTs) have attracted considerable attention for applications using their superior mechanical, thermal and electrical properties. A simple method to controllably align single-walled CNTs (SWNTs) by using magnetic particles embedded with superparamagnetic iron oxide as an accelerator under the magnetic field was developed. The functionalization of SWNTs using biotin, interacted with streptavidin-coupled magnetic particles (micro-to-nano in diameter), and layer-by-layer assembly were performed for the alignment of a particular direction onto the clean silicon and the gold substrate at very low magnetic forces (0.02-0.89 T) at room temperature. The successful alignment of the SWNTs with multi-layer film was observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). By changing the orientation and location of the substrates, crossed-networks of SWNTs-magnetic particle complex could easily be fabricated. We suggest that this approach, which consists of a combination of biological interaction among streptavidin-biotin and magnetite particles, should be useful for lateral orientation of individual SWNTs with controllable direction.

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

PubMed Central

2011-01-01

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

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

PubMed

Trybou, Jeroen; Gemmel, Paul; Annemans, Lieven

2011-02-15

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

Engineering poly(hydroxy butyrate-co-hydroxy valerate) based vascular scaffolds to mimic native artery.

PubMed

Deepthi, S; Nivedhitha Sundaram, M; Vijayan, Ponni; Nair, Shantikumar V; Jayakumar, R

2018-04-01

Electrospun tri-layered fibrous scaffold incorporating VEGF and Platelet Factor Concentrate (PFC) in multiple layers having different layer architectures was designed to mimic native artery. The scaffold consisted of longitudinally aligned poly(hydroxy butyrate-co-hydroxy valerate) (PHBV) and poly(vinyl alcohol) (PVA) nanofibers (inner layer), radially aligned PHBV-elastin nanofibers (middle layer) to provide the bi-directional alignment and combination of longitudinally aligned PHBV-elastin and random PHBV/PVA multiscale fibers (peripheral layer). Tubular constructs of diameter <6 mm were developed. The developed electrospun fibers were characterised by Scanning Electron Microscope (SEM), Fourier Transform Infrared Spectroscopy and Tensile tests. Further the burst strength, compliance and stiffness index of tri-layered tubular scaffold was evaluated. SEM images of fibrous layers showed the typical longitudinal and radial alignment of fibers in the tubular construct. SEM images showed that the prepared PHBV nanofibers were in the range of 500-800 nm and PHBV microfibers were of 1-2 μm in diameter in the tri-layered electrospun membrane. PVA nanofibers were of size 200-250 nm. The tensile strength, percentage compliance and stiffness index of tri-layered membrane was in accordance with that of native small blood vessels. The developed tri-layered membrane was blood compatible, with hemolysis degree 0.85 ± 0.21% and did not activate platelets. Controlled release of VEGF and PFC was observed from the scaffold. The biocompatibility of the tri-layered scaffold was evaluated using HUVECs, SMCs and MSCs and SMCs infiltration from the outer layer was also evaluated. Specific protein expression for the HUVECs and SMCs was evaluated by flow cytometry and immunocytochemistry. HUVECs and SMCs exhibited good elongation and alignment along the direction of fibers and was found to maintain its CD31, VE-Cadherin and αSMA expression respectively. The results highlight the importance of bi-directional fiber alignment on the tri-layered electrospun scaffold as a suitable architectural prototype for vascular scaffolds to mimic the native arteries. Copyright © 2017 Elsevier B.V. All rights reserved.

Two-Piece Screens for Decontaminating Granular Material

NASA Technical Reports Server (NTRS)

