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

High-performance field emission device utilizing vertically aligned carbon nanotubes-based pillar architectures

NASA Astrophysics Data System (ADS)

Gupta, Bipin Kumar; Kedawat, Garima; Gangwar, Amit Kumar; Nagpal, Kanika; Kashyap, Pradeep Kumar; Srivastava, Shubhda; Singh, Satbir; Kumar, Pawan; Suryawanshi, Sachin R.; Seo, Deok Min; Tripathi, Prashant; More, Mahendra A.; Srivastava, O. N.; Hahm, Myung Gwan; Late, Dattatray J.

2018-01-01

The vertical aligned carbon nanotubes (CNTs)-based pillar architectures were created on laminated silicon oxide/silicon (SiO2/Si) wafer substrate at 775 °C by using water-assisted chemical vapor deposition under low pressure process condition. The lamination was carried out by aluminum (Al, 10.0 nm thickness) as a barrier layer and iron (Fe, 1.5 nm thickness) as a catalyst precursor layer sequentially on a silicon wafer substrate. Scanning electron microscope (SEM) images show that synthesized CNTs are vertically aligned and uniformly distributed with a high density. The CNTs have approximately 2-30 walls with an inner diameter of 3-8 nm. Raman spectrum analysis shows G-band at 1580 cm-1 and D-band at 1340 cm-1. The G-band is higher than D-band, which indicates that CNTs are highly graphitized. The field emission analysis of the CNTs revealed high field emission current density (4mA/cm2 at 1.2V/μm), low turn-on field (0.6 V/μm) and field enhancement factor (6917) with better stability and longer lifetime. Emitter morphology resulting in improved promising field emission performances, which is a crucial factor for the fabrication of pillared shaped vertical aligned CNTs bundles as practical electron sources.

Aligned carbon nanotube-silicon sheets: a novel nano-architecture for flexible lithium ion battery electrodes.

PubMed

Fu, Kun; Yildiz, Ozkan; Bhanushali, Hardik; Wang, Yongxin; Stano, Kelly; Xue, Leigang; Zhang, Xiangwu; Bradford, Philip D

2013-09-25

Aligned carbon nanotube sheets provide an engineered scaffold for the deposition of a silicon active material for lithium ion battery anodes. The sheets are low-density, allowing uniform deposition of silicon thin films while the alignment allows unconstrained volumetric expansion of the silicon, facilitating stable cycling performance. The flat sheet morphology is desirable for battery construction. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Channel length scaling behavior in transistors based on individual versus dense arrays of carbon nanotubes

NASA Astrophysics Data System (ADS)

Brady, Gerald J.; Jinkins, Katherine R.; Arnold, Michael S.

2017-09-01

Recent advances in the solution-phase sorting and assembly of semiconducting single-walled carbon nanotubes (SWCNTs) have enabled significant gains in the performance of field-effect transistors (FETs) constructed from dense arrays of aligned SWCNTs. However, the channel length (LCH) downscaling behaviors of these arrays, which contain some organizational disorder (i.e., rotational misalignment and non-uniform pitch), have not yet been studied in detail below LCH of 100 nm. This study compares the behaviors of individualized SWCNTs with arrays of aligned, solution-cast SWCNTs in FETs with LCH ranging from 30 to 240 nm. The on-state conductance of both individual and array SWCNTs rises with decreasing LCH. Nearly ballistic transport is observed for LCH < 40 nm in both cases, reaching a conductance of 0.82 Go per SWCNT in arrays, where Go = 2e2/h is the quantum conductance. In the off-state, the off-current and subthreshold swing of the individual SWCNTs remain nearly invariant with decreasing LCH whereas array SWCNT FETs suffer from increasing off-state current and deteriorating subthreshold swing for LCH below 100 nm. We analyze array disorder using atomic force microscopy, which shows that crossing SWCNTs that arise from misoriented alignment raise SWCNTs off of the substrate for large portions of the channel when LCH is small. Electrostatics modeling analysis indicates that these raised SWCNTs are a likely contributor to the deteriorating off-current and subthreshold characteristics of arrays. These results demonstrate that improved inter-SWCNT pitch uniformity and alignment with minimal inter-SWCNT interactions will be necessary in order for solution processed SWCNT arrays to reach subthreshold performance on par with isolated SWCNTs. These results are also promising because they show that arrays of solution-processed SWCNTs can nearly reach ballistic conductance in the on-state despite imperfections in pitch and alignment.

Data basic to the engineering of reconstituted flakeboard

Treesearch

Robert L. Geimer

1979-01-01

Flakeboards made with uniform densities throughout their thickness and different degrees of flake alignment were used to establish relationships between bending, tension, and compression values of modulus of elasticity or modulus of rupture (or stress to maximum load) and the variables of specific gravity and flake alignment. An equation using sonic velocity as an...

A New Formulation of Time Domain Boundary Integral Equation for Acoustic Wave Scattering in the Presence of a Uniform Mean Flow

NASA Technical Reports Server (NTRS)

Hu, Fang; Pizzo, Michelle E.; Nark, Douglas M.

2017-01-01

It has been well-known that under the assumption of a constant uniform mean flow, the acoustic wave propagation equation can be formulated as a boundary integral equation, in both the time domain and the frequency domain. Compared with solving partial differential equations, numerical methods based on the boundary integral equation have the advantage of a reduced spatial dimension and, hence, requiring only a surface mesh. However, the constant uniform mean flow assumption, while convenient for formulating the integral equation, does not satisfy the solid wall boundary condition wherever the body surface is not aligned with the uniform mean flow. In this paper, we argue that the proper boundary condition for the acoustic wave should not have its normal velocity be zero everywhere on the solid surfaces, as has been applied in the literature. A careful study of the acoustic energy conservation equation is presented that shows such a boundary condition in fact leads to erroneous source or sink points on solid surfaces not aligned with the mean flow. A new solid wall boundary condition is proposed that conserves the acoustic energy and a new time domain boundary integral equation is derived. In addition to conserving the acoustic energy, another significant advantage of the new equation is that it is considerably simpler than previous formulations. In particular, tangential derivatives of the solution on the solid surfaces are no longer needed in the new formulation, which greatly simplifies numerical implementation. Furthermore, stabilization of the new integral equation by Burton-Miller type reformulation is presented. The stability of the new formulation is studied theoretically as well as numerically by an eigenvalue analysis. Numerical solutions are also presented that demonstrate the stability of the new formulation.

Wet catalyst-support films for production of vertically aligned carbon nanotubes.

PubMed

Alvarez, Noe T; Hamilton, Christopher E; Pint, Cary L; Orbaek, Alvin; Yao, Jun; Frosinini, Aldo L; Barron, Andrew R; Tour, James M; Hauge, Robert H

2010-07-01

A procedure for vertically aligned carbon nanotube (VA-CNT) production has been developed through liquid-phase deposition of alumoxanes (aluminum oxide hydroxides, boehmite) as a catalyst support. Through a simple spin-coating of alumoxane nanoparticles, uniform centimer-square thin film surfaces were coated and used as supports for subsequent deposition of metal catalyst. Uniform VA-CNTs are observed to grow from this film following deposition of both conventional evaporated Fe catalyst, as well as premade Fe nanoparticles drop-dried from the liquid phase. The quality and uniformity of the VA-CNTs are comparable to growth from conventional evaporated layers of Al(2)O(3). The combined use of alumoxane and Fe nanoparticles to coat surfaces represents an inexpensive and scalable approach to large-scale VA-CNT production that makes chemical vapor deposition significantly more competitive when compared to other CNT production techniques.

Patterned growth of carbon nanotubes over vertically aligned silicon nanowire bundles for achieving uniform field emission.

PubMed

Hung, Yung-Jr; Huang, Yung-Jui; Chang, Hsuan-Chen; Lee, Kuei-Yi; Lee, San-Liang

2014-01-01

A fabrication strategy is proposed to enable precise coverage of as-grown carbon nanotube (CNT) mats atop vertically aligned silicon nanowire (VA-SiNW) bundles in order to realize a uniform bundle array of CNT-SiNW heterojunctions over a large sample area. No obvious electrical degradation of as-fabricated SiNWs is observed according to the measured current-voltage characteristic of a two-terminal single-nanowire device. Bundle arrangement of CNT-SiNW heterojunctions is optimized to relax the electrostatic screening effect and to maximize the field enhancement factor. As a result, superior field emission performance and relatively stable emission current over 12 h is obtained. A bright and uniform fluorescent radiation is observed from CNT-SiNW-based field emitters regardless of its bundle periodicity, verifying the existence of high-density and efficient field emitters on the proposed CNT-SiNW bundle arrays.

Superior electro-optical properties of electrically controlled birefringence mode using solution-derived La{sub 2}O{sub 3} films

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

Jeong, Hae-Chang; Park, Hong-Gyu; Lee, Ju Hwan

2015-11-15

The authors demonstrate a high performance electrically controlled birefringence (ECB) mode with solution-derived La{sub 2}O{sub 3} films at various molar concentrations. Uniform and homogeneous liquid crystal (LC) alignment was spontaneously achieved on the La{sub 2}O{sub 3} films for lanthanum concentrations at ratios greater than and equal to 0.2. A preferred orientation of LC molecules appeared along the filling direction, and the LC alignment was maintained via van der Waals force by nanocrystals of the La{sub 2}O{sub 3} films. The LC alignment mechanism was confirmed by x-ray photoelectron spectroscopy and high-resolution transmission electron microscopy analysis. Superior electro-optical characteristics of the ECBmore » cells constructed with solution-derived La{sub 2}O{sub 3} films were observed, which suggests that the proposed solution-derived La{sub 2}O{sub 3} films have strong potential for use in the production of advanced LC displays.« less

Field alignment of bent-core smectic liquid crystals for analog optical phase modulation

NASA Astrophysics Data System (ADS)

Shen, Y.; Goodhew, L.; Shao, R.; Moran, M.; Korblova, E.; Walba, D. M.; Clark, N. A.; Maclennan, J. E.; Rudquist, P.

2015-05-01

A general method for aligning bent-core smectic liquid crystal materials is described. Alternating electric fields between interdigitated electrodes patterned on one cell surface create torques on the liquid crystal that result in uniform "bookshelf" orientation of the smectic layers. The aligned cell can then be driven in the conventional way by applying an electric field between all of the stripe electrodes connected together and a monolithic electrode on the other cell surface. Fast, analog, optical phase-only modulation is demonstrated in a device containing a polar, bent-core SmAPF material aligned using this technique.

Optimizing alignment and growth of low-loss YAG single crystal fibers using laser heated pedestal growth technique.

PubMed

Bera, Subhabrata; Nie, Craig D; Soskind, Michael G; Harrington, James A

2017-12-10

The effect of misalignments of different optical components in the laser heated pedestal growth apparatus have been modeled using Zemax optical design software. By isolating the misalignments causing the non-uniformity in the melt zone, the alignment of the components was fine-tuned. Using this optimized alignment, low-loss YAG single crystal fibers of 120 μm diameter were grown, with total attenuation loss as low as 0.5 dB/m at 1064 nm.

A self-aligned dry etching method for mechanical strain enhancement of germanium and its uniformity improvement for photonic applications

NASA Astrophysics Data System (ADS)

Lin, Yiding; Ma, Danhao; Lee, Kwang Hong; Michel, Jurgen; Tan, Chuan Seng

2018-02-01

A self-aligned dry etching method was proposed and verified theoretically to enhance the magnitude and simultaneously improve the uniformity of the tensile strain in a germanium (Ge) wave-guide (WG), with the help of tensile-stressed SiN stressor at the WG sidewalls. The SiN-strained germanium-on-insulator (GOI) WG was also experimentally demonstrated. Significant tensile strain was observed in the Ge material via micro-Raman measurements. This method could potentially facilitate a Ge photodetector with its optical detection range extended further towards longer wavelength and to be comparable with that of state-of-the-art InGaAs detectors.

Simultaneous dual-color fluorescence microscope: a characterization study.

PubMed

Li, Zheng; Chen, Xiaodong; Ren, Liqiang; Song, Jie; Li, Yuhua; Zheng, Bin; Liu, Hong

2013-01-01

High spatial resolution and geometric accuracy is crucial for chromosomal analysis of clinical cytogenetic applications. High resolution and rapid simultaneous acquisition of multiple fluorescent wavelengths can be achieved by utilizing concurrent imaging with multiple detectors. However, such class of microscopic systems functions differently from traditional fluorescence microscopes. To develop a practical characterization framework to assess and optimize the performance of a high resolution and dual-color fluorescence microscope designed for clinical chromosomal analysis. A dual-band microscopic imaging system utilizes a dichroic mirror, two sets of specially selected optical filters, and two detectors to simultaneously acquire two fluorescent wavelengths. The system's geometric distortion, linearity, the modulation transfer function, and the dual detectors' alignment were characterized. Experiment results show that the geometric distortion at lens periphery is less than 1%. Both fluorescent channels show linear signal responses, but there exists discrepancy between the two due to the detectors' non-uniform response ratio to different wavelengths. In terms of the spatial resolution, the two contrast transfer function curves trend agreeably with the spatial frequency. The alignment measurement allows quantitatively assessing the cameras' alignment. A result image of adjusted alignment is demonstrated to show the reduced discrepancy by using the alignment measurement method. In this paper, we present a system characterization study and its methods for a specially designed imaging system for clinical cytogenetic applications. The presented characterization methods are not only unique to this dual-color imaging system but also applicable to evaluation and optimization of other similar multi-color microscopic image systems for improving their clinical utilities for future cytogenetic applications.

Langmuir Films of Flexible Polymers Transferred to Aqueous/Liquid Crystal Interfaces Induce Uniform Azimuthal Alignment of the Liquid Crystal

PubMed Central

Kinsinger, Michael I.; Buck, Maren E.; Meli, Maria-Victoria; Abbott, Nicholas L.; Lynn, David M.

2009-01-01

We reported recently that amphiphilic polymers can be assembled at interfaces created between aqueous phases and thermotropic liquid crystals (LCs) in ways that (i) couple the organization of the polymer to the order of the LC and (ii) respond to changes in the properties of aqueous phases that can be characterized as changes in the optical appearance of the LC. This investigation sought to characterize the behavior of aqueous-LC interfaces decorated with uniaxially compressed thin films of polymers transferred by Langmuir-Schaefer (LS) transfer. Here, we report physicochemical characterization of interfaces created between aqueous phases and the thermotropic LC 4-cyano-4’-pentylbiphenyl (5CB) decorated with Langmuir films of a novel amphiphilic polymer (polymer 1), synthesized by the addition of hydrophobic and hydrophilic side chains to poly(2-vinyl-4,4’-dimethylazlactone). Initial characterization of this system resulted in the unexpected observation of uniform azimuthal alignment of 5CB after LS transfer of the polymer films to aqueous-5CB interfaces. This paper describes characterization of Langmuir films of polymer 1 hosted at aqueous-5CB interfaces as well as the results of our investigations into the origins of the uniform ordering of the LC observed upon LS transfer. Our results, when combined, support the conclusion that uniform azimuthal alignment of 5CB is the result of long-range ordering of polymer chains in the Langmuir films (in a preferred direction orthogonal to the direction of compression) that is generated during uniaxial compression of the films prior to LS transfer. Although past studies of Langmuir films of polymers at aqueous-air interfaces have demonstrated that in-plane alignment of polymer backbones can be induced by uniaxial compression, these past reports have generally made use of polymers with rigid backbones. One important outcome of this current study is thus the observation of anisotropy and long-range order in Langmuir films of a novel flexible polymer. A second important outcome is the observation that the existence, extent, and dynamics of this order can be identified and characterized optically by transfer of the Langmuir film to a thin film of LC. Additional characterization of Langmuir films of two other flexible polymers [poly(methyl methacrylate) and poly(vinyl stearate)] using this method also resulted in uniform azimuthal alignment of 5CB, suggesting that the generation of long-range order in uniaxially compressed Langmuir films of polymers may also occur more generally over a broader range of polymers with flexible backbones. PMID:19836025

Engineered plant biomass feedstock particles

DOEpatents

Dooley, James H [Federal Way, WA; Lanning, David N [Federal Way, WA; Broderick, Thomas F [Lake Forest Park, WA

2012-04-17

A new class of plant biomass feedstock particles characterized by consistent piece size and shape uniformity, high skeletal surface area, and good flow properties. The particles of plant biomass material having fibers aligned in a grain are characterized by a length dimension (L) aligned substantially parallel to the grain and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. In particular, the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.W dimensions define a pair of substantially parallel top and bottom surfaces. The L.times.W surfaces of particles with L/H dimension ratios of 4:1 or less are further elaborated by surface checking between longitudinally arrayed fibers. The length dimension L is preferably aligned within 30.degree. parallel to the grain, and more preferably within 10.degree. parallel to the grain. The plant biomass material is preferably selected from among wood, agricultural crop residues, plantation grasses, hemp, bagasse, and bamboo.

JingleBells: A Repository of Immune-Related Single-Cell RNA-Sequencing Datasets.

PubMed

Ner-Gaon, Hadas; Melchior, Ariel; Golan, Nili; Ben-Haim, Yael; Shay, Tal

2017-05-01

Recent advances in single-cell RNA-sequencing (scRNA-seq) technology increase the understanding of immune differentiation and activation processes, as well as the heterogeneity of immune cell types. Although the number of available immune-related scRNA-seq datasets increases rapidly, their large size and various formats render them hard for the wider immunology community to use, and read-level data are practically inaccessible to the non-computational immunologist. To facilitate datasets reuse, we created the JingleBells repository for immune-related scRNA-seq datasets ready for analysis and visualization of reads at the single-cell level (http://jinglebells.bgu.ac.il/). To this end, we collected the raw data of publicly available immune-related scRNA-seq datasets, aligned the reads to the relevant genome, and saved aligned reads in a uniform format, annotated for cell of origin. We also added scripts and a step-by-step tutorial for visualizing each dataset at the single-cell level, through the commonly used Integrated Genome Viewer (www.broadinstitute.org/igv/). The uniform scRNA-seq format used in JingleBells can facilitate reuse of scRNA-seq data by computational biologists. It also enables immunologists who are interested in a specific gene to visualize the reads aligned to this gene to estimate cell-specific preferences for splicing, mutation load, or alleles. Thus JingleBells is a resource that will extend the usefulness of scRNA-seq datasets outside the programming aficionado realm. Copyright © 2017 by The American Association of Immunologists, Inc.

Comparison of Friction Characteristics on TN and VA Mode Alignment Films with Friction Force Microscopy

NASA Astrophysics Data System (ADS)

Kwak, Musun; Chung, Hanrok; Kwon, Hyukmin; Kim, Jehyun; Han, Daekyung; Yi, Yoonseon; Lee, Sangmun; Lee, Chulgu; Cha, Sooyoul

Using frictional force microscopy (FFM), the friction surface characteristics were compared between twisted nematic (TN) mode and vertical alignment (VA) mode alignment films (AFs). The friction asymmetry was detected depending on temperature conditions on TN mode AF, but not on VA mode AF. The difference between two modes was explained by leaning intermolecular repulsion caused by the pre-tilt angle uniformity and the density of side chain. No level difference according to temperature conditions appeared when the pre-tilt angle were measured after liquid crystal (LC) injection.

Optimized mirror shape tuning using beam weightings based on distance, angle of incidence, reflectivity, and power.

PubMed

Goldberg, Kenneth A; Yashchuk, Valeriy V

2016-05-01

For glancing-incidence optical systems, such as short-wavelength optics used for nano-focusing, incorporating physical factors in the calculations used for shape optimization can improve performance. Wavefront metrology, including the measurement of a mirror's shape or slope, is routinely used as input for mirror figure optimization on mirrors that can be bent, actuated, positioned, or aligned. Modeling shows that when the incident power distribution, distance from focus, angle of incidence, and the spatially varying reflectivity are included in the optimization, higher Strehl ratios can be achieved. Following the works of Maréchal and Mahajan, optimization of the Strehl ratio (for peak intensity with a coherently illuminated system) occurs when the expectation value of the phase error's variance is minimized. We describe an optimization procedure based on regression analysis that incorporates these physical parameters. This approach is suitable for coherently illuminated systems of nearly diffraction-limited quality. Mathematically, this work is an enhancement of the methods commonly applied for ex situ alignment based on uniform weighting of all points on the surface (or a sub-region of the surface). It follows a similar approach to the optimization of apodized and non-uniformly illuminated optical systems. Significantly, it reaches a different conclusion than a more recent approach based on minimization of focal plane ray errors.

Shoe heel abrasion and its possible biomechanical cause: a transversal study with infantry recruits.

PubMed

Baumfeld, Daniel; Raduan, Fernando C; Macedo, Benjamim; Silva, Thiago Alexandre Alves; Baumfeld, Tiago; Favato, Danilo Fabrino; de Andrade, Marco Antonio Percope; Nery, Caio

2015-11-19

Excessive shoe heel abrasion is of concern to patients and shoe manufacturers, but little scientific information is available about this feature and its possible causes. The purpose of this study was to relate this phenomenon with biomechanical factors that could predispose to shoe heel abrasion. Ninety-seven recruits (median age 25) were enrolled in this study. Shoe abrasion was assessed manually with a metric plastic tape on the posterior part of the heel that comes in contact with the ground. The number of sprains, foot alignment, and calf muscle shortening (Silfverskiold test) was also assessed in order to relate it with shoe heel abrasion. After using our exclusion criteria, 86 recruits and 172 were considered for this study. The most common abrasion site was the lateral portion of the heel surface (50 %). Forty-four percent of the participants had neutral hind-foot alignment and 39 % had valgus alignment. Twenty-six (30 %) patients have had previous ankle or foot sprains. Neutral foot was related with less calf muscle shortening. On the other hand, valgus hind-foot alignment was more associated with Achilles shortening (p < 0.05). Patients with neutral alignment were associated with more uniform shoe heel abrasion and varus feet were associated with more central and lateral abrasion (p < 0.05). The pattern of shoe heel abrasion was not statistically related with calf muscle shortening nor with number of sprains. This study was able to correlate shoe heel abrasion with biomechanical causes (neutral alignment-uniform abrasion/varus alignment-central and lateral abrasion). More effort has to be done to continue evaluating outsole abrasion with its possible biomechanical cause in order to predict and treat possible associated injuries.

Analysis of Fringe Field Formed Inside LDA Measurement Volume Using Compact Two Hololens Imaging Systems

NASA Astrophysics Data System (ADS)

Ghosh, Abhijit; Nirala, A. K.; Yadav, H. L.

2018-03-01

We have designed and fabricated four LDA optical setups consisting of aberration compensated four different compact two hololens imaging systems. We have experimentally investigated and realized a hololens recording geometry which is interferogram of converging spherical wavefront with mutually coherent planar wavefront. Proposed real time monitoring and actual fringe field analysis techniques allow complete characterizations of fringes formed at measurement volume and permit to evaluate beam quality, alignment and fringe uniformity with greater precision. After experimentally analyzing the fringes formed at measurement volume by all four imaging systems, it is found that fringes obtained using compact two hololens imaging systems get improved both qualitatively and quantitatively compared to that obtained using conventional imaging system. Results indicate qualitative improvement of non-uniformity in fringe thickness and micro intensity variations perpendicular to the fringes, and quantitative improvement of 39.25% in overall average normalized standard deviations of fringe width formed by compact two hololens imaging systems compare to that of conventional imaging system.

Disorganization of Cortical Microtubules Stimulates Tangential Expansion and Reduces the Uniformity of Cellulose Microfibril Alignment among Cells in the Root of Arabidopsis1

PubMed Central

Baskin, Tobias I.; Beemster, Gerrit T.S.; Judy-March, Jan E.; Marga, Françoise

2004-01-01

To test the role of cortical microtubules in aligning cellulose microfibrils and controlling anisotropic expansion, we exposed Arabidopsis thaliana roots to moderate levels of the microtubule inhibitor, oryzalin. After 2 d of treatment, roots grow at approximately steady state. At that time, the spatial profiles of relative expansion rate in length and diameter were quantified, and roots were cryofixed, freeze-substituted, embedded in plastic, and sectioned. The angular distribution of microtubules as a function of distance from the tip was quantified from antitubulin immunofluorescence images. In alternate sections, the overall amount of alignment among microfibrils and their mean orientation as a function of position was quantified with polarized-light microscopy. The spatial profiles of relative expansion show that the drug affects relative elongation and tangential expansion rates independently. The microtubule distributions averaged to transverse in the growth zone for all treatments, but on oryzalin the distributions became broad, indicating poorly organized arrays. At a subcellular scale, cellulose microfibrils in oryzalin-treated roots were as well aligned as in controls; however, the mean alignment direction, while consistently transverse in the controls, was increasingly variable with oryzalin concentration, meaning that microfibril orientation in one location tended to differ from that of a neighboring location. This conclusion was confirmed by direct observations of microfibrils with field-emission scanning electron microscopy. Taken together, these results suggest that cortical microtubules ensure microfibrils are aligned consistently across the organ, thereby endowing the organ with a uniform mechanical structure. PMID:15299138

New concept for in-line OLED manufacturing

NASA Astrophysics Data System (ADS)

Hoffmann, U.; Landgraf, H.; Campo, M.; Keller, S.; Koening, M.

2011-03-01

A new concept of a vertical In-Line deposition machine for large area white OLED production has been developed. The concept targets manufacturing on large substrates (>= Gen 4, 750 x 920 mm2) using linear deposition source achieving a total material utilization of >= 50 % and tact time down to 80 seconds. The continuously improved linear evaporation sources for the organic material achieve thickness uniformity on Gen 4 substrate of better than +/- 3 % and stable deposition rates down to less than 0.1 nm m/min and up to more than 100 nm m/min. For Lithium-Fluoride but also for other high evaporation temperature materials like Magnesium or Silver a linear source with uniformity better than +/- 3 % has been developed. For Aluminum we integrated a vertical oriented point source using wire feed to achieve high (> 150 nm m/min) and stable deposition rates. The machine concept includes a new vertical vacuum handling and alignment system for Gen 4 shadow masks. A complete alignment cycle for the mask can be done in less than one minute achieving alignment accuracy in the range of several 10 μm.

Multiciliated cell basal bodies align in stereotypical patterns coordinated by the apical cytoskeleton

PubMed Central

Herawati, Elisa; Kanoh, Hatsuho

2016-01-01

Multiciliated cells (MCCs) promote fluid flow through coordinated ciliary beating, which requires properly organized basal bodies (BBs). Airway MCCs have large numbers of BBs, which are uniformly oriented and, as we show here, align linearly. The mechanism for BB alignment is unexplored. To study this mechanism, we developed a long-term and high-resolution live-imaging system and used it to observe green fluorescent protein–centrin2–labeled BBs in cultured mouse tracheal MCCs. During MCC differentiation, the BB array adopted four stereotypical patterns, from a clustering “floret” pattern to the linear “alignment.” This alignment process was correlated with BB orientations, revealed by double immunostaining for BBs and their asymmetrically associated basal feet (BF). The BB alignment was disrupted by disturbing apical microtubules with nocodazole and by a BF-depleting Odf2 mutation. We constructed a theoretical model, which indicated that the apical cytoskeleton, acting like a viscoelastic fluid, provides a self-organizing mechanism in tracheal MCCs to align BBs linearly for mucociliary transport. PMID:27573463

Gum tragacanth/poly(l-lactic acid) nanofibrous scaffolds for application in regeneration of peripheral nerve damage.

PubMed

Ranjbar-Mohammadi, Marziyeh; Prabhakaran, Molamma P; Bahrami, S Hajir; Ramakrishna, Seeram

2016-04-20

Nanofibrous nerve guides have gained huge interest in supporting the peripheral nerve regeneration due to their abilities to simulate the topography, mechanical, biological and extracellular matrix morphology of native tissue. Gum tragacanth (GT) is a biocompatible mixture of polysaccharides that has been used in biomedical applications. During this study, we fabricated aligned and random nanofibers from poly(l-lactic acid) and gum tragacanth (PLLA/GT) in various ratios (100:0, 75:25, and 50:50) by electrospinning. Scanning electron microscope demonstrated smooth and uniform nanofibers with diameters in the range of 733±65nm and 226±73nm for align PLLA and random PLLA/GT 50:50 nanofibers, respectively. FTIR analysis, contact angle, in vitro biodegradation and tensile measurements were carried out to evaluate the chemical and mechanical properties of the different scaffolds. PLLA/GT 75:25 exhibited the most balanced properties compared to other scaffolds and was used for in vitro culture of nerve cells (PC12) to assess the potential of using these scaffolds as a substrate for nerve regeneration. The cells were found to attach and proliferate on aligned PLLA/GT 75:25 scaffolds, expressing bi-polar neurite extensions and the orientation of nerve cells was along the direction of the fiber alignment. Results of 8 days of in vitro culture of PC12 cells on aligned PLLA/GT 75:25 nanofibers, showed 20% increase in cell proliferation compared to PLLA/GT 75:25 random nanofibers. PLLA/GT 75:25 aligned nanofibers acted as a favorable cue to support neurite outgrowth and nerve cell elongation compared with PLLA nanofibers. Our results showed that aligned PLLA/GT 75:25 nanofibers are promising substrates for application as bioengineered grafts for nerve tissue regeneration. Copyright © 2015 Elsevier Ltd. All rights reserved.

Scalable alignment of CdS nanowires based on efficient roll-on transfer technique.

PubMed

Yan, Shancheng; Shi, Yi; Xiao, Zhongdang; Wang, Junzhuan; Hu, Dong; Xul, Xin; Lu, Tao; Liu, Aili; Gao, Fan

2013-06-01

A roll-on transfer strategy is developed to enable large-scale and uniform assembly of CdS nanowires on various rigid and flexible substrate materials. In this method, the CdS nanowires were synthesized by the hydrothermal method. The dispersed CdS NWs could be firstly aligned and selectively deposited at the micro/nanochannels between aligned nanofibers on the surface of the donor roller as a result of evaporation-induced flow and capillary action, and then the directional and aligned transfer of the CdS NWs from the donor roller to a receiver substrate via roll-on transfer technique. Finally, a device structures consisting of the nanowire channel and two metal electrodes was fabricated. The electrical property of this device was observed.

Aligned metal absorbers and the ultraviolet background at the end of reionization

NASA Astrophysics Data System (ADS)

Doughty, Caitlin; Finlator, Kristian; Oppenheimer, Benjamin D.; Davé, Romeel; Zackrisson, Erik

2018-04-01

We use observations of spatially aligned C II, C IV, Si II, Si IV, and O I absorbers to probe the slope and intensity of the ultraviolet background (UVB) at z ˜ 6. We accomplish this by comparing observations with predictions from a cosmological hydrodynamic simulation using three trial UVBs applied in post-processing: a spectrally soft, fluctuating UVB calculated using multifrequency radiative transfer; a soft, spatially uniform UVB; and a hard, spatially uniform `quasars-only' model. When considering our paired high-ionization absorbers (C IV/Si IV), the observed statistics strongly prefer the hard, spatially uniform UVB. This echoes recent findings that cosmological simulations generically underproduce strong C IV absorbers at z > 5. A single low/high ionization pair (Si II/Si IV), by contrast, shows a preference for the HM12 UVB, whereas two more (C II/C IV and O I/C IV) show no preference for any of the three UVBs. Despite this, future observations of specific absorbers, particularly Si IV/C IV, with next-generation telescopes probing to lower column densities should yield tighter constraints on the UVB.

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

PubMed

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

2015-10-01

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

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

PubMed Central

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

2015-01-01

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

Modeling and optimization of atomic layer deposition processes on vertically aligned carbon nanotubes.

PubMed

Yazdani, Nuri; Chawla, Vipin; Edwards, Eve; Wood, Vanessa; Park, Hyung Gyu; Utke, Ivo

2014-01-01

Many energy conversion and storage devices exploit structured ceramics with large interfacial surface areas. Vertically aligned carbon nanotube (VACNT) arrays have emerged as possible scaffolds to support large surface area ceramic layers. However, obtaining conformal and uniform coatings of ceramics on structures with high aspect ratio morphologies is non-trivial, even with atomic layer deposition (ALD). Here we implement a diffusion model to investigate the effect of the ALD parameters on coating kinetics and use it to develop a guideline for achieving conformal and uniform thickness coatings throughout the depth of ultra-high aspect ratio structures. We validate the model predictions with experimental data from ALD coatings of VACNT arrays. However, the approach can be applied to predict film conformality as a function of depth for any porous topology, including nanopores and nanowire arrays.

Detecting and accounting for multiple sources of positional variance in peak list registration analysis and spin system grouping.

PubMed

Smelter, Andrey; Rouchka, Eric C; Moseley, Hunter N B

2017-08-01

Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include automated protein resonance assignment and protein structure calculation software tools. Prior to these analyses, peak lists must be aligned to each other and sets of related peaks must be grouped based on common chemical shift dimensions. Even when programs can perform peak grouping, they require the user to provide uniform match tolerances or use default values. However, peak grouping is further complicated by multiple sources of variance in peak position limiting the effectiveness of grouping methods that utilize uniform match tolerances. In addition, no method currently exists for deriving peak positional variances from single peak lists for grouping peaks into spin systems, i.e. spin system grouping within a single peak list. Therefore, we developed a complementary pair of peak list registration analysis and spin system grouping algorithms designed to overcome these limitations. We have implemented these algorithms into an approach that can identify multiple dimension-specific positional variances that exist in a single peak list and group peaks from a single peak list into spin systems. The resulting software tools generate a variety of useful statistics on both a single peak list and pairwise peak list alignment, especially for quality assessment of peak list datasets. We used a range of low and high quality experimental solution NMR and solid-state NMR peak lists to assess performance of our registration analysis and grouping algorithms. Analyses show that an algorithm using a single iteration and uniform match tolerances approach is only able to recover from 50 to 80% of the spin systems due to the presence of multiple sources of variance. Our algorithm recovers additional spin systems by reevaluating match tolerances in multiple iterations. To facilitate evaluation of the algorithms, we developed a peak list simulator within our nmrstarlib package that generates user-defined assigned peak lists from a given BMRB entry or database of entries. In addition, over 100,000 simulated peak lists with one or two sources of variance were generated to evaluate the performance and robustness of these new registration analysis and peak grouping algorithms.

Controlled growth of ZnO/Zn₁-xPbxSe core-shell nanowires and their interfacial electronic energy alignment.

PubMed

Chen, Z H; Yeung, S Y; Li, H; Qian, J C; Zhang, W J; Li, Y Y; Bello, I

2012-05-21

ZnO/Zn(1-x)Pb(x)Se core-shell nanowires (NWs) have been synthesized by a solution based surface ion transfer method at various temperatures. The energy dispersive spectroscopic (EDS) mapping of single NWs suggests that the Zn, Pb and Se atoms are uniformly distributed in their shell layers. The ternary Zn(1-x)Pb(x)Se layers with tunable bandgaps extend the band-edge of optical absorption from 450 nm to 700 nm contrasting with the binary ZnSe layers. The ultraviolet photoelectron spectroscopic (UPS) analysis reveals a transition from the type I to type II band alignment when the x fraction decreases from 0.66 to the value of 0.36 in the nanoshell layers. This quantitative investigation of electronic energy levels at ZnO and Zn(1-x)Pb(x)Se interfaces indicates that the proper type II band alignment is well suited for photovoltaic energy conversion. The photovoltaic cells comprising a ZnO/Zn(1-x)Pb(x)Se nano-heterojunction with the optimized Pb content are expected to be more efficient than the devices sensitized by binary ZnSe or PbSe.

Aligned Incentives: Could the Army’s Award System Inadvertently be Hindering Counterinsurgency Operations

DTIC Science & Technology

2009-06-01

and dining room facilities, payment by cheque, special uniform and markings on the uniform, admission to the membership of professional bodies ...accompanied President Lincoln’s body to its burial site; Peter Collier, Medal of Honor: Portraits of Valor beyond the Call of Duty (New York: Artisan, 2003...insurgent/counterinsurgent wars are not recent developments; there is a significant body of literature already devoted to them. Discussed below are some of

Functionalized vertically aligned ZnO nanorods for application in electrolyte-insulator-semiconductor based pH sensors and label-free immuno-sensors

NASA Astrophysics Data System (ADS)

Kumar, Narendra; Senapati, Sujata; Kumar, Satyendra; Kumar, Jitendra; Panda, Siddhartha

2016-04-01

Vertically aligned ZnO nanorods were grown on a SiO2/Si surface by optimization of the temperature and atmosphere for annealing of the seed. The seed layer annealed at 500 °C in vacuum provided well separated and uniform seeds which also provided the best condition to get densely packed, uniformly distributed, and vertically aligned nanorods. These nanorods grown on the substrates were used to fabricate electrolyte-insulator-semiconductor (EIS) devices for pH sensing. Etching of ZnO at acidic pH prevents the direct use of nanorods for pH sensing. Therefore, the nanorods functionalised with 3-aminopropyltriethoxysilane (APTES) were utilized for pH sensing and showed the pH sensitivity of 50.1 mV/pH. APTES is also known to be used as a linker to immobilize biomolecules (such as antibodies). The EIS device with APTES functionalized nanorods was used for the label free detection of prostate-specific antigen (PSA). Finally, voltage shifts of 23 mV and 35 mV were observed with PSA concentrations of 1 ng/ml and 100 ng/ml, respectively.

Conformal Fe3O4 sheath on aligned carbon nanotube scaffolds as high-performance anodes for lithium ion batteries.

PubMed

Wu, Yang; Wei, Yang; Wang, Jiaping; Jiang, Kaili; Fan, Shoushan

2013-02-13

A uniform Fe(3)O(4) sheath is magnetron sputtered onto aligned carbon nanotube (CNT) scaffolds that are directly drawn from CNT arrays. The Fe(3)O(4)-CNT composite electrode, with the size of Fe(3)O(4) confined to 5-7 nm, exhibits a high reversible capacity over 800 mAh g(-1) based on the total electrode mass, remarkable capacity retention, as well as high rate capability. The excellent performance is attributable to the superior electrical conductivity of CNTs, the uniform loading of Fe(3)O(4) sheath, and the structural retention of the composite anode on cycling. As Fe(3)O(4) is inexpensive and environmentally friendly, and the synthesis of Fe(3)O(4)-CNT is free of chemical wastes, this composite anode material holds considerable promise for high-performance lithium ion batteries.

Alternative generation of well-aligned uniform lying helix texture in a cholesteric liquid crystal cell

NASA Astrophysics Data System (ADS)

Yu, Chia-Hua; Wu, Po-Chang; Lee, Wei

2017-10-01

This work demonstrates a simple approach for obtaining a well-aligned uniform lying helix (ULH) texture and a tri-bistable feature at ambient temperature in a typical 90°-twisted cell filled with a short-pitch cholesteric liquid crystal. This ULH texture is obtained at room temperature from initially field-induced helix-free homeotropic state by gradually decreasing the applied voltage. Depending on the way and rate of reducing the voltage, three stable states (i.e., Grandjean planar, focal conic, and ULH) are generated and switching between any two of them is realized. Moreover, the electrical operation of the cell in the ULH state enables the tunability in phase retardation via the deformation of the ULH. The observations made in this work may be useful for applications such as tunable phase modulators and energy-efficient photonic devices.

High Efficient THz Emission From Unbiased and Biased Semiconductor Nanowires Fabricated Using Electron Beam Lithography

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

Balci, Soner; Czaplewski, David A.; Jung, Il Woong

Besides having perfect control on structural features, such as vertical alignment and uniform distribution by fabricating the wires via e-beam lithography and etching process, we also investigated the THz emission from these fabricated nanowires when they are applied DC bias voltage. To be able to apply a voltage bias, an interdigitated gold (Au) electrode was patterned on the high-quality InGaAs epilayer grown on InP substrate bymolecular beam epitaxy. Afterwards, perfect vertically aligned and uniformly distributed nanowires were fabricated in between the electrodes of this interdigitated pattern so that we could apply voltage bias to improve the THz emission. As amore » result, we achieved enhancement in the emitted THz radiation by ~four times, about 12 dB increase in power ratio at 0.25 THz with a DC biased electric field compared with unbiased NWs.« less

Strain-induced alignment and phase behavior of blue phase liquid crystals confined to thin films.

PubMed

Bukusoglu, Emre; Martinez-Gonzalez, Jose A; Wang, Xiaoguang; Zhou, Ye; de Pablo, Juan J; Abbott, Nicholas L

2017-12-06

We report on the influence of surface confinement on the phase behavior and strain-induced alignment of thin films of blue phase liquid crystals (BPs). Confining surfaces comprised of bare glass, dimethyloctadecyl [3-(trimethoxysilyl)propyl] ammonium chloride (DMOAP)-functionalized glass, or polyvinyl alcohol (PVA)-coated glass were used with or without mechanically rubbing to influence the azimuthal anchoring of the BPs. These experiments reveal that confinement can change the phase behavior of the BP films. For example, in experiments performed with rubbed-PVA surfaces, we measured the elastic strain of the BPs to change the isotropic-BPII phase boundary, suppressing formation of BPII for film thicknesses incommensurate with the BPII lattice. In addition, we observed strain-induced alignment of the BPs to exhibit a complex dependence on both the surface chemistry and azimuthal alignment of the BPs. For example, when using bare glass surfaces causing azimuthally degenerate and planar anchoring, BPI oriented with (110) planes of the unit cell parallel to the contacting surfaces for thicknesses below 3 μm but transitioned to an orientation with (200) planes aligned parallel to the contacting surfaces for thicknesses above 4 μm. In contrast, BPI aligned with (110) planes parallel to confining surfaces for all other thicknesses and surface treatments, including bare glass with uniform azimuthal alignment. Complementary simulations based on minimization of the total free energy (Landau-de Gennes formalism) confirmed a thickness-dependent reorientation due to strain of BPI unit cells within a window of surface anchoring energies and in the absence of uniform azimuthal alignment. In contrast to BPI, BPII did not exhibit thickness-dependent orientations but did exhibit orientations that were dependent on the surface chemistry, a result that was also captured in simulations by varying the anchoring energies. Overall, the results in this paper reveal that the orientations assumed by BPs in thin films reflect a complex interplay of surface interactions and elastic energies associated with strain of the BP lattice. The results also provide new principles and methods to control the structure and properties of BP thin films, which may find use in BP-templated material synthesis, and BP-based optical and electronic devices.