Backes, Douglas; Poulter, Clay; Godfrey, Max; Dutton, Melinda; Tolman, Dennis

2009-01-01

Two-piece screens have been designed specifically for use in filtering a granular material to remove contaminant particles that are significantly wider or longer than are the desired granules. In the original application for which the twopiece screens were conceived, the granular material is ammonium perchlorate and the contaminant particles tend to be wires and other relatively long, rigid strands. The basic design of the twopiece screens can be adapted to other granular materials and contaminants by modifying critical dimensions to accommodate different grain and contaminant- particle sizes. A two-piece screen of this type consists mainly of (1) a top flat plate perforated with circular holes arranged in a hexagonal pattern and (2) a bottom plate that is also perforated with circular holes (but not in a pure hexagonal pattern) and is folded into an accordion structure. Fabrication of the bottom plate begins with drilling circular holes into a flat plate in a hexagonal pattern that is interrupted, at regular intervals, by parallel gaps. The plate is then folded into the accordion structure along the gaps. Because the folds are along the gaps, there are no holes at the peaks and valleys of the accordion screen. The top flat plate and the bottom accordion plate are secured within a metal frame. The resulting two-piece screen is placed at the bottom opening of a feed hopper containing the granular material to be filtered. Tests have shown that such long, rigid contaminant strands as wires readily can pass through a filter consisting of the flat screen alone and that the addition of the accordion screen below the flat screen greatly increases the effectiveness of removal of wires and other contaminant strands. Part of the reason for increased effectiveness is in the presentation of the contaminant to the filter surface. Testing has shown that wire type contamination will readily align itself parallel to the material direction flow. Since this direction of flow is nearly always perpendicular to the filter surface holes, the contamination is automatically aligned to pass through. The two-filter configuration reduces the likelihood that a given contaminant strand will be aligned with the flow of material by eliminating the perpendicular presentation angle. Thus, for wires of a certain diameter, a two-piece screen is 20 percent more effective than is the corresponding flat perforated plate alone, even if the holes in the flat plate are narrower. An accordion screen alone is similarly effective in catching contaminants, but lumps of agglomerated granules of the desired material often collect in the valleys and clog the screen. The addition of a flat screen above the accordion screen prevents clogging of the accordion screen. Flat wire screens have often been used to remove contaminants from granular materials, and are about as effective as are the corresponding perforated flat plates used alone.

A gaussian mixture + demons deformable registration method for cone-beam CT-guided robotic transoral base-of-tongue surgery

NASA Astrophysics Data System (ADS)

Reaungamornrat, S.; Liu, W. P.; Schafer, S.; Otake, Y.; Nithiananthan, S.; Uneri, A.; Richmon, J.; Sorger, J.; Siewerdsen, J. H.; Taylor, R. H.

2013-03-01

Purpose: An increasingly popular minimally invasive approach to resection of oropharyngeal / base-of-tongue cancer is made possible by a transoral technique conducted with the assistance of a surgical robot. However, the highly deformed surgical setup (neck flexed, mouth open, and tongue retracted) compared to the typical patient orientation in preoperative images poses a challenge to guidance and localization of the tumor target and adjacent critical anatomy. Intraoperative cone-beam CT (CBCT) can account for such deformation, but due to the low contrast of soft-tissue in CBCT images, direct localization of the target and critical tissues in CBCT images can be difficult. Such structures may be more readily delineated in preoperative CT or MR images, so a method to deformably register such information to intraoperative CBCT could offer significant value. This paper details the initial implementation of a deformable registration framework to align preoperative images with the deformed intraoperative scene and gives preliminary evaluation of the geometric accuracy of registration in CBCT-guided TORS. Method: The deformable registration aligns preoperative CT or MR to intraoperative CBCT by integrating two established approaches. The volume of interest is first segmented (specifically, the region of the tongue from the tip to the hyoid), and a Gaussian mixture (GM) mode1 of surface point clouds is used for rigid initialization (GMRigid) as well as an initial deformation (GMNonRigid). Next, refinement of the registration is performed using the Demons algorithm applied to distance transformations of the GM-registered and CBCT volumes. The registration accuracy of the framework was quantified in preliminary studies using a cadaver emulating preoperative and intraoperative setups. Geometric accuracy of registration was quantified in terms of target registration error (TRE) and surface distance error. Result: With each step of the registration process, the framework demonstrated improved registration, achieving mean TRE of 3.0 mm following the GM rigid, 1.9 mm following GM nonrigid, and 1.5 mm at the output of the registration process. Analysis of surface distance demonstrated a corresponding improvement of 2.2, 0.4, and 0.3 mm, respectively. The evaluation of registration error revealed the accurate alignment in the region of interest for base-of-tongue robotic surgery owing to point-set selection in the GM steps and refinement in the deep aspect of the tongue in the Demons step. Conclusions: A promising framework has been developed for CBCT-guided TORS in which intraoperative CBCT provides a basis for registration of preoperative images to the highly deformed intraoperative setup. The registration framework is invariant to imaging modality (accommodating preoperative CT or MR) and is robust against CBCT intensity variations and artifact, provided corresponding segmentation of the volume of interest. The approach could facilitate overlay of preoperative planning data directly in stereo-endoscopic video in support of CBCT-guided TORS.

3D Anisotropy of Solar Wind Turbulence, Tubes, or Ribbons?