Extracting DNA words based on the sequence features: non-uniform distribution and integrity.

PubMed

Li, Zhi; Cao, Hongyan; Cui, Yuehua; Zhang, Yanbo

2016-01-25

DNA sequence can be viewed as an unknown language with words as its functional units. Given that most sequence alignment algorithms such as the motif discovery algorithms depend on the quality of background information about sequences, it is necessary to develop an ab initio algorithm for extracting the "words" based only on the DNA sequences. We considered that non-uniform distribution and integrity were two important features of a word, based on which we developed an ab initio algorithm to extract "DNA words" that have potential functional meaning. A Kolmogorov-Smirnov test was used for consistency test of uniform distribution of DNA sequences, and the integrity was judged by the sequence and position alignment. Two random base sequences were adopted as negative control, and an English book was used as positive control to verify our algorithm. We applied our algorithm to the genomes of Saccharomyces cerevisiae and 10 strains of Escherichia coli to show the utility of the methods. The results provide strong evidences that the algorithm is a promising tool for ab initio building a DNA dictionary. Our method provides a fast way for large scale screening of important DNA elements and offers potential insights into the understanding of a genome.

Highly Anisotropic Adhesive Film Made from Upside-Down, Flat, and Uniform Vertically Aligned CNTs.

PubMed

Hong, Sanghyun; Lundstrom, Troy; Ghosh, Ranajay; Abdi, Hamed; Hao, Ji; Jeoung, Sun Kyoung; Su, Paul; Suhr, Jonghwan; Vaziri, Ashkan; Jalili, Nader; Jung, Yung Joon

2016-12-14

We have created a multifunctional dry adhesive film with transferred vertically aligned carbon nanotubes (VA-CNTs). This unique VA-CNT film was fabricated by a multistep transfer process, converting the flat and uniform bottom of VA-CNTs grown on atomically flat silicon wafer substrates into the top surface of an adhesive layer. Unlike as-grown VA-CNTs, which have a nonuniform surface, randomly entangled CNT arrays, and a weak interface between the CNTs and substrates, this transferred VA-CNT film shows an extremely high coefficient of static friction (COF) of up to 60 and a shear adhesion force 30 times higher (12 N/cm 2 ) than that of the as-grown VA-CNTs under a very small preloading of 0.2 N/cm 2 . Moreover, a near-zero normal adhesion force was observed with 20 mN/cm 2 preloading and a maximum 100-μm displacement in a piezo scanner, demonstrating ideal properties for an artificial gecko foot. Using this unique structural feature and anisotropic adhesion properties, we also demonstrate effective removal and assembly of nanoparticles into organized micrometer-scale circular and line patterns by a single brushing of this flat and uniform VA-CNT film.

On the colour of wing scales in butterflies: iridescence and preferred orientation of single gyroid photonic crystals

PubMed Central

2017-01-01

Lycaenid butterflies from the genera Callophrys, Cyanophrys and Thecla have evolved remarkable biophotonic gyroid nanostructures within their wing scales that have only recently been replicated by nanoscale additive manufacturing. These nanostructures selectively reflect parts of the visible spectrum to give their characteristic non-iridescent, matte-green appearance, despite a distinct blue–green–yellow iridescence predicted for individual crystals from theory. It has been hypothesized that the organism must achieve its uniform appearance by growing crystals with some restrictions on the possible distribution of orientations, yet preferential orientation observed in Callophrys rubi confirms that this distribution need not be uniform. By analysing scanning electron microscope and optical images of 912 crystals in three wing scales, we find no preference for their rotational alignment in the plane of the scales. However, crystal orientation normal to the scale was highly correlated to their colour at low (conical) angles of view and illumination. This correlation enabled the use of optical images, each containing up to 104–105 crystals, for concluding the preferential alignment seen along the at the level of single scales, appears ubiquitous. By contrast, orientations were found to occur at no greater rate than that expected by chance. Above a critical cone angle, all crystals reflected bright green light indicating the dominant light scattering is due to the predicted band gap along the direction, independent of the domain orientation. Together with the natural variation in scale and wing shapes, we can readily understand the detailed mechanism of uniform colour production and iridescence suppression in these butterflies. It appears that the combination of preferential alignment normal to the wing scale, and uniform distribution within the plane is a near optimal solution for homogenizing the angular distribution of the band gap relative to the wings. Finally, the distributions of orientations, shapes, sizes and degree of order of crystals within single scales provide useful insights for understanding the mechanisms at play in the formation of these biophotonic nanostructures. PMID:28630678

Aligning land use with land potential

USDA-ARS?s Scientific Manuscript database

Current agricultural land use is dominated by an emphasis on provisioning services by applying energy-intensive inputs through relatively uniform production systems across variable landscapes. This approach to agricultural land use is not sustainable. Integrated agricultural systems (IAS) are uphe...

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

The effect of axial crucible rotation on microstructural uniformity during horizontal directional solidification

NASA Technical Reports Server (NTRS)

Grugel, R. N.; Kim, Shinwoo; Woodward, Tracey; Wang, T. G.

1992-01-01

The effects on microstructure of crucible orientation with respect to the earth's gravitational vector, g, during directional solidification of low-volume fraction copper and aluminum, Pb-Cu, and Sn-Al alloys are examined. It is demonstrated that horizontal alignment (i.e. perpendicular to g) in combination with axial rotation of the crucible during growth is sufficient to negate factors which initiate macrosegregation, e.g. density gradients attributed to temperature and/or compositional differences, and promotes a uniform microstructure.

Ionization chamber dosimeter

DOEpatents

Renner, Tim R.; Nyman, Mark A.; Stradtner, Ronald

1991-01-01

A method for fabricating an ion chamber dosimeter collecting array of the type utilizing plural discrete elements formed on a uniform collecting surface which includes forming a thin insulating layer over an aperture in a frame having surfaces, forming a predetermined pattern of through holes in the layer, plating both surfaces of the layer and simultaneously tilting and rotating the frame for uniform plate-through of the holes between surfaces. Aligned masking and patterned etching of the surfaces provides interconnects between the through holes and copper leads provided to external circuitry.

Modifying the morphology and properties of aligned CNT foams through secondary CNT growth.

PubMed

Faraji, Shaghayegh; Stano, Kelly; Akyildiz, Halil; Yildiz, Ozkan; Jur, Jesse S; Bradford, Philip D

2018-07-20

In this work, we report for the first time, growth of secondary carbon nanotubes (CNTs) throughout a three-dimensional assembly of CNTs. The assembly of nanotubes was in the form of aligned CNT/carbon (ACNT/C) foams. These low-density CNT foams were conformally coated with an alumina buffer layer using atomic layer deposition. Chemical vapor deposition was further used to grow new CNTs. The CNT foam's extremely high porosity allowed for growth of secondary CNTs inside the bulk of the foams. Due to the heavy growth of new nanotubes, density of the foams increased more than 2.5 times. Secondary nanotubes had the same graphitic quality as the primary CNTs. Microscopy and chemical analysis revealed that the thickness of the buffer layer affected the diameter, nucleation density as well as growth uniformity across the thickness of the foams. The effects of secondary nanotubes on the compressive mechanical properties of the foams was also investigated.

Dynamic switching mechanisms of a CC chemokine, CCL5 (RANTES). A simulation study

NASA Astrophysics Data System (ADS)

Peter, Emanuel; Pivkin, Igor

CCL5 (RANTES) belongs to the class of pro-inflammatory chemokines which are part of the human immune-response. It is known to activate leukocytes through its associated chemokine receptor 5 (CCR5) and plays a key role in several malignancies, including HIV-1 infections and cancer. In this talk, we present our results from enhanced sampling simulations of the CCL5 (RANTES) monomer. We find that this protein can adopt 2 different conformations : a globular form, with an orthogonal alignment of the N-terminal part, and a 'cis' form, in which the N-terminus is aligned parallel to the β-strand interface. A detailed analysis of the structure reveals that each of these states is stabilized by salt-bridges along the sequence, and corresponds to a defined dihedral-geometry of the 2 disulfide bridges Cys10-34 and Cys11-50. We derive a uniform distribution of transitions from the globular form of CCL5 (RANTES), and find that each of the main conformers adopts different electrostatic patterns.

Modifying the morphology and properties of aligned CNT foams through secondary CNT growth

NASA Astrophysics Data System (ADS)

Faraji, Shaghayegh; Stano, Kelly; Akyildiz, Halil; Yildiz, Ozkan; Jur, Jesse S.; Bradford, Philip D.

2018-07-01

In this work, we report for the first time, growth of secondary carbon nanotubes (CNTs) throughout a three-dimensional assembly of CNTs. The assembly of nanotubes was in the form of aligned CNT/carbon (ACNT/C) foams. These low-density CNT foams were conformally coated with an alumina buffer layer using atomic layer deposition. Chemical vapor deposition was further used to grow new CNTs. The CNT foam’s extremely high porosity allowed for growth of secondary CNTs inside the bulk of the foams. Due to the heavy growth of new nanotubes, density of the foams increased more than 2.5 times. Secondary nanotubes had the same graphitic quality as the primary CNTs. Microscopy and chemical analysis revealed that the thickness of the buffer layer affected the diameter, nucleation density as well as growth uniformity across the thickness of the foams. The effects of secondary nanotubes on the compressive mechanical properties of the foams was also investigated.

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

PubMed

Zheng, Qi; Grice, Elizabeth A

2016-10-01

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

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

PubMed

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

2011-11-01

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

Homogeneous alignment of nematic liquid crystals by ion beam etched surfaces

NASA Technical Reports Server (NTRS)

Wintucky, E. G.; Mahmood, R.; Johnson, D. L.

1979-01-01

A wide range of ion beam etch parameters capable of producing uniform homogeneous alignment of nematic liquid crystals on SiO2 films are discussed. The alignment surfaces were generated by obliquely incident (angles of 5 to 25 deg) argon ions with energies in the range of 0.5 to 2.0 KeV, ion current densities of 0.1 to 0.6 mA sq cm and etch times of 1 to 9 min. A smaller range of ion beam parameters (2.0 KeV, 0.2 mA sq cm, 5 to 10 deg and 1 to 5 min.) were also investigated with ZrO2 films and found suitable for homogeneous alignment. Extinction ratios were very high (1000), twist angles were small ( or = 3 deg) and tilt-bias angles very small ( or = 1 deg). Preliminary scanning electron microscopy results indicate a parallel oriented surface structure on the ion beam etched surfaces which may determine alignment.

Multiscale field-aligned current analyzer

NASA Astrophysics Data System (ADS)

Bunescu, C.; Marghitu, O.; Constantinescu, D.; Narita, Y.; Vogt, J.; Blǎgǎu, A.

2015-11-01

The magnetosphere-ionosphere coupling is achieved, essentially, by a superposition of quasi-stationary and time-dependent field-aligned currents (FACs), over a broad range of spatial and temporal scales. The planarity of the FAC structures observed by satellite data and the orientation of the planar FAC sheets can be investigated by the well-established minimum variance analysis (MVA) of the magnetic perturbation. However, such investigations are often constrained to a predefined time window, i.e., to a specific scale of the FAC. The multiscale field-aligned current analyzer, introduced here, relies on performing MVA continuously and over a range of scales by varying the width of the analyzing window, appropriate for the complexity of the magnetic field signatures above the auroral oval. The proposed technique provides multiscale information on the planarity and orientation of the observed FACs. A new approach, based on the derivative of the largest eigenvalue of the magnetic variance matrix with respect to the length of the analysis window, makes possible the inference of the current structures' location (center) and scale (thickness). The capabilities of the FAC analyzer are explored analytically for the magnetic field profile of the Harris sheet and tested on synthetic FAC structures with uniform current density and infinite or finite geometry in the cross-section plane of the FAC. The method is illustrated with data observed by the Cluster spacecraft on crossing the nightside auroral region, and the results are cross checked with the optical observations from the Time History of Events and Macroscale Interactions during Substorms ground network.

Highly uniform and vertically aligned SnO2 nanochannel arrays for photovoltaic applications

NASA Astrophysics Data System (ADS)

Kim, Jae-Yup; Kang, Jin Soo; Shin, Junyoung; Kim, Jin; Han, Seung-Joo; Park, Jongwoo; Min, Yo-Sep; Ko, Min Jae; Sung, Yung-Eun

2015-04-01

Nanostructured electrodes with vertical alignment have been considered ideal structures for electron transport and interfacial contact with redox electrolytes in photovoltaic devices. Here, we report large-scale vertically aligned SnO2 nanochannel arrays with uniform structures, without lateral cracks fabricated by a modified anodic oxidation process. In the modified process, ultrasonication is utilized to avoid formation of partial compact layers and lateral cracks in the SnO2 nanochannel arrays. Building on this breakthrough, we first demonstrate the photovoltaic application of these vertically aligned SnO2 nanochannel arrays. These vertically aligned arrays were directly and successfully applied in quasi-solid state dye-sensitized solar cells (DSSCs) as photoanodes, yielding reasonable conversion efficiency under back-side illumination. In addition, a significantly short process time (330 s) for achieving the optimal thickness (7.0 μm) and direct utilization of the anodized electrodes enable a simple, rapid and low-cost fabrication process. Furthermore, a TiO2 shell layer was coated on the SnO2 nanochannel arrays by the atomic layer deposition (ALD) process for enhancement of dye-loading and prolonging the electron lifetime in the DSSC. Owing to the presence of the ALD TiO2 layer, the short-circuit photocurrent density (Jsc) and conversion efficiency were increased by 20% and 19%, respectively, compared to those of the DSSC without the ALD TiO2 layer. This study provides valuable insight into the development of efficient SnO2-based photoanodes for photovoltaic application by a simple and rapid fabrication process.Nanostructured electrodes with vertical alignment have been considered ideal structures for electron transport and interfacial contact with redox electrolytes in photovoltaic devices. Here, we report large-scale vertically aligned SnO2 nanochannel arrays with uniform structures, without lateral cracks fabricated by a modified anodic oxidation process. In the modified process, ultrasonication is utilized to avoid formation of partial compact layers and lateral cracks in the SnO2 nanochannel arrays. Building on this breakthrough, we first demonstrate the photovoltaic application of these vertically aligned SnO2 nanochannel arrays. These vertically aligned arrays were directly and successfully applied in quasi-solid state dye-sensitized solar cells (DSSCs) as photoanodes, yielding reasonable conversion efficiency under back-side illumination. In addition, a significantly short process time (330 s) for achieving the optimal thickness (7.0 μm) and direct utilization of the anodized electrodes enable a simple, rapid and low-cost fabrication process. Furthermore, a TiO2 shell layer was coated on the SnO2 nanochannel arrays by the atomic layer deposition (ALD) process for enhancement of dye-loading and prolonging the electron lifetime in the DSSC. Owing to the presence of the ALD TiO2 layer, the short-circuit photocurrent density (Jsc) and conversion efficiency were increased by 20% and 19%, respectively, compared to those of the DSSC without the ALD TiO2 layer. This study provides valuable insight into the development of efficient SnO2-based photoanodes for photovoltaic application by a simple and rapid fabrication process. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00202h

Synthesis of an ultradense forest of vertically aligned triple-walled carbon nanotubes of uniform diameter and length using hollow catalytic nanoparticles.

PubMed

Baliyan, Ankur; Nakajima, Yoshikata; Fukuda, Takahiro; Uchida, Takashi; Hanajiri, Tatsuro; Maekawa, Toru

2014-01-22

It still remains a crucial challenge to actively control carbon nanotube (CNT) structure such as the alignment, area density, diameter, length, chirality, and number of walls. Here, we synthesize an ultradense forest of CNTs of a uniform internal diameter by the plasma-enhanced chemical vapor deposition (PECVD) method using hollow nanoparticles (HNPs) modified with ligand as a catalyst. The diameters of the HNPs and internal cavities in the HNPs are uniform. A monolayer of densely packed HNPs is self-assembled on a silicon substrate by spin coating. HNPs shrink via the collapse of the internal cavities and phase transition from iron oxide to metallic iron in hydrogen plasma during the PECVD process. Agglomeration of catalytic NPs is avoided on account of the shrinkage of the NPs and ligand attached to the NPs. Diffusion of NPs into the substrate, which would inactivate the growth of CNTs, is also avoided on account of the ligand. As a result, an ultradense forest of triple-walled CNTs of a uniform internal diameter is successfully synthesized. The area density of the grown CNTs is as high as 0.6 × 10(12) cm(-2). Finally, the activity of the catalytic NPs and the NP/carbon interactions during the growth process of CNTs are investigated and discussed. We believe that the present approach may make a great contribution to the development of an innovative synthetic method for CNTs with selective properties.

Exploration of a possible cause of magnetic reconfiguration/reconnection due to generation, rather than annihilation, of magnetic field in a nun-uniform thin current sheet

NASA Astrophysics Data System (ADS)

Huang, Y. C.; Lyu, L. H.

2014-12-01

Magnetic reconfiguration/reconnection plays an important role on energy and plasma transport in the space plasma. It is known that magnetic field lines on two sides of a tangential discontinuity can connect to each other only at a neutral point, where the strength of the magnetic field is equal to zero. Thus, the standard reconnection picture with magnetic field lines intersecting at the neutral point is not applicable to the component reconnection events observed at the magnetopause and in the solar corona. In our early study (Yu, Lyu, & Wu, 2011), we have shown that annihilation of magnetic field near a thin current sheet can lead to the formation of normal magnetic field component (normal to the current sheet) to break the frozen-in condition and to accelerate the reconnected plasma flux, even without the presence of a neutral point. In this study, we examine whether or not a generation, rather than annihilation, of magnetic field in a nun-uniform thin current sheet can also lead to reconnection of plasma flux. Our results indicate that a non-uniform enhancement of electric current can yield formation of field-aligned currents. The normal-component magnetic field generated by the field-aligned currents can yield reconnection of plasma flux just outside the current-enhancement region. The particle motion that can lead to non-uniform enhancement of electric currents will be discussed.

Aligning land use with land potential: The role of integrated agriculture

USDA-ARS?s Scientific Manuscript database

Contemporary agricultural land use is dominated by an emphasis on provisioning services by applying energy-intensive inputs through relatively uniform production systems across variable landscapes. This approach to agricultural land use is not sustainable. Achieving sustainable use of agricultural...

Field-Induced Alignment of Polar Bent-Ccore Smectic A Liquid Crystals

NASA Astrophysics Data System (ADS)

Shen, Yongqiang; Goodhew, Lisa; Shao, Renfan; Maclennan, Joseph; Clark, Noel; Rudquist, Per

2014-03-01

The SmAPF phase is a promising phase modulator mode. To use the SmAPF materials for applications, we need to obtain uniform, large-area alignment of the samples. However, bent-core liquid crystals are notoriously difficult to align with conventional surface treatment methods because most of them have no nematic phase. We have developed a powerful, new method using in-plane applied electric fields that allows us to create a perfect bookshelf alignment of orthogonal bent-core smectics. By using an interdigitated, finger-like electrode arrangement on one of the cell surfaces, we can align the materials by applying in-plane electric fields. This stripe geometry, which produces curved field lines, allows for only one smectic layer orientation, normal both to the cell walls and to the finger electrodes. After alignment, the cell can be operated in the conventional way by connecting the finger electrodes together to make one effective electrode, opposing continuous, common electrode on the opposite side of the cell. This alignment method opens up the use of these materials in perfectly aligned cells for both amplitude and phase-only modulation applications. This work was supported by NSF MRSEC Grant No. DMR-0820579, by NSF Grant No. DMR-1008300, and by Swedish Research Council (VR) Grant No. 621-2009-3621.

Functionalization of vertically aligned carbon nanotubes.

PubMed

Van Hooijdonk, Eloise; Bittencourt, Carla; Snyders, Rony; Colomer, Jean-François

2013-01-01

This review focuses and summarizes recent studies on the functionalization of carbon nanotubes oriented perpendicularly to their substrate, so-called vertically aligned carbon nanotubes (VA-CNTs). The intrinsic properties of individual nanotubes make the VA-CNTs ideal candidates for integration in a wide range of devices, and many potential applications have been envisaged. These applications can benefit from the unidirectional alignment of the nanotubes, the large surface area, the high carbon purity, the outstanding electrical conductivity, and the uniformly long length. However, practical uses of VA-CNTs are limited by their surface characteristics, which must be often modified in order to meet the specificity of each particular application. The proposed approaches are based on the chemical modifications of the surface by functionalization (grafting of functional chemical groups, decoration with metal particles or wrapping of polymers) to bring new properties or to improve the interactions between the VA-CNTs and their environment while maintaining the alignment of CNTs.

Functionalization of vertically aligned carbon nanotubes

PubMed Central

Snyders, Rony; Colomer, Jean-François

2013-01-01

Summary This review focuses and summarizes recent studies on the functionalization of carbon nanotubes oriented perpendicularly to their substrate, so-called vertically aligned carbon nanotubes (VA-CNTs). The intrinsic properties of individual nanotubes make the VA-CNTs ideal candidates for integration in a wide range of devices, and many potential applications have been envisaged. These applications can benefit from the unidirectional alignment of the nanotubes, the large surface area, the high carbon purity, the outstanding electrical conductivity, and the uniformly long length. However, practical uses of VA-CNTs are limited by their surface characteristics, which must be often modified in order to meet the specificity of each particular application. The proposed approaches are based on the chemical modifications of the surface by functionalization (grafting of functional chemical groups, decoration with metal particles or wrapping of polymers) to bring new properties or to improve the interactions between the VA-CNTs and their environment while maintaining the alignment of CNTs. PMID:23504581

Periodically striped films produced from super-aligned carbon nanotube arrays.

PubMed

Liu, Kai; Sun, Yinghui; Liu, Peng; Wang, Jiaping; Li, Qunqing; Fan, Shoushan; Jiang, Kaili

2009-08-19

We report a novel way to draw films from super-aligned carbon nanotube arrays at large drawing angles. The obtained super-aligned carbon nanotube films have a periodically striped configuration with alternating thinner and thicker film sections, and the width of the stripes is equal to the height of the original arrays. Compared with ordinary uniform films, the striped films provide a better platform for understanding the mechanism of spinning films from arrays because carbon nanotube junctions are easily observed and identified at the boundary of the stripes. Further studies show that the carbon nanotube junctions are bottleneck positions for thermal conduction and mechanical strength of the film, but do not limit its electrical conduction. These films can be utilized as striped and high-degree polarized light emission sources. Our results will be valuable for new applications and future large-scale production of tunable super-aligned carbon nanotube films.

A Two-Phase Spherical Electric Machine for Generating Rotating Uniform Magnetic Fields

DTIC Science & Technology

2007-06-01

data prior to processing in Matlab 65 5-6 Probe and sensor alignment apparatus with GMW sensor removed. The circular tip of the F.W. Bell probe can be...again using the Biot-Savart Law. The field, B, at a point, P, given in cylindrical geometry by the coordinates (r, ¢J, z), due to a circular loop of...alignment apparatus with GMW sensor removed. The circular tip of the F.W. Bell probe can be seen; it is flush with the bottom of the milled slot for the

Tunable band alignment in two-phase-coexistence Nb3O7F nanocrystals with enhanced light harvesting and photocatalytic performance

NASA Astrophysics Data System (ADS)

Li, Zhen; Huang, Fei; Feng, Xin; Yan, Aihua; Dong, Haiming; Hu, Miao; Li, Qi

2018-06-01

A two-phase-coexistence technique offers intriguing variables to maneuver novel and enhanced functionality in a single-component material. Most importantly, new band alignment and perfect interfaces between two phases can strongly affect local photoelectronic properties. However, previous efforts to achieve two-phase coexistence were mainly restricted to specific systems and methods. Here we demonstrate a phase-transition route to acquire two-phase-coexistence niobium oxyfluoride (Nb3O7F) nanocrystals for the first time. Based on key distinguishing features of the experimental results and theoretical analysis, the phase transition of Nb3O7F involves an organic/inorganic hybrid, heat treating, Al-doping, lattice deformation and structural rearrangement. The band gap can be effectively tuned from 3.03 eV to 2.84 eV, and the VBM can be tuned from 1.49 eV to 1.69 eV according to the phase proportion. Benefiting from uniform nanocrystal size, tunable band alignment and an optimized interfacial structure, the two-phase coexistence markedly enhances visible-light harvesting and the photocatalytic performance of Nb3O7F nanocrystals. The results not only demonstrate an opportunity to explore two-phase coexistence of novel nanocrystals, but also illustrate the role of two-phase coexistence in achieving enhanced photoelectronic properties.

Tunable band alignment in two-phase-coexistence Nb3O7F nanocrystals with enhanced light harvesting and photocatalytic performance.

PubMed

Li, Zhen; Huang, Fei; Feng, Xin; Yan, Aihua; Dong, Haiming; Hu, Miao; Li, Qi

2018-06-01

A two-phase-coexistence technique offers intriguing variables to maneuver novel and enhanced functionality in a single-component material. Most importantly, new band alignment and perfect interfaces between two phases can strongly affect local photoelectronic properties. However, previous efforts to achieve two-phase coexistence were mainly restricted to specific systems and methods. Here we demonstrate a phase-transition route to acquire two-phase-coexistence niobium oxyfluoride (Nb 3 O 7 F) nanocrystals for the first time. Based on key distinguishing features of the experimental results and theoretical analysis, the phase transition of Nb 3 O 7 F involves an organic/inorganic hybrid, heat treating, Al-doping, lattice deformation and structural rearrangement. The band gap can be effectively tuned from 3.03 eV to 2.84 eV, and the VBM can be tuned from 1.49 eV to 1.69 eV according to the phase proportion. Benefiting from uniform nanocrystal size, tunable band alignment and an optimized interfacial structure, the two-phase coexistence markedly enhances visible-light harvesting and the photocatalytic performance of Nb 3 O 7 F nanocrystals. The results not only demonstrate an opportunity to explore two-phase coexistence of novel nanocrystals, but also illustrate the role of two-phase coexistence in achieving enhanced photoelectronic properties.

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

PubMed Central

Zheng, Qi; Grice, Elizabeth A.

2016-01-01

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

Assembly and evaluation of a pyroelectric detector bonded to vertically aligned multiwalled carbon nanotubes over thin silicon.

PubMed

Theocharous, E; Theocharous, S P; Lehman, J H

2013-11-20

A novel pyroelectric detector consisting of a vertically aligned nanotube array on thin silicon (VANTA/Si) bonded to a 60 μm thick crystal of LiTaO₃ has been fabricated. The performance of the VANTA/Si-coated pyroelectric detector was evaluated using National Physical Laboratory's (NPL's) detector-characterization facilities. The relative spectral responsivity of the detector was found to be spectrally flat in the 0.8-24 μm wavelength range, in agreement with directional-hemispherical reflectance measurements of witness samples of the VANTA. The spatial uniformity of response of the test detector exhibited good uniformity, although the nonuniformity increased with increasing modulation frequency. The nonuniformity may be assigned either to the dimensions of the VANTA or the continuity of the bond between the VANTA/Si coating and the pyroelectric crystal substrate. The test detector exhibited a small superlinear response, which is similar to that of pyroelectric detectors coated with good quality gold-black coatings.

Method for gas-metal arc deposition

DOEpatents

Buhrmaster, C.L.; Clark, D.E.; Smartt, H.B.

1990-11-13

Method and apparatus for gas-metal arc deposition of metal, metal alloys, and metal matrix composites are disclosed. The apparatus contains an arc chamber for confining a D.C. electrical arc discharge, the arc chamber containing an outlet orifice in fluid communication with a deposition chamber having a deposition opening in alignment with the orifice for depositing metal droplets on a coatable substrate. Metal wire is passed continuously into the arc chamber in alignment with the orifice. Electric arcing between the metal wire anode and the orifice cathode produces droplets of molten metal from the wire which pass through the orifice and into the deposition chamber for coating a substrate exposed at the deposition opening. When producing metal matrix composites, a suspension of particulates in an inert gas enters the deposition chamber via a plurality of feed openings below and around the orifice so that reinforcing particulates join the metal droplets to produce a uniform mixture which then coats the exposed substrate with a uniform metal matrix composite. 1 fig.

Method for gas-metal arc deposition

DOEpatents

Buhrmaster, Carol L.; Clark, Denis E.; Smartt, Herschel B.

1990-01-01

Method and apparatus for gas-metal arc deposition of metal, metal alloys, and metal matrix composites. The apparatus contains an arc chamber for confining a D.C. electrical arc discharge, the arc chamber containing an outlet orifice in fluid communication with a deposition chamber having a deposition opening in alignment wiht the orifice for depositing metal droplets on a coatable substrate. Metal wire is passed continuously into the arc chamber in alignment with the orifice. Electric arcing between the metal wire anode and the orifice cathode produces droplets of molten metal from the wire which pass through the orifice and into the deposition chamber for coating a substrate exposed at the deposition opening. When producing metal matrix composites, a suspension of particulates in an inert gas enters the deposition chamber via a plurality of feed openings below and around the orifice so that reinforcing particulates join the metal droplets to produce a uniform mixture which then coats the exposed substrate with a uniform metal matrix composite.

Apparatus for gas-metal arc deposition

DOEpatents

Buhrmaster, Carol L.; Clark, Denis E.; Smartt, Herschel B.

1991-01-01

Apparatus for gas-metal arc deposition of metal, metal alloys, and metal matrix composites. The apparatus contains an arc chamber for confining a D.C. electrical arc discharge, the arc chamber containing an outlet orifice in fluid communication with a deposition chamber having a deposition opening in alignment with the orifice for depositing metal droplets on a coatable substrate. Metal wire is passed continuously into the arc chamber in alignment with the orifice. Electric arcing between the metal wire anode and the orifice cathode produces droplets of molten metal from the wire which pass through the orifice and into the deposition chamber for coating a substrate exposed at the deposition opening. When producing metal matrix composites, a suspenion of particulates in an inert gas enters the deposition chamber via a plurality of feed openings below and around the orifice so that reinforcing particulates join the metal droplets to produce a uniform mixture which then coats the exposed substrate with a uniform metal matrix composite.

Zooming in: high resolution 3D reconstruction of differently stained histological whole slide images

NASA Astrophysics Data System (ADS)

Lotz, Johannes; Berger, Judith; Müller, Benedikt; Breuhahn, Kai; Grabe, Niels; Heldmann, Stefan; Homeyer, André; Lahrmann, Bernd; Laue, Hendrik; Olesch, Janine; Schwier, Michael; Sedlaczek, Oliver; Warth, Arne

2014-03-01

Much insight into metabolic interactions, tissue growth, and tissue organization can be gained by analyzing differently stained histological serial sections. One opportunity unavailable to classic histology is three-dimensional (3D) examination and computer aided analysis of tissue samples. In this case, registration is needed to reestablish spatial correspondence between adjacent slides that is lost during the sectioning process. Furthermore, the sectioning introduces various distortions like cuts, folding, tearing, and local deformations to the tissue, which need to be corrected in order to exploit the additional information arising from the analysis of neighboring slide images. In this paper we present a novel image registration based method for reconstructing a 3D tissue block implementing a zooming strategy around a user-defined point of interest. We efficiently align consecutive slides at increasingly fine resolution up to cell level. We use a two-step approach, where after a macroscopic, coarse alignment of the slides as preprocessing, a nonlinear, elastic registration is performed to correct local, non-uniform deformations. Being driven by the optimization of the normalized gradient field (NGF) distance measure, our method is suitable for differently stained and thus multi-modal slides. We applied our method to ultra thin serial sections (2 μm) of a human lung tumor. In total 170 slides, stained alternately with four different stains, have been registered. Thorough visual inspection of virtual cuts through the reconstructed block perpendicular to the cutting plane shows accurate alignment of vessels and other tissue structures. This observation is confirmed by a quantitative analysis. Using nonlinear image registration, our method is able to correct locally varying deformations in tissue structures and exceeds the limitations of globally linear transformations.

Tensil Film Clamps And Mounting Block For Viscoelastometers

NASA Technical Reports Server (NTRS)

Stoakley, Diane M.; St. Clair, Anne K.; Little, Bruce D.

1989-01-01

Set of clamps and mounting block developed for use in determining tensile moduli and damping properties of films in manually operated or automated commercial viscoelastometer. These clamps and block provide uniformity of sample gripping and alignment in instrument. Dependence on operator and variability of data greatly reduced.

On the colour of wing scales in butterflies: iridescence and preferred orientation of single gyroid photonic crystals.

PubMed

Corkery, Robert W; Tyrode, Eric C

2017-08-06

Lycaenid butterflies from the genera Callophrys , Cyanophrys and Thecla have evolved remarkable biophotonic gyroid nanostructures within their wing scales that have only recently been replicated by nanoscale additive manufacturing. These nanostructures selectively reflect parts of the visible spectrum to give their characteristic non-iridescent, matte-green appearance, despite a distinct blue-green-yellow iridescence predicted for individual crystals from theory. It has been hypothesized that the organism must achieve its uniform appearance by growing crystals with some restrictions on the possible distribution of orientations, yet preferential orientation observed in Callophrys rubi confirms that this distribution need not be uniform. By analysing scanning electron microscope and optical images of 912 crystals in three wing scales, we find no preference for their rotational alignment in the plane of the scales. However, crystal orientation normal to the scale was highly correlated to their colour at low (conical) angles of view and illumination. This correlation enabled the use of optical images, each containing up to 10 4 -10 5 crystals, for concluding the preferential alignment seen along the [Formula: see text] at the level of single scales, appears ubiquitous. By contrast, [Formula: see text] orientations were found to occur at no greater rate than that expected by chance. Above a critical cone angle, all crystals reflected bright green light indicating the dominant light scattering is due to the predicted band gap along the [Formula: see text] direction, independent of the domain orientation. Together with the natural variation in scale and wing shapes, we can readily understand the detailed mechanism of uniform colour production and iridescence suppression in these butterflies. It appears that the combination of preferential alignment normal to the wing scale, and uniform distribution within the plane is a near optimal solution for homogenizing the angular distribution of the [Formula: see text] band gap relative to the wings. Finally, the distributions of orientations, shapes, sizes and degree of order of crystals within single scales provide useful insights for understanding the mechanisms at play in the formation of these biophotonic nanostructures.

Transition of vertically aligned liquid crystal driven by fan-shaped electric field

NASA Astrophysics Data System (ADS)

Tsung, J. W.; Ting, T. L.; Chen, C. Y.; Liang, W. L.; Lai, C. W.; Lin, T. H.; Hsu, W. H.

2017-09-01

Interdigital electrodes are implemented in many commercial and novel liquid crystal devices to align molecules. Although many empirical principles and patents apply to electrode design, only a few numerical simulations of alignment have been conducted. Why and how the molecules align in an ordered manner has never been adequately explained. Hence, this investigation addresses the Fréedericksz transition of vertically aligned liquid crystal that is driven by fishbone electrodes, and thereafter identifies the mechanism of liquid crystal alignment. Theoretical calculations suggest that the periodic deformation that is caused by the fan-shaped fringe field minimizes the free energy in the liquid crystal cell, and the optimal alignment can be obtained when the cell parameters satisfy the relation p /2 d =√{k11/k33 } , where p is the spatial period of the strips of the electrode; d denotes the cell gap; and k11 and k33 are the splay and bend elastic constants of the liquid crystal, respectively. Polymer-stabilized vertical alignment test cells with various p values and spacings between the electrodes were fabricated, and the process of liquid crystal alignment was observed under an optical microscope. The degree of alignment was evaluated by measuring the transmittance of the test cell. The experimental results were consistent with the theoretical predictions. The principle of design, p /2 d =√{k11/k33 } , greatly improves the uniformity and stability of the aligned liquid crystal. The methods that are presented here can be further applied to cholesteric liquid crystal and other self-assembled soft materials.

Spontaneous liquid crystal and ferromagnetic ordering of colloidal magnetic nanoplates

PubMed Central

Shuai, M.; Klittnick, A.; Shen, Y.; Smith, G. P.; Tuchband, M. R.; Zhu, C.; Petschek, R. G.; Mertelj, A.; Lisjak, D.; Čopič, M.; Maclennan, J. E.; Glaser, M. A.; Clark, N. A.

2016-01-01

Ferrofluids are familiar as colloidal suspensions of ferromagnetic nanoparticles in aqueous or organic solvents. The dispersed particles are randomly oriented but their moments become aligned if a magnetic field is applied, producing a variety of exotic and useful magnetomechanical effects. A longstanding interest and challenge has been to make such suspensions macroscopically ferromagnetic, that is having uniform magnetic alignment in the absence of a field. Here we report a fluid suspension of magnetic nanoplates that spontaneously aligns into an equilibrium nematic liquid crystal phase that is also macroscopically ferromagnetic. Its zero-field magnetization produces distinctive magnetic self-interaction effects, including liquid crystal textures of fluid block domains arranged in closed flux loops, and makes this phase highly sensitive, with it dramatically changing shape even in the Earth's magnetic field. PMID:26817823

Aligning flaky FeSiAl particles with a two-dimensional rotating magnetic field to improve microwave-absorbing and shielding properties of composites

NASA Astrophysics Data System (ADS)

Liu, Chang; Cai, Jun; Duan, Yubing; Li, Xinghao; Zhang, Deyuan

2018-07-01

In order to enhance the microwave-absorbing and shielding properties of the composites, the flaky FeSiAl particles embedded in an epoxy polymer were aligned with a two-dimensional rotating magnetic field. The morphologies, electromagnetic (EM) characteristics, and microwave-absorbing and shielding properties of the unaligned and aligned FeSiAl/epoxy composites were investigated. The results showed that after alignment treatment, the flaky FeSiAl particles tend to orient uniformly in the rotating magnetic field, and the permittivity and permeability of the aligned composites were increased in the frequency range of 1-18 GHz compared with that of randomly distributed composites. The calculated microwave-absorbing properties indicated that the peak value of the return loss (RL) of the aligned composites can reach 8.8 dB, compared with 5.8 dB of the unaligned composites of 2.5 mm in thickness (60 wt%); and the bandwidth with RL value more than 6 dB is in a wider frequency range from 1 to 2.8 GHz. And the calculated shielding effectiveness (SE) of the aligned composites is 1.1-3 times higher than that of unaligned one in every thickness, and the maximum SE of the aligned one is 31.8 dB at 18 GHz with a thickness of 2.5 mm.

Large deformation analysis of axisymmetric inhomogeneities including coupled elastic and plastic anisotropy

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

Brannon, R.M.

1996-12-31

A mathematical framework is developed for the study of materials containing axisymmetric inclusions or flaws such as ellipsoidal voids, penny-shaped cracks, or fibers of circular cross-section. The general case of nonuniform statistical distributions of such heterogeneities is attacked by first considering a spatially uniform distribution of flaws that are all oriented in the same direction. Assuming an isotropic substrate, the macroscopic material properties of this simpler microstructure naturally should be transversely isotropic. An orthogonal basis for the linear subspace consisting of all double-symmetric transversely-isotropic fourth-order tensors associated with a given material vector is applied to deduce the explicit functional dependencemore » of the material properties of these aligned materials on the shared symmetry axis. The aligned and uniform microstructure seems geometrically simple enough that the macroscopic transversely isotropic properties could be derived in closed form. Since the resulting properties are transversely isotropic, the analyst must therefore be able to identify the appropriate coefficients of the transverse basis. Once these functions are identified, a principle of superposition of strain rates ay be applied to define an expectation integral for the composite properties of a material containing arbitrary anisotropic distributions of axisymmetric inhomogeneities. A proposal for coupling plastic anisotropy to the elastic anisotropy is presented in which the composite yield surface is interpreted as a distortion of the isotropic substrate yield surface; the distortion directions are coupled to the elastic anisotropy directions. Finally, some commonly assumed properties (such as major symmetry) of the Cauchy tangent stiffness tensor are shown to be inappropriate for large distortions of anisotropic materials.« less

Coated carbon nanotube array electrodes

DOEpatents

Ren, Zhifeng; Wen, Jian; Chen, Jinghua; Huang, Zhongping; Wang, Dezhi

2006-12-12

The present invention provides conductive carbon nanotube (CNT) electrode materials comprising aligned CNT substrates coated with an electrically conducting polymer, and the fabrication of electrodes for use in high performance electrical energy storage devices. In particular, the present invention provides conductive CNTs electrode material whose electrical properties render them especially suitable for use in high efficiency rechargeable batteries. The present invention also provides methods for obtaining surface modified conductive CNT electrode materials comprising an array of individual linear, aligned CNTs having a uniform surface coating of an electrically conductive polymer such as polypyrrole, and their use in electrical energy storage devices.

Coated carbon nanotube array electrodes

DOEpatents

Ren, Zhifeng [Newton, MA; Wen, Jian [Newton, MA; Chen, Jinghua [Chestnut Hill, MA; Huang, Zhongping [Belmont, MA; Wang, Dezhi [Wellesley, MA

2008-10-28

The present invention provides conductive carbon nanotube (CNT) electrode materials comprising aligned CNT substrates coated with an electrically conducting polymer, and the fabrication of electrodes for use in high performance electrical energy storage devices. In particular, the present invention provides conductive CNTs electrode material whose electrical properties render them especially suitable for use in high efficiency rechargeable batteries. The present invention also provides methods for obtaining surface modified conductive CNT electrode materials comprising an array of individual linear, aligned CNTs having a uniform surface coating of an electrically conductive polymer such as polypyrrole, and their use in electrical energy storage devices.

Truncation Without Shape Constraints: The Latter Stages of Prosodic Acquisition.

ERIC Educational Resources Information Center

Kehoe, Margaret M.

2000-01-01

Evaluates the claim of uniform size and shape restrictions in prosodic development using a cross-sectional database of English-speaking children's multisyllabic word productions. Suggests children's increasing faithfulness to unstressed syllables can be explained by different constraint rankings that relate to edge alignment, syllable structure,…

Growth of different V2O5 nanostructures as a function of deposition duration

NASA Astrophysics Data System (ADS)

Saini, Sujit K.; Sharma, Rabindar K.; Singh, Megha; Kumar, Prabhat; Reddy, G. B.