NASA Astrophysics Data System (ADS)

Verdini, Andrea; Grappin, Roland; Alexandrova, Olga; Lion, Sonny

2018-01-01

We study the anisotropy with respect to the local magnetic field of turbulent magnetic fluctuations at magnetofluid scales in the solar wind. Previous measurements in the fast solar wind obtained axisymmetric anisotropy, despite that the analysis method allows nonaxisymmetric structures. These results are probably contaminated by the wind expansion that introduces another symmetry axis, namely, the radial direction, as indicated by recent numerical simulations. These simulations also show that while the expansion is strong, the principal fluctuations are in the plane perpendicular to the radial direction. Using this property, we separate 11 yr of Wind spacecraft data into two subsets characterized by strong and weak expansion and determine the corresponding turbulence anisotropy. Under strong expansion, the small-scale anisotropy is consistent with the Goldreich & Sridhar critical balance. As in previous works, when the radial symmetry axis is not eliminated, the turbulent structures are field-aligned tubes. Under weak expansion, we find 3D anisotropy predicted by the Boldyrev model, that is, turbulent structures are ribbons and not tubes. However, the very basis of the Boldyrev phenomenology, namely, a cross-helicity increasing at small scales, is not observed in the solar wind: the origin of the ribbon formation is unknown.

Helical waves in easy-plane antiferromagnets

NASA Astrophysics Data System (ADS)

Semenov, Yuriy G.; Li, Xi-Lai; Xu, Xinyi; Kim, Ki Wook

2017-12-01

Effective spin torques can generate the Néel vector oscillations in antiferromagnets (AFMs). Here, it is theoretically shown that these torques applied at one end of a normal AFM strip can excite a helical type of spin wave in the strip whose properties are drastically different from characteristic spin waves. An analysis based on both a Néel vector dynamical equation and the micromagnetic simulation identifies the direction of magnetic anisotropy and the damping factor as the two key parameters determining the dynamics. Helical wave propagation requires the hard axis of the easy-plane AFM to be aligned with the traveling direction, while the damping limits its spatial extent. If the damping is neglected, the calculation leads to a uniform periodic domain wall structure. On the other hand, finite damping decelerates the helical wave rotation around the hard axis, ultimately causing stoppage of its propagation along the strip. With the group velocity staying close to spin-wave velocity at the wave front, the wavelength becomes correspondingly longer away from the excitation point. In a sufficiently short strip, a steady-state oscillation can be established whose frequency is controlled by the waveguide length as well as the excitation energy or torque.

A dual-satellite study of the spatial properties of FTEs. [flux transfer events

NASA Technical Reports Server (NTRS)

Saunders, M. A.; Russell, C. T.; Sckopke, N.

1984-01-01

Reconnection at the earth's dayside magnetopause may manifest itself primarily as a localized and transient process called a flux-transfer event (FTE). The spatial properties of FTEs are investigated directly by examining data from the ISEE satellite pair when the satellites were separated by more than 1000 km in the vicinity of the magnetopause. Examples of magnetosheath and boundary layer FTEs, each having a dimension normal to the magnetopause of order an earth radius, R(E), are shown, and this scale-size result is substantiated statistically for magnetosheath FTEs. When combined with other information, a 1-R(E) normal dimension implies that the voltage associated with the FTE process at one magnetopause location is at least 10 kV. These findings strengthen the view that the magnetic field comprising an FTE is twisted, this twisting appearing to be continuous in sense across the magnetopause and corresponding to a core field-aligned current of magnitude a few hundred kA. Changes in plasma flow speed and direction are found to be associated with FTEs. The transverse field and flow perturbations accompanying the three magnetosheath FTEs studied here satisfy approximately the Walen relation, the relation which describes a propagating Alfven wave.

Airborne and spaceborne radar images for geologic and environmental mapping in the Amazon rain forest, Brazil

NASA Technical Reports Server (NTRS)

Hurtak, James J.; Ford, John P.

1986-01-01

Spaceborne and airborne radar image of portions of the Middle and Upper Amazon basin in the state of Amazonas and the Territory of Roraima are compared for purposes of geological and environmental mapping. The contrasted illumination geometries and imaging parameters are related to terrain slope and surface roughness characteristics for corresponding areas that were covered by each of the radar imaging systems. Landforms range from deeply dissected mountain and plateau with relief up to 500 m in Roraima, revealing ancient layered rocks through folded residual mountains to deeply beveled pediplain in Amazonas. Geomorphic features provide distinct textural signatures that are characteristic of different rock associations. The principle drainages in the areas covered are the Rio Negro, Rio Branco, and the Rio Japura. Shadowing effects and low radar sensitivity to subtle linear fractures that are aligned parallel or nearly parallel to the direction of radar illumination illustrate the need to obtain multiple coverage with viewing directions about 90 degrees. Perception of standing water and alluvial forest in floodplains varies with incident angle and with season. Multitemporal data sets acquired over periods of years provide an ideal method of monitoring environmental changes.