2018-05-01

Vanadium pentoxide nanostructured thin films are synthesized using plasma assisted sublimation process (PASP). The effect of deposition duration on the growth of V2O5 nanostructured thin films (NSTs) is studied in present paper. Raman and XRD results depict that all films exhibited only orthorhombic crystalline phase of vanadium oxide (i.e. V2O5). As duration increases the growth of V2O5 nanostructures preferentially aligned along (101) crystallographic plane. Scanning electron micrographs show that different morphologies are obtained with different duration of deposition. For low durations (i.e. 30 and 40 min.) the 1D nanostructures with random alignments are obtained, whereas for prolonged durations of deposition (50 and 60 min) the embedded nanopillers having vertical alignments with uniform distribution on entire substrate are found. The occurrence of remarkable increase in visible radiation from 8% to 13% on increasing duration again implies that the crystallinity and alignments of V2O5 nanostructures is getting improved with duration.

Shape-dependent dispersion and alignment of nonaggregating plasmonic gold nanoparticles in lyotropic and thermotropic liquid crystals.

PubMed

Liu, Qingkun; Tang, Jianwei; Zhang, Yuan; Martinez, Angel; Wang, Shaowei; He, Sailing; White, Timothy J; Smalyukh, Ivan I

2014-05-01

We use both lyotropic liquid crystals composed of prolate micelles and thermotropic liquid crystals made of rod-like molecules to uniformly disperse and unidirectionally align relatively large gold nanorods and other complex-shaped nanoparticles at high concentrations. We show that some of these ensuing self-assembled orientationally ordered soft matter systems exhibit polarization-dependent plasmonic properties with strongly pronounced molar extinction exceeding that previously achieved in self-assembled composites. The long-range unidirectional alignment of gold nanorods is mediated mainly by anisotropic surface anchoring interactions at the surfaces of gold nanoparticles. Polarization-sensitive absorption, scattering, and extinction are used to characterize orientations of nanorods and other nanoparticles. The experimentally measured unique optical properties of these composites, which stem from the collective plasmonic effect of the gold nanorods with long-range order in a liquid crystal matrix, are reproduced in computer simulations. A simple phenomenological model based on anisotropic surface interaction explains the alignment of gold nanorods dispersed in liquid crystals and the physical underpinnings behind our observations.

Continuous high-yield production of vertically aligned carbon nanotubes on 2D and 3D substrates.

PubMed

Guzmán de Villoria, Roberto; Hart, A John; Wardle, Brian L

2011-06-28

Vertically aligned carbon nanotubes (VACNTs) have certain advantages over bulk CNT powders and randomly oriented CNT mats for applications in flexible electronic devices, filtration membranes, biosensors and multifunctional aerospace materials. Here, a machine and a process to synthesize VACNTs in a continuous manner are presented showing uniform growth on 2D and 3D substrates, including alumina fibers, silicon wafer pieces, and stainless steel foils. Aligned multiwalled carbon nanotubes (MWNT) are synthesized at substrate feed rates of up to 6.8 cm/min, and the CNTs reach up to 60 μm in length depending on residence time in the reactor. In addition to the aligned morphology indicative of high yield growth, transmission electron microscopy and Raman spectroscopy reveal that the CNTs are of comparable quality to CNTs grown via a similar batch process. A significant reduction in time, reaction products, gases, and energy is demonstrated relative to batch processing, paving the way for industrial production of VACNTs.

Conformal atomic layer deposition of alumina on millimeter tall, vertically-aligned carbon nanotube arrays.

PubMed

Stano, Kelly L; Carroll, Murphy; Padbury, Richard; McCord, Marian; Jur, Jesse S; Bradford, Philip D

2014-11-12

Atomic layer deposition (ALD) can be used to coat high aspect ratio and high surface area substrates with conformal and precisely controlled thin films. Vertically aligned arrays of multiwalled carbon nanotubes (MWCNTs) with lengths up to 1.5 mm were conformally coated with alumina from base to tip. The nucleation and growth behaviors of Al2O3 ALD precursors on the MWCNTs were studied as a function of CNT surface chemistry. CNT surfaces were modified through a series of post-treatments including pyrolytic carbon deposition, high temperature thermal annealing, and oxygen plasma functionalization. Conformal coatings were achieved where post-treatments resulted in increased defect density as well as the extent of functionalization, as characterized by X-ray photoelectron spectroscopy and Raman spectroscopy. Using thermogravimetric analysis, it was determined that MWCNTs treated with pyrolytic carbon and plasma functionalization prior to ALD coating were more stable to thermal oxidation than pristine ALD coated samples. Functionalized and ALD coated arrays had a compressive modulus more than two times higher than a pristine array coated for the same number of cycles. Cross-sectional energy dispersive X-ray spectroscopy confirmed that Al2O3 could be uniformly deposited through the entire thickness of the vertically aligned MWCNT array by manipulating sample orientation and mounting techniques. Following the ALD coating, the MWCNT arrays demonstrated hydrophilic wetting behavior and also exhibited foam-like recovery following compressive strain.

Transient shear banding in the nematic dumbbell model of liquid crystalline polymers

NASA Astrophysics Data System (ADS)

Adams, J. M.; Corbett, D.

2018-05-01

In the shear flow of liquid crystalline polymers (LCPs) the nematic director orientation can align with the flow direction for some materials but continuously tumble in others. The nematic dumbbell (ND) model was originally developed to describe the rheology of flow-aligning semiflexible LCPs, and flow-aligning LCPs are the focus in this paper. In the shear flow of monodomain LCPs, it is usually assumed that the spatial distribution of the velocity is uniform. This is in contrast to polymer solutions, where highly nonuniform spatial velocity profiles have been observed in experiments. We analyze the ND model, with an additional gradient term in the constitutive model, using a linear stability analysis. We investigate the separate cases of constant applied shear stress and constant applied shear rate. We find that the ND model has a transient flow instability to the formation of a spatially inhomogeneous flow velocity for certain starting orientations of the director. We calculate the spatially resolved flow profile in both constant applied stress and constant applied shear rate in start up from rest, using a model with one spatial dimension to illustrate the flow behavior of the fluid. For low shear rates flow reversal can be seen as the director realigns with the flow direction, whereas for high shear rates the director reorientation occurs simultaneously across the gap. Experimentally, this inhomogeneous flow is predicted to be observed in flow reversal experiments in LCPs.

INDUCTION OF RABBIT ANTIBODY WITH MOLECULAR UNIFORMITY AFTER IMMUNIZATION WITH GROUP C STREPTOCOCCI

PubMed Central

Eichmann, Klaus; Lackland, Henry; Hood, Leroy; Krause, Richard M.

1970-01-01

Antibodies with uniform properties may occur in rabbits after immunization with Group C streptococci. These precipitating antibodies possess specificity for the group-specific carbohydrate. Not uncommonly, their concentration is between 20 and 40 mg/ml of antiserum. Evidence for molecular uniformity in the case of one of these antibodies, described in detail here, includes: individual antigenic specificity; monodisperse distribution of the light chains by alkaline urea polyacrylamide disc electrophoresis; and a single amino acid in each of the first three N-terminal positions of the light chains. When the amino acid sequence of rabbit antibody b+ light chains (κ type) are aligned against their human κ counterparts, a definite homology is observed between the N-terminus of the human and the rabbit variable region. PMID:5409946

High-yield growth of vertically aligned carbon nanotubes on a continuously moving substrate.

PubMed

Guzmán de Villoria, R; Figueredo, S L; Hart, A J; Steiner, S A; Slocum, A H; Wardle, B L

2009-10-07

Vertically aligned carbon nanotube (CNT) arrays are grown on a moving substrate, demonstrating continuous growth of nanoscale materials with long-range order. A cold-wall chamber with an oscillating moving platform is used to locally heat a silicon growth substrate coated with an Fe/Al2O3 catalyst film for CNT growth via chemical vapor deposition. The reactant gases are introduced over the substrate through a directed nozzle to attain high-yield CNT growth. Aligned multi-wall carbon nanotube arrays (or 'forests') with heights of approximately 1 mm are achieved at substrate speeds up to 2.4 mm s(-1). Arrays grown on moving substrates at different velocities are studied in order to identify potential physical limitations of repeatable and fast growth on a continuous basis. No significant differences are noted between static and moving growth as characterized by scanning electron microscopy and Raman spectroscopy, although overall growth height is marginally reduced at the highest substrate velocity. CNT arrays produced on moving substrates are also found to be comparable to those produced through well-characterized batch processes consistent with a base-growth mechanism. Growth parameters required for the moving furnace are found to differ only slightly from those used in a comparable batch process; thermal uniformity appears to be the critical parameter for achieving large-area uniform array growth. If the continuous-growth technology is combined with a reaction zone isolation scheme common in other types of processing (e.g., in the manufacture of carbon fibers), large-scale dense and aligned CNT arrays may be efficiently grown and harvested for numerous applications including providing interlayers for advanced composite reinforcement and improved electrical and thermal transport.

MATHEMATICAL ANALYSIS OF STEADY-STATE SOLUTIONS IN COMPARTMENT AND CONTINUUM MODELS OF CELL POLARIZATION

PubMed Central

ZHENG, ZHENZHEN; CHOU, CHING-SHAN; YI, TAU-MU; NIE, QING

2013-01-01

Cell polarization, in which substances previously uniformly distributed become asymmetric due to external or/and internal stimulation, is a fundamental process underlying cell mobility, cell division, and other polarized functions. The yeast cell S. cerevisiae has been a model system to study cell polarization. During mating, yeast cells sense shallow external spatial gradients and respond by creating steeper internal gradients of protein aligned with the external cue. The complex spatial dynamics during yeast mating polarization consists of positive feedback, degradation, global negative feedback control, and cooperative effects in protein synthesis. Understanding such complex regulations and interactions is critical to studying many important characteristics in cell polarization including signal amplification, tracking dynamic signals, and potential trade-off between achieving both objectives in a robust fashion. In this paper, we study some of these questions by analyzing several models with different spatial complexity: two compartments, three compartments, and continuum in space. The step-wise approach allows detailed characterization of properties of the steady state of the system, providing more insights for biological regulations during cell polarization. For cases without membrane diffusion, our study reveals that increasing the number of spatial compartments results in an increase in the number of steady-state solutions, in particular, the number of stable steady-state solutions, with the continuum models possessing infinitely many steady-state solutions. Through both analysis and simulations, we find that stronger positive feedback, reduced diffusion, and a shallower ligand gradient all result in more steady-state solutions, although most of these are not optimally aligned with the gradient. We explore in the different settings the relationship between the number of steady-state solutions and the extent and accuracy of the polarization. Taken together these results furnish a detailed description of the factors that influence the tradeoff between a single correctly aligned but poorly polarized stable steady-state solution versus multiple more highly polarized stable steady-state solutions that may be incorrectly aligned with the external gradient. PMID:21936604

Unifying cancer and normal RNA sequencing data from different sources

PubMed Central

Wang, Qingguo; Armenia, Joshua; Zhang, Chao; Penson, Alexander V.; Reznik, Ed; Zhang, Liguo; Minet, Thais; Ochoa, Angelica; Gross, Benjamin E.; Iacobuzio-Donahue, Christine A.; Betel, Doron; Taylor, Barry S.; Gao, Jianjiong; Schultz, Nikolaus

2018-01-01

Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data, such as the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA). While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources remains challenging, due to differences in sample and data processing. Here, we developed a pipeline that processes and unifies RNA-seq data from different studies, which includes uniform realignment, gene expression quantification, and batch effect removal. We find that uniform alignment and quantification is not sufficient when combining RNA-seq data from different sources and that the removal of other batch effects is essential to facilitate data comparison. We have processed data from GTEx and TCGA and successfully corrected for study-specific biases, enabling comparative analysis between TCGA and GTEx. The normalized datasets are available for download on figshare. PMID:29664468

Spontaneous liquid crystal and ferromagnetic ordering of colloidal magnetic nanoplates

DOE PAGES

Shuai, M.; Klittnick, A.; Shen, Y.; ...

2016-01-28

Ferrofluids are familiar as colloidal suspensions of ferromagnetic nanoparticles in aqueous or organic solvents. The dispersed particles are randomly oriented but their moments become aligned if a magnetic field is applied, producing a variety of exotic and useful magnetomechanical effects. A longstanding interest and challenge has been to make such suspensions macroscopically ferromagnetic, that is having uniform magnetic alignment in the absence of a field. Here we report a fluid suspension of magnetic nanoplates that spontaneously aligns into an equilibrium nematic liquid crystal phase that is also macroscopically ferromagnetic. We find Its zero-field magnetization produces distinctive magnetic self-interaction effects, includingmore » liquid crystal textures of fluid block domains arranged in closed flux loops, and makes this phase highly sensitive, with it dramatically changing shape even in the Earth’s magnetic field.« less

Nucleation, Growth Mechanism, and Controlled Coating of ZnO ALD onto Vertically Aligned N-Doped CNTs.

PubMed

Silva, R M; Ferro, M C; Araujo, J R; Achete, C A; Clavel, G; Silva, R F; Pinna, N

2016-07-19

Zinc oxide thin films were deposited on vertically aligned nitrogen-doped carbon nanotubes (N-CNTs) by atomic layer deposition (ALD) from diethylzinc and water. The study demonstrates that doping CNTs with nitrogen is an effective approach for the "activation" of the CNTs surface for the ALD of metal oxides. Conformal ZnO coatings are already obtained after 50 ALD cycles, whereas at lower ALD cycles an island growth mode is observed. Moreover, the process allows for a uniform growth from the top to the bottom of the vertically aligned N-CNT arrays. X-ray photoelectron spectroscopy demonstrates that ZnO nucleation takes place at the N-containing species on the surface of the CNTs by the formation of the Zn-N bonds at the interface between the CNTs and the ZnO film.

Large-scale horizontally aligned ZnO microrod arrays with controlled orientation, periodic distribution as building blocks for chip-in piezo-phototronic LEDs.

PubMed

Guo, Zhen; Li, Haiwen; Zhou, Lianqun; Zhao, Dongxu; Wu, Yihui; Zhang, Zhiqiang; Zhang, Wei; Li, Chuanyu; Yao, Jia

2015-01-27

A novel method of fabricating large-scale horizontally aligned ZnO microrod arrays with controlled orientation and periodic distribution via combing technology is introduced. Horizontally aligned ZnO microrod arrays with uniform orientation and periodic distribution can be realized based on the conventional bottom-up method prepared vertically aligned ZnO microrod matrix via the combing method. When the combing parameters are changed, the orientation of horizontally aligned ZnO microrod arrays can be adjusted (θ = 90° or 45°) in a plane and a misalignment angle of the microrods (0.3° to 2.3°) with low-growth density can be obtained. To explore the potential applications based on the vertically and horizontally aligned ZnO microrods on p-GaN layer, piezo-phototronic devices such as heterojunction LEDs are built. Electroluminescence (EL) emission patterns can be adjusted for the vertically and horizontally aligned ZnO microrods/p-GaN heterojunction LEDs by applying forward bias. Moreover, the emission color from UV-blue to yellow-green can be tuned by investigating the piezoelectric properties of the materials. The EL emission mechanisms of the LEDs are discussed in terms of band diagrams of the heterojunctions and carrier recombination processes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Talking Circles, Leadership Competencies, and Inclusive Learning: Expanding the Frame of Business Education

ERIC Educational Resources Information Center

Cowan, David A.; Beard Adams, Kathy M.

2008-01-01

Business education typically embodies traditional organizational values, structures, and processes that focus learning mostly on uniformity and efficiency. In contrast, many First Nation peoples have long used the imagery of a circle as a guiding metaphor for both organizing and educating in ways that respect diversity and align themselves with…

Engineered plant biomass feedstock particles

DOEpatents

Dooley, James H [Federal Way, WA; Lanning, David N [Federal Way, WA; Broderick, Thomas F [Lake Forest Park, WA

2011-10-11

A novel class of flowable biomass feedstock particles with unusually large surface areas that can be manufactured in remarkably uniform sizes using low-energy comminution techniques. The feedstock particles are roughly parallelepiped in shape and characterized by a length dimension (L) aligned substantially with the grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. The particles exhibit a disrupted grain structure with prominent end and surface checks that greatly enhances their skeletal surface area as compared to their envelope surface area. The L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers. The W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers. The L.times.W dimensions define a pair of substantially parallel top surfaces characterized by some surface checking between longitudinally arrayed fibers. The feedstock particles are manufactured from a variety of plant biomass materials including wood, crop residues, plantation grasses, hemp, bagasse, and bamboo.

Hydrothermal Growth of Vertically Aligned ZnO Nanorods Using a Biocomposite Seed Layer of ZnO Nanoparticles.

PubMed

Ibupoto, Zafar Hussain; Khun, Kimleang; Eriksson, Martin; AlSalhi, Mohammad; Atif, Muhammad; Ansari, Anees; Willander, Magnus

2013-08-19

Well aligned ZnO nanorods have been prepared by a low temperature aqueous chemical growth method, using a biocomposite seed layer of ZnO nanoparticles prepared in starch and cellulose bio polymers. The effect of different concentrations of biocomposite seed layer on the alignment of ZnO nanorods has been investigated. ZnO nanorods grown on a gold-coated glass substrate have been characterized by X-ray diffraction (XRD) and field emission scanning electron microscopy (FESEM) techniques. These techniques have shown that the ZnO nanorods are well aligned and perpendicular to the substrate, and grown with a high density and uniformity on the substrate. Moreover, ZnO nanorods can be grown with an orientation along the c -axis of the substrate and exhibit a wurtzite crystal structure with a dominant (002) peak in an XRD spectrum and possessed a high crystal quality. A photoluminescence (PL) spectroscopy study of the ZnO nanorods has revealed a conventional near band edge ultraviolet emission, along with emission in the visible part of the electromagnetic spectrum due to defect emission. This study provides an alternative method for the fabrication of well aligned ZnO nanorods. This method can be helpful in improving the performance of devices where alignment plays a significant role.

Hydrothermal Growth of Vertically Aligned ZnO Nanorods Using a Biocomposite Seed Layer of ZnO Nanoparticles

PubMed Central

Ibupoto, Zafar Hussain; Khun, Kimleang; Eriksson, Martin; AlSalhi, Mohammad; Atif, Muhammad; Ansari, Anees; Willander, Magnus

2013-01-01

Well aligned ZnO nanorods have been prepared by a low temperature aqueous chemical growth method, using a biocomposite seed layer of ZnO nanoparticles prepared in starch and cellulose bio polymers. The effect of different concentrations of biocomposite seed layer on the alignment of ZnO nanorods has been investigated. ZnO nanorods grown on a gold-coated glass substrate have been characterized by X-ray diffraction (XRD) and field emission scanning electron microscopy (FESEM) techniques. These techniques have shown that the ZnO nanorods are well aligned and perpendicular to the substrate, and grown with a high density and uniformity on the substrate. Moreover, ZnO nanorods can be grown with an orientation along the c-axis of the substrate and exhibit a wurtzite crystal structure with a dominant (002) peak in an XRD spectrum and possessed a high crystal quality. A photoluminescence (PL) spectroscopy study of the ZnO nanorods has revealed a conventional near band edge ultraviolet emission, along with emission in the visible part of the electromagnetic spectrum due to defect emission. This study provides an alternative method for the fabrication of well aligned ZnO nanorods. This method can be helpful in improving the performance of devices where alignment plays a significant role. PMID:28811454

Macroscale lateral alignment of semiconductor nanorods into freestanding thin films.

PubMed

Wang, Tie; Wang, Xirui; LaMontagne, Derek; Wang, Zhongwu; Cao, Y Charles

2013-04-24

This Communication reports that needle-like supercrystalline colloidal particles can be synthesized through anisotropy-driven self-assembly of 1,12-dodecanediamine-functionalized CdSe/CdS core/shell nanorods. The resulting superparticles exhibit both 1D lamellar and 2D hexagonal supercrystalline orders along directions parallel and perpendicular to the long axis of constituent nanorods, respectively. Our results show that the needle-like superparticles can be unidirectionally aligned through capillary forces on a patterned solid surface and further transferred into macroscopic, uniform, freestanding polymer films, which exhibit strong linear polarized PL with an enhanced polarization ratio, and are useful as energy down-conversion phosphors in polarized LEDs.

Magnetically actuated tissue engineered scaffold: insights into mechanism of physical stimulation

NASA Astrophysics Data System (ADS)

Sapir-Lekhovitser, Yulia; Rotenberg, Menahem Y.; Jopp, Juergen; Friedman, Gary; Polyak, Boris; Cohen, Smadar

2016-02-01

Providing the right stimulatory conditions resulting in efficient tissue promoting microenvironment in vitro and in vivo is one of the ultimate goals in tissue development for regenerative medicine. It has been shown that in addition to molecular signals (e.g. growth factors) physical cues are also required for generation of functional cell constructs. These cues are particularly relevant to engineering of biological tissues, within which mechanical stress activates mechano-sensitive receptors, initiating biochemical pathways which lead to the production of functionally mature tissue. Uniform magnetic fields coupled with magnetizable nanoparticles embedded within three dimensional (3D) scaffold structures remotely create transient physical forces that can be transferrable to cells present in close proximity to the nanoparticles. This study investigated the hypothesis that magnetically responsive alginate scaffold can undergo reversible shape deformation due to alignment of scaffold's walls in a uniform magnetic field. Using custom made Helmholtz coil setup adapted to an Atomic Force Microscope we monitored changes in matrix dimensions in situ as a function of applied magnetic field, concentration of magnetic particles within the scaffold wall structure and rigidity of the matrix. Our results show that magnetically responsive scaffolds exposed to an externally applied time-varying uniform magnetic field undergo a reversible shape deformation. This indicates on possibility of generating bending/stretching forces that may exert a mechanical effect on cells due to alternating pattern of scaffold wall alignment and relaxation. We suggest that the matrix structure deformation is produced by immobilized magnetic nanoparticles within the matrix walls resulting in a collective alignment of scaffold walls upon magnetization. The estimated mechanical force that can be imparted on cells grown on the scaffold wall at experimental conditions is in the order of 1 pN, which correlates well with reported threshold to induce mechanotransduction effects on cellular level. This work is our next step in understanding of how to accurately create proper stimulatory microenvironment for promotion of cellular organization to form mature tissue engineered constructs.

Magnetically actuated tissue engineered scaffold: insights into mechanism of physical stimulation

PubMed Central

Sapir-Lekhovitser, Yulia; Rotenberg, Menahem Y.; Jopp, Juergen; Friedman, Gary; Polyak, Boris; Cohen, Smadar

2016-01-01

Providing the right stimulatory conditions resulting in efficient tissue promoting microenvironment in vitro and in vivo is one of the ultimate goals in tissue development for regenerative medicine. It has been shown that in addition to molecular signals (e.g. growth factors) physical cues are also required for generation of functional cell constructs. These cues are particularly relevant to engineering of biological tissues, within which mechanical stress activates mechano-sensitive receptors, initiating biochemical pathways which lead to the production of functionally mature tissue. Uniform magnetic fields coupled with magnetizable nanoparticles embedded within three dimensional (3D) scaffold structures remotely create transient physical forces that can be transferrable to cells present in close proximity to the nanoparticles. This study investigated the hypothesis that magnetically responsive alginate scaffold can undergo reversible shape deformation due to alignment of scaffold’s walls in a uniform magnetic field. Using custom made Helmholtz coil setup adapted to an Atomic Force Microscope we monitored changes in matrix dimensions in situ as a function of applied magnetic field, concentration of magnetic particles within the scaffold wall structure and rigidity of the matrix. Our results show that magnetically responsive scaffolds exposed to an externally applied time-varying uniform magnetic field undergo a reversible shape deformation. This indicates on possibility of generating bending/stretching forces that may exert a mechanical effect on cells due to alternating pattern of scaffold wall alignment and relaxation. We suggest that the matrix structure deformation is produced by immobilized magnetic nanoparticles within the matrix walls resulting in a collective alignment of scaffold walls upon magnetization. The estimated mechanical force that can be imparted on cells grown on the scaffold wall at experimental conditions is in the order of 1 pN, which correlates well with reported threshold to induce mechanotransduction effects on cellular level. This work is our next step in understanding of how to accurately create proper stimulatory microenvironment for promotion of cellular organization to form mature tissue engineered constructs. PMID:26790538

Collective alignment of nanorods in thin Newtonian films

NASA Astrophysics Data System (ADS)

Gu, Yu; Burtovyy, Ruslan; Townsend, James; Owens, Jeffery; Luzinov, Igor; Kornev, Konstantin

2013-11-01

We provide a complete analytical description of the alignment kinetics of magnetic nanorods in magnetic field. Nickel nanorods were formed by template electrochemical deposition in alumina membranes from a dispersion in a water-glycerol mixture. To ensure uniformity of the dispersion, the surface of the nickel nanorods was covered with polyvinylpyrrolidone (PVP). A 40-70 nm coating prevented aggregation of nanoroda. These modifications allowed us to control alignment of the nanorods in a magnetic field and test the proposed theory. An orientational distribution function of nanorods was introduced. We demonstrated that the 0.04% volume fraction of nanorods in the glycerol-water mixture behaves as a system of non-interacting particles. However, the kinetics of alignment of a nanorod assembly does not follow the predictions of the single-nanorod theory. The distribution function theory explains the kinetics of alignment of a nanorod assembly and shows the significance of the initial distribution of nanorods in the film. It can be used to develop an experimental protocol for controlled ordering of magnetic nanorods in thin films. This work was supported by the Air Force Office of Scientific Research, Grant numbers FA9550-12-1-0459 and FA8650-09-D-507 5900.

Field gradients can control the alignment of nanorods.

PubMed

Ooi, Chinchun; Yellen, Benjamin B

2008-08-19

This work is motivated by the unexpected experimental observation that field gradients can control the alignment of nonmagnetic nanorods immersed inside magnetic fluids. In the presence of local field gradients, nanorods were observed to align perpendicular to the external field at low field strengths, but parallel to the external field at high field strengths. The switching behavior results from the competition between a preference to align with the external field (orientational potential energy) and preference to move into regions of minimum magnetic field (positional potential energy). A theoretical model is developed to explain this experimental behavior by investigating the statistics of nanorod alignment as a function of both the external uniform magnetic field strength and the local magnetic field variation above a periodic array of micromagnets. Computational phase diagrams are developed which indicate that the relative population of nanorods in parallel and perpendicular states can be adjusted through several control parameters. However, an energy barrier to rotation was discovered to influence the rate kinetics and restrict the utility of this assembly technique to nanorods which are slightly shorter than the micromagnet length. Experimental results concerning the orientation of nanorods inside magnetic fluid are also presented and shown to be in strong agreement with the theoretical work.

The use of patterns to disguise environmental cues during an anticipatory judgment task.

PubMed

Causer, Joe; Williams, A Mark

2015-02-01

A number of novel manipulations to the design of playing uniforms were used to try to disguise the actions of penalty takers in soccer. Skilled and less-skilled soccer goalkeepers were required to anticipate penalty kick outcome while their opponent wore one of three different uniform designs that were intended to disguise the availability of potentially key information from the hip region. Variations of shapes/patterns were designed to conceal the actual alignment of the hips. Three occlusion points were used in the test film: -160 ms, -80 ms before, and at foot-ball contact. Skilled individuals reported higher accuracy scores than their less-skilled counterparts (p < .05). There were no performance decrements for the less-skilled group across the different uniform conditions (p > .05); however, the skilled group decreased their accuracy on the experimental conditions compared with the control (p < .05). Findings highlight the potential benefits of designing playing uniforms that facilitate disguise in sport.

Electrorotation of colloidal particles in liquid crystals

NASA Astrophysics Data System (ADS)

Liao, G.; Smalyukh, I. I.; Kelly, J. R.; Lavrentovich, O. D.; Jákli, A.

2005-09-01

We present the first observations of dc electric-field-induced rotational motion of finite particles in liquid crystals. We show that the electrorotation is essentially identical to the well-known Quincke rotation, which in liquid crystals triggers an additional translational motion at higher fields. In the smectic phase the translational motion is confined to the two-dimensional geometry of smectic layers, in contrast to the isotropic and nematic phases, where the particles can move in all three dimensions. We demonstrate that by a proper analysis of the electrorotation, one can determine the in-plane viscosity of smectic liquid crystals. This method needs only a small amount of material, does not require uniform alignment over large areas, and enables probing rheological properties locally.

Method of constructing dished ion thruster grids to provide hole array spacing compensation

NASA Technical Reports Server (NTRS)

Banks, B. A. (Inventor)

1976-01-01

The center-to-center spacings of a photoresist pattern for an array of holes applied to a thin metal sheet are increased by uniformly stretching the thin metal sheet in all directions along the plane of the sheet. The uniform stretching is provided by securely clamping the periphery of the sheet and applying an annular force against the face of the sheet, within the periphery of the sheet and around the photoresist pattern. The technique is used in the construction of ion thruster grid units where the outer or downstream grid is subjected to uniform stretching prior to convex molding. The technique provides alignment of the holes of grid pairs so as to direct the ion beamlets in a direction parallel to the axis of the grid unit and thereby provide optimization of the available thrust.

Enhanced room temperature gas sensing of aligned Mn3O4 nanorod assemblies functionalized by aluminum anodic membranes.

PubMed

John, Neetha; Thomas, Paulose; Divya, K V; Abraham, K E

2018-08-17

The study includes a conductometric chemical sensor design using aligned Mn 3 O 4 nanorods. Nanostructuring is an emerging field of prominence due to its capacity to introduce unprecedented properties in materials with potential applications. A hydrothermally prepared in situ Mn 3 O 4 sample appears with an urchin rod-like morphology, which changes to a spherical shape upon annealing. An aluminum anodic membrane/template (AAO) is used for the growth of the nanorods and also as a medium to support the sensor. The aligned Mn 3 O 4 nanorods are formed in the pores of the AAO by vacuum infiltration approach, which is later on annealed. The gold electrical contacts are deposited on the top or bottom ends of the Mn 3 O 4 -embedded AAO to ensure conductometric sensing along the length of the Mn 3 O 4 nanorods. In comparison to the Mn 3 O 4 film-based sensor, the Mn 3 O 4 nanorods in the AAO template have enhanced sensitivity for detecting ethanol and acetone vapor at room temperature. The novel property observed is a result of the large surface area and number of oxygen vacancies of the uniformly aligned and parallel assemblies of the nanorods. The sensor exhibits the lowest response time at 4 s for ethanol and 2 s for acetone at room temperature with a concentration of 50 ppm. The response time is 7 and 5 s, respectively, for 25 ppm. The maximum sensitivities of the sensor at room temperature for ethanol and acetone gases are 67% and 68%, respectively, for 50 ppm concentration. The growth mechanism of the aligned nanorods formed in the AAO template is well established through FESEM analysis. The XPS and HRTEM study give additional evidence for the presence of oxidation states and structure of the prepared nanostructures, respectively.

Diffraction phase microscopy realized with an automatic digital pinhole

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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.

Tensile film clamps and mounting block for the rheovibron and autovibron viscoelastometer

NASA Technical Reports Server (NTRS)

Stoakley, Diane M. (Inventor); St.clair, Anne K. (Inventor); Little, Bruce D. (Inventor)

1989-01-01

A set of film clamps and a mounting block for use in the determination of tensile modulus and damping properties of films in a manually operated or automated Rheovibron is diagrammed. These clamps and mounting block provide uniformity of sample gripping and alignment in the instrument. Operator dependence and data variability are greatly reduced.

Single element laser beam shaper

DOEpatents

Zhang, Shukui [Yorktown, VA; Shinn, Michelle D [Newport News, VA

2005-09-13

A single lens laser beam shaper for converting laser beams from any spatial profile to a flat-top or uniform spatial profile. The laser beam shaper includes a lens having two aspheric surfaces. The beam shaper significantly simplifies the overall structure in comparison with conventional 2-element systems and therefore provides great ease in alignment and reduction of cost.

The development and progress of XeCl Excimer laser system

NASA Astrophysics Data System (ADS)

Zhang, Yongsheng; Ma, Lianying; Wang, Dahui; Zhao, Xueqing; Zhu, Yongxiang; Hu, Yun; Qian, Hang; Shao, Bibo; Yi, Aiping; Liu, Jingru

2015-05-01

A large angularly multiplexed XeCl Excimer laser system is under development at the Northwest Institute of Nuclear Technology (NINT). It is designed to explore the technical issues of uniform and controllable target illumination. Short wavelength, uniform and controllable target illumination is the fundamental requirement of high energy density physics research using large laser facility. With broadband, extended light source and multi-beam overlapping techniques, rare gas halide Excimer laser facility will provide uniform target illumination theoretically. Angular multiplexing and image relay techniques are briefly reviewed and some of the limitations are examined to put it more practical. The system consists of a commercial oscillator front end, three gas discharge amplifiers, two electron beam pumped amplifiers and the optics required to relay, encode and decode the laser beam. An 18 lens array targeting optics direct and focus the laser in the vacuum target chamber. The system is operational and currently undergoing tests. The total 18 beams output energy is more than 100J and the pulse width is 7ns (FWHM), the intensities on the target will exceed 1013W/cm2. The aberration of off-axis imaging optics at main amplifier should be minimized to improve the final image quality at the target. Automatic computer controlled alignment of the whole system is vital to efficiency and stability of the laser system, an array of automatic alignment model is under test and will be incorporated in the system soon.

Synchrotron x-ray scattering measurements of bulk structural properties in superconducting (Bi,Pb){sub 2}Sr{sub 2}Ca{sub 2}Cu{sub 3}O{sub 10}{endash}Ag tapes

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

Thurston, T.R.; Wildgruber, U.; Jisrawi, N.

The structural properties of superconducting (Bi,Pb){sub 2}Sr{sub 2}Ca{sub 2}Cu{sub 3}O{sub 10}{endash}Ag (2223) tapes have been measured using synchrotron x-ray scattering techniques. The x-ray photon energy was tuned just below the silver {ital K} absorption edge so the penetration depth was large, which allowed the measurements to be performed in a transmission geometry without removing the silver cladding. Analysis of the peaks in 2{theta} scans indicates that residual (Bi,Pb){sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8} (2212) superconductor starting material is present in all samples studied. The amount of 2212 varied widely among the tapes, and was not homogeneous along the length of eachmore » individual tape. Residual 2212 content increased near the ends of most samples, suggesting that 2223 phase development is sensitive to whether the superconducting material is encased in silver or not. The bulk {ital c}-axis alignment was measured in {approximately}100 mono- and multifilament samples, and correlations between {ital c}-axis alignment and current carrying capacity at 77 K were found. Multifilament samples generally had better alignment than monofilament samples. The {ital c}-axis alignment along the length of the tapes was uniform, and the superconducting material within {approximately}1 {mu}m of the Ag was better textured than the bulk of the sample. Intermediate pressings were directly shown to have an adverse affect on {ital c}-axis alignment. Finally, the evolution of texture and phase development was examined in a series of samples annealed for varying times. The 2212 starting material acquired the final {ital c}-axis alignment state after brief heating times, and only after much longer heating times did the 2212 transform into the 2223 phase. These results and their implications for improving processing procedures are discussed. {copyright} {ital 1996 American Institute of Physics.}« less

Engineered plant biomass particles coated with biological agents

DOEpatents

Dooley, James H.; Lanning, David N.

2014-06-24

Plant biomass particles coated with a biological agent such as a bacterium or seed, characterized by a length dimension (L) aligned substantially parallel to a grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. In particular, the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.W dimensions define a pair of substantially parallel top and bottom surfaces.

Stable Fe nanomagnets encapsulated inside vertically-aligned carbon nanotubes.

PubMed

Bondino, Federica; Magnano, Elena; Ciancio, Regina; Castellarin Cudia, Carla; Barla, Alessandro; Carlino, Elvio; Yakhou-Harris, Flora; Rupesinghe, Nalin; Cepek, Cinzia

2017-12-06

Well-defined sized (5-10 nm) metallic iron nanoparticles (NPs) with body-centered cubic structure encapsulated inside the tip of millimeter-long vertically aligned carbon nanotubes (VACNTs) of uniform length have been investigated with high-resolution transmission electron microscopy and soft X-ray spectroscopy techniques. Surface-sensitive and chemically-selective measurements have been used to evaluate the magnetic properties of the encapsulated NPs. The encapsulated Fe NPs display magnetic remanence up to room temperature, low coercivity, high chemical stability and no significant anisotropy. Our surface-sensitive measurements combined with the specific morphology of the studied VACNTs allow us to pinpoint the contribution of the surface oxidized or hydroxidized iron catalysts present at the VACNT-substrate interface.

Carbon nanotube bundles with tensile strength over 80 GPa.

PubMed

Bai, Yunxiang; Zhang, Rufan; Ye, Xuan; Zhu, Zhenxing; Xie, Huanhuan; Shen, Boyuan; Cai, Dali; Liu, Bofei; Zhang, Chenxi; Jia, Zhao; Zhang, Shenli; Li, Xide; Wei, Fei

2018-05-14

Carbon nanotubes (CNTs) are one of the strongest known materials. When assembled into fibres, however, their strength becomes impaired by defects, impurities, random orientations and discontinuous lengths. Fabricating CNT fibres with strength reaching that of a single CNT has been an enduring challenge. Here, we demonstrate the fabrication of CNT bundles (CNTBs) that are centimetres long with tensile strength over 80 GPa using ultralong defect-free CNTs. The tensile strength of CNTBs is controlled by the Daniels effect owing to the non-uniformity of the initial strains in the components. We propose a synchronous tightening and relaxing strategy to release these non-uniform initial strains. The fabricated CNTBs, consisting of a large number of components with parallel alignment, defect-free structures, continuous lengths and uniform initial strains, exhibit a tensile strength of 80 GPa (corresponding to an engineering tensile strength of 43 GPa), which is far higher than that of any other strong fibre.

Process for making carbon foam

DOEpatents

Klett, James W.

2000-01-01

The process obviates the need for conventional oxidative stabilization. The process employs mesophase or isotropic pitch and a simplified process using a single mold. The foam has a relatively uniform distribution of pore sizes and a highly aligned graphic structure in the struts. The foam material can be made into a composite which is useful in high temperature sandwich panels for both thermal and structural applications.

Automatic Configuration of Programmable Logic Controller Emulators

DTIC Science & Technology

2015-03-01

25 11 Example tree generated using UPGMA [Edw13] . . . . . . . . . . . . . . . . . . . . 33 12 Example sequence alignment for two... UPGMA Unweighted Pair Group Method with Arithmetic Mean URL uniform resource locator VM virtual machine XML Extensible Markup Language xx List of...appearance in the ses- sion, and then they are clustered again using Unweighted Pair Group Method with Arithmetic Mean ( UPGMA ) with a distance matrix based

Scalar Fluxes Near a Tall Building in an Aligned Array of Rectangular Buildings

NASA Astrophysics Data System (ADS)

Fuka, Vladimír; Xie, Zheng-Tong; Castro, Ian P.; Hayden, Paul; Carpentieri, Matteo; Robins, Alan G.

2018-04-01

Scalar dispersion from ground-level sources in arrays of buildings is investigated using wind-tunnel measurements and large-eddy simulation (LES). An array of uniform-height buildings of equal dimensions and an array with an additional single tall building (wind tunnel) or a periodically repeated tall building (LES) are considered. The buildings in the array are aligned and form long streets. The sensitivity of the dispersion pattern to small changes in wind direction is demonstrated. Vertical scalar fluxes are decomposed into the advective and turbulent parts and the influences of wind direction and of the presence of the tall building on the scalar flux components are evaluated. In the uniform-height array turbulent scalar fluxes are dominant, whereas the tall building produces an increase of the magnitude of advective scalar fluxes that yields the largest component. The presence of the tall building causes either an increase or a decrease to the total vertical scalar flux depending on the position of the source with respect to the tall building. The results of the simulations can be used to develop parametrizations for street-canyon dispersion models and enhance their capabilities in areas with tall buildings.

15N and 31P solid-state NMR study of transmembrane domain alignment of M2 protein of influenza A virus in hydrated cylindrical lipid bilayers confined to anodic aluminum oxide nanopores.

PubMed

Chekmenev, Eduard Y; Hu, Jun; Gor'kov, Peter L; Brey, William W; Cross, Timothy A; Ruuge, Andres; Smirnov, Alex I

2005-04-01

This communication reports the first example of a high resolution solid-state 15N 2D PISEMA NMR spectrum of a transmembrane peptide aligned using hydrated cylindrical lipid bilayers formed inside nanoporous anodic aluminum oxide (AAO) substrates. The transmembrane domain SSDPLVVA(A-15N)SIIGILHLILWILDRL of M2 protein from influenza A virus was reconstituted in hydrated 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine bilayers that were macroscopically aligned by a conventional micro slide glass support or by the AAO nanoporous substrate. 15N and 31P NMR spectra demonstrate that both the phospholipids and the protein transmembrane domain are uniformly aligned in the nanopores. Importantly, nanoporous AAO substrates may offer several advantages for membrane protein alignment in solid-state NMR studies compared to conventional methods. Specifically, higher thermal conductivity of aluminum oxide is expected to suppress thermal gradients associated with inhomogeneous radio frequency heating. Another important advantage of the nanoporous AAO substrate is its excellent accessibility to the bilayer surface for exposure to solute molecules. Such high accessibility achieved through the substrate nanochannel network could facilitate a wide range of structure-function studies of membrane proteins by solid-state NMR.

Automated cell tracking identifies mechanically oriented cell divisions during Drosophila axis elongation.

PubMed

Wang, Michael F Z; Hunter, Miranda V; Wang, Gang; McFaul, Christopher; Yip, Christopher M; Fernandez-Gonzalez, Rodrigo

2017-04-01

Embryos extend their anterior-posterior (AP) axis in a conserved process known as axis elongation. Drosophila axis elongation occurs in an epithelial monolayer, the germband, and is driven by cell intercalation, cell shape changes, and oriented cell divisions at the posterior germband. Anterior germband cells also divide during axis elongation. We developed image analysis and pattern-recognition methods to track dividing cells from confocal microscopy movies in a generally applicable approach. Mesectoderm cells, forming the ventral midline, divided parallel to the AP axis, while lateral cells displayed a uniform distribution of division orientations. Mesectoderm cells did not intercalate and sustained increased AP strain before cell division. After division, mesectoderm cell density increased along the AP axis, thus relieving strain. We used laser ablation to isolate mesectoderm cells from the influence of other tissues. Uncoupling the mesectoderm from intercalating cells did not affect cell division orientation. Conversely, separating the mesectoderm from the anterior and posterior poles of the embryo resulted in uniformly oriented divisions. Our data suggest that mesectoderm cells align their division angle to reduce strain caused by mechanical forces along the AP axis of the embryo. © 2017. Published by The Company of Biologists Ltd.