Double-grooved nanofibre surfaces with enhanced anisotropic hydrophobicity.

PubMed

Liang, Meimei; Chen, Xin; Xu, Yang; Zhu, Lei; Jin, Xiangyu; Huang, Chen

2017-11-02

This study reports a facile method for fabricating double-grooved fibrous surfaces. The primary grooves of the surface are formed by aligned fibres, while the secondary grooves are achieved by oriented nanogrooves on the fibre surface. Investigation into the formation mechanism reveals that the nanogrooves can be readily tailored through adjusting the solvent ratio and relative humidity. With this understanding, a variety of polymers have been successfully electrospun into fibres having the same nanogrooved feature. These fibres show high resemblance to natural hierarchical structures, and thereby endowing the corresponding double-grooved surface with enhanced anisotropic hydrophobicity. A water droplet at a parallel direction to the grooves exhibits a much higher contact angle and a lower roll-off angle than the droplet at a perpendicular direction. The application potential of such anisotropic hydrophobicity has been demonstrated via a fog collection experiment, in which the double-grooved surface can harvest the largest amount of water. Moreover, the fabrication method requires neither post-treatment nor sophisticated equipment, making us anticipate that the double-grooved surface would be competitive in areas where a highly ordered surface, a large surface area and an anisotropic hydrophobicity are preferred.

The transient oxidation of single crystal NiAl+Zr. M.S. Thesis. Final Report

NASA Technical Reports Server (NTRS)

Doychak, J. K.

1983-01-01

The 800 C oxidation of oriented single crystals of Zr doped beta-NiAl was studied using transmission electron microscopy. The oxide phases and metal-oxide orientation relationships were determined to characterize the transient stages of oxidation prior to the transformation to or formation of alpha-Al2O3. On (001) and (012) metal orientations, NiAl2O4 was the first oxide to form followed by delta-Al2O3 which becomes the predominant oxide phase. All oxides were highly epitaxially related to the metal; the orientation relationships being function of parallel cation close-packed directions in the meta and oxide. On (011) and (111) metal orientations, gamma-Al2O3 became the predominant oxide phase rather than delta-Al2O3, indicating a structural stability from the highly epitaxial oxides. The relative concentration of aluminum in the oxide scales increased with time indicating preferential gamma-or delta-Al2O3 growth. The striking feature common to the orientation relationships is the alignment of 100 m and 110 ox directions, believed to result from the minimal 3 percent mismatch between the corresponding (100)m and (110)ox planes.

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.

The Spin and Orientation of Dark Matter Halos Within Cosmic Filaments

NASA Astrophysics Data System (ADS)

Zhang, Youcai; Yang, Xiaohu; Faltenbacher, Andreas; Springel, Volker; Lin, Weipeng; Wang, Huiyuan

2009-11-01

Clusters, filaments, sheets, and voids are the building blocks of the cosmic web. Forming dark matter halos respond to these different large-scale environments, and this in turn affects the properties of galaxies hosted by the halos. It is therefore important to understand the systematic correlations of halo properties with the morphology of the cosmic web, as this informs both about galaxy formation physics and possible systematics of weak lensing studies. In this study, we present and compare two distinct algorithms for finding cosmic filaments and sheets, a task which is far less well established than the identification of dark matter halos or voids. One method is based on the smoothed dark matter density field and the other uses the halo distributions directly. We apply both techniques to one high-resolution N-body simulation and reconstruct the filamentary/sheet like network of the dark matter density field. We focus on investigating the properties of the dark matter halos inside these structures, in particular, on the directions of their spins and the orientation of their shapes with respect to the directions of the filaments and sheets. We find that both the spin and the major axes of filament halos with masses lsim1013 h -1 M sun are preferentially aligned with the direction of the filaments. The spins and major axes of halos in sheets tend to lie parallel to the sheets. There is an opposite mass dependence of the alignment strength for the spin (negative) and major (positive) axes, i.e. with increasing halo mass the major axis tends to be more strongly aligned with the direction of the filament, whereas the alignment between halo spin and filament becomes weaker with increasing halo mass. The alignment strength as a function of the distance to the most massive node halo indicates that there is a transit large-scale environment impact: from the two-dimensional collapse phase of the filament to the three-dimensional collapse phase of the cluster/node halo at small separation. Overall, the two algorithms for filament/sheet identification investigated here agree well with each other. The method based on halos alone can be easily adapted for use with observational data sets.