Uniformly wound superconducting coil and method of making same

DOEpatents

Mookerjee, S.; Weijun, S.; Yager, B.

1994-03-08

A coil of superconducting wire for a superconducting magnet is described having a relatively dense and uniformly spaced winding to enhance the homogeneity and strength of the magnetic field surrounding the coil and a method of winding the same wherein the mandrel used to wind said coil comprises removable spacers and retainers forming a plurality of outwardly opening slots, each of said slots extending generally about the periphery of the mandrel and being sized to receive and outwardly align and retain successive turns of the superconducting wire within each slot as the wire is wound around and laterally across the mandrel to form a plurality of wire ribbons of a predetermined thickness laterally across the mandrel. 8 figures.

Uniformly wound superconducting coil and method of making same

DOEpatents

Mookerjee, Sumit; Weijun, Shen; Yager, Billy

1994-01-01

A coil of superconducting wire for a superconducting magnet having a relaely dense and uniformly spaced winding to enhance the homogeneity and strength of the magnetic field surrounding the coil and a method of winding the same wherein the mandrel used to wind said coil comprises removable spacers and retainers forming a plurality of outwardly opening slots, each of said slots extending generally about the periphery of the mandrel and being sized to receive and outwardly align and retain successive turns of the superconducting wire within each slot as the wire is wound around and laterally across the mandrel to form a plurality of wire ribbons of a predetermined thickness laterally across the mandrel.

Study of Image Quality From CT Scanner Multi-Detector by using Americans College of Radiology (ACR) Phantom

NASA Astrophysics Data System (ADS)

Mulyadin; Dewang, Syamsir; Abdullah, Bualkar; Tahir, Dahlang

2018-03-01

In this study, the image quality of CT scan using phantom American College of Radiology (ACR) was determined. Scanning multidetector CT is used to know the image quality parameters by using a solid phantom containing four modules and primarily from materials that are equivalent to water. Each module is 4 cm in diameter and 20 cm in diameter. There is white alignment marks painted white to reflect the alignment laser and there are also “HEAD”, “FOOT”, and “TOP” marks on the phantom to help align. This test obtains CT images of each module according to the routine inspection protocol of the head. Acceptance of image quality obtained for determination: CT Number Accuracy (CTN), CT Number Uniformity and Noise, Linearity CT Number, Slice Technique, Low Contrast Resolution and High Contrast Resolution represent image quality parameters. In testing CT Number Accuracy (CTN), CT Uniform number and Noise are in the range of tolerable values allowed. In the test, Linearity CT Number obtained correlation value above 0.99 is the relationship between electron density and CT Number. In a low contrast resolution test, the smallest contrast groups are visible. In contrast, the high resolution is seen up to 7 lp/cm. The quality of GE CT Scan is very high, as all the image quality tests obtained are within the tolerance brackets of values permitted by the Nuclear Power Control Agency (BAPETEN). Image quality test is a way to get very important information about the accuracy of snoring result by using phantom ACR.

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

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.

Fabrication of Highly Ordered Anodic Aluminium Oxide Templates on Silicon Substrates

DTIC Science & Technology

2007-01-01

highly ordered anodic aluminium oxide ( AAO ) templates of unprecedented pore uniformity directly on Si, enabled by new advances on two fronts – direct...field emitter, sensors, oscillators and photodetectors. 15. SUBJECT TERMS Anodic aluminum oxide , template-assisted nanofabrication, carbon nanotube...Fabrication of the aligned and patterned carbon nanotube field emitters using the anodic aluminum oxide nano-template on a Si wafer’, Synth. Met

Method of casting pitch based foam

DOEpatents

Klett, James W.

2002-01-01

A process for producing molded pitch based foam is disclosed which minimizes cracking. The process includes forming a viscous pitch foam in a container, and then transferring the viscous pitch foam from the container into a mold. The viscous pitch foam in the mold is hardened to provide a carbon foam having a relatively uniform distribution of pore sizes and a highly aligned graphic structure in the struts.

Lithographic process window optimization for mask aligner proximity lithography

NASA Astrophysics Data System (ADS)

Voelkel, Reinhard; Vogler, Uwe; Bramati, Arianna; Erdmann, Andreas; Ünal, Nezih; Hofmann, Ulrich; Hennemeyer, Marc; Zoberbier, Ralph; Nguyen, David; Brugger, Juergen

2014-03-01

We introduce a complete methodology for process window optimization in proximity mask aligner lithography. The commercially available lithography simulation software LAB from GenISys GmbH was used for simulation of light propagation and 3D resist development. The methodology was tested for the practical example of lines and spaces, 5 micron half-pitch, printed in a 1 micron thick layer of AZ® 1512HS1 positive photoresist on a silicon wafer. A SUSS MicroTec MA8 mask aligner, equipped with MO Exposure Optics® was used in simulation and experiment. MO Exposure Optics® is the latest generation of illumination systems for mask aligners. MO Exposure Optics® provides telecentric illumination and excellent light uniformity over the full mask field. MO Exposure Optics® allows the lithography engineer to freely shape the angular spectrum of the illumination light (customized illumination), which is a mandatory requirement for process window optimization. Three different illumination settings have been tested for 0 to 100 micron proximity gap. The results obtained prove, that the introduced process window methodology is a major step forward to obtain more robust processes in mask aligner lithography. The most remarkable outcome of the presented study is that a smaller exposure gap does not automatically lead to better print results in proximity lithography - what the "good instinct" of a lithographer would expect. With more than 5'000 mask aligners installed in research and industry worldwide, the proposed process window methodology might have significant impact on yield improvement and cost saving in industry.

Engineered plant biomass particles coated with bioactive agents

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

Dooley, James H; Lanning, David N

Plant biomass particles coated with a bioactive agent such as a fertilizer or pesticide, characterized by a length dimension (L) aligned substantially parallel to a grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. In particular, the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.Wmore » dimensions define a pair of substantially parallel top and bottom surfaces.« less

Template-Assisted Hydrothermal Growth of Aligned Zinc Oxide Nanowires for Piezoelectric Energy Harvesting Applications

PubMed Central

2016-01-01

A flexible and robust piezoelectric nanogenerator (NG) based on a polymer-ceramic nanocomposite structure has been successfully fabricated via a cost-effective and scalable template-assisted hydrothermal synthesis method. Vertically aligned arrays of dense and uniform zinc oxide (ZnO) nanowires (NWs) with high aspect ratio (diameter ∼250 nm, length ∼12 μm) were grown within nanoporous polycarbonate (PC) templates. The energy conversion efficiency was found to be ∼4.2%, which is comparable to previously reported values for ZnO NWs. The resulting NG is found to have excellent fatigue performance, being relatively immune to detrimental environmental factors and mechanical failure, as the constituent ZnO NWs remain embedded and protected inside the polymer matrix. PMID:27172933

Femtosecond laser-induced surface structures on carbon fibers.

PubMed

Sajzew, Roman; Schröder, Jan; Kunz, Clemens; Engel, Sebastian; Müller, Frank A; Gräf, Stephan

2015-12-15

The influence of different polarization states during the generation of periodic nanostructures on the surface of carbon fibers was investigated using a femtosecond laser with a pulse duration τ=300  fs, a wavelength λ=1025  nm, and a peak fluence F=4  J/cm². It was shown that linear polarization results in a well-aligned periodic pattern with different orders of magnitude concerning their period and an alignment parallel and perpendicular to fiber direction, respectively. For circular polarization, both types of uniform laser-induced periodic surface structures (LIPSS) patterns appear simultaneously with different dominance in dependence on the position at the fiber surface. Their orientation was explained by the polarization-dependent absorptivity and the geometrical anisotropy of the carbon fibers.

Vertically aligned N-doped CNTs growth using Taguchi experimental design

NASA Astrophysics Data System (ADS)

Silva, Ricardo M.; Fernandes, António J. S.; Ferro, Marta C.; Pinna, Nicola; Silva, Rui F.

2015-07-01

The Taguchi method with a parameter design L9 orthogonal array was implemented for optimizing the nitrogen incorporation in the structure of vertically aligned N-doped CNTs grown by thermal chemical deposition (TCVD). The maximization of the ID/IG ratio of the Raman spectra was selected as the target value. As a result, the optimal deposition configuration was NH3 = 90 sccm, growth temperature = 825 °C and catalyst pretreatment time of 2 min, the first parameter having the main effect on nitrogen incorporation. A confirmation experiment with these values was performed, ratifying the predicted ID/IG ratio of 1.42. Scanning electron microscopy (SEM) characterization revealed a uniform completely vertically aligned array of multiwalled CNTs which individually exhibit a bamboo-like structure, consisting of periodically curved graphitic layers, as depicted by high resolution transmission electron microscopy (HRTEM). The X-ray photoelectron spectroscopy (XPS) results indicated a 2.00 at.% of N incorporation in the CNTs in pyridine-like and graphite-like, as the predominant species.

Fabrication of large diffractive optical elements in thick film on a concave lens surface.

PubMed

Xie, Yongjun; Lu, Zhenwu; Li, Fengyou

2003-05-05

We demonstrate experimentally the technique of fabricating large diffractive optical elements (DOEs) in thick film on a concave lens surface (mirrors) with precise alignment by using the strategy of double exposure. We adopt the method of double exposure to overcome the difficulty of processing thick photoresist on a large curved substrate. A uniform thick film with arbitrary thickness on a concave lens can be obtained with this technique. We fabricate a large concentric circular grating with a 10-ìm period on a concave lens surface in film with a thickness of 2.0 ìm after development. It is believed that this technique can also be used to fabricate larger DOEs in thicker film on the concave or convex lens surface with precise alignment. There are other potential applications of this technique, such as fabrication of micro-optoelectromechanical systems (MOEMS) or microelectromechanical systems (MEMS) and fabrication of microlens arrays on a large concave lens surface or convex lens surface with precise alignment.

Silicon cells made by self-aligned selective-emitter plasma-etchback process

DOEpatents

Ruby, Douglas S.; Schubert, William K.; Gee, James M.; Zaidi, Saleem H.

2000-01-01

Photovoltaic cells and methods for making them are disclosed wherein the metallized grids of the cells are used to mask portions of cell emitter regions to allow selective etching of phosphorus-doped emitter regions. The preferred etchant is SF.sub.6 or a combination of SF.sub.6 and O.sub.2. This self-aligned selective etching allows for enhanced blue response (versus cells with uniform heavy doping of the emitter) while preserving heavier doping in the region beneath the gridlines needed for low contact resistance. Embodiments are disclosed for making cells with or without textured surfaces. Optional steps include plasma hydrogenation and PECVD nitride deposition, each of which are suited to customized applications for requirements of given cells to be manufactured. The techniques disclosed could replace expensive and difficult alignment methodologies used to obtain selectively etched emitters, and they may be easily integrated with existing plasma processing methods and techniques of the invention may be accomplished in a single plasma-processing chamber.

Fundamental radiological and geometric performance of two types of proton beam modulated discrete scanning systems.

PubMed

Farr, J B; Dessy, F; De Wilde, O; Bietzer, O; Schönenberg, D

2013-07-01

The purpose of this investigation was to compare and contrast the measured fundamental properties of two new types of modulated proton scanning systems. This provides a basis for clinical expectations based on the scanned beam quality and a benchmark for computational models. Because the relatively small beam and fast scanning gave challenges to the characterization, a secondary purpose was to develop and apply new approaches where necessary to do so. The following performances of the proton scanning systems were investigated: beamlet alignment, static in-air beamlet size and shape, scanned in-air penumbra, scanned fluence map accuracy, geometric alignment of scanning system to isocenter, maximum field size, lateral and longitudinal field uniformity of a 1 l cubic uniform field, output stability over time, gantry angle invariance, monitoring system linearity, and reproducibility. A range of detectors was used: film, ionization chambers, lateral multielement and longitudinal multilayer ionization chambers, and a scintillation screen combined with a digital video camera. Characterization of the scanned fluence maps was performed with a software analysis tool. The resulting measurements and analysis indicated that the two types of delivery systems performed within specification for those aspects investigated. The significant differences were observed between the two types of scanning systems where one type exhibits a smaller spot size and associated penumbra than the other. The differential is minimum at maximum energy and increases inversely with decreasing energy. Additionally, the large spot system showed an increase in dose precision to a static target with layer rescanning whereas the small spot system did not. The measured results from the two types of modulated scanning types of system were consistent with their designs under the conditions tested. The most significant difference between the types of system was their proton spot size and associated resolution, factors of magnetic optics, and vacuum length. The need and benefit of mutielement detectors and high-resolution sensors was also shown. The use of a fluence map analytical software tool was particularly effective in characterizing the dynamic proton energy-layer scanning.

Moire interferometry patterns for rotational alignment of structures

NASA Astrophysics Data System (ADS)

Heidari, Esmaeil; Harding, Kevin

2016-08-01

In some manufacturing applications the alignment of fine structures formed on the surface of a part such as micro-scribed patterns on solar panels can be critical to the panel performance. Variations in pattern uniformity may degrade the efficiency of the solar panel if the pattern deviates significantly from designed parameters. This paper will explore the use of moire patterns to interpret the angular alignment of such structures on 3 dimensional non-planar shapes. The moire interferometry pattern creates a beat between the scribed pattern and a reference pattern that is a function of both the shape of the part as well as the shape of the scribed pattern. Both the part shape variations and the patterns of interest are typically much smaller than can be seen visually. Similar challenges exist when inspecting specular models or testing low quality optics. The moire effect allows small displacements to be measured from patterns that are well below the resolution of the camera systems that are used to view the patterns. Issues such as the separation of the shape of the part from the alignment of the fine structure as well as resolution and robustness of the technique will be explored in this paper.

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

Barnes, Jason W., E-mail: jwbarnes@uidaho.ed

Main-sequence stars earlier than spectral-type approxF6 or so are expected to rotate rapidly due to their radiative exteriors. This rapid rotation leads to an oblate stellar figure. It also induces the photosphere to be hotter (by up to several thousand kelvin) at the pole than at the equator as a result of a process called gravity darkening that was first predicted by von Zeipel. Transits of extrasolar planets across such a non-uniform, oblate disk yield unusual and distinctive lightcurves that can be used to determine the relative alignment of the stellar rotation pole and the planet orbit normal. This spin-orbitmore » alignment can be used to constrain models of planet formation and evolution. Orderly planet formation and migration within a disk that is coplanar with the stellar equator will result in spin-orbit alignment. More violent planet-planet scattering events should yield spin-orbit misaligned planets. Rossiter-McLaughlin measurements of transits of lower-mass stars show that some planets are spin-orbit aligned, and some are not. Since Rossiter-McLaughlin measurements are difficult around rapid rotators, lightcurve photometry may be the best way to determine the spin-orbit alignment of planets around massive stars. The Kepler mission will monitor approx10{sup 4} of these stars within its sample. The lightcurves of any detected planets will allow us to probe the planet formation process around high-mass stars for the first time.« less

Gold nano-decorated aligned polyurethane nanofibers for enhancement of neurite outgrowth and elongation.

PubMed

Demir, Ulku Selcen; Shahbazi, Reza; Calamak, Semih; Ozturk, Sukru; Gultekinoglu, Merve; Ulubayram, Kezban

2018-06-01

Neurite outgrowth and elongation of neural cells is the most important subject that is considered in nerve tissue engineering. In this regard, aligned nanofibers have taken much attention in terms of providing guidance for newly outgrown neurites. The main objective of this study was to fabricate aligned polyurethane nanofibers by electrospinning process and decorate them with gold nanoparticles to further investigate the synergistic effects of nanotopography, biological nerve growth factor (NGF) and electrical stimulations on neurite outgrowth and elongation of pheochromocytoma (PC-12) model cells. In this regard, smooth and uniform aligned polyurethane nanofibers with the average diameter of 519 ± 56 nm were fabricated and decorated with the gold nanoparticles with the average diameter of ∼50 nm. PC-12 cells were cultured on the various nanofiber surfaces inside the bio-mimetic bioreactor system and exposed either to NGF alone or combination of NGF and electrical stimulation. It was found that 50 ng/mL NGF concentration is an optimal value for the stimulation of neurite outgrowth. After 4 days of culture under 100 mV, 10 ms electrical stimulation in 1 h/day period it was found that the gold nanoparticle decorated aligned polyurethane nanofibers increased the neurite outgrowth and elongation more with the combinational NGF and electrical stimulation. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 1604-1613, 2018. © 2018 Wiley Periodicals, Inc.

Permeability of C2C12 myotube membranes is influenced by stretch velocity.

PubMed

Burkholder, Thomas J

2003-05-30

Mechanical signals are critical to the growth and maintenance of skeletal muscle, but the mechanism by which these signals are transduced by the cell remains unknown. This work examined the hypothesis that stretch conditions influence membrane permeability consistent with a role for membrane permeability in mechanotransduction. C2C12 myotubes were grown in conditions that encourage uniform alignment and subjected to uniform mechanical deformation in the presence of fluorescein labeled dextran to evaluate membrane permeability as a function of stretch amplitude and velocity. Within a physiologically relevant range of conditions, a complex interaction between the two aspects of stretch was observed, with velocity contributing most strongly at large stretch amplitudes. This suggests that membrane viscosity could contribute to mechanotransduction.

Effect of tow alignment on the mechanical performance of 3D woven textile composites

NASA Technical Reports Server (NTRS)

Norman, Timothy L.; Allison, Patti; Baldwin, Jack W.; Gracias, Brian K.; Seesdorf, Dave

1993-01-01

Three-dimensional (3D) woven preforms are currently being considered for use as primary structural components. Lack of technology to properly manufacture, characterize and predict mechanical properties, and predict damage mechanisms leading to failure are problems facing designers of textile composite materials. Two material systems with identical specifications but different manufacturing approaches are investigated. One manufacturing approach resulted in an irregular (nonuniform) preform geometry. The other approach yielded the expected preform geometry (uniform). The objectives are to compare the mechanical properties of the uniform and nonuniform angle interlock 3D weave constructions. The effect of adding layers of laminated tape to the outer surfaces of the textile preform is also examined. Damage mechanisms are investigated and test methods are evaluated.

Fabrication of Tunnel Junctions For Direct Detector Arrays With Single-Electron Transistor Readout Using Electron-Beam Lithography

NASA Technical Reports Server (NTRS)

Stevenson, T. R.; Hsieh, W.-T.; Li, M. J.; Stahle, C. M.; Rhee, K. W.; Teufel, J.; Schoelkopf, R. J.

2002-01-01

This paper will describe the fabrication of small aluminum tunnel junctions for applications in astronomy. Antenna-coupled superconducting tunnel junctions with integrated single-electron transistor readout have the potential for photon-counting sensitivity at sub-millimeter wavelengths. The junctions for the detector and single-electron transistor can be made with electron-beam lithography and a standard self-aligned double-angle deposition process. However, high yield and uniformity of the junctions is required for large-format detector arrays. This paper will describe how measurement and modification of the sensitivity ratio in the resist bilayer was used to greatly improve the reliability of forming devices with uniform, sub-micron size, low-leakage junctions.

Wide-field-of-view nanoscale Bragg liquid crystal polarization gratings

NASA Astrophysics Data System (ADS)

Xiang, Xiao; Kim, Jihwan; Escuti, Michael J.

2018-02-01

Here, we demonstrate a liquid crystal (LC) polymer Bragg polarization grating (PG) with large angular band- width and high efficiency in transmission-mode for 532 nm wavelength and 400 nm period. The field-of-view (FOV ) is increased significantly while preserving high diffraction efficiency by realizing a monolithic grating comprising two different slants. Using rigorous coupled-wave analysis simulation, we identified a structure with 48° FOV and 70% average first-order efficiency. We then experimentally fabricated and characterized the grating with a photo-aligned LC polymer network, also known as reactive mesogens. We measured 40° FOV and nearly 80% average diffraction efficiency. With this broadened and fairly uniform angular response, this wide FOV Bragg PG is a compelling option for large deflection-angle applications, including near-eye display in augmented reality systems, waveguide based illumination, and beam steering.

Electrohydrodynamic instabilities of viscous drops*

NASA Astrophysics Data System (ADS)

Vlahovska, Petia M.

2016-10-01

A classic result due to Taylor is that a weakly conducting drop bearing zero net charge placed in a uniform electric field adopts a prolate or oblate spheroidal shape, the flow and shape being axisymmetrically aligned with the applied field. Here I overview some intriguing symmetry-breaking instabilities occurring in strong applied dc fields: Quincke rotation resulting in drop steady tilt or tumbling, and pattern formation on the surface of a particle-coated drop.

Engineered plant biomass feedstock particles

DOEpatents

Dooley, James H [Federal Way, WA; Lanning, David N [Federal Way, WA; Broderick, Thomas F [Lake Forest Park, WA

2011-10-18

A novel class of flowable biomass feedstock particles with unusually large surface areas that can be manufactured in remarkably uniform sizes using low-energy comminution techniques. The feedstock particles are roughly parallelepiped in shape and characterized by a length dimension (L) aligned substantially with the grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. The particles exhibit a disrupted grain structure with prominent end and surface checks that greatly enhances their skeletal surface area as compared to their envelope surface area. The L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers. The W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers. The L.times.W dimensions define a pair of substantially parallel top surfaces characterized by some surface checking between longitudinally arrayed fibers. At least 80% of the particles pass through a 1/4 inch screen having a 6.3 mm nominal sieve opening but are retained by a No. 10 screen having a 2 mm nominal sieve opening. The feedstock particles are manufactured from a variety of plant biomass materials including wood, crop residues, plantation grasses, hemp, bagasse, and bamboo.

Equilibrium state of a cylindrical particle with flat ends in nematic liquid crystals.

PubMed

Hashemi, S Masoomeh; Ejtehadi, Mohammad Reza

2015-01-01

A continuum theory is employed to numerically study the equilibrium orientation and defect structures of a circular cylindrical particle with flat ends under a homeotropic anchoring condition in a uniform nematic medium. Different aspect ratios of this colloidal geometry from thin discotic to long rodlike shapes and several colloidal length scales ranging from mesoscale to nanoscale are investigated. We show that the equilibrium state of this colloidal geometry is sensitive to the two geometrical parameters: aspect ratio and length scale of the particle. For a large enough mesoscopic particle, there is a specific asymptotic equilibrium angle associated to each aspect ratio. Upon reducing the particle size to nanoscale, the equilibrium angle follows a descending or ascending trend in such a way that the equilibrium angle of a particle with the aspect ratio bigger than 1:1 (a discotic particle) goes to a parallel alignment with respect to the far-field nematic, whereas the equilibrium angle for a particle with the aspect ratio 1:1 and smaller (a rodlike particle) tends toward a perpendicular alignment to the uniform nematic direction. The discrepancy between the equilibrium angles of the mesoscopic and nanoscopic particles originates from the significant differences between their defect structures. The possible defect structures related to mesoscopic and nanoscopic colloidal particles of this geometry are also introduced.

Direct spectroscopic evidence for competition between thermal molecular agitation and magnetic field in a tetrameric protein in aqueous solution

NASA Astrophysics Data System (ADS)

Calabrò, Emanuele; Magazù, Salvatore

2018-05-01

Samples of a typical tetrameric protein, the hemoglobin, at the concentration of 150 mg/ml in bidistilled water solution, were exposed to a uniform magnetic field at 200 mT at different temperatures of 15∘C, 40∘C and 65∘C. Fourier Transform Infrared Spectroscopy was used to analyze the response of the secondary structure of the protein to both stress agents, heating and static magnetic field. The most relevant result which was observed was the significant increasing in intensity of the Amide I band after exposure to the uniform magnetic field at the room temperature of 15∘C. This result can be explained assuming that protein's α-helices aligned along the direction of the applied magnetic field due to their large dipole moment, inducing the alignment of the entire protein. Increasing of temperature up to 40∘C and 65∘C induced a significant reduction of the increasing in intensity of the Amide I band. This effect may be easily explained assuming that Brownian motion of the protein in water solution caused by thermal molecular agitation increased with increasing of temperature, contrasting the effect of the torque of the magnetic field applied to the protein in water solution.

Uniform hexagonal graphene flakes and films grown on liquid copper surface.

PubMed

Geng, Dechao; Wu, Bin; Guo, Yunlong; Huang, Liping; Xue, Yunzhou; Chen, Jianyi; Yu, Gui; Jiang, Lang; Hu, Wenping; Liu, Yunqi

2012-05-22

Unresolved problems associated with the production of graphene materials include the need for greater control over layer number, crystallinity, size, edge structure and spatial orientation, and a better understanding of the underlying mechanisms. Here we report a chemical vapor deposition approach that allows the direct synthesis of uniform single-layered, large-size (up to 10,000 μm(2)), spatially self-aligned, and single-crystalline hexagonal graphene flakes (HGFs) and their continuous films on liquid Cu surfaces. Employing a liquid Cu surface completely eliminates the grain boundaries in solid polycrystalline Cu, resulting in a uniform nucleation distribution and low graphene nucleation density, but also enables self-assembly of HGFs into compact and ordered structures. These HGFs show an average two-dimensional resistivity of 609 ± 200 Ω and saturation current density of 0.96 ± 0.15 mA/μm, demonstrating their good conductivity and capability for carrying high current density.

Uniform hexagonal graphene flakes and films grown on liquid copper surface

PubMed Central

Geng, Dechao; Wu, Bin; Guo, Yunlong; Huang, Liping; Xue, Yunzhou; Chen, Jianyi; Yu, Gui; Jiang, Lang; Hu, Wenping; Liu, Yunqi

2012-01-01

Unresolved problems associated with the production of graphene materials include the need for greater control over layer number, crystallinity, size, edge structure and spatial orientation, and a better understanding of the underlying mechanisms. Here we report a chemical vapor deposition approach that allows the direct synthesis of uniform single-layered, large-size (up to 10,000 μm2), spatially self-aligned, and single-crystalline hexagonal graphene flakes (HGFs) and their continuous films on liquid Cu surfaces. Employing a liquid Cu surface completely eliminates the grain boundaries in solid polycrystalline Cu, resulting in a uniform nucleation distribution and low graphene nucleation density, but also enables self-assembly of HGFs into compact and ordered structures. These HGFs show an average two-dimensional resistivity of 609 ± 200 Ω and saturation current density of 0.96 ± 0.15 mA/μm, demonstrating their good conductivity and capability for carrying high current density. PMID:22509001

Method for fabricating boron carbide articles

DOEpatents

Ardary, Zane L.; Reynolds, Carl D.

1980-01-01

The present invention is directed to the fabrication of boron carbide articles having length-to-diameter or width ratios greater than 2 to 1. The process of the present invention is practiced by the steps comprising hot pressing boron carbide powder into article segments or portions in which the segments have a length-to-diameter or width ratio less than 1.5, aligning a plurality of the initially hot-pressed segments in a hot-pressing die with the end surfaces of the segments placed in intimate contact with one another, and then hot pressing the aligned segments into an article of the desired configuration. The resulting article exhibits essentially uniform density throughout the structure with the bonds between the segments being equivalent in hardness, strength, and density to the remainder of the article.

Effect of Ply Orientation and Crack Location on SIFs in Finite Multilayers with Aligned Cracks

NASA Astrophysics Data System (ADS)

Chen, Linfeng; Pindera, Marek-Jerzy

2008-02-01

An exact elasticity solution is presented for arbitrarily laminated finite multilayers in a state of generalized plane deformation under horizontally pinned end constraints that are weakened by aligned cracks. Based on half-range Fourier series and the local/global stiffness matrix approach, the mixed boundary-value problem is reduced to Cauchy-type singular integral equations in the unknown displacement discontinuities. Solution to these equations is obtained using the approach developed by Erdogan and co-workers. Numerical results quantify the thus-far undocumented geometric and material effects on Mode I, II and III stress intensity factors in composite multilayers with interacting cracks under uniform vertical displacement. These effects include finite dimensions, crack location, material anisotropy due to a unidirectional fiber-reinforced layer/s orientation, and orientational grading.

A MISO UCA Beamforming Dimmable LED System for Indoor Positioning

PubMed Central

Taparugssanagorn, Attaphongse; Siwamogsatham, Siwaruk; Pomalaza-Ráez, Carlos

2014-01-01

The use of a multiple input single output (MISO) transmit beamforming system using dimmable light emitting arrays (LEAs) in the form of a uniform circular array (UCA) of transmitters is proposed in this paper. With this technique, visible light communications between a transmitter and a receiver (LED reader) can be achieved with excellent performance and the receiver's position can be estimated. A hexagonal lattice alignment of LED transmitters is deployed to reduce the coverage holes and the areas of overlapping radiation. As a result, the accuracy of the position estimation is better than when using a typical rectangular grid alignment. The dimming control is done with pulse width modulation (PWM) to obtain an optimal closed loop beamforming and minimum energy consumption with acceptable lighting. PMID:24481234

One-dimensional magnetic nanocomposites with attapulgites as templates: Growth, formation mechanism and magnetic alignment

NASA Astrophysics Data System (ADS)

Fu, Meng; Li, Xiangming; Jiang, Rui; Zhang, Zepeng

2018-05-01

Magnetic nanocomposite composed of attapulgite and Fe3O4 was synthesized by a simple and facile co-precipitation method. Its structure and morphology was verified using X-ray diffraction, transmission electron microscopy, scanning electron microscopy and Fourier transform infrared spectroscopy. Although the difficulty of forming uniform Fe3O4 on the attapulgite surface was discussed in detail in this study, one-dimensional magnetic nanorod with attapulgites as core and Fe3O4 as uniform shell was implemented for the first time using a cationic polymer surfactant, polyethylenimine. Polyethylenimine concentration, Fe3+/Fe2+ concentration and temperature were controlled to investigate the morphological evolutions of this nanocomposite. It was found that a uniform shell could be available with thickness tuning from 10 nm to 40 nm when Fe3+ concentration ranged from 0.01 mol/L to 0.03 mol/L meanwhile the polyethylenimine concentration was kept at 0.2 mg/mL and the temperature was kept at 60-80 °C. Finally, a possible mechanism for the formation of the Fe3O4 shell was suggested. The polyethylenimine on the surface of the attapulgites first adsorbed Fe3+/Fe2+ and then released under the action of alkali. It acted as a linker for the Fe3O4 nanoparticles nucleation in situ. The synthesized one-dimensional nanocomposites exhibit the superparamagnetism and fast response to an external magnetic field. The alignment of attapulgite-Fe3O4 one-dimensional nanocomposite along the external magnetic field was demonstrated. It provides promising candidates for building blocks and functional devices, which are low cost, non-toxic and eco-friendly, and opens the door for the application of attapulgite as one-dimensional nanomaterials.

Carbon nanotubes on a substrate

DOEpatents

Gao, Yufei [Kennewick, WA; Liu, Jun [West Richland, WA

2002-03-26

The present invention includes carbon nanotubes whose hollow cores are 100% filled with conductive filler. The carbon nanotubes are in uniform arrays on a conductive substrate and are well-aligned and can be densely packed. The uniformity of the carbon nanotube arrays is indicated by the uniform length and diameter of the carbon nanotubes, both which vary from nanotube to nanotube on a given array by no more than about 5%. The alignment of the carbon nanotubes is indicated by the perpendicular growth of the nanotubes from the substrates which is achieved in part by the simultaneous growth of the conductive filler within the hollow core of the nanotube and the densely packed growth of the nanotubes. The present invention provides a densely packed carbon nanotube growth where each nanotube is in contact with at least one nearest-neighbor nanotube. The substrate is a conductive substrate coated with a growth catalyst, and the conductive filler can be single crystals of carbide formed by a solid state reaction between the substrate material and the growth catalyst. The present invention further provides a method for making the filled carbon nanotubes on the conductive substrates. The method includes the steps of depositing a growth catalyst onto the conductive substrate as a prepared substrate, creating a vacuum within a vessel which contains the prepared substrate, flowing H2/inert (e.g. Ar) gas within the vessel to increase and maintain the pressure within the vessel, increasing the temperature of the prepared substrate, and changing the H2/Ar gas to ethylene gas such that the ethylene gas flows within the vessel. Additionally, varying the density and separation of the catalyst particles on the conductive substrate can be used to control the diameter of the nanotubes.

Method of making carbon nanotubes on a substrate

DOEpatents

Gao, Yufei; Liu, Jun

2006-03-14

The present invention includes carbon nanotubes whose hollow cores are 100% filled with conductive filler. The carbon nanotubes are in uniform arrays on a conductive substrate and are well-aligned and can be densely packed. The uniformity of the carbon nanotube arrays is indicated by the uniform length and diameter of the carbon nanotubes, both which vary from nanotube to nanotube on a given array by no more than about 5%. The alignment of the carbon nanotubes is indicated by the perpendicular growth of the nanotubes from the substrates which is achieved in part by the simultaneous growth of the conductive filler within the hollow core of the nanotube and the densely packed growth of the nanotubes. The present invention provides a densely packed carbon nanotube growth where each nanotube is in contact with at least one nearest-neighbor nanotube. The substrate is a conductive substrate coated with a growth catalyst, and the conductive filler can be single crystals of carbide formed by a solid state reaction between the substrate material and the growth catalyst. The present invention further provides a method for making the filled carbon nanotubes on the conductive substrates. The method includes the steps of depositing a growth catalyst onto the conductive substrate as a prepared substrate, creating a vacuum within a vessel which contains the prepared substrate, flowing H2/inert (e.g. Ar) gas within the vessel to increase and maintain the pressure within the vessel, increasing the temperature of the prepared substrate, and changing the H2/Ar gas to ethylene gas such that the ethylene gas flows within the vessel. Additionally, varying the density and separation of the catalyst particles on the conductive substrate can be used to control the diameter of the nanotubes.

IUS prerelease alignment

NASA Technical Reports Server (NTRS)

Evans, F. A.

1978-01-01

Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

Modeling, design, packing and experimental analysis of liquid-phase shear-horizontal surface acoustic wave sensors

NASA Astrophysics Data System (ADS)

Pollard, Thomas B

Recent advances in microbiology, computational capabilities, and microelectromechanical-system fabrication techniques permit modeling, design, and fabrication of low-cost, miniature, sensitive and selective liquid-phase sensors and lab-on-a-chip systems. Such devices are expected to replace expensive, time-consuming, and bulky laboratory-based testing equipment. Potential applications for devices include: fluid characterization for material science and industry; chemical analysis in medicine and pharmacology; study of biological processes; food analysis; chemical kinetics analysis; and environmental monitoring. When combined with liquid-phase packaging, sensors based on surface-acoustic-wave (SAW) technology are considered strong candidates. For this reason such devices are focused on in this work; emphasis placed on device modeling and packaging for liquid-phase operation. Regarding modeling, topics considered include mode excitation efficiency of transducers; mode sensitivity based on guiding structure materials/geometries; and use of new piezoelectric materials. On packaging, topics considered include package interfacing with SAW devices, and minimization of packaging effects on device performance. In this work novel numerical models are theoretically developed and implemented to study propagation and transduction characteristics of sensor designs using wave/constitutive equations, Green's functions, and boundary/finite element methods. Using developed simulation tools that consider finite-thickness of all device electrodes, transduction efficiency for SAW transducers with neighboring uniform or periodic guiding electrodes is reported for the first time. Results indicate finite electrode thickness strongly affects efficiency. Using dense electrodes, efficiency is shown to approach 92% and 100% for uniform and periodic electrode guiding, respectively; yielding improved sensor detection limits. A numerical sensitivity analysis is presented targeting viscosity using uniform-electrode and shear-horizontal mode configurations on potassium-niobate, langasite, and quartz substrates. Optimum configurations are determined yielding maximum sensitivity. Results show mode propagation-loss and sensitivity to viscosity are correlated by a factor independent of substrate material. The analysis is useful for designing devices meeting sensitivity and signal level requirements. A novel, rapid and precise microfluidic chamber alignment/bonding method was developed for SAW platforms. The package is shown to have little effect on device performance and permits simple macrofluidic interfacing. Lastly, prototypes were designed, fabricated, and tested for viscosity and biosensor applications; results show ability to detect as low as 1% glycerol in water and surface-bound DNA crosslinking.

Computerized Design and Analysis of Face-Milled, Uniform Tooth Height, Low-Noise Spiral Bevel Gear Drives

NASA Technical Reports Server (NTRS)

Litvin, F. L.; Zhao, X.

1996-01-01

A new method for design and generation of spiral bevel gears of uniform tooth depth with localized bearing contact and low level of transmission errors is considered. The main features of the proposed approach are as follows: (1) The localization of the bearing contact is achieved by the mismatch of the generating surfaces. The bearing contact may be provided in the longitudinal direction, or in the direction across the surface; and (2) The low level of transmission errors is achieved due to application of nonlinear relations between the motions of the gear and the gear head-cutter. Such relations may be provided by application of a CNC machine. The generation of the pinion is based on application of linear relations between the motions of the tool and the pinion being generated. The relations described above permit a parabolic function of transmission errors to be obtained that is able to absorb almost linear functions caused by errors of gear alignment. A computer code has been written for the meshing and contact of the spiral bevel gears with the proposed geometry. The effect of misalignment on the proposed geometry has also been determined. Numerical examples for illustration of the proposed theory have been provided.

Computerized Design and Analysis of Face-Milled, Uniform Tooth Height, Low-Noise Spiral Bevel Gear Drives

NASA Technical Reports Server (NTRS)

Litvin, F. L.; Zhao, X.

1996-01-01

A new method for design and generation of spiral bevel gears of uniform tooth depth with localized bearing contact and low level of transmission errors is considered. The main features of the proposed approach are as follows: (1) the localization of the bearing contact is achieved by the mismatch of the generating surfaces. The bearing contact may be provided in the longitudinal direction, or in the direction across the surface; and (2) the low level of transmission errors is achieved due to application of nonlinear relations between the motions of the gear and the gear head-cutter. Such relations may be provided by application of a CNC machine. The generation of the pinion is based on application of linear relations between the motions of the tool and the pinion being generated. The relations described above permit a parabolic function of transmission errors to be obtained that is able to absorb almost linear functions caused by errors of gear alignment. A computer code has been written for the meshing and contact of the spiral bevel gears with the proposed geometry. The effect of misalignment on the proposed geometry has also been determined. Numerical examples for illustration of the proposed theory have been provided.

Template-guided highly aligned, nano-scale wrinkle structure on a large-area

NASA Astrophysics Data System (ADS)

Lim, Jongcheon; Kim, Pilnam

This study presents a novel technique to induce aligned, nano-scale wrinkle on a polysiloxane-based UV curable resin. There have been studies on generating randomized sub-micron wrinkle using oxygen plasma treatment which causes equibiaxial compressive stress on the film surface. Few works have been reported on how to control the surface wrinkle orientation. Currently available approaches for regulating the wrinkle pattern typically require polydimethylsiloxane (PDMS)-based bilayer system under uniaxial stress condition which hampers various technological applications. Here, we demonstrate a method to generate aligned wrinkle with UV curable polymers. Highly regular array of nanoscale wrinkles were formed by elastic buckling of bilayered UV curable resin, resulting from a combination of confinement effect and anchor-guided propagation of structure. The wrinkle tends to align uniformly lateral to the template pattern as the resin filled in the pattern forms more convex meniscus. The wavelength of the wrinkle was controlled by UV exposure time yielding as small as 170nm. From our results, we suggest the confinement provided by the template pattern may have affected the direction of thin film's expansion yielding unidirectional compressive stress. This work was supported by Samsung Research Funding Center of Samsung Electronics under Project Number SRFC-IT1402-02.

Resolving the Southern African Large Telescope's image quality problems

NASA Astrophysics Data System (ADS)

O'Donoghue, Darragh E.; Crause, Lisa A.; O'Connor, James; Strümpfer, Francois; Strydom, Ockert J.; Sass, Craig; Brink, Janus D.; Plessis, Charl du; Wiid, Eben; Love, Jonathan

2013-08-01

Images obtained with the Southern African Large Telescope (SALT) during its commissioning phase in 2006 showed degradation due to a large focus gradient, astigmatism, and higher order optical aberrations. An extensive forensic investigation exonerated the primary mirror and the science instruments before pointing to the mechanical interface between the telescope and the spherical aberration corrector, the complex optical subassembly which corrects the spherical aberration introduced by the 11-m primary mirror. Having diagnosed the problem, a detailed repair plan was formulated and implemented when the corrector was removed from the telescope in April 2009. The problematic interface was replaced, and the four aspheric mirrors were optically tested and re-aligned. Individual mirror surface figures were confirmed to meet specification, and a full system test after the re-alignment yielded a root mean square wavefront error of 0.15 waves. The corrector was reinstalled in August 2010 and aligned with respect to the payload and primary mirror. Subsequent on-sky tests revealed spurious signals being sent to the tracker by the auto-collimator, the instrument that maintains the alignment of the corrector with respect to the primary mirror. After rectifying this minor issue, the telescope yielded uniform 1.1 arcsec star images over the full 10-arcmin field of view.

GeneSilico protein structure prediction meta-server.

PubMed

Kurowski, Michal A; Bujnicki, Janusz M

2003-07-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta.

GeneSilico protein structure prediction meta-server

PubMed Central

Kurowski, Michal A.; Bujnicki, Janusz M.

2003-01-01

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta. PMID:12824313

Self-aligned photolithography for the fabrication of fully transparent high-voltage devices

NASA Astrophysics Data System (ADS)

Zhang, Yonghui; Mei, Zengxia; Huo, Wenxing; Wang, Tao; Liang, Huili; Du, Xiaolong

2018-05-01

High-voltage devices, working in the range of hundreds of volts, are indispensable elements in the driving or readout circuits for various kinds of displays, integrated microelectromechanical systems and x-ray imaging sensors. However, the device performances are found hardly uniform or repeatable due to the misalignment issue, which are extremely common for offset drain high-voltage devices. To resolve this issue, this article reports a set of self-aligned photolithography technology for the fabrication of high-voltage devices. High-performance fully-transparent high-voltage thin film transistors, diodes and logic inverters are successfully fabricated with this technology. Unlike other self-aligned routes, opaque masks are introduced on the backside of the transparent substrate to facilitate proximity exposure method. The photolithography process is simulated and analyzed with technology computer aided design simulation to explain the working principle of the proximity exposure method. The substrate thickness is found to be vital for the implementation of this technology based on both simulation and experimental results. The electrical performance of high-voltage devices is dependent on the offset length, which can be delicately modulated by changing the exposure dose. The presented self-aligned photolithography technology is proved to be feasible in high-voltage circuits, demonstrating its huge potential in practical industrial applications.

Wafer-scale fabrication of glass-FEP-glass microfluidic devices for lipid bilayer experiments.

PubMed

Bomer, Johan G; Prokofyev, Alexander V; van den Berg, Albert; Le Gac, Séverine

2014-12-07

We report a wafer-scale fabrication process for the production of glass-FEP-glass microdevices using UV-curable adhesive (NOA81) as gluing material, which is applied using a novel "spin & roll" approach. Devices are characterized for the uniformity of the gluing layer, presence of glue in the microchannels, and alignment precision. Experiments on lipid bilayers with electrophysiological recordings using a model pore-forming polypeptide are demonstrated.

Advanced CFD Methods for Hypervelocity Wind Tunnels

DTIC Science & Technology

2011-03-10

Mach 14 nozzle produces non-uniformities in the test section flow that are not desirable [1,2]. Calibration runs with Pitot pressure rakes suggest...flows is presented. The grid is based on the characteristic lines of the supersonic regions of the flow. This allows for grid alignment and clustering...novel grid generation scheme for hypersonic nozzle flows is presented. The grid is based on the characteristic lines of the supersonic regions of the

Pitch-based carbon foam and composites

DOEpatents

Klett, James W.

2001-01-01

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

Pitch-based carbon foam and composites

DOEpatents

Klett, James W.

2003-12-16

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

Pitch-based carbon foam and composites

DOEpatents

Klett, James W.

2003-12-02

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

Pitch-based carbon foam and composites

DOEpatents

Klett, James W.

2002-01-01

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

Generalized Effective Medium Theory for Particulate Nanocomposite Materials

PubMed Central

Siddiqui, Muhammad Usama; Arif, Abul Fazal M.

2016-01-01

The thermal conductivity of particulate nanocomposites is strongly dependent on the size, shape, orientation and dispersion uniformity of the inclusions. To correctly estimate the effective thermal conductivity of the nanocomposite, all these factors should be included in the prediction model. In this paper, the formulation of a generalized effective medium theory for the determination of the effective thermal conductivity of particulate nanocomposites with multiple inclusions is presented. The formulated methodology takes into account all the factors mentioned above and can be used to model nanocomposites with multiple inclusions that are randomly oriented or aligned in a particular direction. The effect of inclusion dispersion non-uniformity is modeled using a two-scale approach. The applications of the formulated effective medium theory are demonstrated using previously published experimental and numerical results for several particulate nanocomposites. PMID:28773817

Loosely coupled coaxial TEM applicators for deep-heating.

PubMed

Harrison, W H; Storm, F K

1989-01-01

The development of a coaxial TEM (transverse electromagnetic) deep-heating, non-contacting applicator employing two axially spaced concentric sleeves is described which has electrostatic characteristics and has been named the ESA. Thermal data obtained with the FDA/CDRH elliptic-shaped human torso phantom (with fat overlay) showed nearly uniform heating (+/- 10%) throughout the inner cross-section. Saline tank measurements on a torso cross-section confirmed similar SAR uniformity. Animal experiments with a pig, both with and without blood flow, verified deep-heating and suggested that some preferential central heating occurred. The absence of excessive surface heating indicated that the major portion of the E-field excitation is axially aligned. The non-contacting applicator does not require a water bolus, and experiments showed that moderate patient movement had minor effect on performance.

The Størmer problem for an aligned rotator

NASA Astrophysics Data System (ADS)

Epp, V.; Pervukhina, O. N.

2018-03-01

The effective potential energy of the particles in the field of rotating uniformly magnetized celestial body is investigated. The axis of rotation coincides with the axis of the magnetic field. Electromagnetic field of the body is composed of a dipole magnetic and quadrupole electric fields. The geometry of the trapping regions is studied as a function of the magnetic field magnitude and the rotation speed of the body. Examples of the potential energy topology for different values of these parameters are given. The main difference from the classical Størmer problem is that the single toroidal trapping region predicted by Størmer is divided into equatorial and off-equatorial trapping regions. Applicability of the idealized model of a rotating uniformly magnetized sphere with a vacuum magnetosphere to real celestial bodies is discussed.

Method For Plasma Source Ion Implantation And Deposition For Cylindrical Surfaces

DOEpatents

Fetherston, Robert P. , Shamim, Muhammad M. , Conrad, John R.

1997-12-02

Uniform ion implantation and deposition onto cylindrical surfaces is achieved by placing a cylindrical electrode in coaxial and conformal relation to the target surface. For implantation and deposition of an inner bore surface the electrode is placed inside the target. For implantation and deposition on an outer cylindrical surface the electrode is placed around the outside of the target. A plasma is generated between the electrode and the target cylindrical surface. Applying a pulse of high voltage to the target causes ions from the plasma to be driven onto the cylindrical target surface. The plasma contained in the space between the target and the electrode is uniform, resulting in a uniform implantation or deposition of the target surface. Since the plasma is largely contained in the space between the target and the electrode, contamination of the vacuum chamber enclosing the target and electrodes by inadvertent ion deposition is reduced. The coaxial alignment of the target and the electrode may be employed for the ion assisted deposition of sputtered metals onto the target, resulting in a uniform coating of the cylindrical target surface by the sputtered material. The independently generated and contained plasmas associated with each cylindrical target/electrode pair allows for effective batch processing of multiple cylindrical targets within a single vacuum chamber, resulting in both uniform implantation or deposition, and reduced contamination of one target by adjacent target/electrode pairs.

A simple and transparent well-aligned ZnO nanowire array ultraviolet photodetector with high responsivity

NASA Astrophysics Data System (ADS)

Yin, Lei; Ding, Hesheng; Yuan, Zhaolin; Huang, Wendeng; Shuai, Chunjiang; Xiong, Zhaoxin; Deng, Jianping; Lv, Tengbo

2018-06-01

Well-aligned zinc oxide (ZnO) nanowire arrays were grown on an interdigital patterned fluorine tin oxide (FTO)-coated glass substrate by a facile chemical bath deposition at low temperature. Morphology, crystalline structure, and optical properties of the ZnO nanowire arrays were analyzed in detail. The results revealed that the ZnO nanowires had wurtzite structure, typically ∼40-60 nm in diameter, and ∼700-800 nm in length, a great number of highly uniform and dense nanowires grew vertically on the substrate to form the well-aligned ZnO nanowire arrays, which had very high optical transmission (>86%) in the visible light region. In addition, the performance of ZnO nanowire arrays ultraviolet (UV) photodetector was systematically examined. The photosensitivity (S), responsivity (R), response and decay time of the photodetector were 703 at +0.2 V, 113 A/W at +5 V, 23 s and 73 s respectively. Also, the photoresponse mechanism of the UV photodetector was illuminated in terms of the oxygen adsorption-photodesorption process.

Room temperature infrared imaging sensors based on highly purified semiconducting carbon nanotubes.

PubMed

Liu, Yang; Wei, Nan; Zhao, Qingliang; Zhang, Dehui; Wang, Sheng; Peng, Lian-Mao

2015-04-21

High performance infrared (IR) imaging systems usually require expensive cooling systems, which are highly undesirable. Here we report the fabrication and performance characteristics of room temperature carbon nanotube (CNT) IR imaging sensors. The CNT IR imaging sensor is based on aligned semiconducting CNT films with 99% purity, and each pixel or device of the imaging sensor consists of aligned strips of CNT asymmetrically contacted by Sc and Pd. We found that the performance of the device is dependent on the CNT channel length. While short channel devices provide a large photocurrent and a rapid response of about 110 μs, long channel length devices exhibit a low dark current and a high signal-to-noise ratio which are critical for obtaining high detectivity. In total, 36 CNT IR imagers are constructed on a single chip, each consists of 3 × 3 pixel arrays. The demonstrated advantages of constructing a high performance IR system using purified semiconducting CNT aligned films include, among other things, fast response, excellent stability and uniformity, ideal linear photocurrent response, high imaging polarization sensitivity and low power consumption.

Transparent silicon strip sensors for the optical alignment of particle detector systems

NASA Astrophysics Data System (ADS)

Blum, W.; Kroha, H.; Widmann, P.

1996-02-01

Modern large-area precision tracking detectors require increasing accuracy for the alignment of their components. A novel multi-point laser alignment system has been developed for such applications. The position of detector components with respect to reference laser beams is monitored by semi-transparent optical position sensors which work on the principle of silicon strip photodiodes. Two types of custom designed transparent strip sensors, based on crystalline and on amorphous silicon as active material, have been studied. The sensors are optimized for the typical diameters of collimated laser beams of 3-5 mm over distances of 10-20 m. They provide very high position resolution, on the order of 1 μm, uniformly over a wide measurement range of several centimeters. The preparation of the sensor surfaces requires special attention in order to achieve high light transmittance and minimum distortion of the traversing laser beams. At selected wavelengths, produced by laser diodes, transmission rates above 90% have been achieved. This allows to position more than 30 sensors along one laser beam. The sensors will be equipped with custom designed integrated readout electronics.

Effect of angular momentum alignment and strong magnetic fields on the formation of protostellar discs

NASA Astrophysics Data System (ADS)

Gray, William J.; McKee, Christopher F.; Klein, Richard I.

2018-01-01

Star-forming molecular clouds are observed to be both highly magnetized and turbulent. Consequently, the formation of protostellar discs is largely dependent on the complex interaction between gravity, magnetic fields, and turbulence. Studies of non-turbulent protostellar disc formation with realistic magnetic fields have shown that these fields are efficient in removing angular momentum from the forming discs, preventing their formation. However, once turbulence is included, discs can form in even highly magnetized clouds, although the precise mechanism remains uncertain. Here, we present several high-resolution simulations of turbulent, realistically magnetized, high-mass molecular clouds with both aligned and random turbulence to study the role that turbulence, misalignment, and magnetic fields have on the formation of protostellar discs. We find that when the turbulence is artificially aligned so that the angular momentum is parallel to the initial uniform field, no rotationally supported discs are formed, regardless of the initial turbulent energy. We conclude that turbulence and the associated misalignment between the angular momentum and the magnetic field are crucial in the formation of protostellar discs in the presence of realistic magnetic fields.

Current progress and technical challenges of flexible liquid crystal displays

NASA Astrophysics Data System (ADS)

Fujikake, Hideo; Sato, Hiroto

2009-02-01

We focused on several technical approaches to flexible liquid crystal (LC) display in this report. We have been developing flexible displays using plastic film substrates based on polymer-dispersed LC technology with molecular alignment control. In our representative devices, molecular-aligned polymer walls keep plastic-substrate gap constant without LC alignment disorder, and aligned polymer networks create monostable switching of fast-response ferroelectric LC (FLC) for grayscale capability. In the fabrication process, a high-viscosity FLC/monomer solution was printed, sandwiched and pressed between plastic substrates. Then the polymer walls and networks were sequentially formed based on photo-polymerization-induced phase separation in the nematic phase by two exposure processes of patterned and uniform ultraviolet light. The two flexible backlight films of direct illumination and light-guide methods using small three-primary-color light-emitting diodes were fabricated to obtain high-visibility display images. The fabricated flexible FLC panels were driven by external transistor arrays, internal organic thin film transistor (TFT) arrays, and poly-Si TFT arrays. We achieved full-color moving-image displays using the flexible FLC panel and the flexible backlight film based on field-sequential-color driving technique. Otherwise, for backlight-free flexible LC displays, flexible reflective devices of twisted guest-host nematic LC and cholesteric LC were discussed with molecular-aligned polymer walls. Singlesubstrate device structure and fabrication method using self-standing polymer-stabilized nematic LC film and polymer ceiling layer were also proposed for obtaining LC devices with excellent flexibility.

Fabrication of Well-Aligned ZnO Nanorods Using a Composite Seed Layer of ZnO Nanoparticles and Chitosan Polymer.

PubMed

Khun, Kimleang; Ibupoto, Zafar Hussain; AlSalhi, Mohamad S; Atif, Muhammad; Ansari, Anees A; Willander, Magnus

2013-09-30

In this study, by taking the advantage of both inorganic ZnO nanoparticles and the organic material chitosan as a composite seed layer, we have fabricated well-aligned ZnO nanorods on a gold-coated glass substrate using the hydrothermal growth method. The ZnO nanoparticles were characterized by the Raman spectroscopic techniques, which showed the nanocrystalline phase of the ZnO nanoparticles. Different composites of ZnO nanoparticles and chitosan were prepared and used as a seed layer for the fabrication of well-aligned ZnO nanorods. Field emission scanning electron microscopy, energy dispersive X-ray, high-resolution transmission electron microscopy, X-ray diffraction, and infrared reflection absorption spectroscopic techniques were utilized for the structural characterization of the ZnO nanoparticles/chitosan seed layer-coated ZnO nanorods on a gold-coated glass substrate. This study has shown that the ZnO nanorods are well-aligned, uniform, and dense, exhibit the wurtzite hexagonal structure, and are perpendicularly oriented to the substrate. Moreover, the ZnO nanorods are only composed of Zn and O atoms. An optical study was also carried out for the ZnO nanoparticles/chitosan seed layer-coated ZnO nanorods, and the obtained results have shown that the fabricated ZnO nanorods exhibit good crystal quality. This study has provided a cheap fabrication method for the controlled morphology and good alignment of ZnO nanorods, which is of high demand for enhancing the working performance of optoelectronic devices.

Fabrication of Well-Aligned ZnO Nanorods Using a Composite Seed Layer of ZnO Nanoparticles and Chitosan Polymer

PubMed Central

Khun, Kimleang; Ibupoto, Zafar Hussain; AlSalhi, Mohamad S.; Atif, Muhammad; Ansari, Anees A.; Willander, Magnus

2013-01-01

In this study, by taking the advantage of both inorganic ZnO nanoparticles and the organic material chitosan as a composite seed layer, we have fabricated well-aligned ZnO nanorods on a gold-coated glass substrate using the hydrothermal growth method. The ZnO nanoparticles were characterized by the Raman spectroscopic techniques, which showed the nanocrystalline phase of the ZnO nanoparticles. Different composites of ZnO nanoparticles and chitosan were prepared and used as a seed layer for the fabrication of well-aligned ZnO nanorods. Field emission scanning electron microscopy, energy dispersive X-ray, high-resolution transmission electron microscopy, X-ray diffraction, and infrared reflection absorption spectroscopic techniques were utilized for the structural characterization of the ZnO nanoparticles/chitosan seed layer-coated ZnO nanorods on a gold-coated glass substrate. This study has shown that the ZnO nanorods are well-aligned, uniform, and dense, exhibit the wurtzite hexagonal structure, and are perpendicularly oriented to the substrate. Moreover, the ZnO nanorods are only composed of Zn and O atoms. An optical study was also carried out for the ZnO nanoparticles/chitosan seed layer-coated ZnO nanorods, and the obtained results have shown that the fabricated ZnO nanorods exhibit good crystal quality. This study has provided a cheap fabrication method for the controlled morphology and good alignment of ZnO nanorods, which is of high demand for enhancing the working performance of optoelectronic devices. PMID:28788336

Evolution of grid-wide access to database resident information in ATLAS using Frontier

NASA Astrophysics Data System (ADS)

Barberis, D.; Bujor, F.; de Stefano, J.; Dewhurst, A. L.; Dykstra, D.; Front, D.; Gallas, E.; Gamboa, C. F.; Luehring, F.; Walker, R.

2012-12-01

The ATLAS experiment deployed Frontier technology worldwide during the initial year of LHC collision data taking to enable user analysis jobs running on the Worldwide LHC Computing Grid to access database resident data. Since that time, the deployment model has evolved to optimize resources, improve performance, and streamline maintenance of Frontier and related infrastructure. In this presentation we focus on the specific changes in the deployment and improvements undertaken, such as the optimization of cache and launchpad location, the use of RPMs for more uniform deployment of underlying Frontier related components, improvements in monitoring, optimization of fail-over, and an increasing use of a centrally managed database containing site specific information (for configuration of services and monitoring). In addition, analysis of Frontier logs has allowed us a deeper understanding of problematic queries and understanding of use cases. Use of the system has grown beyond user analysis and subsystem specific tasks such as calibration and alignment, extending into production processing areas, such as initial reconstruction and trigger reprocessing. With a more robust and tuned system, we are better equipped to satisfy the still growing number of diverse clients and the demands of increasingly sophisticated processing and analysis.

Tape tracking and handling for magnetic tape recorders. [aboard spacecraft

NASA Technical Reports Server (NTRS)

Paroby, W.; Disilvestre, R.

1975-01-01

One of the critical performance and life limiting elements of a spacecraft tape recorder instrumentation system which has received little attention in technical literature is magnetic tape tracking and handling technology. This technology is required to understand how to gently transfer tape from one reel to another with proper alignment and a desirable uniform velocity at the read and write transducer heads. The increased demand for high data rate (i.e., multi-track spacecraft recording instrumentation systems), coupled with performance under extreme environmental conditions, requires a thorough knowledge of the various parameters which establish an optimum designed tape tracking and handling system. Stress analysis techniques are required to evaluate these parameters substantiated with test tape tracking data, to show the effect of each parameter on a tape recorder instrumentation tracking system. The technology is applicable to ground type tape recorders where the detrimental effects of edge guidance can be eliminated.

Banded whistlers observed on OGO-4

NASA Technical Reports Server (NTRS)

Paymar, E. M.

1972-01-01

Inspection of broadband VLF records from OGO-4 shows that some whistlers exhibit a banded structure in which one or more bands of frequencies are missing from the whistler's spectrum. The phenomenon is commonly observed by satellites on midlatitude field lines at all local times and at various longitudes around the world. The dispersion of banded whistlers (BW) is of several tens of sec to the 1/2 power, indicating that they originated in the opposite hemisphere and are propagating downward at the satellite. BW are generally spread in time (tenths of seconds) rather than sharply defined and tend to occur at random. The frequency spacing of the bands may be either uniform or irregular, and may vary radically between successive events. Several possible explanations for BW are considered. In particular, an analysis of the interaction of plane electromagnetic waves traveling in an anisotropic plasma with a field aligned slab of enhanced ionization is presented with promising results.

The Muon g-2 Experiment overview and status as of June 2016

DOE PAGES

Holzbauer, J. L.

2016-12-09

The Muon g-2 Experiment at Fermilab will measure the anomalous magnetic moment of the muon to a precision of 140 parts per billion, which is a factor of four improvement over the previous E821 measurement at Brookhaven. The experiment will also extend the search for the electric dipole moment (EDM) of the muon by approximately two orders of magnitude, with a sensitivity down to 10 -21 e.cm. Both of these measurements are made by combining a precise measurement of the 1.45T storage ring magnetic field with an analysis of the modulation of the decay rate of higher-energy positrons (from anti-muons),more » recorded by 24 calorimeters and 3 straw tracking detectors. Furthermore, the recent progress in the alignment of the electrostatic quadrapole plates and the trolley rails inside the vacuum chambers, and in establishing the uniform storage ring magnetic field will be described.« less

Multiple-reflection optical gas cell

DOEpatents

Matthews, Thomas G.

1983-01-01

A multiple-reflection optical cell for Raman or fluorescence gas analysis consists of two spherical mirrors positioned transverse to a multiple-pass laser cell in a confronting plane-parallel alignment. The two mirrors are of equal diameter but possess different radii of curvature. The spacing between the mirrors is uniform and less than half of the radius of curvature of either mirror. The mirror of greater curvature possesses a small circular portal in its center which is the effective point source for conventional F1 double lens collection optics of a monochromator-detection system. Gas to be analyzed is flowed into the cell and irradiated by a multiply-reflected composite laser beam centered between the mirrors of the cell. Raman or fluorescence radiation originating from a large volume within the cell is (1) collected via multiple reflections with the cell mirrors, (2) partially collimated and (3) directed through the cell portal in a geometric array compatible with F1 collection optics.

Medical education in India: current challenges and the way forward.

PubMed

Solanki, Anjali; Kashyap, Surender

2014-12-01

Medical education in India is suffering from various shortcomings at conceptual as well as implementation level. With the expansion in medical education, the doctor to patient ratio has increased but these numbers do not align well with the overall quality of medical care in the country. To address this issue, a comprehensive analysis of various associated factors is essential. Indian medical education is suffering from a maldistribution of resources, unregulated growth in the private sector, lack of uniform admission procedures and traditional curricula lacking innovative approaches. To achieve higher standards of medical education, our goal should be to re-evaluate each and every aspect; create an efficient accreditation system; promote an equal distribution of resources, redesign curricula with stricter implementation and improved assessment methodologies; all of which will generate efficient medical graduates and consequently better health care delivery, and resulting in desired change within the system.

The Muon g-2 Experiment Overview and Status as of June 2016

NASA Astrophysics Data System (ADS)

Holzbauer, J.

2016-11-01

The Muon g-2 Experiment at Fermilab will measure the anomalous magnetic moment of the muon to a precision of 140 parts per billion, which is a factor of four improvement over the previous E821 measurement at Brookhaven. The experiment will also extend the search for the electric dipole moment (EDM) of the muon by approximately two orders of magnitude, with a sensitivity down to 10-21 e.cm. Both of these measurements are made by combining a precise measurement of the 1.45T storage ring magnetic field with an analysis of the modulation of the decay rate of higher-energy positrons (from anti-muons), recorded by 24 calorimeters and 3 straw tracking detectors. The recent progress in the alignment of the electrostatic quadrapole plates and the trolley rails inside the vacuum chambers, and in establishing the uniform storage ring magnetic field will be described.

Influence of the extrinsic curvature on two-dimensional nematic films.

PubMed

Napoli, Gaetano; Vergori, Luigi

2018-05-01

Nematic films are thin fluid structures, ideally two dimensional, endowed with an in-plane degenerate nematic order. In this paper we examine a generalization of the classical Plateau problem to an axisymmetric nematic film bounded by two coaxial parallel rings. At equilibrium, the shape of the nematic film results from the competition between surface tension, which favors the minimization of the area, and the nematic elasticity, which instead promotes the alignment of the molecules along a common direction. We find two classes of equilibrium solutions in which the molecules are uniformly aligned along the meridians or parallels. Depending on two dimensionless parameters, one related to the geometry of the film and the other to the constitutive moduli, the Gaussian curvature of the equilibrium shape may be everywhere negative, vanishing, or positive. The stability of these equilibrium configurations is investigated.

Influence of the extrinsic curvature on two-dimensional nematic films

NASA Astrophysics Data System (ADS)

Napoli, Gaetano; Vergori, Luigi

2018-05-01

Nematic films are thin fluid structures, ideally two dimensional, endowed with an in-plane degenerate nematic order. In this paper we examine a generalization of the classical Plateau problem to an axisymmetric nematic film bounded by two coaxial parallel rings. At equilibrium, the shape of the nematic film results from the competition between surface tension, which favors the minimization of the area, and the nematic elasticity, which instead promotes the alignment of the molecules along a common direction. We find two classes of equilibrium solutions in which the molecules are uniformly aligned along the meridians or parallels. Depending on two dimensionless parameters, one related to the geometry of the film and the other to the constitutive moduli, the Gaussian curvature of the equilibrium shape may be everywhere negative, vanishing, or positive. The stability of these equilibrium configurations is investigated.

Uniformed Diplomacy: Reviewing the Army Leader Development Strategy in Light of the Regional Alignment of Forces Construct

DTIC Science & Technology

2014-06-13

Component Command. Developing this operational flexibility, Army Chief of Staff General Raymond Odierno believes, will help improve the effectiveness of...days of arriving in Africa, he and 45 other soldiers found themselves “working with local forces and U.S. Embassy staff to stiffen protection at the...missions, neither USARAF nor DOS have fully developed measure of effectiveness criteria for these deployments.35 Thus far each mission’s after action

Synthesis of Ferroelectric Lead Titanate Nanohoneycomb Arrays via Lead Supplement Process

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

Kim, Bongsoo; Hong, Seungbum; Ahn, Gun

In this paper, we demonstrate a novel process to convert TiO 2 nanotubes into ferroelectric nanohoneycombs, comprised of vertically aligned PbTiO 3 nanotubes. Tube bottom opening process enabled effective infiltration of lead acetate precursor into the nanotubes. Finally, nanohoneycombs, which were converted via additional lead supplement process, showed uniform conversion and well-defined ferroelectric properties with the effective piezoelectric coefficient of approximately 20 pm/V, which was measured by piezoresponse force microscopy.

Semiconductor Laser Diode Arrays by MOCVD (Metalorganic Chemical Vapor Deposition)

DTIC Science & Technology

1987-09-01

laser diode arrays are intended to be used as an optical pump for solid state yttrium aluminum garnet (YAG) lasers. In particular, linear uniform...corresponds to about . , 8080A. Such thin layer structures, while difficult to grow by such conventional growth methods as liquid phase epitaxy ( LPE ...lower yet than for DH lasers grown by LPE . , - Conventional self-aligned stripe laser This structure is formed by growing (on an n-type GaAs substrate

Synthesis of Ferroelectric Lead Titanate Nanohoneycomb Arrays via Lead Supplement Process

DOE PAGES

Kim, Bongsoo; Hong, Seungbum; Ahn, Gun; ...

2016-05-14

In this paper, we demonstrate a novel process to convert TiO 2 nanotubes into ferroelectric nanohoneycombs, comprised of vertically aligned PbTiO 3 nanotubes. Tube bottom opening process enabled effective infiltration of lead acetate precursor into the nanotubes. Finally, nanohoneycombs, which were converted via additional lead supplement process, showed uniform conversion and well-defined ferroelectric properties with the effective piezoelectric coefficient of approximately 20 pm/V, which was measured by piezoresponse force microscopy.

Solvothermal Vapor Annealing of Lamellar Poly(styrene)-block-poly(d,l-lactide) Block Copolymer Thin Films for Directed Self-Assembly Application.

PubMed

Cummins, Cian; Mokarian-Tabari, Parvaneh; Andreazza, Pascal; Sinturel, Christophe; Morris, Michael A

2016-03-01

Solvothermal vapor annealing (STVA) was employed to induce microphase separation in a lamellar forming block copolymer (BCP) thin film containing a readily degradable block. Directed self-assembly of poly(styrene)-block-poly(d,l-lactide) (PS-b-PLA) BCP films using topographically patterned silicon nitride was demonstrated with alignment over macroscopic areas. Interestingly, we observed lamellar patterns aligned parallel as well as perpendicular (perpendicular microdomains to substrate in both cases) to the topography of the graphoepitaxial guiding patterns. PS-b-PLA BCP microphase separated with a high degree of order in an atmosphere of tetrahydrofuran (THF) at an elevated vapor pressure (at approximately 40-60 °C). Grazing incidence small-angle X-ray scattering (GISAXS) measurements of PS-b-PLA films reveal the through-film uniformity of perpendicular microdomains after STVA. Perpendicular lamellar orientation was observed on both hydrophilic and relatively hydrophobic surfaces with a domain spacing (L0) of ∼32.5 nm. The rapid removal of the PLA microdomains is demonstrated using a mild basic solution for the development of a well-defined PS mask template. GISAXS data reveal the through-film uniformity is retained following wet etching. The experimental results in this article demonstrate highly oriented PS-b-PLA microdomains after a short annealing period and facile PLA removal to form porous on-chip etch masks for nanolithography application.

Analysis of Basis Weight Uniformity of Microfiber Nonwovens and Its Impact on Permeability and Filtration Properties

NASA Astrophysics Data System (ADS)

Amirnasr, Elham

It is widely recognized that nonwoven basis weight non-uniformity affects various properties of nonwovens. However, few studies can be found in this topic. The development of uniformity definition and measurement methods and the study of their impact on various web properties such as filtration properties and air permeability would be beneficial both in industrial applications and in academia. They can be utilized as a quality control tool and would provide insights about nonwoven behaviors that cannot be solely explained by average values. Therefore, for quantifying nonwoven web basis weight uniformity we purse to develop an optical analytical tool. The quadrant method and clustering analysis was utilized in an image analysis scheme to help define "uniformity" and its spatial variation. Implementing the quadrant method in an image analysis system allows the establishment of a uniformity index that can be used to quantify the degree of uniformity. Clustering analysis has also been modified and verified using uniform and random simulated images with known parameters. Number of clusters and cluster properties such as cluster size, member and density was determined. We also utilized this new measurement method to evaluate uniformity of nonwovens produced with different processes and investigated impacts of uniformity on filtration and permeability. The results of quadrant method shows that uniformity index computed from quadrant method demonstrate a good range for non-uniformity of nonwoven webs. Clustering analysis is also been applied on reference nonwoven with known visual uniformity. From clustering analysis results, cluster size is promising to be used as uniformity parameter. It is been shown that non-uniform nonwovens has provide lager cluster size than uniform nonwovens. It was been tried to find a relationship between web properties and uniformity index (as a web characteristic). To achieve this, filtration properties, air permeability, solidity and uniformity index of meltblown and spunbond samples was measured. Results for filtration test show some deviation between theoretical and experimental filtration efficiency by considering different types of fiber diameter. This deviation can occur due to variation in basis weight non-uniformity. So an appropriate theory is required to predict the variation of filtration efficiency with respect to non-uniformity of nonwoven filter media. And the results for air permeability test showed that uniformity index determined by quadrant method and measured properties have some relationship. In the other word, air permeability decreases as uniformity index on nonwoven web increase.

A statistically harmonized alignment-classification in image space enables accurate and robust alignment of noisy images in single particle analysis.

PubMed

Kawata, Masaaki; Sato, Chikara

2007-06-01

In determining the three-dimensional (3D) structure of macromolecular assemblies in single particle analysis, a large representative dataset of two-dimensional (2D) average images from huge number of raw images is a key for high resolution. Because alignments prior to averaging are computationally intensive, currently available multireference alignment (MRA) software does not survey every possible alignment. This leads to misaligned images, creating blurred averages and reducing the quality of the final 3D reconstruction. We present a new method, in which multireference alignment is harmonized with classification (multireference multiple alignment: MRMA). This method enables a statistical comparison of multiple alignment peaks, reflecting the similarities between each raw image and a set of reference images. Among the selected alignment candidates for each raw image, misaligned images are statistically excluded, based on the principle that aligned raw images of similar projections have a dense distribution around the correctly aligned coordinates in image space. This newly developed method was examined for accuracy and speed using model image sets with various signal-to-noise ratios, and with electron microscope images of the Transient Receptor Potential C3 and the sodium channel. In every data set, the newly developed method outperformed conventional methods in robustness against noise and in speed, creating 2D average images of higher quality. This statistically harmonized alignment-classification combination should greatly improve the quality of single particle analysis.

Enhanced cold wall CVD reactor growth of horizontally aligned single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Mu, Wei; Kwak, Eun-Hye; Chen, Bingan; Huang, Shirong; Edwards, Michael; Fu, Yifeng; Jeppson, Kjell; Teo, Kenneth; Jeong, Goo-Hwan; Liu, Johan

2016-05-01

HASynthesis of horizontally-aligned single-walled carbon nanotubes (HA-SWCNTs) by chemical vapor deposition (CVD) directly on quartz seems very promising for the fabrication of future nanoelectronic devices. In comparison to hot-wall CVD, synthesis of HA-SWCNTs in a cold-wall CVD chamber not only means shorter heating, cooling and growth periods, but also prevents contamination of the chamber. However, since most synthesis of HA-SWCNTs is performed in hot-wall reactors, adapting this well-established process to a cold-wall chamber becomes extremely crucial. Here, in order to transfer the CVD growth technology from a hot-wall to a cold-wall chamber, a systematic investigation has been conducted to determine the influence of process parameters on the HA-SWCNT's growth. For two reasons, the cold-wall CVD chamber was upgraded with a top heater to complement the bottom substrate heater; the first reason to maintain a more uniform temperature profile during HA-SWCNTs growth, and the second reason to preheat the precursor gas flow before projecting it onto the catalyst. Our results show that the addition of a top heater had a significant effect on the synthesis. Characterization of the CNTs shows that the average density of HA-SWCNTs is around 1 - 2 tubes/ μm with high growth quality as shown by Raman analysis. [Figure not available: see fulltext.

Dependence of Sum Frequency Generation (SFG) Spectral Features on the Mesoscale Arrangement of SFG-Active Crystalline Domains Interspersed in SFG-Inactive Matrix: A Case Study with Cellulose in Uniaxially Aligned Control Samples and Alkali-Treated Secondary Cell Walls of Plants

DOE PAGES

Makarem, Mohamadamin; Sawada, Daisuke; O'Neill, Hugh M.; ...

2017-04-21

Vibrational sum frequency generation (SFG) spectroscopy can selectively detect not only molecules at two-dimensional (2D) interfaces but also noncentrosymmetric domains interspersed in amorphous three-dimensional (3D) matrixes. However, the SFG analysis of 3D systems is more complicated than 2D systems because more variables are involved. One such variable is the distance between SFG-active domains in SFG-inactive matrixes. In this study, we fabricated control samples in which SFG-active cellulose crystals were uniaxially aligned in an amorphous matrix. Assuming uniform separation distances between cellulose crystals, the relative intensities of alkyl (CH) and hydroxyl (OH) SFG peaks of cellulose could be related to themore » intercrystallite distance. The experimentally measured CH/OH intensity ratio as a function of the intercrystallite distance could be explained reasonably well with a model constructed using the theoretically calculated hyperpolarizabilities of cellulose and the symmetry cancellation principle of dipoles antiparallel to each other. In conclusion, this comparison revealed physical insights into the intercrystallite distance dependence of the CH/OH SFG intensity ratio of cellulose, which can be used to interpret the SFG spectral features of plant cell walls in terms of mesoscale packing of cellulose microfibrils.« less

CAFE: aCcelerated Alignment-FrEe sequence analysis.

PubMed

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

2017-07-03

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

Nanofiber alignment of a small diameter elastic electrospun scaffold

NASA Astrophysics Data System (ADS)

Patel, Jignesh

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

Ceramic-metal composites prepared via tape casting and melt infiltration methods

NASA Astrophysics Data System (ADS)

Kim, Hyun Jun

Melt infiltration of preforms prepared by tape casting and lamination has been accomplished using a short-time infiltration process that significantly suppresses reaction product formation. For layered materials produced via infiltration of laminated ceramic tapes, of particular interest is the effect that a large change in microstructure has on infiltration, phase formation, and mechanical properties. Hardness of the fine scale composite layers is approximately three times higher than coarse scale layers, due to greater strength of the fine B4C network. Fractography showed that crack propagation occurred by brittle fracture of the carbide and ductile extension of the metal. Despite large differences in hardness, the fracture mode of the fine and coarse scale microstructures appears identical. Fluid flow modeling for tape casting was conducted with a Newtonian slurry under a parallel blade, and the effect of beveling the blade based on a one dimensional flow model is shown. The discussion on slurry deformation after the blade exit suggests that the mode of slurry deformation depends on the relative importance of the pressure gradient and wall shear and that the existence of zero shear plane might have a negative effect on particle alignment in the tape. The analysis of the flow under a beveled blade predicts that this configuration is more advantageous than the parallel blade for productivity and parallel blade is better for producing uniform particle alignment and thinner tape. Also, the one dimensional flow model for the beveled blade is shown to be a valid approximation of the fluid behavior below a blade angle of 45 degrees. The flow visualization study on tape casting was conducted with a transparent apparatus and model slurry. Most investigators have concluded that the shear stress between the doctor blade and moving carrier causes the particle alignment, but, according to the result of visualization experiment, some degree of particle alignment is already established in the reservoir. The fluid flow concept of tape casting is incorporated with a metal infiltration technique to prepare the ceramic-metal composites with tailored porosity and pore orientation. Boron carbide-aluminum system was used to prepare the composites, and its stiffness constants were investigated. The aligned metal ligaments rarely affect the stiffness constant anisotropy which appears to be caused by tape casting operation.

Octahedral Tin Dioxide Nanocrystals Anchored on Vertically Aligned Carbon Aerogels as High Capacity Anode Materials for Lithium-Ion Batteries.

PubMed

Liu, Mingkai; Liu, Yuqing; Zhang, Yuting; Li, Yiliao; Zhang, Peng; Yan, Yan; Liu, Tianxi

2016-08-11

A novel binder-free graphene - carbon nanotubes - SnO2 (GCNT-SnO2) aerogel with vertically aligned pores was prepared via a simple and efficient directional freezing method. SnO2 octahedrons exposed of {221} high energy facets were uniformly distributed and tightly anchored on multidimensional graphene/carbon nanotube (GCNT) composites. Vertically aligned pores can effectively prevent the emersion of "closed" pores which cannot load the active SnO2 nanoparticles, further ensure quick immersion of electrolyte throughout the aerogel, and can largely shorten the transport distance between lithium ions and active sites of SnO2. Especially, excellent electrical conductivity of GCNT-SnO2 aerogel was achieved as a result of good interconnected networks of graphene and CNTs. Furthermore, meso- and macroporous structures with large surface area created by the vertically aligned pores can provide great benefit to the favorable transport kinetics for both lithium ion and electrons and afford sufficient space for volume expansion of SnO2. Due to the well-designed architecture of GCNT-SnO2 aerogel, a high specific capacity of 1190 mAh/g with good long-term cycling stability up to 1000 times was achieved. This work provides a promising strategy for preparing free-standing and binder-free active electrode materials with high performance for lithium ion batteries and other energy storage devices.

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.

Octahedral Tin Dioxide Nanocrystals Anchored on Vertically Aligned Carbon Aerogels as High Capacity Anode Materials for Lithium-Ion Batteries

NASA Astrophysics Data System (ADS)

Liu, Mingkai; Liu, Yuqing; Zhang, Yuting; Li, Yiliao; Zhang, Peng; Yan, Yan; Liu, Tianxi

2016-08-01

A novel binder-free graphene - carbon nanotubes - SnO2 (GCNT-SnO2) aerogel with vertically aligned pores was prepared via a simple and efficient directional freezing method. SnO2 octahedrons exposed of {221} high energy facets were uniformly distributed and tightly anchored on multidimensional graphene/carbon nanotube (GCNT) composites. Vertically aligned pores can effectively prevent the emersion of “closed” pores which cannot load the active SnO2 nanoparticles, further ensure quick immersion of electrolyte throughout the aerogel, and can largely shorten the transport distance between lithium ions and active sites of SnO2. Especially, excellent electrical conductivity of GCNT-SnO2 aerogel was achieved as a result of good interconnected networks of graphene and CNTs. Furthermore, meso- and macroporous structures with large surface area created by the vertically aligned pores can provide great benefit to the favorable transport kinetics for both lithium ion and electrons and afford sufficient space for volume expansion of SnO2. Due to the well-designed architecture of GCNT-SnO2 aerogel, a high specific capacity of 1190 mAh/g with good long-term cycling stability up to 1000 times was achieved. This work provides a promising strategy for preparing free-standing and binder-free active electrode materials with high performance for lithium ion batteries and other energy storage devices.

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.

Alignment verification procedures

NASA Technical Reports Server (NTRS)

Edwards, P. R.; Phillips, E. P.; Newman, J. C., Jr.

1988-01-01

In alignment verification procedures each laboratory is required to align its test machines and gripping fixtures to produce a nearly uniform tensile stress field on an un-notched sheet specimen. The blank specimens (50 mm w X 305 mm l X 2.3 mm th) supplied by the coordinators were strain gauged. Strain gauge readings were taken at all gauges (n = 1 through 10). The alignment verification procedures are as follows: (1) zero all strain gauges while specimen is in a free-supported condition; (2) put strain-gauged specimen in the test machine so that specimen front face (face 1) is in contact with reference jaw (standard position of specimen), tighten grips, and at zero load measure strains on all gauges. (epsilon sub nS0 is strain at gauge n, standard position, zero load); (3) with specimen in machine and at a tensile load of 10 kN measure strains (specimen in standard position). (Strain = epsilon sub nS10); (4) remove specimen from machine. Put specimen in machine so that specimen back face (face 2) is in contact with reference jaw (reverse position of specimen), tighten grips, and at zero load measure strains on all gauges. (Strain - epsilon sub nR0); and (5) with specimen in machine and at tensile load of 10 kN measure strains (specimen in reverse position). (epsilon sub nR10 is strain at gauge n, reverse position, 10 kN load).

United States Air Force Summer Research Program 1991. Graduate Student Research Program (GSRP) Reports. Volume 9. Wright Laboratory

DTIC Science & Technology

1992-01-09

Materials 22 Deply of Laminated Panels with Perforation due to Impact John Lair 23 Actuator Location and Optimal Control Design for Flexible Structures...procedure is the focusing and alignment of the UV souce. Though the output of a vapor lamp is nonuniform ., intensity peaks can be smoothed by expanding the...surface, localized surface heatig may occur. Secondly, the output of a mercury vapor lame is nonuniform , requiring diffusion tc obtain a more- uniform

Prototype Superconducting Planar Transformers Using High-Tc Thin and Thick Films

DTIC Science & Technology

1992-01-01

AUG27 0%2 and Thick FilmsS A D W. C. McGinnis J. S. Briggs T. E . Jones L. J. Johnson 92-23707 Approved for public release; distribution Is unlimited. 92...platelet-like crystals, given the opportunity, will lie flat against each other. Reasonably good alignment can be produced by simply pressing the...these latter films, only the step-cooled sample (FCS-75) produced a reasonably smooth, uniform-looking film, and therefore only that film was

Insights into the phylogenetic positions of photosynthetic bacteria obtained from 5S rRNA and 16S rRNA sequence data

NASA Technical Reports Server (NTRS)

Fox, G. E.

1985-01-01

Comparisons of complete 16S ribosomal ribonucleic acid (rRNA) sequences established that the secondary structure of these molecules is highly conserved. Earlier work with 5S rRNA secondary structure revealed that when structural conservation exists the alignment of sequences is straightforward. The constancy of structure implies minimal functional change. Under these conditions a uniform evolutionary rate can be expected so that conditions are favorable for phylogenetic tree construction.

MHD Turbulence Sheared in Fixed and Rotating Frames

NASA Technical Reports Server (NTRS)

Kassinos, S. C.; Knaepen, B.; Wray, A.