Angular dependence of coercivity derived from alignment dependence of coercivity in Nd-Fe-B sintered magnets

NASA Astrophysics Data System (ADS)

Matsuura, Yutaka; Nakamura, Tetsuya; Sumitani, Kazushi; Kajiwara, Kentaro; Tamura, Ryuji; Osamura, Kozo

2018-01-01

Experimental results of the alignment dependence of the coercivity in Nd-Fe-B sintered magnets showed that the angle of magnetization reversal for anisotropically aligned magnets was bigger than that obtained from the theoretical results calculated using the postulation that every grain independently reverses its magnetization direction following the 1/cos θ law. The angles of reversed magnetization (θ1) for Nd13.48Co0.55B5.76Febal. with alignment α=0.95 and for Nd12.75Dy0.84B5.81Co0.55Febal. with α=0.96 were 30° and 36°, respectively, which were very similar to that of an ideal magnet with a Gaussian distribution (σ=31° and 44°, respectively) of the grain alignment. In this model, we postulated that every grain independently reversed according to the 1/cos θ law. The calculation results for the angular dependence of the coercivity using the values θ1=ω1(0°)=30°, σ=31° and θ1=ω1(0°)=36°, σ=44° could qualitatively and convincingly explain the observed angular dependence of the coercivity of Nd14.2B6.2Co1.0Febal. and Nd14.2Dy0.3B6.2Co1.0Febal.. It is speculated that the magnetic domain wall is pinned at grains tilted away from the easy magnetization direction, and when the magnetic domain wall de-pins from the tilted grains, the magnetic domain wall jumps through several grains. We suggest that the coercive force of the aligned magnet behaves like a low-aligned magnet owing to the magnetization reversal of the crust of the grains induced by the pinning and subsequent jumping of the magnetic domain wall.

Reduction of the field-aligned potential drop in the polar cap during large geomagnetic storms

NASA Astrophysics Data System (ADS)

Kitamura, N.; Seki, K.; Nishimura, Y.; Hori, T.; Terada, N.; Ono, T.; Strangeway, R. J.

2013-12-01

We have studied photoelectron flows and the inferred field-aligned potential drop in the polar cap during 5 large geomagnetic storms that occurred in the periods when the photoelectron observations in the polar cap were available near the apogee of the FAST satellite (~4000 km) at solar maximum, and the footprint of the satellite paths in the polar cap was under sunlit conditions most of the time. In contrast to the ~20 V potential drop during geomagnetically quiet periods at solar maximum identified by Kitamura et al. [JGR, 2012], the field-aligned potential drop frequently became smaller than ~5 V during the main and early recovery phases of the large geomagnetic storms. Because the potential acts to inhibit photoelectron escape, this result indicates that the corresponding acceleration of ions by the field-aligned potential drop in the polar cap and the lobe region is smaller during the main and early recovery phases of large geomagnetic storms compared to during geomagnetically quiet periods. Under small field-aligned current conditions, the number flux of outflowing ions should be nearly equal to the net escaping electron number flux. Since ions with large flux originating from the cusp/cleft ionosphere convect into the polar cap during geomagnetic storms [e.g., Kitamura et al., JGR, 2010], the net escaping electron number flux should increase to balance the enhanced ion outflows. The magnitude of the field-aligned potential drop would be reduced to let a larger fraction of photoelectrons escape.

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Shear induced alignment of short nanofibers in 3D printed polymer composites.

PubMed

Yunus, Doruk Erdem; Shi, Wentao; Sohrabi, Salman; Liu, Yaling

2016-12-09

3D printing of composite materials offers an opportunity to combine the desired properties of composite materials with the flexibility of additive manufacturing in geometric shape and complexity. In this paper, the shear-induced alignment of aluminum oxide nanowires during stereolithography printing was utilized to fabricate a nanowire reinforced polymer composite. To align the fibers, a lateral oscillation mechanism was implemented and combined with wall pattern printing technique to generate shear flow in both vertical and horizontal directions. A series of specimens were fabricated for testing the composite material's tensile strength. The results showed that mechanical properties of the composite were improved by reinforcement of nanofibers through shear induced alignment. The improvement of tensile strength was approximately ∼28% by aligning the nanowires at 5 wt% (∼1.5% volume fraction) loading of aluminum oxide nanowires.

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.