2004-01-01

We consider homogeneous turbulence in a conducting fluid that is exposed to a uniform external magnetic field while being sheared in fixed and rotating frames. We take both the frame-rotation axis and the applied magnetic field to be aligned in the direction normal to the plane of the mean shear. Here a systematic parametric study is carried out in a series of Direct Numerical Simulations (DNS) in order to clarify the main effects determining the structural anisotropy and stability of the flow.

Fiber coating method

DOEpatents

Corman, Gregory Scot

2003-04-15

A coating is applied to reinforcing fibers arranged into a tow by coaxially aligning the tow with an adjacent separation layer and winding or wrapping the tow and separation layer onto a support structure in an interleaved manner so that the separation layer separates a wrap of the tow from an adjacent wrap of the tow. A coating can then be uniformly applied to the reinforcing fibers without defects caused by fiber tow to fiber tow contact. The separation layer can be a carbon fiber veil.

Beginning Learners' Development of Interactional Competence: Alignment Activity

ERIC Educational Resources Information Center

Tecedor, Marta

2016-01-01

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

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments

PubMed Central

Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

2016-01-01

The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. PMID:26978354

Sub-5 nm, globally aligned graphene nanoribbons on Ge(001)

DOE PAGES

Kiraly, Brian; Mannix, Andrew J.; Jacobberger, Robert M.; ...

2016-05-23

Graphene nanoribbons (GNRs) hold great promise for future electronics because of their edge and width dependent electronic bandgaps and exceptional transport properties. While significant progress toward such devices has been made, the field has been limited by difficulties achieving narrow widths, global alignment, and atomically pristine GNR edges on technologically relevant substrates. A recent advance has challenged these limits by using Ge(001) substrates to direct the bottom-up growth of GNRs with nearly pristine armchair edges and widths near ~10 nm via atmospheric pressure chemical vapor deposition. In this work, we extend the growth of GNRs on Ge(001) to ultra-high vacuummore » conditions and realize GNRs narrower than 5 nm. Armchair graphene nanoribbons directed along the Ge <110> surface directions are achieved with excellent width control and relatively large bandgaps. As a result, the bandgap magnitude and electronic uniformity make these new materials excellent candidates for future developments in nanoelectronics.« less

The rapid growth of vertically aligned carbon nanotubes using laser heating.

PubMed

Park, J B; Jeong, S H; Jeong, M S; Lim, S C; Lee, I H; Lee, Y H

2009-05-06

Growth of densely packed vertically aligned carbon nanotubes (VA-CNTs) using laser-induced chemical vapor deposition with visible laser (lambda = 532 nm) irradiation at room temperature is reported. Using a multiple-catalyst layer (Fe/Al/Cr) on quartz as the substrate and an acetylene-hydrogen mixture as the precursor gas, VA-CNT pillars with 60 microm height and 4 microm diameter were grown at a high rate of around 1 microm s(-1) with good reproducibility. It is demonstrated that the fabrication of uniform pillar arrays of VA-CNTs can be achieved with a single irradiation for each pillar using LCVD with no annealing or preprocessing of the substrate. Here, laser fast heating is considered the primary mechanism facilitating the growth of VA-CNT pillars. Field emission characteristics of an array of VA-CNT pillars were then examined to investigate their potential application in vacuum electronic devices.

Novel anisotropic engineered cardiac tissues: studies of electrical propagation.

PubMed

Bursac, Nenad; Loo, Yihua; Leong, Kam; Tung, Leslie

2007-10-05

The goal of this study was to engineer cardiac tissue constructs with uniformly anisotropic architecture, and to evaluate their electrical function using multi-site optical mapping of cell membrane potentials. Anisotropic polymer scaffolds made by leaching of aligned sucrose templates were seeded with neonatal rat cardiac cells and cultured in rotating bioreactors for 6-14 days. Cells aligned and interconnected inside the scaffolds and when stimulated by a point electrode, supported macroscopically continuous, anisotropic impulse propagation. By culture day 14, the ratio of conduction velocities along vs. across cardiac fibers reached a value of 2, similar to that in native neonatal ventricles, while action potential duration and maximum capture rate, respectively, decreased to 120ms and increased to approximately 5Hz. The shorter culture time and larger scaffold thickness were associated with increased incidence of sustained reentrant arrhythmias. In summary, this study is the first successful attempt to engineer a cm(2)-size, functional anisotropic cardiac tissue patch.

Production of aligned microfibers and nanofibers and derived functional monoliths

DOEpatents

Hu, Michael Z [Knoxville, TN; DePaoli, David W [Knoxville, TN; Kuritz, Tanya [Kingston, TN; Omatete, Ogbemi [New Port Richey, FL

2007-08-14

The present invention comprises a method for producing microfibers and nanofibers and further fabricating derived solid monolithic materials having aligned uniform micro- or nanofibrils. A method for producing fibers ranging in diameter from micrometer-sized to nanometer-sized comprises the steps of producing an electric field and preparing a solid precipitative reaction media wherein the media comprises at least one chemical reactive precursor and a solvent having low electrical conductivity and wherein a solid precipitation reaction process for nucleation and growth of a solid phase occurs within the media. Then, subjecting the media to the electric field to induce in-situ growth of microfibers or nanofibers during the reaction process within the media causing precipitative growth of solid phase particles wherein the reaction conditions and reaction kinetics control the size, morphology and composition of the fibers. The fibers can then be wet pressed while under electric field into a solid monolith slab, dried and consolidated.

Growth of well-aligned ZnO nanorods using auge catalyst by vapor phase transportation.

PubMed

Ha, S Y; Jung, M N; Park, S H; Ko, H J; Ko, H; Oh, D C; Yao, T; Chang, J H

2006-11-01

Well-aligned ZnO nanorods have been achieved using new alloy (AuGe) catalyst. Zn powder was used as a source material and it was transported in a horizontal tube furnace onto an AuGe deposited Si substrates. The structural and optical properties of ZnO nanorods were characterized by scanning electron microscopy, high resolution X-ray diffraction, and photoluminescence. ZnO nanorods grown at 650 degrees C on 53 nm thick AuGe layer show uniform shape with the length of 8 +/- 0.5 microm and the diameter of 150 +/- 5 nm. Also, the tilting angle of ZnO nanorods (+/- 5.5 degrees) is confirmed by HRXRD. High structural quality of the nanorods is conformed by the photoluminescence measurement. All samples show strong UV emission without considerable deep level emission. However, weak deep level emission appears at high (700 degrees C) temperature due to the increase of oxygen desertion.

Planarized arrays of aligned, untangled multiwall carbon nanotubes with Ohmic back contacts

DOE PAGES

Rochford, C.; Limmer, S. J.; Howell, S. W.; ...

2014-11-26

Vertically aligned, untangled planarized arrays of multiwall carbon nanotubes (MWNTs) with Ohmic back contacts were grown in nanopore templates on arbitrary substrates. The templates were prepared by sputter depositing Nd-doped Al films onto W-coated substrates, followed by anodization to form an aluminum oxide nanopore array. The W underlayer helps eliminate the aluminum oxide barrier that typically occurs at the nanopore bottoms by instead forming a thin WO 3 layer. The WO 3 can be selectively etched to enable electrodeposition of Co catalysts with control over the Co site density. This led to control of the site density of MWNTs grownmore » by thermal chemical vapor deposition, with the W also serving as a back electrical contact. As a result, Ohmic contact to MWNTs was confirmed, even following ultrasonic cutting of the entire array to a uniform height.« less

Aligned hierarchical Ag/ZnO nano-heterostructure arrays via electrohydrodynamic nanowire template for enhanced gas-sensing properties.

PubMed

Yin, Zhouping; Wang, Xiaomei; Sun, Fazhe; Tong, Xiaohu; Zhu, Chen; Lv, Qiying; Ye, Dong; Wang, Shuai; Luo, Wei; Huang, YongAn

2017-09-22

Gas sensing performance can be improved significantly by the increase in both the effective gas exposure area and the surface reactivitiy of ZnO nanorods. Here, we propose aligned hierarchical Ag/ZnO nano-heterostructure arrays (h-Ag/ZnO-NAs) via electrohydrodynamic nanowire template, together with a subsequent hydrothermal synthesis and photoreduction reaction. The h-Ag/ZnO-NAs scatter at top for higher specific surface areas with the air, simultaneously contact at root for the electrical conduction. Besides, the ZnO nanorods are uniformly coated with dispersed Ag nanoparticles, resulting in a tremendous enhancement of the surface reactivity. Compared with pure ZnO, such h-Ag/ZnO-NAs exhibit lower electrical resistance and faster responses. Moreover, they demonstrate enhanced NO 2 gas sensing properties. Self-assembly via electrohydrodynamic nanowire template paves a new way for the preparation of high performance gas sensors.

Visualization of three pathways for macromolecule transport across cultured endothelium and their modification by flow.

PubMed

Ghim, Mean; Alpresa, Paola; Yang, Sung-Wook; Braakman, Sietse T; Gray, Stephen G; Sherwin, Spencer J; van Reeuwijk, Maarten; Weinberg, Peter D

2017-11-01

Transport of macromolecules across vascular endothelium and its modification by fluid mechanical forces are important for normal tissue function and in the development of atherosclerosis. However, the routes by which macromolecules cross endothelium, the hemodynamic stresses that maintain endothelial physiology or trigger disease, and the dependence of transendothelial transport on hemodynamic stresses are controversial. We visualized pathways for macromolecule transport and determined the effect on these pathways of different types of flow. Endothelial monolayers were cultured under static conditions or on an orbital shaker producing different flow profiles in different parts of the wells. Fluorescent tracers that bound to the substrate after crossing the endothelium were used to identify transport pathways. Maps of tracer distribution were compared with numerical simulations of flow to determine effects of different shear stress metrics on permeability. Albumin-sized tracers dominantly crossed the cultured endothelium via junctions between neighboring cells, high-density lipoprotein-sized tracers crossed at tricellular junctions, and low-density lipoprotein-sized tracers crossed through cells. Cells aligned close to the angle that minimized shear stresses across their long axis. The rate of paracellular transport under flow correlated with the magnitude of these minimized transverse stresses, whereas transport across cells was uniformly reduced by all types of flow. These results contradict the long-standing two-pore theory of solute transport across microvessel walls and the consensus view that endothelial cells align with the mean shear vector. They suggest that endothelial cells minimize transverse shear, supporting its postulated proatherogenic role. Preliminary data show that similar tracer techniques are practicable in vivo. NEW & NOTEWORTHY Solutes of increasing size crossed cultured endothelium through intercellular junctions, through tricellular junctions, or transcellularly. Cells aligned to minimize the shear stress acting across their long axis. Paracellular transport correlated with the level of this minimized shear, but transcellular transport was reduced uniformly by flow regardless of the shear profile. Copyright © 2017 the American Physiological Society.

Roughness and uniformity improvements on self-aligned quadruple patterning technique for 10nm node and beyond by wafer stress engineering

NASA Astrophysics Data System (ADS)

Liu, Eric; Ko, Akiteru; O'Meara, David; Mohanty, Nihar; Franke, Elliott; Pillai, Karthik; Biolsi, Peter

2017-05-01

Dimension shrinkage has been a major driving force in the development of integrated circuit processing over a number of decades. The Self-Aligned Quadruple Patterning (SAQP) technique is widely adapted for sub-10nm node in order to achieve the desired feature dimensions. This technique provides theoretical feasibility of multiple pitch-halving from 193nm immersion lithography by using various pattern transferring steps. The major concept of this approach is to a create spacer defined self-aligned pattern by using single lithography print. By repeating the process steps, double, quadruple, or octuple are possible to be achieved theoretically. In these small architectures, line roughness control becomes extremely important since it may contribute to a significant portion of process and device performance variations. In addition, the complexity of SAQP in terms of processing flow makes the roughness improvement indirective and ineffective. It is necessary to discover a new approach in order to improve the roughness in the current SAQP technique. In this presentation, we demonstrate a novel method to improve line roughness performances on 30nm pitch SAQP flow. We discover that the line roughness performance is strongly related to stress management. By selecting different stress level of film to be deposited onto the substrate, we can manipulate the roughness performance in line and space patterns. In addition, the impact of curvature change by applied film stress to SAQP line roughness performance is also studied. No significant correlation is found between wafer curvature and line roughness performance. We will discuss in details the step-by-step physical performances for each processing step in terms of critical dimension (CD)/ critical dimension uniformity (CDU)/line width roughness (LWR)/line edge roughness (LER). Finally, we summarize the process needed to reach the full wafer performance targets of LWR/LER in 1.07nm/1.13nm on 30nm pitch line and space pattern.

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

PubMed

Hashemifar, Somaye; Xu, Jinbo

2014-09-01

High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

A happy conclusion to the SALT image quality saga

NASA Astrophysics Data System (ADS)

Crause, Lisa A.; O'Donoghue, Darragh E.; O'Connor, James E.; Strumpfer, Francois; Strydom, Ockert J.; Sass, Craig; du Plessis, Charl A.; Wiid, Eben; Love, Jonathan; Brink, Janus D.; Wilkinson, Martin; Coetzee, Chris

2012-09-01

Images obtained with the Southern African Large Telescope (SALT) during its commissioning phase showed degradation due to a large focus gradient and a variety of other optical aberrations. An extensive forensic investigation eventually traced the problem to the mechanical interface between the telescope and the secondary optics that form the Spherical Aberration Corrector (SAC). The SAC was brought down from the telescope in 2009 April, the problematic interface was replaced and the four corrector mirrors were optically tested and re-aligned. The surface figures of the SAC mirrors were confirmed to be within specification and a full system test following the re-alignment process yielded a RMS wavefront error of just 0.15 waves. The SAC was re-installed on the tracker in 2010 August and aligned with respect to the payload and primary mirror. Subsequent on-sky tests produced alarming results which were due to spurious signals being sent to the tracker by the auto-collimator, the instrument responsible for controlling the attitude of the SAC with respect to the primary mirror. Once this minor issue was resolved, we obtained uniform 1.1 arcsecond star images over the full 10 arcminute field of view of the telescope.

WC Nanocrystals Grown on Vertically Aligned Carbon Nanotubes: An Efficient and Stable Electrocatalyst for Hydrogen Evolution Reaction.

PubMed

Fan, Xiujun; Zhou, Haiqing; Guo, Xia

2015-05-26

Single nanocrystalline tungsten carbide (WC) was first synthesized on the tips of vertically aligned carbon nanotubes (VA-CNTs) with a hot filament chemical vapor deposition (HF-CVD) method through the directly reaction of tungsten metal with carbon source. The VA-CNTs with preservation of vertical structure integrity and alignment play an important role to support the nanocrystalline WC growth. With the high crystallinity, small size, and uniform distribution of WC particles on the carbon support, the formed WC-CNTs material exhibited an excellent catalytic activity for hydrogen evolution reaction (HER), giving a η10 (the overpotential for driving a current of 10 mA cm(-2)) of 145 mV, onset potential of 15 mV, exchange current density@ 300 mV of 117.6 mV and Tafel slope values of 72 mV dec(-1) in acid solution, and η10 of 137 mV, onset potential of 16 mV, exchange current density@ 300 mV of 33.1 mV and Tafel slope values of 106 mV dec(-1) in alkaline media, respectively. Electrochemical stability test further confirms the long-term operation of the catalyst in both acidic and alkaline media.

The current impact flux on Mars and its seasonal variation

NASA Astrophysics Data System (ADS)

JeongAhn, Youngmin; Malhotra, Renu

2015-12-01

We calculate the present-day impact flux on Mars and its variation over the martian year, using the current data on the orbital distribution of known Mars-crossing minor planets. We adapt the Öpik-Wetherill formulation for calculating collision probabilities, paying careful attention to the non-uniform distribution of the perihelion longitude and the argument of perihelion owed to secular planetary perturbations. We find that, at the current epoch, the Mars crossers have an axial distribution of the argument of perihelion, and the mean direction of their eccentricity vectors is nearly aligned with Mars' eccentricity vector. These previously neglected angular non-uniformities have the effect of depressing the mean annual impact flux by a factor of about 2 compared to the estimate based on a uniform random distribution of the angular elements of Mars-crossers; the amplitude of the seasonal variation of the impact flux is likewise depressed by a factor of about 4-5. We estimate that the flux of large impactors (of absolute magnitude H < 16) within ±30° of Mars' aphelion is about three times larger than when the planet is near perihelion. Extrapolation of our results to a model population of meter-size Mars-crossers shows that if these small impactors have a uniform distribution of their angular elements, then their aphelion-to-perihelion impact flux ratio would be 11-15, but if they track the orbital distribution of the large impactors, including their non-uniform angular elements, then this ratio would be about 3. Comparison of our results with the current dataset of fresh impact craters on Mars (detected with Mars-orbiting spacecraft) appears to rule out the uniform distribution of angular elements.

The use of zeolites to generate PET phantoms for the validation of quantification strategies in oncology.

PubMed

Zito, Felicia; De Bernardi, Elisabetta; Soffientini, Chiara; Canzi, Cristina; Casati, Rosangela; Gerundini, Paolo; Baselli, Giuseppe

2012-09-01

In recent years, segmentation algorithms and activity quantification methods have been proposed for oncological (18)F-fluorodeoxyglucose (FDG) PET. A full assessment of these algorithms, necessary for a clinical transfer, requires a validation on data sets provided with a reliable ground truth as to the imaged activity distribution, which must be as realistic as possible. The aim of this work is to propose a strategy to simulate lesions of uniform uptake and irregular shape in an anthropomorphic phantom, with the possibility to easily obtain a ground truth as to lesion activity and borders. Lesions were simulated with samples of clinoptilolite, a family of natural zeolites of irregular shape, able to absorb aqueous solutions of (18)F-FDG, available in a wide size range, and nontoxic. Zeolites were soaked in solutions of (18)F-FDG for increasing times up to 120 min and their absorptive properties were characterized as function of soaking duration, solution concentration, and zeolite dry weight. Saturated zeolites were wrapped in Parafilm, positioned inside an Alderson thorax-abdomen phantom and imaged with a PET-CT scanner. The ground truth for the activity distribution of each zeolite was obtained by segmenting high-resolution finely aligned CT images, on the basis of independently obtained volume measurements. The fine alignment between CT and PET was validated by comparing the CT-derived ground truth to a set of zeolites' PET threshold segmentations in terms of Dice index and volume error. The soaking time necessary to achieve saturation increases with zeolite dry weight, with a maximum of about 90 min for the largest sample. At saturation, a linear dependence of the uptake normalized to the solution concentration on zeolite dry weight (R(2) = 0.988), as well as a uniform distribution of the activity over the entire zeolite volume from PET imaging were demonstrated. These findings indicate that the (18)F-FDG solution is able to saturate the zeolite pores and that the concentration does not influence the distribution uniformity of both solution and solute, at least at the trace concentrations used for zeolite activation. An additional proof of uniformity of zeolite saturation was obtained observing a correspondence between uptake and adsorbed volume of solution, corresponding to about 27.8% of zeolite volume. As to the ground truth for zeolites positioned inside the phantom, the segmentation of finely aligned CT images provided reliable borders, as demonstrated by a mean absolute volume error of 2.8% with respect to the PET threshold segmentation corresponding to the maximum Dice. The proposed methodology allowed obtaining an experimental phantom data set that can be used as a feasible tool to test and validate quantification and segmentation algorithms for PET in oncology. The phantom is currently under consideration for being included in a benchmark designed by AAPM TG211, which will be available to the community to evaluate PET automatic segmentation methods.

Symmetry breaking and chaos in droplet electrohydrodynamics

NASA Astrophysics Data System (ADS)

Salipante, Paul; Vlahovska, Petia

2010-11-01

A classic result due to G.I.Taylor is that a drop placed in a uniform electric field adopts a prolate or oblate spheroidal shape, the flow and shape being axisymmetrically aligned with the applied field. However, recent studies have revealed an instability and transition to a nonaxisymmetric rotational flow in strong fields, similar to the rotation of solid dielectric particles observed by Quincke in the 19th century. We present an experimental and theoretical study of this phenomenon in DC uniform fields, focusing on nonlinear behavior arising from electromechanial coupling at the fluid-fluid interface. Charge convection by the both rotational and straining flows is included in the our model to explain the dependence of critical electric field on viscosity ratio. Hysteresis in the transition is observed for large low-viscosity drops. At stronger fields, chaotic drop tumbling and sustained shape oscillations are observed.

One-pot template-free synthesis of uniform-sized fullerene-like magnetite hollow spheres

NASA Astrophysics Data System (ADS)

Zhu, Qing; Zhang, Yue; Liu, Zheng; Zhou, Xinrui; Zhang, Xinmei; Zeng, Lintao

2015-11-01

Uniform-sized Fe3O4 hollow spheres with average diameter of 250 nm and shell thickness of ∼50 nm have been successfully synthesized through a simple hydrothermal route with the presence of di-n-propylamine (DPA) as a weak-base. The reaction time and DPA amount play important roles in the formation of the magnetite hollow spheres. The structures of the products were characterized by X-ray diffraction, X-ray photoelectron spectroscopy, Fourier transform infrared spectra, scanning electron microscopy, transmission electron microscopy, and high-resolution transmission electron microscopy. The results show that the single-crystalline Fe3O4 hollow spheres are composed of well-aligned magnetite nanoparticles (NPs). The magnetic property investigation shows that these hollow spheres have a higher saturation magnetization (Ms) than the solid spheres. Furthermore, a possible mechanism for the formation of magnetite hollow spheres is proposed based on the experimental observations.

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

PubMed Central

2013-01-01

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

Magnetization reversal of in-plane uniaxial Co films and its dependence on epitaxial alignment

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

Idigoras, O., E-mail: o.idigoras@nanogune.eu; Suszka, A. K.; Berger, A.

2014-02-28

This work studies the influence of crystallographic alignment onto magnetization reversal in partially epitaxial Co films. A reproducible growth sequence was devised that allows for the continuous tuning of grain orientation disorder in Co films with uniaxial in-plane anisotropy by the controlled partial suppression of epitaxy. While all stable or meta-stable magnetization states occurring during a magnetic field cycle exhibit a uniform magnetization for fully epitaxial samples, non-uniform states appear for samples with sufficiently high grain orientation disorder. Simultaneously with the occurrence of stable domain states during the magnetization reversal, we observe a qualitative change of the applied field anglemore » dependence of the coercive field. Upon increasing the grain orientation disorder, we observe a disappearance of transient domain wall propagation as the dominating reversal process, which is characterized by an increase of the coercive field for applied field angles away from the easy axis for well-ordered epitaxial samples. Upon reaching a certain disorder threshold level, we also find an anomalous magnetization reversal, which is characterized by a non-monotonic behavior of the remanent magnetization and coercive field as a function of the applied field angle in the vicinity of the nominal hard axis. This anomaly is a collective reversal mode that is caused by disorder-induced frustration and it can be qualitatively and even quantitatively explained by means of a two Stoner-Wohlfarth particle model. Its predictions are furthermore corroborated by Kerr microscopy and by Brillouin light scattering measurements.« less

Node fingerprinting: an efficient heuristic for aligning biological networks.

PubMed

Radu, Alex; Charleston, Michael

2014-10-01

With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

Optical Analysis And Alignment Applications Using The Infrared Smartt Interferometer

NASA Astrophysics Data System (ADS)

Viswanathan, V. K.; Bolen, P. D.; Liberman, I.; Seery, B. D.

1981-12-01

The possiblility of using the infrared Smartt interferometer for optical analysis and alignment of infrared laser systems has been discussed previously. In this paper, optical analysis of the Gigawatt Test Facility at Los Alamos, as well as a deformable mirror manufactured by Rocketdyne, are discussed as examples of the technique. The possibility of optically characterizing, as well as aligning, pulsed high energy laser systems like Helios and Antares is discussed in some detail.

Optical analysis and alignment applications using the infrared Smartt interferometer

NASA Astrophysics Data System (ADS)

Viswanathan, V. K.; Bolen, P. D.; Liberman, I.; Seery, B. D.

The possibility of using the infrared Smartt interferometer for optical analysis and alignment of infrared laser systems has been discussed previously. In this paper, optical analysis of the Gigawatt Test Facility at Los Alamos, as well as a deformable mirror manufactured by Rocketdyne, are discussed as examples of the technique. The possibility of optically characterizing, as well as aligning, pulsed high energy laser systems like Helios and Antares is discussed in some detail.

SU-E-I-20: Comprehensive Quality Assurance Test of Second Generation Toshiba Aquilion Large Bore CT Simulator Based On AAPM TG-66 Recommendations

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

Zhang, D

2015-06-15

Purpose: AAPM radiation therapy committee task group No. 66 (TG-66) published a report which described a general approach to CT simulator QA. The report outlines the testing procedures and specifications for the evaluation of patient dose, radiation safety, electromechanical components, and image quality for a CT simulator. The purpose of this study is to thoroughly evaluate the performance of a second generation Toshiba Aquilion Large Bore CT simulator with 90 cm bore size (Toshiba, Nasu, JP) based on the TG-66 criteria. The testing procedures and results from this study provide baselines for a routine QA program. Methods: Different measurements andmore » analysis were performed including CTDIvol measurements, alignment and orientation of gantry lasers, orientation of the tabletop with respect to the imaging plane, table movement and indexing accuracy, Scanogram location accuracy, high contrast spatial resolution, low contrast resolution, field uniformity, CT number accuracy, mA linearity and mA reproducibility using a number of different phantoms and measuring devices, such as CTDI phantom, ACR image quality phantom, TG-66 laser QA phantom, pencil ion chamber (Fluke Victoreen) and electrometer (RTI Solidose 400). Results: The CTDI measurements were within 20% of the console displayed values. The alignment and orientation for both gantry laser and tabletop, as well as the table movement and indexing and scanogram location accuracy were within 2mm as specified in TG66. The spatial resolution, low contrast resolution, field uniformity and CT number accuracy were all within ACR’s recommended limits. The mA linearity and reproducibility were both well below the TG66 threshold. Conclusion: The 90 cm bore size second generation Toshiba Aquilion Large Bore CT simulator that comes with 70 cm true FOV can consistently meet various clinical needs. The results demonstrated that this simulator complies with the TG-66 protocol in all aspects including electromechanical component, radiation safety component, and image quality component. Employee of Toshiba America Medical Systems.« less

Students Wearing Police Uniforms Exhibit Biased Attention toward Individuals Wearing Hoodies.

PubMed

Civile, Ciro; Obhi, Sukhvinder S

2017-01-01

Police provide an essential public service and they often operate in difficult circumstances, requiring high-speed cognition. Recent incidents involving apparent profiling and aggressive behavior have led to accusations that the police are sometimes biased. Given that previous research has shown a link between clothing and cognition, we investigated the question of whether the police uniform itself might induce a bias in social attention. To address this question, and using a Canadian university student sample, we assessed whether wearing a police uniform biases attention toward black faces compared to white faces, and low-status individuals compared to high-status individuals. In Experiment 1 ( n = 28), participants wore either a police-style uniform or mechanic overalls, and performed a shape categorization task in the presence of a distractor that could be either: a black face, a white face, a person wearing a hoodie (whom we propose will be associated with low SES), or a person wearing a suit (whom we propose will be associated with high SES). Participants wearing the police-style uniform exhibited biased attention, indexed by slower reaction times (RTs), in the presence of low-SES images. In Experiment 2 ( n = 28), we confirmed this bias using a modified Dot-Probe task - an alternate measure of attentional bias in which we observed faster RTs to a dot probe that was spatially aligned with a low SES image. Experiment 3 ( n = 56) demonstrated that attentional bias toward low-SES targets appears only when participants wear the police-style uniform, and not when they are simply exposed to it - by having it placed on the desk in front of them. Our results demonstrate that wearing a police-style uniform biases attention toward low-SES targets. Thus, wearing a police-style uniform may induce a kind of "status-profiling" in which individuals from low-status groups become salient and capture attention. We note that our results are limited to university students and that it will be important to extend them to members of the community and law-enforcement officers. We discuss how uniforms might exert their effects on cognition by virtue of the power and cultural associations they evoke in the wearer.

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.

PubMed

Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris

2011-10-20

Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down-to-earth quantitative analysis works well for the CluPA-aligned spectra. The whole workflow is embedded into a modular and statistically sound framework that is implemented as an R package called "speaq" ("spectrum alignment and quantitation"), which is freely available from http://code.google.com/p/speaq/.

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.

EphA2 and Src regulate equatorial cell morphogenesis during lens development

PubMed Central

Cheng, Catherine; Ansari, Moham M.; Cooper, Jonathan A.; Gong, Xiaohua

2013-01-01

High refractive index and transparency of the eye lens require uniformly shaped and precisely aligned lens fiber cells. During lens development, equatorial epithelial cells undergo cell-to-cell alignment to form meridional rows of hexagonal cells. The mechanism that controls this morphogenesis from randomly packed cuboidal epithelial cells to highly organized hexagonal fiber cells remains unknown. In Epha2-/- mouse lenses, equatorial epithelial cells fail to form precisely aligned meridional rows; moreover, the lens fulcrum, where the apical tips of elongating epithelial cells constrict to form an anchor point before fiber cell differentiation and elongation at the equator, is disrupted. Phosphorylated Src-Y424 and cortactin-Y466, actin and EphA2 cluster at the vertices of wild-type hexagonal epithelial cells in organized meridional rows. However, phosphorylated Src and phosphorylated cortactin are not detected in disorganized Epha2-/- cells with altered F-actin distribution. E-cadherin junctions, which are normally located at the basal-lateral ends of equatorial epithelial cells and are diminished in newly differentiating fiber cells, become widely distributed in the apical, lateral and basal sides of epithelial cells and persist in differentiating fiber cells in Epha2-/- lenses. Src-/- equatorial epithelial cells also fail to form precisely aligned meridional rows and lens fulcrum. These results indicate that EphA2/Src signaling is essential for the formation of the lens fulcrum. EphA2 also regulates Src/cortactin/F-actin complexes at the vertices of hexagonal equatorial cells for cell-to-cell alignment. This mechanistic information explains how EphA2 mutations lead to disorganized lens cells that subsequently contribute to altered refractive index and cataracts in humans and mice. PMID:24026120

Enhanced method of magnetic powder alignment for production of PLP Nd-Fe-B magnets

NASA Astrophysics Data System (ADS)

Popov, A. G.; Golovnia, O. A.; Protasov, A. V.

2017-04-01

It is demonstrated how the high degree of powder alignment in PLP magnets can be achieved by loading the powder into a container placed in a magnetic field of moderate strength. The strip-cast alloy with a composition of 30.00 Nd, 1.95 Dy, 66.42 Fe, 0.99 B, 0.54 Co, 0.1 Ga (wt%) was subjected to hydrogen decrepitation and then milled in a vibratory mill in toluene to an average particle size of 2.9 μm determined by the FSSS method. The powder was compacted in the magnetic field of 0.2 - 1.2 T to the filling density 2.6 - 3.2×103 kg/m3. It is shown that loading the powder into a container placed in a magnetic field enhances the degree of powder alignment in sintered Nd-Fe-B magnets produced from non-pressed powder. At the filling density less than 3.2×103 kg/m3, the density of magnets is high but insufficient, because of the formation of magnetostatic chains of particles, which impedes the powder compaction. The simulation by the discrete-element method qualitatively proves that the magnetostatic interaction of the chains of particles that are formed in the course of loading in the magnetic field stimulates a decrease in the density of the sintered magnets and its non-uniform distribution over the sample. As a result of the optimization of the parameters of the alignment and compaction of the powder loaded in a magnetic field, PLP magnets with Br ≥1.34 T, Hc ≥950 kA/m, (BH)max ≥340 kJ/m3, and the degree of alignment exceeding 96% were produced.

CAFE: aCcelerated Alignment-FrEe sequence analysis

PubMed Central

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

2017-01-01

Abstract Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^*$\\end{document} and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^S$\\end{document} are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. PMID:28472388

The use of Long-Lived Tracer Observations to Examine Transport Characteristics in the Lower Stratosphere

NASA Astrophysics Data System (ADS)

Lingenfelser, Gretchen Scott

This thesis explores the problem of uniformly aligning Ferroelectric Liquid Crystals (FLCs) over large areas whilst retaining bistability. A novel high tilt alignment (HTA) is presented and its electro-optic performance is compared to the traditional surface stabilised (SS) alignment using three different devices; test cells, displays and all-fibre optic devices. Evidence is presented to show that the SS alignment has a small surface pretilt of the director which reduces the number of zig-zag defects in parallel aligned cells. This is related to the layer structure and a review of the latest proposed structures of SS devices is presented. The HTA device is shown to have many advantages over the SS device; no zig-zag defects, excellent bistability in up to 6 mum thick cells, good mechanical stability and excellent viewing characteristics when multiplexed. These properties are explored and culminate in the production of two FLC displays, one HTA and one SS aligned. The properties of these displays are compared. In order to improve the appearance and frame time of the displays, multiplexing schemes were investigated, including a novel two slot scheme that was successfully used to drive both displays. It was found that the SS display could be driven in a reverse contrast mode by taking advantage of the relaxation process. This decreased the line address time and produced a higher contrast display. A nematic LC all-fibre optic polariser was produced with excellent extinction ratio (45 dB) and low loss (0.2 dB) using evanescent field coupling. A nematic LC modulator was then demonstrated using a novel electrode arrangement. A modulation depth of 28 dB was achieved using low voltages ( 10V) but with 10 kHz but the modulation depth was poor (8.2 dB) because of the unsuitable refractive indices. The potential and uses of LC all-fibre optic devices are discussed.

A Sustainable Substitute for Ivory: the Jarina Seed from the Amazon

NASA Astrophysics Data System (ADS)

Chu, Yinghao; Meyers A, Marc A.; Wang, Bin; Yang, Wen; Jung, Jae-Young; Coimbra, Carlos F. M.

2015-09-01

The dried endosperm of the seed of Phytelephas sp is widely used for artisanal work in the Amazon region due to its favorable mechanical properties and pleasant appearance that resemble elephant ivory. While the seeds have enjoyed popularity and limited use by selected industries (e.g., military uniform buttons and piano keys) and handicraft applications, little is known about the mechanical properties and structure of this sustainable material. This work is the first to characterize the dried Jarina endosperm and to investigate its functionality as a viable substitute for elephant ivory. Structural analysis of typical seeds reveals the prevalence of tubules that align in rings and radiate from the (usually hollow) core of the seed. This seed, in the absence of a reinforcement structure or mineral phase, possesses mechanical properties slightly inferior to elephant ivory and selected plastics, while retaining the visual appeal of a naturally occurring material. A synthetic structure inspired on the seed is created and suggestions for further development are discussed.

A Sustainable Substitute for Ivory: the Jarina Seed from the Amazon

PubMed Central

Chu, Yinghao; Meyers A, Marc A.; Wang, Bin; Yang, Wen; Jung, Jae-Young; Coimbra, Carlos F. M.

2015-01-01

The dried endosperm of the seed of Phytelephas sp is widely used for artisanal work in the Amazon region due to its favorable mechanical properties and pleasant appearance that resemble elephant ivory. While the seeds have enjoyed popularity and limited use by selected industries (e.g., military uniform buttons and piano keys) and handicraft applications, little is known about the mechanical properties and structure of this sustainable material. This work is the first to characterize the dried Jarina endosperm and to investigate its functionality as a viable substitute for elephant ivory. Structural analysis of typical seeds reveals the prevalence of tubules that align in rings and radiate from the (usually hollow) core of the seed. This seed, in the absence of a reinforcement structure or mineral phase, possesses mechanical properties slightly inferior to elephant ivory and selected plastics, while retaining the visual appeal of a naturally occurring material. A synthetic structure inspired on the seed is created and suggestions for further development are discussed. PMID:26399626

Stress-strain state of reinforced bimodulus beam on an elastic foundation

NASA Astrophysics Data System (ADS)

Beskopylny, A. N.; Kadomtseva, E. E.; Strelnikov, G. P.; Berdnik, Y. A.

2017-10-01

The paper provides the calculation theory of an arbitrary supported and arbitrary loaded reinforced beam filled with bimodulus material. The formulas determining normal stresses, bending moments, shear forces, rotation angles and a deflection of a rectangular crosssection beam reinforced with any number of bars aligned parallel to the beam axis have been obtained. The numerical study has been carried out to investigate an influence of a modulus of subgrade reaction on values of maximum normal stresses, maximum bending moments and a maximum deflection of a hinged supported beam loaded with a point force or uniform distributed load. The estimation is based on the method of initial parameters for a beam on elastic foundation and the Bubnov-Galerkin method. Values of maximum deflections, maximum bending moments and maximum stresses obtained by these methods coincide. The numerical studies show that taking into consideration the bimodulus of material leads to the necessity to calculate the strength analysis of both tensile stresses and compressive stresses.

Effect of polyethyleneimine modified graphene on the mechanical and water vapor barrier properties of methyl cellulose composite films.

PubMed

Liu, Hongyu; Liu, Cuiyun; Peng, Shuge; Pan, Bingli; Lu, Chang

2018-02-15

A series of novel methyl cellulose (MC) composite films were prepared using polyethyleneimine reduced graphene oxide (PEI-RGO) as an effective filler for water vapor barrier application. The as-prepared PEI-RGO/MC composites were characterized by Fourier transform infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, tensile test and scanning electron microscopy. The experimental and theoretical results exhibited that PEI-RGO was uniformly dispersed in the MC matrix without aggregation and formed an aligned dispersion. The addition of PEI-RGO resulted in an enhanced surface hydrophobicity and a tortuous diffusion pathway for water molecules. Water vapor permeability of PEI-RGO/MC with loading of 3.0% of surface modified graphene was as low as 5.98×10 -11 gmm -2 s -1 Pa -1 . The synergistic effects of enhanced surface hydrophobicity and tortuous diffusion pathway were accounted for the improved water vapor barrier performance of the PEI-RGO/MC composite films. Copyright © 2017 Elsevier Ltd. All rights reserved.

Grain size tuning of nanostructured Cu{sub 2}O films through vapour phase supersaturation control and their characterization for practical applications

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

Anu, A.; Abdul Khadar, M., E-mail: mabdulkhadar@rediffmail.com

2015-09-15

A strategy for creating nanostructured films is the alignment of nanoparticles into ordered superstructures as living organisms synthesize biomaterials with superior physical properties using nanoparticle building blocks. We synthesized nanostructured films of Cu{sub 2}O of variable grain size by establishing the condition of supersaturation for creation of nanoparticles of copper which deposited as nanograined films and which was then oxidized. This technique has the advantage of being compatible with conventional vacuum processes for electronic device fabrication. The Cu{sub 2}O film samples consisted of a secondary structure of spherical particles of almost uniform size, each particle being an agglomerate of primarymore » nanocrystals. Fractal analysis of the AFM images of the samples is carried out for studying the aggregation mechanism. Grain size tuning of the nanostructured Cu{sub 2}O films has been studied using XRD, and micro-Raman and photoluminescence spectroscopy.« less

Structure and Thermoelectric Properties of Bi2−xSbxTe3 Nanowires Grown in Flexible Nanoporous Polycarbonate Templates

PubMed Central

Datta, Anuja; Sangle, Abhijeet; Hardingham, Nick; Cooper, Charles; Kraan, Max; Ritchie, David; Narayan, Vijay; Kar-Narayan, Sohini

2017-01-01

We report the room-temperature growth of vertically aligned ternary Bi2−xSbxTe3 nanowires of diameter ~200 nm and length ~12 µm, within flexible track-etched nanoporous polycarbonate (PC) templates via a one-step electrodeposition process. Bi2−xSbxTe3 nanowires with compositions spanning the entire range from pure Bi2Te3 (x = 0) to pure Sb2Te3 (x = 2) were systematically grown within the nanoporous channels of PC templates from a tartaric–nitric acid based electrolyte, at the end of which highly crystalline nanowires of uniform composition were obtained. Compositional analysis showed that the Sb concentration could be tuned by simply varying the electrolyte composition without any need for further annealing of the samples. Thermoelectric properties of the Bi2−xSbxTe3 nanowires were measured using a standardized bespoke setup while they were still embedded within the flexible PC templates. PMID:28772915

Winston Solar Concentrators and Evaluation Support. Phase 2: Non-imaging Concentrators for Space Applications

NASA Technical Reports Server (NTRS)

Winston, R.; Ogallagher, J.; Greenman, P.

1978-01-01

A 4.67X, plus or minus 5 deg. compound parabolic concentrator (CPC) for a large photovoltaic array in space was analyzed. The design was demonstrated to be effective in achieving a net power gain which can be varied from more than a factor of 3 down to approximately unity. A method for reducing nonuniformities in illumination to a given desired level was found. The effectiveness of this method, which involves the introduction of a degree of non-specularity in the reflector surface, was confirmed by direct measurements with prepared foil reflectors in a CPC in terrestrial sunshine as well as by computer ray tracing. Further ray tracing confirms that the CPC design is extremely tolerant to pointing and alignment errors, minor distortions, etc. A two stage non-imaging design was shown, by preliminary measurements and analysis, to provide both the desired angular tolerance and the required degree of intensity uniformity if higher concentrations (4X-10X) are necessary.

Compact laser amplifier system

DOEpatents

Carr, R.B.

1974-02-26

A compact laser amplifier system is described in which a plurality of face-pumped annular disks, aligned along a common axis, independently radially amplify a stimulating light pulse. Partially reflective or lasing means, coaxially positioned at the center of each annualar disk, radially deflects a stimulating light directed down the common axis uniformly into each disk for amplification, such that the light is amplified by the disks in a parallel manner. Circumferential reflecting means coaxially disposed around each disk directs amplified light emission, either toward a common point or in a common direction. (Official Gazette)

A High-Performance Lithium-Ion Battery Anode Based on the Core-Shell Heterostructure of Silicon-Coated Vertically Aligned Carbon Nanofibers

DTIC Science & Technology

2013-01-01

nanotubes ( MWCNTs ) using chemical vapour deposition (CVD) to form a hybrid Si– MWCNT structure consisting of 54 to 57 wt% of Si.16 The initial specic...retained less than 70% aer 100 cycles.16 The wavy and partially entangled structure may still have prevented uniform Si deposition deep into the MWCNT ...silicon shells, as illustrated in Fig. 1. The VACNFs are a special type of MWCNTs which are grown with DC-biased plasma chemical vapour deposition (PECVD

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

PubMed

Rajan, Vaibhav

2013-03-01

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

Forced Alignment for Understudied Language Varieties: Testing Prosodylab-Aligner with Tongan Data

ERIC Educational Resources Information Center

Johnson, Lisa M.; Di Paolo, Marianna; Bell, Adrian

2018-01-01

Automated alignment of transcriptions to audio files expedites the process of preparing data for acoustic analysis. Unfortunately, the benefits of auto-alignment have generally been available only to researchers studying majority languages, for which large corpora exist and for which acoustic models have been created by large-scale research…

A qualitative content analysis of global health engagements in Peacekeeping and Stability Operations Institute's stability operations lessons learned and information management system.

PubMed

Nang, Roberto N; Monahan, Felicia; Diehl, Glendon B; French, Daniel

2015-04-01

Many institutions collect reports in databases to make important lessons-learned available to their members. The Uniformed Services University of the Health Sciences collaborated with the Peacekeeping and Stability Operations Institute to conduct a descriptive and qualitative analysis of global health engagements (GHEs) contained in the Stability Operations Lessons Learned and Information Management System (SOLLIMS). This study used a summative qualitative content analysis approach involving six steps: (1) a comprehensive search; (2) two-stage reading and screening process to identify first-hand, health-related records; (3) qualitative and quantitative data analysis using MAXQDA, a software program; (4) a word cloud to illustrate word frequencies and interrelationships; (5) coding of individual themes and validation of the coding scheme; and (6) identification of relationships in the data and overarching lessons-learned. The individual codes with the most number of text segments coded included: planning, personnel, interorganizational coordination, communication/information sharing, and resources/supplies. When compared to the Department of Defense's (DoD's) evolving GHE principles and capabilities, the SOLLIMS coding scheme appeared to align well with the list of GHE capabilities developed by the Department of Defense Global Health Working Group. The results of this study will inform practitioners of global health and encourage additional qualitative analysis of other lessons-learned databases. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

Joint Multi-Leaf Segmentation, Alignment, and Tracking for Fluorescence Plant Videos.

PubMed

Yin, Xi; Liu, Xiaoming; Chen, Jin; Kramer, David M

2018-06-01

This paper proposes a novel framework for fluorescence plant video processing. The plant research community is interested in the leaf-level photosynthetic analysis within a plant. A prerequisite for such analysis is to segment all leaves, estimate their structures, and track them over time. We identify this as a joint multi-leaf segmentation, alignment, and tracking problem. First, leaf segmentation and alignment are applied on the last frame of a plant video to find a number of well-aligned leaf candidates. Second, leaf tracking is applied on the remaining frames with leaf candidate transformation from the previous frame. We form two optimization problems with shared terms in their objective functions for leaf alignment and tracking respectively. A quantitative evaluation framework is formulated to evaluate the performance of our algorithm with four metrics. Two models are learned to predict the alignment accuracy and detect tracking failure respectively in order to provide guidance for subsequent plant biology analysis. The limitation of our algorithm is also studied. Experimental results show the effectiveness, efficiency, and robustness of the proposed method.

Luminaire layout: Design and implementation

NASA Technical Reports Server (NTRS)

Both, A. J.

1994-01-01

The information contained in this report was presented during the discussion regarding guidelines for PAR uniformity in greenhouses. The data shows a lighting uniformity analysis in a research greenhouse for rose production at the Cornell University campus. The luminaire layout was designed using the computer program Lumen-Micro. After implementation of the design, accurate measurements were taken in the greenhouse and the uniformity analysis for both the design and implementation were compared. A study of several supplemental lighting installations resulted in the following recommendations: include only the actual growing area in the lighting uniformity analysis; for growing areas up to 20 square meters, take four measurements per square meter; for growing areas above 20 square meters, take one measurement per square meter; use one of the uniformity criteria and frequency graphs to compare lighting uniformity amongst designs; and design for uniformity criterion of a least 0.75 and the fraction within +/- 15% of the average PAR value should be close to one.

Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution.

PubMed

Brody, Thomas; Yavatkar, Amarendra S; Park, Dong Sun; Kuzin, Alexander; Ross, Jermaine; Odenwald, Ward F

2017-06-01

Flavivirus and Filovirus infections are serious epidemic threats to human populations. Multi-genome comparative analysis of these evolving pathogens affords a view of their essential, conserved sequence elements as well as progressive evolutionary changes. While phylogenetic analysis has yielded important insights, the growing number of available genomic sequences makes comparisons between hundreds of viral strains challenging. We report here a new approach for the comparative analysis of these hemorrhagic fever viruses that can superimpose an unlimited number of one-on-one alignments to identify important features within genomes of interest. We have adapted EvoPrinter alignment algorithms for the rapid comparative analysis of Flavivirus or Filovirus sequences including Zika and Ebola strains. The user can input a full genome or partial viral sequence and then view either individual comparisons or generate color-coded readouts that superimpose hundreds of one-on-one alignments to identify unique or shared identity SNPs that reveal ancestral relationships between strains. The user can also opt to select a database genome in order to access a library of pre-aligned genomes of either 1,094 Flaviviruses or 460 Filoviruses for rapid comparative analysis with all database entries or a select subset. Using EvoPrinter search and alignment programs, we show the following: 1) superimposing alignment data from many related strains identifies lineage identity SNPs, which enable the assessment of sublineage complexity within viral outbreaks; 2) whole-genome SNP profile screens uncover novel Dengue2 and Zika recombinant strains and their parental lineages; 3) differential SNP profiling identifies host cell A-to-I hyper-editing within Ebola and Marburg viruses, and 4) hundreds of superimposed one-on-one Ebola genome alignments highlight ultra-conserved regulatory sequences, invariant amino acid codons and evolutionarily variable protein-encoding domains within a single genome. EvoPrinter allows for the assessment of lineage complexity within Flavivirus or Filovirus outbreaks, identification of recombinant strains, highlights sequences that have undergone host cell A-to-I editing, and identifies unique input and database SNPs within highly conserved sequences. EvoPrinter's ability to superimpose alignment data from hundreds of strains onto a single genome has allowed us to identify unique Zika virus sublineages that are currently spreading in South, Central and North America, the Caribbean, and in China. This new set of integrated alignment programs should serve as a useful addition to existing tools for the comparative analysis of these viruses.

Effects on diameter and morphology of polycaprolactone nanofibers infused with various concentrations of selenium nanoparticles

NASA Astrophysics Data System (ADS)

Kamaruzaman, Nurul Asyikin; Yusoff, Abdull Rahim Mohd; Buang, Nor Aziah; Salleh, Nik Ghazali Nik

2017-12-01

Electrospinning is one of the techniques used in the fabrication of nanofibers. Polycaprolactone (PCL), is a biodegradable polymer which was commonly electrospun without the presence of nanoparticles as additives and/or filler in the applications such as tissue engineering, biosensors, filtration, wound dressings, drug delivery and enzyme immobilization. In this study, via FESEM analyses, the effects on the diameter and morphology of PCL nanofibers was investigated with respect to various concentration of selenium nanoparticles (SeNP). Increasing the concentration of SeNP from 0.2 to 1.0% (w/v) resulted in increased of fiber diameter as well as the density of the nanofiber networking. Consequently, the formation of beads have also increased with the increment of the concentration of SeNP. The images from FESEM micrographs showed the formation of "aligned fibers" with the average size of less than 550 nm. The optimized concentration of SeNP obtained was 0.4 % w/v for the formation of aligned fibers with a uniform diameter in size and the least formation of beads in the matrices. Aligned nanofibers are biocompatible and can be used in tissue engineering and wound dressing applications. Meanwhile, nanofibers with beads are suitable for filtration design in water and gaseous applications.

The doubling of stellar black hole nuclei

NASA Astrophysics Data System (ADS)

Kazandjian, Mher V.; Touma, J. R.

2013-04-01

It is strongly believed that Andromeda's double nucleus signals a disc of stars revolving around its central supermassive black hole on eccentric Keplerian orbits with nearly aligned apsides. A self-consistent stellar dynamical origin for such apparently long-lived alignment has so far been lacking, with indications that cluster self-gravity is capable of sustaining such lopsided configurations if and when stimulated by external perturbations. Here, we present results of N-body simulations which show unstable counter-rotating stellar clusters around supermassive black holes saturating into uniformly precessing lopsided nuclei. The double nucleus in our featured experiment decomposes naturally into a thick eccentric disc of apo-apse aligned stars which is embedded in a lighter triaxial cluster. The eccentric disc reproduces key features of Keplerian disc models of Andromeda's double nucleus; the triaxial cluster has a distinctive kinematic signature which is evident in Hubble Space Telescope observations of Andromeda's double nucleus, and has been difficult to reproduce with Keplerian discs alone. Our simulations demonstrate how the combination of an eccentric disc and a triaxial cluster arises naturally when a star cluster accreted over a preexisting and counter-rotating disc of stars drives disc and cluster into a mutually destabilizing dance. Such accretion events are inherent to standard galaxy formation scenarios. They are here shown to double stellar black hole nuclei as they feed them.

Alternating current electric fields of varying frequencies: effects on proliferation and differentiation of porcine neural progenitor cells.

PubMed

Lim, Ji-Hey; McCullen, Seth D; Piedrahita, Jorge A; Loboa, Elizabeth G; Olby, Natasha J

2013-10-01

Application of sinusoidal electric fields (EFs) has been observed to affect cellular processes, including alignment, proliferation, and differentiation. In the present study, we applied low-frequency alternating current (AC) EFs to porcine neural progenitor cells (pNPCs) and investigated the effects on cell patterning, proliferation, and differentiation. pNPCs were grown directly on interdigitated electrodes (IDEs) localizing the EFs to a region accessible visually for fluorescence-based assays. Cultures of pNPCs were exposed to EFs (1 V/cm) of 1 Hz, 10 Hz, and 50 Hz for 3, 7, and 14 days and compared to control cultures. Immunocytochemistry was performed to evaluate the expression of neural markers. pNPCs grew uniformly with no evidence of alignment to the EFs and no change in cell numbers when compared with controls. Nestin expression was shown in all groups at 3 and 7 days, but not at 14 days. NG2 expression was low in all groups. Co-expression of glial fibrillary acidic protein (GFAP) and TUJ1 was significantly higher in the cultures exposed to 10- and 50-Hz EFs than the controls. In summary, sinusoidal AC EFs via IDEs did not alter the alignment and proliferation of pNPCs, but higher frequency stimulation appeared to delay differentiation into mature astrocytes.

An Analysis of the Alignment of the Grade 12 Physical Sciences Examination and the Core Curriculum in South Africa

ERIC Educational Resources Information Center

Edwards, Nazeem

2010-01-01

I report on an analysis of the alignment between the South African Grade 12 Physical Sciences core curriculum content and the exemplar papers of 2008, and the final examination papers of 2008 and 2009. A two-dimensional table was used for both the curriculum and the examination in order to calculate the Porter alignment index, which indicates the…

Aligning Arrays of Lenses and Single-Mode Optical Fibers

NASA Technical Reports Server (NTRS)

Liu, Duncan

2004-01-01

A procedure now under development is intended to enable the precise alignment of sheet arrays of microscopic lenses with the end faces of a coherent bundle of as many as 1,000 single-mode optical fibers packed closely in a regular array (see Figure 1). In the original application that prompted this development, the precise assembly of lenses and optical fibers serves as a single-mode spatial filter for a visible-light nulling interferometer. The precision of alignment must be sufficient to limit any remaining wavefront error to a root-mean-square value of less than 1/10 of a wavelength of light. This wavefront-error limit translates to requirements to (1) ensure uniformity of both the lens and fiber arrays, (2) ensure that the lateral distance from the central axis of each lens and the corresponding optical fiber is no more than a fraction of a micron, (3) angularly align the lens-sheet planes and the fiber-bundle end faces to within a few arc seconds, and (4) axially align the lenses and the fiber-bundle end faces to within tens of microns of the focal distance. Figure 2 depicts the apparatus used in the alignment procedure. The beam of light from a Zygo (or equivalent) interferometer is first compressed by a ratio of 20:1 so that upon its return to the interferometer, the beam will be magnified enough to enable measurement of wavefront quality. The apparatus includes relay lenses that enable imaging of the arrays of microscopic lenses in a charge-coupled-device (CCD) camera that is part of the interferometer. One of the arrays of microscopic lenses is mounted on a 6-axis stage, in proximity to the front face of the bundle of optical fibers. The bundle is mounted on a separate stage. A mirror is attached to the back face of the bundle of optical fibers for retroreflection of light. When a microscopic lens and a fiber are aligned with each other, the affected portion of the light is reflected back by the mirror, recollimated by the microscopic lens, transmitted through the relay lenses and the beam compressor/expander, then split so that half goes to a detector and half to the interferometer. The output of the detector is used as a feedback control signal for the six-axis stage to effect alignment.

Uniformity testing: assessment of a centralized web-based uniformity analysis system.

PubMed

Klempa, Meaghan C

2011-06-01

Uniformity testing is performed daily to ensure adequate camera performance before clinical use. The aim of this study is to assess the reliability of Beth Israel Deaconess Medical Center's locally built, centralized, Web-based uniformity analysis system by examining the differences between manufacturer and Web-based National Electrical Manufacturers Association integral uniformity calculations measured in the useful field of view (FOV) and the central FOV. Manufacturer and Web-based integral uniformity calculations measured in the useful FOV and the central FOV were recorded over a 30-d period for 4 cameras from 3 different manufacturers. These data were then statistically analyzed. The differences between the uniformity calculations were computed, in addition to the means and the SDs of these differences for each head of each camera. There was a correlation between the manufacturer and Web-based integral uniformity calculations in the useful FOV and the central FOV over the 30-d period. The average differences between the manufacturer and Web-based useful FOV calculations ranged from -0.30 to 0.099, with SD ranging from 0.092 to 0.32. For the central FOV calculations, the average differences ranged from -0.163 to 0.055, with SD ranging from 0.074 to 0.24. Most of the uniformity calculations computed by this centralized Web-based uniformity analysis system are comparable to the manufacturers' calculations, suggesting that this system is reasonably reliable and effective. This finding is important because centralized Web-based uniformity analysis systems are advantageous in that they test camera performance in the same manner regardless of the manufacturer.

An analysis of cross-coupling of a multicomponent jet engine test stand using finite element modeling techniques

NASA Technical Reports Server (NTRS)

Schweikhard, W. G.; Singnoi, W. N.

1985-01-01

A two axis thrust measuring system was analyzed by using a finite a element computer program to determine the sensitivities of the thrust vectoring nozzle system to misalignment of the load cells and applied loads, and the stiffness of the structural members. Three models were evaluated: (1) the basic measuring element and its internal calibration load cells; (2) the basic measuring element and its external load calibration equipment; and (3) the basic measuring element, external calibration load frame and the altitude facility support structure. Alignment of calibration loads was the greatest source of error for multiaxis thrust measuring systems. Uniform increases or decreases in stiffness of the members, which might be caused by the selection of the materials, have little effect on the accuracy of the measurements. It is found that the POLO-FINITE program is a viable tool for designing and analyzing multiaxis thrust measurement systems. The response of the test stand to step inputs that might be encountered with thrust vectoring tests was determined. The dynamic analysis show a potential problem for measuring the dynamic response characteristics of thrust vectoring systems because of the inherently light damping of the test stand.

Effect of foot shape on the three-dimensional position of foot bones.

PubMed

Ledoux, William R; Rohr, Eric S; Ching, Randal P; Sangeorzan, Bruce J

2006-12-01

To eliminate some of the ambiguity in describing foot shape, we developed three-dimensional (3D), objective measures of foot type based on computerized tomography (CT) scans. Feet were classified via clinical examination as pes cavus (high arch), neutrally aligned (normal arch), asymptomatic pes planus (flat arch with no pain), or symptomatic pes planus (flat arch with pain). We enrolled 10 subjects of each foot type; if both feet were of the same foot type, then each foot was scanned (n=65 total). Partial weightbearing (20% body weight) CT scans were performed. We generated embedded coordinate systems for each foot bone by assuming uniform density and calculating the inertial matrix. Cardan angles were used to describe five bone-to-bone relationships, resulting in 15 angular measurements. Significant differences were found among foot types for 12 of the angles. The angles were also used to develop a classification tree analysis, which determined the correct foot type for 64 of the 65 feet. Our measure provides insight into how foot bone architecture differs between foot types. The classification tree analysis demonstrated that objective measures can be used to discriminate between feet with high, normal, and low arches. Copyright (c) 2006 Orthopaedic Research Society.

High efficiency virtual impactor

DOEpatents

Loo, Billy W.

1981-01-01

Environmental monitoring of atmospheric air is facilitated by a single stage virtual impactor (11) for separating an inlet flow (Q.sub.O) having particulate contaminants into a coarse particle flow (Q.sub.1) and a fine particle flow (Q.sub.2) to enable collection of such particles on different filters (19a, 19b) for separate analysis. An inlet particle acceleration nozzle (28) and coarse particle collection probe member (37) having a virtual impaction opening (41) are aligned along a single axis (13) and spaced apart to define a flow separation region (14) at which the fine particle flow (Q.sub.2) is drawn radially outward into a chamber (21) while the coarse particle flow (Q.sub.1) enters the virtual impaction opening (41). Symmetrical outlet means (47) for the chamber (21) provide flow symmetry at the separation region (14) to assure precise separation of particles about a cutpoint size and to minimize losses by wall impaction and gravitational settling. Impulse defocusing means (42) in the probe member (37) provides uniform coarse particle deposition on the filter (19a) to aid analysis. Particle losses of less than 1% for particles in the 0 to 20 micron range may be realized.

Transfer and alignment of random single-walled carbon nanotube films by contact printing.

PubMed

Liu, Huaping; Takagi, Daisuke; Chiashi, Shohei; Homma, Yoshikazu

2010-02-23

We present a simple method to transfer large-area random single-walled carbon nanotube (SWCNT) films grown on SiO(2) substrates onto another surface through a simple contact printing process. The transferred random SWCNT films can be assembled into highly ordered, dense regular arrays with high uniformity and reproducibility by sliding the growth substrate during the transfer process. The position of the transferred SWCNT film can be controlled by predefined patterns on the receiver substrates. The process is compatible with a variety of substrates, and even metal meshes for transmission electron microscopy (TEM) can be used as receiver substrates. Thus, suspended web-like SWCNT networks and aligned SWCNT arrays can be formed over the grids of TEM meshes, so that the structures of the transferred SWCNTs can be directly observed by TEM. This simple technique can be used to controllably transfer SWCNTs for property studies, for the fabrication of devices, or even as support films for TEM meshes.

MollDE: a homology modeling framework you can click with.

PubMed

Canutescu, Adrian A; Dunbrack, Roland L

2005-06-15

Molecular Integrated Development Environment (MolIDE) is an integrated application designed to provide homology modeling tools and protocols under a uniform, user-friendly graphical interface. Its main purpose is to combine the most frequent modeling steps in a semi-automatic, interactive way, guiding the user from the target protein sequence to the final three-dimensional protein structure. The typical basic homology modeling process is composed of building sequence profiles of the target sequence family, secondary structure prediction, sequence alignment with PDB structures, assisted alignment editing, side-chain prediction and loop building. All of these steps are available through a graphical user interface. MolIDE's user-friendly and streamlined interactive modeling protocol allows the user to focus on the important modeling questions, hiding from the user the raw data generation and conversion steps. MolIDE was designed from the ground up as an open-source, cross-platform, extensible framework. This allows developers to integrate additional third-party programs to MolIDE. http://dunbrack.fccc.edu/molide/molide.php rl_dunbrack@fccc.edu.

Oriented nanofibers embedded in a polymer matrix

NASA Technical Reports Server (NTRS)

Barrera, Enrique V. (Inventor); Lozano, Karen (Inventor); Rodriguez-Macias, Fernando J. (Inventor); Chibante, Luis Paulo Felipe (Inventor); Stewart, David Harris (Inventor)

2011-01-01

A method of forming a composite of embedded nanofibers in a polymer matrix is disclosed. The method includes incorporating nanofibers in a plastic matrix forming agglomerates, and uniformly distributing the nanofibers by exposing the agglomerates to hydrodynamic stresses. The hydrodynamic said stresses force the agglomerates to break apart. In combination or additionally elongational flow is used to achieve small diameters and alignment. A nanofiber reinforced polymer composite system is disclosed. The system includes a plurality of nanofibers that are embedded in polymer matrices in micron size fibers. A method for producing nanotube continuous fibers is disclosed. Nanofibers are fibrils with diameters of 100 nm, multiwall nanotubes, single wall nanotubes and their various functionalized and derivatized forms. The method includes mixing a nanofiber in a polymer; and inducing an orientation of the nanofibers that enables the nanofibers to be used to enhance mechanical, thermal and electrical properties. Orientation is induced by high shear mixing and elongational flow, singly or in combination. The polymer may be removed from said nanofibers, leaving micron size fibers of aligned nanofibers.

Ultrathin Optical Panel And A Method Of Making An Ultrathin Optical Panel.

DOEpatents

Biscardi, Cyrus; Brewster, Calvin; DeSanto, Leonard; Veligdan, James T.

2005-02-15

An ultrathin optical panel, and a method of producing an ultrathin optical panel, are disclosed, including stacking a plurality of glass sheets, which sheets may be coated with a transparent cladding substance or may be uncoated, fastening together the plurality of stacked coated glass sheets using an epoxy or ultraviolet adhesive, applying uniform pressure to the stack, curing the stack, sawing the stack to form an inlet face on a side of the stack and an outlet face on an opposed side of the stack, bonding a coupler to the inlet face of the stack, and fastening the stack, having the coupler bonded thereto, within a rectangular housing having an open front which is aligned with the outlet face, the rectangular housing having therein a light generator which is optically aligned with the coupler. The light generator is preferably placed parallel to and proximate with the inlet face, thereby allowing for a reduction in the depth of the housing.

Ultrathin Optical Panel And A Method Of Making An Ultrathin Optical Panel.

DOEpatents

Biscardi, Cyrus; Brewster, Calvin; DeSanto, Leonard; Veligdan, James T.

2005-05-17

An ultrathin optical panel, and a method of producing an ultrathin optical panel, are disclosed, including stacking a plurality of glass sheets, which sheets may be coated with a transparent cladding substance or may be uncoated, fastening together the plurality of stacked coated glass sheets using an epoxy or ultraviolet adhesive, applying uniform pressure to the stack, curing the stack, sawing the stack to form an inlet face on a side of the stack and an outlet face on an opposed side of the stack, bonding a coupler to the inlet face of the stack, and fastening the stack, having the coupler bonded thereto, within a rectangular housing having an open front which is aligned with the outlet face, the rectangular housing having therein a light generator which is optically aligned with the coupler. The light generator is preferably placed parallel to and proximate with the inlet face, thereby allowing for a reduction in the depth of the housing.

Ultrathin optical panel and a method of making an ultrathin optical panel

DOEpatents

Biscardi, Cyrus; Brewster, Calvin; DeSanto, Leonard; Veligdan, James T.

2003-02-11

An ultrathin optical panel, and a method of producing an ultrathin optical panel, are disclosed, including stacking a plurality of glass sheets, which sheets may be coated with a transparent cladding substance or may be uncoated, fastening together the plurality of stacked coated glass sheets using an epoxy or ultraviolet adhesive, applying uniform pressure to the stack, curing the stack, sawing the stack to form an inlet face on a side of the stack and an outlet face on an opposed side of the stack, bonding a coupler to the inlet face of the stack, and fastening the stack, having the coupler bonded thereto, within a rectangular housing having an open front which is aligned with the outlet face, the rectangular housing having therein a light generator which is optically aligned with the coupler. The light generator is preferably placed parallel to and proximate with the inlet face, thereby allowing for a reduction in the depth of the housing.

Ultrathin optical panel and a method of making an ultrathin optical panel

DOEpatents

Biscardi, Cyrus; Brewster, Calvin; DeSanto, Leonard; Veligdan, James T.

2001-10-09

An ultrathin optical panel, and a method of producing an ultrathin optical panel, are disclosed, including stacking a plurality of glass sheets, which sheets may be coated with a transparent cladding substance or may be uncoated, fastening together the plurality of stacked coated glass sheets using an epoxy or ultraviolet adhesive, applying uniform pressure to the stack, curing the stack, sawing the stack to form an inlet face on a side of the stack and an outlet face on an opposed side of the stack, bonding a coupler to the inlet face of the stack, and fastening the stack, having the coupler bonded thereto, within a rectangular housing having an open front which is aligned with the outlet face, the rectangular housing having therein a light generator which is optically aligned with the coupler. The light generator is preferably placed parallel to and proximate with the inlet face, thereby allowing for a reduction in the depth of the housing.

Ultrathin optical panel and a method of making an ultrathin optical panel

DOEpatents

Biscardi, Cyrus; Brewster, Calvin; DeSanto, Leonard; Veligdan, James T.

2002-01-01

An ultrathin optical panel, and a method of producing an ultrathin optical panel, are disclosed, including stacking a plurality of glass sheets, which sheets may be coated With a transparent cladding substance or may be uncoated, fastening together the plurality of stacked coated glass sheets using an epoxy or ultraviolet adhesive, applying uniform pressure to the stack, curing the stack, sawing the stack to form an inlet face on a side of the stack and an outlet face on an opposed side of the stack, bonding a coupler to the inlet face of the stack, and fastening the stack, having the coupler bonded thereto, within a rectangular housing having an open front which is aligned with the outlet face, the rectangular housing having therein a light generator which is optically aligned with the coupler. The light generator is preferably placed parallel to and proximate with the inlet face, thereby allowing for a reduction in the depth of the housing.

System for maintaining the alignment of mandrels in filament winding operations

DOEpatents

Robinson, S.C.; Dodge, W.G.; Pollard, R.E.

1983-10-12

The present invention is directed to a system for sensing and correcting the alignment of a mandrel being wound with filamentary material with respect to the filamentary material winding mechanism. A positioned reference pin attached to the mandrel is positioned in a beam of collimated light emanating from a laser so as to bisect the light beam and create a shadow therebetween. A pair of photocells are positioned to receive the bisected light beam with the shadow uniformly located between the photocells when the pin is in a selected position. The mandrel is supported in the selected position for the winding of a filamentary material by a position adjustable roller mechanism which is coupled by a screw drive to a reversible motor. Changes in the pin position such as caused by winding growth are sensed by the photocells to provide the displacement of the roller mechanism in the direction necessary to return the mandrel to the selected position.

System for maintaining the alignment of mandrels in filament winding operations

DOEpatents

Robinson, Samuel C.; Dodge, William G.; Pollard, Roy E.

1984-01-01

The present invention is directed to a system for sensing and correcting the alignment of a mandrel being wound with filamentary material with respect to the filamentary material winding mechanism. A positioned reference pin attached to the mandrel is positioned in a beam of collimated light emanating from a laser so as to bisect the light beam and create a shadow therebetween. A pair of photocells are positioned to receive the bisected light beam with the shadow uniformly located between the photocells when the pin is in a selected position. The mandrel is supported in the selected position for the winding of a filamentary material by a position adjustable roller mechanism which is coupled by a screw drive to a reversible motor. Changes in the pin position such as caused by winding growth are sensed by the photocells to provide the displacement of the roller mechanism in the direction necessary to return the mandrel to the selected position.

Alignment of crystal orientations of the multi-domain photonic crystals in Parides sesostris wing scales

PubMed Central

Yoshioka, S.; Fujita, H.; Kinoshita, S.; Matsuhana, B.

2014-01-01

It is known that the wing scales of the emerald-patched cattleheart butterfly, Parides sesostris, contain gyroid-type photonic crystals, which produce a green structural colour. However, the photonic crystal is not a single crystal that spreads over the entire scale, but it is separated into many small domains with different crystal orientations. As a photonic crystal generally has band gaps at different frequencies depending on the direction of light propagation, it seems mysterious that the scale is observed to be uniformly green under an optical microscope despite the multi-domain structure. In this study, we have carefully investigated the structure of the wing scale and discovered that the crystal orientations of different domains are not perfectly random, but there is a preferred crystal orientation that is aligned along the surface normal of the scale. This finding suggests that there is an additional factor during the developmental process of the microstructure that regulates the crystal orientation. PMID:24352678

Rotating states of self-propelling particles in two dimensions.

PubMed

Chen, Hsuan-Yi; Leung, Kwan-Tai

2006-05-01

We present particle-based simulations and a continuum theory for steady rotating flocks formed by self-propelling particles (SPPs) in two-dimensional space. Our models include realistic but simple rules for the self-propelling, drag, and interparticle interactions. Among other coherent structures, in particle-based simulations we find steady rotating flocks when the velocity of the particles lacks long-range alignment. Physical characteristics of the rotating flock are measured and discussed. We construct a phenomenological continuum model and seek steady-state solutions for a rotating flock. We show that the velocity and density profiles become simple in two limits. In the limit of weak alignment, we find that all particles move with the same speed and the density of particles vanishes near the center of the flock due to the divergence of centripetal force. In the limit of strong body force, the density of particles within the flock is uniform and the velocity of the particles close to the center of the flock becomes small.

Large-area formation of self-aligned crystalline domains of organic semiconductors on transistor channels using CONNECT

PubMed Central

Park, Steve; Giri, Gaurav; Shaw, Leo; Pitner, Gregory; Ha, Jewook; Koo, Ja Hoon; Gu, Xiaodan; Park, Joonsuk; Lee, Tae Hoon; Nam, Ji Hyun; Hong, Yongtaek; Bao, Zhenan

2015-01-01

The electronic properties of solution-processable small-molecule organic semiconductors (OSCs) have rapidly improved in recent years, rendering them highly promising for various low-cost large-area electronic applications. However, practical applications of organic electronics require patterned and precisely registered OSC films within the transistor channel region with uniform electrical properties over a large area, a task that remains a significant challenge. Here, we present a technique termed “controlled OSC nucleation and extension for circuits” (CONNECT), which uses differential surface energy and solution shearing to simultaneously generate patterned and precisely registered OSC thin films within the channel region and with aligned crystalline domains, resulting in low device-to-device variability. We have fabricated transistor density as high as 840 dpi, with a yield of 99%. We have successfully built various logic gates and a 2-bit half-adder circuit, demonstrating the practical applicability of our technique for large-scale circuit fabrication. PMID:25902502

B-MIC: An Ultrafast Three-Level Parallel Sequence Aligner Using MIC.

PubMed

Cui, Yingbo; Liao, Xiangke; Zhu, Xiaoqian; Wang, Bingqiang; Peng, Shaoliang

2016-03-01

Sequence alignment is the central process for sequence analysis, where mapping raw sequencing data to reference genome. The large amount of data generated by NGS is far beyond the process capabilities of existing alignment tools. Consequently, sequence alignment becomes the bottleneck of sequence analysis. Intensive computing power is required to address this challenge. Intel recently announced the MIC coprocessor, which can provide massive computing power. The Tianhe-2 is the world's fastest supercomputer now equipped with three MIC coprocessors each compute node. A key feature of sequence alignment is that different reads are independent. Considering this property, we proposed a MIC-oriented three-level parallelization strategy to speed up BWA, a widely used sequence alignment tool, and developed our ultrafast parallel sequence aligner: B-MIC. B-MIC contains three levels of parallelization: firstly, parallelization of data IO and reads alignment by a three-stage parallel pipeline; secondly, parallelization enabled by MIC coprocessor technology; thirdly, inter-node parallelization implemented by MPI. In this paper, we demonstrate that B-MIC outperforms BWA by a combination of those techniques using Inspur NF5280M server and the Tianhe-2 supercomputer. To the best of our knowledge, B-MIC is the first sequence alignment tool to run on Intel MIC and it can achieve more than fivefold speedup over the original BWA while maintaining the alignment precision.

The 10 Conditions That Increased Vermont's Readiness to Implement Statewide Health System Transformation.

PubMed

Grembowski, David; Marcus-Smith, Miriam

2018-06-01

Following an arduous, 6-year policy-making process, Vermont is the first state implementing a unified, statewide all-payer integrated delivery system with value-based payment, along with aligned medical and social service reforms, for almost all residents and providers in a state. Commercial, Medicare, and Medicaid value-based payment for most Vermonters will be administered through a new statewide accountable care organization in 2018-2022. The purpose of this article is to describe the 10 conditions that increased Vermont's readiness to implement statewide system transformation. The authors reviewed documents, conducted internet searches of public information, interviewed key informants annually in 2014-2016, cross-validated factual and narrative interpretation, and performed content analyses to derive conditions that increased readiness and their implications for policy and practice. Four social conditions (leadership champions; a common vision; collaborative culture; social capital and collective efficacy) and 6 support conditions (money; statewide data; legal infrastructure; federal policy promoting payment reform; delivery system transformation aligned with payment reform; personnel skilled in system reform) increased Vermont's readiness for system transformation. Vermont's experience indicates that increasing statewide readiness for reform is slow, incremental, and exhausting to overcome the sheer inertia of large fee-based systems. The new payments may work because statewide, uniform population-based payment will affect the health care of almost all Vermonters, creating statewide, uniform provider incentives to reduce volume and making the current fee-based system less viable. The conditions for readiness and statewide system transformation may be more likely in states with regulated markets, like Vermont, than in states with highly competitive markets.

Optical properties of orthodontic aligners--spectrophotometry analysis of three types before and after aging.

PubMed

Lombardo, Luca; Arreghini, Angela; Maccarrone, Roberta; Bianchi, Anna; Scalia, Santo; Siciliani, Giuseppe

2015-01-01

The aim was to assess and compare absorbance and transmittance values of three types of clear orthodontic aligners before and after two cycles of in vitro aging. Nine samples of orthodontic aligners from three different manufacturers (Invisalign, Align Technology, Santa Clara, CA, USA; All-In, Micerium, Avegno, GE, Italy; F22 Aligner, Sweden & Martina, Due Carrare, PD, Italy) were selected, and each sample was subjected to spectrophotometry analysis of both its transmittance and absorbance a total of 27 times. Samples were subsequently aged in vitro at a constant temperature in artificial saliva supplemented with food colouring for two cycles of 14 days each. The spectrophotometry protocol was then repeated, and the resulting data were analysed and compared by means of ANOVA (p < 0.05). All types of aligners tested yielded lower transmittance and higher absorbance values after aging, but the difference was not significant in any case. That being said, the F22 aligners were found to be most transparent, both before and after aging, followed by Invisalign and All-In, and these differences were statistically significant. Commercial aligners possess significantly different optical, and therefore aesthetic, properties, both as delivered and following aging.

Students Wearing Police Uniforms Exhibit Biased Attention toward Individuals Wearing Hoodies

PubMed Central

Civile, Ciro; Obhi, Sukhvinder S.

2017-01-01

Police provide an essential public service and they often operate in difficult circumstances, requiring high-speed cognition. Recent incidents involving apparent profiling and aggressive behavior have led to accusations that the police are sometimes biased. Given that previous research has shown a link between clothing and cognition, we investigated the question of whether the police uniform itself might induce a bias in social attention. To address this question, and using a Canadian university student sample, we assessed whether wearing a police uniform biases attention toward black faces compared to white faces, and low-status individuals compared to high-status individuals. In Experiment 1 (n = 28), participants wore either a police-style uniform or mechanic overalls, and performed a shape categorization task in the presence of a distractor that could be either: a black face, a white face, a person wearing a hoodie (whom we propose will be associated with low SES), or a person wearing a suit (whom we propose will be associated with high SES). Participants wearing the police-style uniform exhibited biased attention, indexed by slower reaction times (RTs), in the presence of low-SES images. In Experiment 2 (n = 28), we confirmed this bias using a modified Dot-Probe task – an alternate measure of attentional bias in which we observed faster RTs to a dot probe that was spatially aligned with a low SES image. Experiment 3 (n = 56) demonstrated that attentional bias toward low-SES targets appears only when participants wear the police-style uniform, and not when they are simply exposed to it – by having it placed on the desk in front of them. Our results demonstrate that wearing a police-style uniform biases attention toward low-SES targets. Thus, wearing a police-style uniform may induce a kind of “status-profiling” in which individuals from low-status groups become salient and capture attention. We note that our results are limited to university students and that it will be important to extend them to members of the community and law-enforcement officers. We discuss how uniforms might exert their effects on cognition by virtue of the power and cultural associations they evoke in the wearer. PMID:28220086

The influence of atomic alignment on absorption and emission spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Heshou; Yan, Huirong; Richter, Philipp

2018-06-01

Spectroscopic observations play essential roles in astrophysics. They are crucial for determining physical parameters in the universe, providing information about the chemistry of various astronomical environments. The proper execution of the spectroscopic analysis requires accounting for all the physical effects that are compatible to the signal-to-noise ratio. We find in this paper the influence on spectroscopy from the atomic/ground state alignment owing to anisotropic radiation and modulated by interstellar magnetic field, has significant impact on the study of interstellar gas. In different observational scenarios, we comprehensively demonstrate how atomic alignment influences the spectral analysis and provide the expressions for correcting the effect. The variations are even more pronounced for multiplets and line ratios. We show the variation of the deduced physical parameters caused by the atomic alignment effect, including alpha-to-iron ratio ([X/Fe]) and ionisation fraction. Synthetic observations are performed to illustrate the visibility of such effect with current facilities. A study of PDRs in ρ Ophiuchi cloud is presented to demonstrate how to account for atomic alignment in practice. Our work has shown that due to its potential impact, atomic alignment has to be included in an accurate spectroscopic analysis of the interstellar gas with current observational capability.

Electrospinning fundamentals: optimizing solution and apparatus parameters.

PubMed

Leach, Michelle K; Feng, Zhang-Qi; Tuck, Samuel J; Corey, Joseph M

2011-01-21

Electrospun nanofiber scaffolds have been shown to accelerate the maturation, improve the growth, and direct the migration of cells in vitro. Electrospinning is a process in which a charged polymer jet is collected on a grounded collector; a rapidly rotating collector results in aligned nanofibers while stationary collectors result in randomly oriented fiber mats. The polymer jet is formed when an applied electrostatic charge overcomes the surface tension of the solution. There is a minimum concentration for a given polymer, termed the critical entanglement concentration, below which a stable jet cannot be achieved and no nanofibers will form - although nanoparticles may be achieved (electrospray). A stable jet has two domains, a streaming segment and a whipping segment. While the whipping jet is usually invisible to the naked eye, the streaming segment is often visible under appropriate lighting conditions. Observing the length, thickness, consistency and movement of the stream is useful to predict the alignment and morphology of the nanofibers being formed. A short, non-uniform, inconsistent, and/or oscillating stream is indicative of a variety of problems, including poor fiber alignment, beading, splattering, and curlicue or wavy patterns. The stream can be optimized by adjusting the composition of the solution and the configuration of the electrospinning apparatus, thus optimizing the alignment and morphology of the fibers being produced. In this protocol, we present a procedure for setting up a basic electrospinning apparatus, empirically approximating the critical entanglement concentration of a polymer solution and optimizing the electrospinning process. In addition, we discuss some common problems and troubleshooting techniques.

Dust Polarization toward Embedded Protostars in Ophiuchus with ALMA. I. VLA 1623

NASA Astrophysics Data System (ADS)

Sadavoy, Sarah I.; Myers, Philip C.; Stephens, Ian W.; Tobin, John; Commerçon, Benoît; Henning, Thomas; Looney, Leslie; Kwon, Woojin; Segura-Cox, Dominique; Harris, Robert

2018-06-01

We present high-resolution (∼30 au) ALMA Band 6 dust polarization observations of VLA 1623. The VLA 1623 data resolve compact ∼40 au inner disks around the two protobinary sources, VLA 1623-A and VLA 1623-B, and also an extended ∼180 au ring of dust around VLA 1623-A. This dust ring was previously identified as a large disk in lower-resolution observations. We detect highly structured dust polarization toward the inner disks and the extended ring with typical polarization fractions ≈1.7% and ≈2.4%, respectively. The two components also show distinct polarization morphologies. The inner disks have uniform polarization angles aligned with their minor axes. This morphology is consistent with expectations from dust scattering. By contrast, the extended dust ring has an azimuthal polarization morphology not previously seen in lower-resolution observations. We find that our observations are well-fit by a static, oblate spheroid model with a flux-frozen, poloidal magnetic field. We propose that the polarization traces magnetic grain alignment likely from flux freezing on large scales and magnetic diffusion on small scales. Alternatively, the azimuthal polarization may be attributed to grain alignment by the anisotropic radiation field. If the grains are radiatively aligned, then our observations indicate that large (∼100 μm) dust grains grow quickly at large angular extents. Finally, we identify significant proper motion of VLA 1623 using our observations and those in the literature. This result indicates that the proper motion of nearby systems must be corrected for when combining ALMA data from different epochs.

A Comprehensive Two-Dimensional Retention Time Alignment Algorithm To Enhance Chemometric Analysis of Comprehensive Two-Dimensional Separation Data

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

Pierce, Karisa M.; Wood, Lianna F.; Wright, Bob W.

2005-12-01

A comprehensive two-dimensional (2D) retention time alignment algorithm was developed using a novel indexing scheme. The algorithm is termed comprehensive because it functions to correct the entire chromatogram in both dimensions and it preserves the separation information in both dimensions. Although the algorithm is demonstrated by correcting comprehensive two-dimensional gas chromatography (GC x GC) data, the algorithm is designed to correct shifting in all forms of 2D separations, such as LC x LC, LC x CE, CE x CE, and LC x GC. This 2D alignment algorithm was applied to three different data sets composed of replicate GC x GCmore » separations of (1) three 22-component control mixtures, (2) three gasoline samples, and (3) three diesel samples. The three data sets were collected using slightly different temperature or pressure programs to engender significant retention time shifting in the raw data and then demonstrate subsequent corrections of that shifting upon comprehensive 2D alignment of the data sets. Thirty 12-min GC x GC separations from three 22-component control mixtures were used to evaluate the 2D alignment performance (10 runs/mixture). The average standard deviation of the first column retention time improved 5-fold from 0.020 min (before alignment) to 0.004 min (after alignment). Concurrently, the average standard deviation of second column retention time improved 4-fold from 3.5 ms (before alignment) to 0.8 ms (after alignment). Alignment of the 30 control mixture chromatograms took 20 min. The quantitative integrity of the GC x GC data following 2D alignment was also investigated. The mean integrated signal was determined for all components in the three 22-component mixtures for all 30 replicates. The average percent difference in the integrated signal for each component before and after alignment was 2.6%. Singular value decomposition (SVD) was applied to the 22-component control mixture data before and after alignment to show the restoration of trilinearity to the data, since trilinearity benefits chemometric analysis. By applying comprehensive 2D retention time alignment to all three data sets (control mixtures, gasoline samples, and diesel samples), classification by principal component analysis (PCA) substantially improved, resulting in 100% accurate scores clustering.« less

Improving AIRS Radiance Spectra in High Contrast Scenes Using MODIS

NASA Technical Reports Server (NTRS)

Pagano, Thomas S.; Aumann, Hartmut H.; Manning, Evan M.; Elliott, Denis A.; Broberg, Steven E.

2015-01-01

The Atmospheric Infrared Sounder (AIRS) on the EOS Aqua Spacecraft was launched on May 4, 2002. AIRS acquires hyperspectral infrared radiances in 2378 channels ranging in wavelength from 3.7-15.4 microns with spectral resolution of better than 1200, and spatial resolution of 13.5 km with global daily coverage. The AIRS is designed to measure temperature and water vapor profiles for improvement in weather forecast accuracy and improved understanding of climate processes. As with most instruments, the AIRS Point Spread Functions (PSFs) are not the same for all detectors. When viewing a non-uniform scene, this causes a significant radiometric error in some channels that is scene dependent and cannot be removed without knowledge of the underlying scene. The magnitude of the error depends on the combination of non-uniformity of the AIRS spatial response for a given channel and the non-uniformity of the scene, but is typically only noticeable in about 1% of the scenes and about 10% of the channels. The current solution is to avoid those channels when performing geophysical retrievals. In this effort we use data from the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument to provide information on the scene uniformity that is used to correct the AIRS data. For the vast majority of channels and footprints the technique works extremely well when compared to a Principal Component (PC) reconstruction of the AIRS channels. In some cases where the scene has high inhomogeneity in an irregular pattern, and in some channels, the method can actually degrade the spectrum. Most of the degraded channels appear to be slightly affected by random noise introduced in the process, but those with larger degradation may be affected by alignment errors in the AIRS relative to MODIS or uncertainties in the PSF. Despite these errors, the methodology shows the ability to correct AIRS radiances in non-uniform scenes under some of the worst case conditions and improves the ability to match AIRS and MODIS radiances in non-uniform scenes.

Simulation of Turbulent Flow Inside and Above Wind Farms: Model Validation and Layout Effects

NASA Astrophysics Data System (ADS)

Wu, Yu-Ting; Porté-Agel, Fernando

2013-02-01

A recently-developed large-eddy simulation framework is validated and used to investigate turbulent flow within and above wind farms under neutral conditions. Two different layouts are considered, consisting of thirty wind turbines occupying the same total area and arranged in aligned and staggered configurations, respectively. The subgrid-scale (SGS) turbulent stress is parametrized using a tuning-free Lagrangian scale-dependent dynamic SGS model. The turbine-induced forces are modelled using two types of actuator-disk models: (a) the `standard' actuator-disk model (ADM-NR), which calculates only the thrust force based on one-dimensional momentum theory and distributes it uniformly over the rotor area; and (b) the actuator-disk model with rotation (ADM-R), which uses blade-element momentum theory to calculate the lift and drag forces (that produce both thrust and rotation), and distributes them over the rotor disk based on the local blade and flow characteristics. Validation is performed by comparing simulation results with turbulence measurements collected with hot-wire anemometry inside and above an aligned model wind farm placed in a boundary-layer wind tunnel. In general, the ADM-R model yields improved predictions compared with the ADM-NR in the wakes of all the wind turbines, where including turbine-induced flow rotation and accounting for the non-uniformity of the turbine-induced forces in the ADM-R appear to be important. Another advantage of the ADM-R model is that, unlike the ADM-NR, it does not require a priori specification of the thrust coefficient (which varies within a wind farm). Finally, comparison of simulations of flow through both aligned and staggered wind farms shows important effects of farm layout on the flow structure and wind-turbine performance. For the limited-size wind farms considered in this study, the lateral interaction between cumulated wakes is stronger in the staggered case, which results in a farm wake that is more homogeneous in the spanwise direction, thus resembling more an internal boundary layer. Inside the staggered farm, the relatively longer separation between consecutive downwind turbines allows the wakes to recover more, exposing the turbines to higher local wind speeds (leading to higher turbine efficiency) and lower turbulence intensity levels (leading to lower fatigue loads), compared with the aligned farm. Above the wind farms, the area-averaged velocity profile is found to be logarithmic, with an effective wind-farm aerodynamic roughness that is larger for the staggered case.

Onorbit IMU alignment error budget

NASA Technical Reports Server (NTRS)

Corson, R. W.

1980-01-01

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

Selective and directional actuation of elastomer films using chained magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Mishra, Sumeet R.; Dickey, Michael D.; Velev, Orlin D.; Tracy, Joseph B.

2016-01-01

We report selective and directional actuation of elastomer films utilizing magnetic anisotropy introduced by chains of Fe3O4 magnetic nanoparticles (MNPs). Under uniform magnetic fields or field gradients, dipolar interactions between the MNPs favor magnetization along the chain direction and cause selective lifting. This mechanism is described using a simple model.We report selective and directional actuation of elastomer films utilizing magnetic anisotropy introduced by chains of Fe3O4 magnetic nanoparticles (MNPs). Under uniform magnetic fields or field gradients, dipolar interactions between the MNPs favor magnetization along the chain direction and cause selective lifting. This mechanism is described using a simple model. Electronic supplementary information (ESI) available: Two videos for actuation while rotating the sample, experimental details of nanoparticle synthesis, polymer composite preparation, and alignment and bending studies, details of the theoretical model of actuation, and supplemental figures for understanding the behavior of rotating samples and results from modelling. See DOI: 10.1039/c5nr07410j

Proposal for generating synthetic magnetic fields in hexagonal optical lattices

NASA Astrophysics Data System (ADS)

Tian, Binbin; Endres, Manuel; Pekker, David

2015-05-01

We propose a new approach to generating synthetic magnetic fields in ultra cold atom systems that does not rely on either Raman transitions nor periodic drive. Instead, we consider a hexagonal optical lattice produced by the intersection of three laser beams at 120 degree angles, where the intensity of one or more of the beams is spatially non-uniform. The resulting optical lattice remains hexagonal, but has spatially varying hopping matrix elements. For atoms near the Dirac points, these spatial variations appear as a gauge field, similar to the fictitious gauge field that is induced for for electrons in strained graphene. We suggest that a robust way to generate a gauge field that corresponds to a uniform flux is to aligning three gaussian beams to intersect in an equilateral triangle. Using realistic experimental parameters, we show how the proposed setup can be used to observe cyclotron motion of an atom cloud - the conventional Hall effect and distinct Landau levels - the integer quantum Hall effect.

Comminution process to produce precision wood particles of uniform size and shape with disrupted grain structure from wood chips

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

Dooley, James H; Lanning, David N

A process of comminution of wood chips (C) having a grain direction to produce a mixture of wood particles (P), wherein the wood chips are characterized by an average length dimension (L.sub.C) as measured substantially parallel to the grain, an average width dimension (W.sub.C) as measured normal to L.sub.C and aligned cross grain, and an average height dimension (H.sub.C) as measured normal to W.sub.C and L.sub.C, and wherein the comminution process comprises the step of feeding the wood chips in a direction of travel substantially randomly to the grain direction through a counter rotating pair of intermeshing arrays of cuttingmore » discs (D) arrayed axially perpendicular to the direction of wood chip travel, wherein the cutting discs have a uniform thickness (T.sub.D), and wherein at least one of L.sub.C, W.sub.C, and H.sub.C is greater than T.sub.D.« less

Tracking Simulation of Third-Integer Resonant Extraction for Fermilab's Mu2e Experiment

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

Park, Chong Shik; Amundson, James; Michelotti, Leo

2015-02-13

The Mu2e experiment at Fermilab requires acceleration and transport of intense proton beams in order to deliver stable, uniform particle spills to the production target. To meet the experimental requirement, particles will be extracted slowly from the Delivery Ring to the external beamline. Using Synergia2, we have performed multi-particle tracking simulations of third-integer resonant extraction in the Delivery Ring, including space charge effects, physical beamline elements, and apertures. A piecewise linear ramp profile of tune quadrupoles was used to maintain a constant averaged spill rate throughout extraction. To study and minimize beam losses, we implemented and introduced a number ofmore » features, beamline element apertures, and septum plane alignments. Additionally, the RF Knockout (RFKO) technique, which excites particles transversely, is employed for spill regulation. Combined with a feedback system, it assists in fine-tuning spill uniformity. Simulation studies were carried out to optimize the RFKO feedback scheme, which will be helpful in designing the final spill regulation system.« less

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

DOEpatents

Zemla, Adam T [Brentwood, CA

2011-09-20

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

SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform.

PubMed

Lin, Jie; Wei, Jing; Adjeroh, Donald; Jiang, Bing-Hua; Jiang, Yue

2018-05-02

Alignment-free sequence similarity analysis methods often lead to significant savings in computational time over alignment-based counterparts. A new alignment-free sequence similarity analysis method, called SSAW is proposed. SSAW stands for Sequence Similarity Analysis using the Stationary Discrete Wavelet Transform (SDWT). It extracts k-mers from a sequence, then maps each k-mer to a complex number field. Then, the series of complex numbers formed are transformed into feature vectors using the stationary discrete wavelet transform. After these steps, the original sequence is turned into a feature vector with numeric values, which can then be used for clustering and/or classification. Using two different types of applications, namely, clustering and classification, we compared SSAW against the the-state-of-the-art alignment free sequence analysis methods. SSAW demonstrates competitive or superior performance in terms of standard indicators, such as accuracy, F-score, precision, and recall. The running time was significantly better in most cases. These make SSAW a suitable method for sequence analysis, especially, given the rapidly increasing volumes of sequence data required by most modern applications.

Alignment and Initial Operation of an Advanced Solar Simulator

NASA Technical Reports Server (NTRS)

Jaworske, Donald A.; Jefferies, Kent S.; Mason, Lee S.

1996-01-01

A solar simulator utilizing nine 30-kW xenon arc lamps was built to provide radiant power for testing a solar dynamic space power system in a thermal vacuum environment. The advanced solar simulator achieved the following values specific to the solar dynamic system: (1) a subtense angle of 1 deg; (2) the ability to vary solar simulator intensity up to 1.7 kW/sq m; (3) a beam diameter of 4.8 m; and (4) uniformity of illumination on the order of +/-10%. The flexibility of the solar simulator design allows for other potential uses of the facility.

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2004-08-24

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

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2007-01-02

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

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2006-03-21

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

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2002-01-01

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

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2000-01-01

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

Pitch-based carbon foam heat sink with phase change material

DOEpatents

Klett, James W.; Burchell, Timothy D.

2007-01-23

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

Fluid Physics

NASA Image and Video Library

2003-05-10

These images, from David Weitz’s liquid crystal research, show ordered uniform sized droplets (upper left) before they are dried from their solution. After the droplets are dried (upper right), they are viewed with crossed polarizers that show the deformation caused by drying, a process that orients the bipolar structure of the liquid crystal within the droplets. When an electric field is applied to the dried droplets (lower left), and then increased (lower right), the liquid crystal within the droplets switches its alignment, thereby reducing the amount of light that can be scattered by the droplets when a beam is shone through them.

Polar POLICRYPS diffractive structures generate cylindrical vector beams

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

Alj, Domenico; Caputo, Roberto, E-mail: roberto.caputo@fis.unical.it; Umeton, Cesare

2015-11-16

Local shaping of the polarization state of a light beam is appealing for a number of applications. This can be achieved by employing devices containing birefringent materials. In this article, we present one such enables converting a uniformly circularly polarized beam into a cylindrical vector beam (CVB). This device has been fabricated by exploiting the POLICRYPS (POlymer-LIquid CRYstals-Polymer-Slices) photocuring technique. It is a liquid-crystal-based optical diffraction grating featuring polar symmetry of the director alignment. We have characterized the resulting CVB profile and polarization for the cases of left and right circularly polarized incoming beams.

Controlled growth of vertically aligned carbon nanotubes on metal substrates

NASA Astrophysics Data System (ADS)

Gao, Zhaoli

Carbon nanotube (CNT) is a fascinating material with extraordinary electrical thermal and mechanical properties. Growing vertically aligned CNT (VACNT) arrays on metal substrates is an important step in bringing CNT into practical applications such as thermal interface materials (TIMs) and microelectrodes. However, the growth process is challenging due to the difficulties in preventing catalyst diffusion and controlling catalyst dewetting on metal substrates with physical surface heterogeneity. In this work, the catalyst diffusion mechanism and catalyst dewetting theory were studied for the controlled growth of VACNTs on metal substrates. The diffusion time of the catalyst, the diffusion coefficients for the catalyst in the substrate materials and the number density of catalyst nanoparticles after dewetting are identified as the key parameters, based on which three strategies are developed. Firstly, a fast-heating catalyst pretreatment strategy was used, aiming at preserving the amount of catalyst prior to CNT growth by reducing the catalyst diffusion time. The catalyst lifetime is extended from half an hour to one hour on a patterned Al thin film and a VACNT height of 106 mum, about twenty fold of that reported in the literature, was attained. Secondly, a diffusion barrier layer strategy is employed for a reduction of catalyst diffusion into the substrate materials. Enhancement of VACNT growth on Cu substrates was achieved by adopting a conformal Al2O 3 diffusion barrier layer fabricated by a specially designed atomic layer deposition (ALD) system. Lastly, a novel catalyst glancing angle deposition (GLAD) strategy is performed to manipulate the morphology of a relatively thick catalyst on metal substrates with physical surface heterogeneity, aiming to obtain uniform and dense catalyst nanoparticles after dewetting in the pretreatment process for enhanced VACNT growth. We are able to control the VACNT growth conditions on metal substrates in terms of their distribution, heights and alignments. Catalyst loss is controlled by the catalyst diffusion time and catalyst diffusion coefficients. A shorter catalyst diffusion time and smaller diffusion coefficient enhance VACNT growth on metals due to reduced catalyst loss during the pretreatment process. The dewetting behaviors of the thin film catalysts are influenced by the physical surface heterogeneity of the substrates which leads to non-uniform growth of VACNTs. The GLAD process facilitates the deposition of a relatively thick catalyst layer for the creation of dense and uniform catalyst nanoparticles. Applications of VACNT-metal structures in TIMs and microelectrodes are demonstrated. The VACNT-TIMs fabricated on Al alloy substrates have a typical thermal contact resistivity of 17.1 mm2˙K/W and their effective application in high-brightness LED thermal management was demonstrated. Electrochemical characterization was carried out on VACNT microelectrodes for the development of high resolution retinal prostheses and a satisfactory electrochemical property was again demonstrated.

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.

Alignment control study for the solar optical telescope

NASA Technical Reports Server (NTRS)

1976-01-01

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

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.

A simplified implementation of edge detection in MATLAB is faster and more sensitive than fast fourier transform for actin fiber alignment quantification.

PubMed

Kemeny, Steven Frank; Clyne, Alisa Morss

2011-04-01

Fiber alignment plays a critical role in the structure and function of cells and tissues. While fiber alignment quantification is important to experimental analysis and several different methods for quantifying fiber alignment exist, many studies focus on qualitative rather than quantitative analysis perhaps due to the complexity of current fiber alignment methods. Speed and sensitivity were compared in edge detection and fast Fourier transform (FFT) for measuring actin fiber alignment in cells exposed to shear stress. While edge detection using matrix multiplication was consistently more sensitive than FFT, image processing time was significantly longer. However, when MATLAB functions were used to implement edge detection, MATLAB's efficient element-by-element calculations and fast filtering techniques reduced computation cost 100 times compared to the matrix multiplication edge detection method. The new computation time was comparable to the FFT method, and MATLAB edge detection produced well-distributed fiber angle distributions that statistically distinguished aligned and unaligned fibers in half as many sample images. When the FFT sensitivity was improved by dividing images into smaller subsections, processing time grew larger than the time required for MATLAB edge detection. Implementation of edge detection in MATLAB is simpler, faster, and more sensitive than FFT for fiber alignment quantification.

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

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

Characterization of tannase protein sequences of bacteria and fungi: an in silico study.

PubMed

Banerjee, Amrita; Jana, Arijit; Pati, Bikash R; Mondal, Keshab C; Das Mohapatra, Pradeep K

2012-04-01

The tannase protein sequences of 149 bacteria and 36 fungi were retrieved from NCBI database. Among them only 77 bacterial and 31 fungal tannase sequences were taken which have different amino acid compositions. These sequences were analysed for different physical and chemical properties, superfamily search, multiple sequence alignment, phylogenetic tree construction and motif finding to find out the functional motif and the evolutionary relationship among them. The superfamily search for these tannase exposed the occurrence of proline iminopeptidase-like, biotin biosynthesis protein BioH, O-acetyltransferase, carboxylesterase/thioesterase 1, carbon-carbon bond hydrolase, haloperoxidase, prolyl oligopeptidase, C-terminal domain and mycobacterial antigens families and alpha/beta hydrolase superfamily. Some bacterial and fungal sequence showed similarity with different families individually. The multiple sequence alignment of these tannase protein sequences showed conserved regions at different stretches with maximum homology from amino acid residues 389-469 and 482-523 which could be used for designing degenerate primers or probes specific for tannase producing bacterial and fungal species. Phylogenetic tree showed two different clusters; one has only bacteria and another have both fungi and bacteria showing some relationship between these different genera. Although in second cluster near about all fungal species were found together in a corner which indicates the sequence level similarity among fungal genera. The distributions of fourteen motifs analysis revealed Motif 1 with a signature amino acid sequence of 29 amino acids, i.e. GCSTGGREALKQAQRWPHDYDGIIANNPA, was uniformly observed in 83.3 % of studied tannase sequences representing its participation with the structure and enzymatic function.

Strategic Planning to Conduct Joint Force Network Operations: A Content Analysis of NETOPS Organizations Strategic Plans

DTIC Science & Technology

2007-03-01

information dominance , Joint Network Operations (NETOPS) organizations need to be strategically aligned. As result, to enhance the capabilities-based effects of NETOPS and reduce our NETOP infrastructures susceptibility to compromise. Once the key organizations were identified, their strategic plans were analyzed using a structured content analysis framework. The results illustrated that the strategic plans were aligned with the community of interests tasking to conduct NETOPS. Further research is required into the strategic alignment beyond the strategic

Statistical Significance of Optical Map Alignments

PubMed Central

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

2012-01-01

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

Comparative Analysis of the Measurement of Total Instructional Alignment

ERIC Educational Resources Information Center

Kick, Laura C.

2013-01-01

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

Effect of grain alignment distribution on magnetic properties in (MM, Nd)-Fe-B sintered magnets

NASA Astrophysics Data System (ADS)

Yu, Xiaoqiang; Yue, Ming; Zhu, Minggang; Liu, Weiqiang; Li, Yuqing; Xi, Longlong; Li, Jiajie; Zhang, Jiuxing; Li, Wei

2018-03-01

H cj of (MM x Nd1-x )-Fe-B sintered magnets decreases distinctly with x increasing when misch metal (MM) content (x) ranges from 0.3 to 1. Practical application is taken into consideration so that the (MM0.6Nd0.4)-Fe-B components are chosen to analyze the changes in behavior of the magnetic properties. Both Magnet II and Magnet III belong to (MM0.6Nd0.4)-Fe-B sintered magnets, however, it should be noted that Magnet II is prepared by the single alloying method (SAM) and Magnet III is prepared by the double main phase alloy method (DMPAM). Core-shell structures of the magnets prepared by DMPAM can result in the higher H cj and lower knee-point coercivity (H k) compared with that by SAM. Furthermore, for Magnet II, the abnormal grain growth contributes to a better grain alignment and smaller distribution coefficient (σ) defined as the degree of grain alignment, which will enforce a higher tendency of the H cj decreasing and H k increasing. The expression of their normalized coercivity h(σ) is deduced by combining Gao’s starting field model with Kronmüller’s nucleation mechanism. Based on the overall h(σ) ~ σ curve, the best desirable h(σ) value is calculated when σ  =  0.09. Theoretically, for Magnet III, the resultant larger σ should be attributed to the more uniform grain alignment. In addition, the deviations of grain size distributions on the c-plane become more remarkable with more MM concentrates, which can be presented by SEM images. Meanwhile, by means of the pole figures, it is also verified that the grain alignment distribution becomes much more diverse with x increasing. Therefore, it can be predicted whether the grain alignment distribution is significant for H k and H cj of (MM x Nd1-x )-Fe-B sintered magnets (x  ≠  0.6) prepared by SAM/DMPAM or not.

AlignMe—a membrane protein sequence alignment web server

PubMed Central

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

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

PubMed

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

2017-01-29

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

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

PubMed

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

2016-08-01

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

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

PubMed Central

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

2017-01-01

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

SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments.

PubMed

Ajawatanawong, Pravech; Atkinson, Gemma C; Watson-Haigh, Nathan S; Mackenzie, Bryony; Baldauf, Sandra L

2012-07-01

Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.

SU-F-I-59: Quality Assurance Phantom for PET/CT Alignment and Attenuation Correction

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

Lin, T; Hamacher, K

2016-06-15

Purpose: This study utilizes a commercial PET/CT phantom to investigate two specific properties of a PET/CT system: the alignment accuracy of PET images with those from CT used for attenuation correction and the accuracy of this correction in PET images. Methods: A commercial PET/CT phantom consisting of three aluminum rods, two long central cylinders containing uniform activity, and attenuating materials such as air, water, bone and iodine contrast was scanned using a standard PET/CT protocol. Images reconstructed with 2 mm slice thickness and a 512 by 512 matrix were obtained. The center of each aluminum rod in the PET andmore » CT images was compared to evaluate alignment accuracy. ROIs were drawn on transaxial images of the central rods at each section of attenuating material to determine the corrected activity (in BQML). BQML values were graphed as a function of slice number to provide a visual representation of the attenuation-correction throughout the whole phantom. Results: Alignment accuracy is high between the PET and CT images. The maximum deviation between the two in the axial plane is less than 1.5 mm, which is less than the width of a single pixel. BQML values measured along different sections of the large central rods are similar among the different attenuating materials except iodine contrast. Deviation of BQML values in the air and bone sections from the water section is less than 1%. Conclusion: Accurate alignment of PET and CT images is critical to ensure proper calculation and application of CT-based attenuation correction. This study presents a simple and quick method to evaluate the two with a single acquisition. As the phantom also includes spheres of increasing diameter, this could serve as a straightforward means to annually evaluate the status of a modern PET/CT system.« less

The Morphologies and Alignments of Gas, Mass, and the Central Galaxies of CLASH Clusters of Galaxies

NASA Astrophysics Data System (ADS)

Donahue, Megan; Ettori, Stefano; Rasia, Elena; Sayers, Jack; Zitrin, Adi; Meneghetti, Massimo; Voit, G. Mark; Golwala, Sunil; Czakon, Nicole; Yepes, Gustavo; Baldi, Alessandro; Koekemoer, Anton; Postman, Marc

2016-03-01

Morphology is often used to infer the state of relaxation of galaxy clusters. The regularity, symmetry, and degree to which a cluster is centrally concentrated inform quantitative measures of cluster morphology. The Cluster Lensing and Supernova survey with Hubble Space Telescope (CLASH) used weak and strong lensing to measure the distribution of matter within a sample of 25 clusters, 20 of which were deemed to be “relaxed” based on their X-ray morphology and alignment of the X-ray emission with the Brightest Cluster Galaxy. Toward a quantitative characterization of this important sample of clusters, we present uniformly estimated X-ray morphological statistics for all 25 CLASH clusters. We compare X-ray morphologies of CLASH clusters with those identically measured for a large sample of simulated clusters from the MUSIC-2 simulations, selected by mass. We confirm a threshold in X-ray surface brightness concentration of C ≳ 0.4 for cool-core clusters, where C is the ratio of X-ray emission inside 100 h70-1 kpc compared to inside 500 {h}70-1 kpc. We report and compare morphologies of these clusters inferred from Sunyaev-Zeldovich Effect (SZE) maps of the hot gas and in from projected mass maps based on strong and weak lensing. We find a strong agreement in alignments of the orientation of major axes for the lensing, X-ray, and SZE maps of nearly all of the CLASH clusters at radii of 500 kpc (approximately 1/2 R500 for these clusters). We also find a striking alignment of clusters shapes at the 500 kpc scale, as measured with X-ray, SZE, and lensing, with that of the near-infrared stellar light at 10 kpc scales for the 20 “relaxed” clusters. This strong alignment indicates a powerful coupling between the cluster- and galaxy-scale galaxy formation processes.

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

PubMed

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

2007-10-11

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

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

Three-Dimensional Printed Thermal Regulation Textiles.

PubMed

Gao, Tingting; Yang, Zhi; Chen, Chaoji; Li, Yiju; Fu, Kun; Dai, Jiaqi; Hitz, Emily M; Xie, Hua; Liu, Boyang; Song, Jianwei; Yang, Bao; Hu, Liangbing

2017-11-28

Space cooling is a predominant part of energy consumption in people's daily life. Although cooling the whole building is an effective way to provide personal comfort in hot weather, it is energy-consuming and high-cost. Personal cooling technology, being able to provide personal thermal comfort by directing local heat to the thermally regulated environment, has been regarded as one of the most promising technologies for cooling energy and cost savings. Here, we demonstrate a personal thermal regulated textile using thermally conductive and highly aligned boron nitride (BN)/poly(vinyl alcohol) (PVA) composite (denoted as a-BN/PVA) fibers to improve the thermal transport properties of textiles for personal cooling. The a-BN/PVA composite fibers are fabricated through a fast and scalable three-dimensional (3D) printing method. Uniform dispersion and high alignment of BN nanosheets (BNNSs) can be achieved during the processing of fiber fabrication, leading to a combination of high mechanical strength (355 MPa) and favorable heat dispersion. Due to the improved thermal transport property imparted by the thermally conductive and highly aligned BNNSs, better cooling effect (55% improvement over the commercial cotton fiber) can be realized in the a-BN/PVA textile. The wearable a-BN/PVA textiles containing the 3D-printed a-BN/PVA fibers offer a promising selection for meeting the personal cooling requirement, which can significantly reduce the energy consumption and cost for cooling the whole building.

An anisotropic hydrogel with electrostatic repulsion between cofacially aligned nanosheets

NASA Astrophysics Data System (ADS)

Liu, Mingjie; Ishida, Yasuhiro; Ebina, Yasuo; Sasaki, Takayoshi; Hikima, Takaaki; Takata, Masaki; Aida, Takuzo

2015-01-01

Machine technology frequently puts magnetic or electrostatic repulsive forces to practical use, as in maglev trains, vehicle suspensions or non-contact bearings. In contrast, materials design overwhelmingly focuses on attractive interactions, such as in the many advanced polymer-based composites, where inorganic fillers interact with a polymer matrix to improve mechanical properties. However, articular cartilage strikingly illustrates how electrostatic repulsion can be harnessed to achieve unparalleled functional efficiency: it permits virtually frictionless mechanical motion within joints, even under high compression. Here we describe a composite hydrogel with anisotropic mechanical properties dominated by electrostatic repulsion between negatively charged unilamellar titanate nanosheets embedded within it. Crucial to the behaviour of this hydrogel is the serendipitous discovery of cofacial nanosheet alignment in aqueous colloidal dispersions subjected to a strong magnetic field, which maximizes electrostatic repulsion and thereby induces a quasi-crystalline structural ordering over macroscopic length scales and with uniformly large face-to-face nanosheet separation. We fix this transiently induced structural order by transforming the dispersion into a hydrogel using light-triggered in situ vinyl polymerization. The resultant hydrogel, containing charged inorganic structures that align cofacially in a magnetic flux, deforms easily under shear forces applied parallel to the embedded nanosheets yet resists compressive forces applied orthogonally. We anticipate that the concept of embedding anisotropic repulsive electrostatics within a composite material, inspired by articular cartilage, will open up new possibilities for developing soft materials with unusual functions.

An anisotropic hydrogel with electrostatic repulsion between cofacially aligned nanosheets.

PubMed

Liu, Mingjie; Ishida, Yasuhiro; Ebina, Yasuo; Sasaki, Takayoshi; Hikima, Takaaki; Takata, Masaki; Aida, Takuzo

2015-01-01

Machine technology frequently puts magnetic or electrostatic repulsive forces to practical use, as in maglev trains, vehicle suspensions or non-contact bearings. In contrast, materials design overwhelmingly focuses on attractive interactions, such as in the many advanced polymer-based composites, where inorganic fillers interact with a polymer matrix to improve mechanical properties. However, articular cartilage strikingly illustrates how electrostatic repulsion can be harnessed to achieve unparalleled functional efficiency: it permits virtually frictionless mechanical motion within joints, even under high compression. Here we describe a composite hydrogel with anisotropic mechanical properties dominated by electrostatic repulsion between negatively charged unilamellar titanate nanosheets embedded within it. Crucial to the behaviour of this hydrogel is the serendipitous discovery of cofacial nanosheet alignment in aqueous colloidal dispersions subjected to a strong magnetic field, which maximizes electrostatic repulsion and thereby induces a quasi-crystalline structural ordering over macroscopic length scales and with uniformly large face-to-face nanosheet separation. We fix this transiently induced structural order by transforming the dispersion into a hydrogel using light-triggered in situ vinyl polymerization. The resultant hydrogel, containing charged inorganic structures that align cofacially in a magnetic flux, deforms easily under shear forces applied parallel to the embedded nanosheets yet resists compressive forces applied orthogonally. We anticipate that the concept of embedding anisotropic repulsive electrostatics within a composite material, inspired by articular cartilage, will open up new possibilities for developing soft materials with unusual functions.

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

PubMed Central

2010-01-01

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

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

NASA Technical Reports Server (NTRS)

Kneifel, A. A.; Guerrero, C.

2003-01-01

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

'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.

A high resolution hand-held focused beam profiler

NASA Astrophysics Data System (ADS)

Zapata-Farfan, J.; Garduño-Mejía, J.; Rosete-Aguilar, M.; Ascanio, G.; Román-Moreno, C. J.

2017-05-01

The shape of a beam is important in any laser application and depending on the final implementation, there exists a preferred one which is defined by the irradiance distribution.1 The energy distribution (or laser beam profile) is an important parameter in a focused beam, for instance, in laser cut industry, where the beam shape determines the quality of the cut. In terms of alignment and focusing, the energy distribution also plays an important role since the system must be configured in order to reduce the aberration effects and achieve the highest intensity. Nowadays a beam profiler is used in both industry and research laboratories with the aim to characterize laser beams used in free-space communications, focusing and welding, among other systems. The purpose of the profile analyzers is to know the main parameters of the beam, to control its characteristics as uniformity, shape and beam size as a guide to align the focusing system. In this work is presented a high resolution hand-held and compact design of a beam profiler capable to measure at the focal plane, with covered range from 400 nm to 1000 nm. The detection is reached with a CMOS sensor sized in 3673.6 μm x 2738.4 μm which acquire a snap shot of the previously attenuated focused beam to avoid the sensor damage, the result is an image of beam intensity distribution, which is digitally processed with a RaspberryTMmodule gathering significant parameters such as beam waist, centroid, uniformity and also some aberrations. The profiler resolution is 1.4 μm and was probed and validated in three different focusing systems. The spot sizes measurements were compared with the Foucault knife-edge test.

Reduction of a grid moiré pattern by integrating a carbon-interspaced high precision x-ray grid with a digital radiographic detector.

PubMed

Yoon, Jai-Woong; Park, Young-Guk; Park, Chun-Joo; Kim, Do-Il; Lee, Jin-Ho; Chung, Nag-Kun; Choe, Bo-Young; Suh, Tae-Suk; Lee, Hyoung-Koo

2007-11-01

The stationary grid commonly used with a digital x-ray detector causes a moiré interference pattern due to the inadequate sampling of the grid shadows by the detector pixels. There are limitations with the previous methods used to remove the moiré such as imperfect electromagnetic interference shielding and the loss of image information. A new method is proposed for removing the moiré pattern by integrating a carbon-interspaced high precision x-ray grid with high grid line uniformity with the detector for frequency matching. The grid was aligned to the detector by translating and rotating the x-ray grid with respect to the detector using microcontrolled alignment mechanism. The gap between the grid and the detector surface was adjusted with micrometer precision to precisely match the projected grid line pitch to the detector pixel pitch. Considering the magnification of the grid shadows on the detector plane, the grids were manufactured such that the grid line frequency was slightly higher than the detector sampling frequency. This study examined the factors that affect the moiré pattern, particularly the line frequency and displacement. The frequency of the moiré pattern was found to be sensitive to the angular displacement of the grid with respect to the detector while the horizontal translation alters the phase but not the moiré frequency. The frequency of the moiré pattern also decreased with decreasing difference in frequency between the grid and the detector, and a moiré-free image was produced after complete matching for a given source to detector distance. The image quality factors including the contrast, signal-to-noise ratio and uniformity in the images with and without the moiré pattern were investigated.

Analysis of condition for uniform lighting generated by array of light emitting diodes with large view angle.

PubMed

Qin, Zong; Wang, Kai; Chen, Fei; Luo, Xiaobing; Liu, Sheng

2010-08-02

In this research, the condition for uniform lighting generated by array of LEDs with large view angle was studied. The luminous intensity distribution of LED is not monotone decreasing with view angle. A LED with freeform lens was designed as an example for analysis. In a system based on LEDs designed in house with a thickness of 20mm and rectangular arrangement, the condition for uniform lighting was derived and the analytical results demonstrated that the uniformity was not decreasing monotonously with the increasing of LED-to-LED spacing. The illuminance uniformities were calculated with Monte Carlo ray tracing simulations and the uniformity was found to increase with the increasing of certain LED-to-LED spacings anomalously. Another type of large view angle LED and different arrangements were discussed in addition. Both analysis and simulation results showed that the method is available for LED array lighting system design on the basis of large view angle LED..

Chromaligner: a web server for chromatogram alignment.

PubMed

Wang, San-Yuan; Ho, Tsung-Jung; Kuo, Ching-Hua; Tseng, Yufeng J

2010-09-15

Chromaligner is a tool for chromatogram alignment to align retention time for chromatographic methods coupled to spectrophotometers such as high performance liquid chromatography and capillary electrophoresis for metabolomics works. Chromaligner resolves peak shifts by a constrained chromatogram alignment. For a collection of chromatograms and a set of defined peaks, Chromaligner aligns the chromatograms on defined peaks using correlation warping (COW). Chromaligner is faster than the original COW algorithm by k(2) times, where k is the number of defined peaks in a chromatogram. It also provides alignments based on known component peaks to reach the best results for further chemometric analysis. Chromaligner is freely accessible at http://cmdd.csie.ntu.edu.tw/~chromaligner.

MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer

PubMed Central

Gauthier, Nicholas Paul; Reznik, Ed; Gao, Jianjiong; Sumer, Selcuk Onur; Schultz, Nikolaus; Sander, Chris; Miller, Martin L.

2016-01-01

The MutationAligner web resource, available at http://www.mutationaligner.org, enables discovery and exploration of somatic mutation hotspots identified in protein domains in currently (mid-2015) more than 5000 cancer patient samples across 22 different tumor types. Using multiple sequence alignments of protein domains in the human genome, we extend the principle of recurrence analysis by aggregating mutations in homologous positions across sets of paralogous genes. Protein domain analysis enhances the statistical power to detect cancer-relevant mutations and links mutations to the specific biological functions encoded in domains. We illustrate how the MutationAligner database and interactive web tool can be used to explore, visualize and analyze mutation hotspots in protein domains across genes and tumor types. We believe that MutationAligner will be an important resource for the cancer research community by providing detailed clues for the functional importance of particular mutations, as well as for the design of functional genomics experiments and for decision support in precision medicine. MutationAligner is slated to be periodically updated to incorporate additional analyses and new data from cancer genomics projects. PMID:26590264

RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

PubMed Central

Munger, Steven C.; Raghupathy, Narayanan; Choi, Kwangbom; Simons, Allen K.; Gatti, Daniel M.; Hinerfeld, Douglas A.; Svenson, Karen L.; Keller, Mark P.; Attie, Alan D.; Hibbs, Matthew A.; Graber, Joel H.; Chesler, Elissa J.; Churchill, Gary A.

2014-01-01

Massively parallel RNA sequencing (RNA-seq) has yielded a wealth of new insights into transcriptional regulation. A first step in the analysis of RNA-seq data is the alignment of short sequence reads to a common reference genome or transcriptome. Genetic variants that distinguish individual genomes from the reference sequence can cause reads to be misaligned, resulting in biased estimates of transcript abundance. Fine-tuning of read alignment algorithms does not correct this problem. We have developed Seqnature software to construct individualized diploid genomes and transcriptomes for multiparent populations and have implemented a complete analysis pipeline that incorporates other existing software tools. We demonstrate in simulated and real data sets that alignment to individualized transcriptomes increases read mapping accuracy, improves estimation of transcript abundance, and enables the direct estimation of allele-specific expression. Moreover, when applied to expression QTL mapping we find that our individualized alignment strategy corrects false-positive linkage signals and unmasks hidden associations. We recommend the use of individualized diploid genomes over reference sequence alignment for all applications of high-throughput sequencing technology in genetically diverse populations. PMID:25236449

Photo-elastic stress analysis of initial alignment archwires.

PubMed

Badran, Serene A; Orr, John F; Stevenson, Mike; Burden, Donald J

2003-04-01

Photo-elastic models replicating a lower arch with a moderate degree of lower incisor crowding and a palatally displaced maxillary canine were used to evaluate the stresses transmitted to the roots of the teeth by initial alignment archwires. Six initial alignment archwires were compared, two multi-strand stainless steel wires, two non-super-elastic (stabilized martensitic form) nickel titanium wires, and two stress-induced super-elastic (austenitic active) nickel titanium wires. Three specimens of each archwire type were tested. Analysis of the photo-elastic fringe patterns, in the medium supporting the teeth, revealed that the non-super-elastic nickel titanium archwires produced the highest shear stresses (P = 0.001). However, the shear stresses generated by the super-elastic alignment archwires and the multi-strand stainless steel archwires were very similar (P = 1.00). These results show that even in situations where large deflections of initial alignment archwires are required, super-elastic archwires do not appear to have any marked advantage over multi-strand stainless steel alignment archwires in terms of the stresses transferred to the roots of the teeth.

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

PubMed Central

Steele, Joe; Bastola, Dhundy

2014-01-01

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

Monitoring fibrous scaffold guidance of three-dimensional collagen organisation using minimally-invasive second harmonic generation.

PubMed

Delaine-Smith, Robin M; Green, Nicola H; Matcher, Stephen J; MacNeil, Sheila; Reilly, Gwendolen C

2014-01-01

The biological and mechanical function of connective tissues is largely determined by controlled cellular alignment and therefore it seems appropriate that tissue-engineered constructs should be architecturally similar to the in vivo tissue targeted for repair or replacement. Collagen organisation dictates the tensile properties of most tissues and so monitoring the deposition of cell-secreted collagen as the construct develops is essential for understanding tissue formation. In this study, electrospun fibres with a random or high degree of orientation, mimicking two types of tissue architecture found in the body, were used to culture human fibroblasts for controlling cell alignment. The minimally-invasive technique of second harmonic generation was used with the aim of monitoring and profiling the deposition and organisation of collagen at different construct depths over time while construct mechanical properties were also determined over the culture period. It was seen that scaffold fibre organisation affected cell migration and orientation up to 21 days which in turn had an effect on collagen organisation. Collagen in random fibrous constructs was deposited in alternating configurations at different depths however a high degree of organisation was observed throughout aligned fibrous constructs orientated in the scaffold fibre direction. Three-dimensional second harmonic generation images showed that deposited collagen was more uniformly distributed in random constructs but aligned constructs were more organised and had higher intensities. The tensile properties of all constructs increased with increasing collagen deposition and were ultimately dictated by collagen organisation. This study highlights the importance of scaffold architecture for controlling the development of well-organised tissue engineered constructs and the usefulness of second harmonic generation imaging for monitoring collagen maturation in a minimally invasive manner.

Mid-infrared imaging- and spectro-polarimetric subarcsecond observations of NGC 1068

NASA Astrophysics Data System (ADS)

Lopez-Rodriguez, E.; Packham, C.; Roche, P. F.; Alonso-Herrero, A.; Díaz-Santos, T.; Nikutta, R.; González-Martín, O.; Álvarez, C. A.; Esquej, P.; Espinosa, J. M. Rodríguez; Perlman, E.; Ramos Almeida, C.; Telesco, C. M.

2016-06-01

We present subarcsecond 7.5-13 μm imaging- and spectro-polarimetric observations of NGC 1068 using CanariCam on the 10.4-m Gran Telescopio CANARIAS. At all wavelengths, we find: (1) A 90 × 60 pc extended polarized feature in the northern ionization cone, with a uniform ˜44° polarization angle. Its polarization arises from dust and gas emission in the ionization cone, heated by the active nucleus and jet, and further extinguished by aligned dust grains in the host galaxy. The polarization spectrum of the jet-molecular cloud interaction at ˜24 pc from the core is highly polarized, and does not show a silicate feature, suggesting that the dust grains are different from those in the interstellar medium. (2) A southern polarized feature at ˜9.6 pc from the core. Its polarization arises from a dust emission component extinguished by a large concentration of dust in the galaxy disc. We cannot distinguish between dust emission from magnetically aligned dust grains directly heated by the jet close to the core, and aligned dust grains in the dusty obscuring material surrounding the central engine. Silicate-like grains reproduce the polarized dust emission in this feature, suggesting different dust compositions in both ionization cones. (3) An upper limit of polarization degree of 0.3 per cent in the core. Based on our polarization model, the expected polarization of the obscuring dusty material is ≲0.1 per cent in the 8-13 μm wavelength range. This low polarization may be arising from the passage of radiation through aligned dust grains in the shielded edges of the clumps.

Elaborate analysis and design of filter-bank-based sensing for wideband cognitive radios

NASA Astrophysics Data System (ADS)

Maliatsos, Konstantinos; Adamis, Athanasios; Kanatas, Athanasios G.

2014-12-01

The successful operation of a cognitive radio system strongly depends on its ability to sense the radio environment. With the use of spectrum sensing algorithms, the cognitive radio is required to detect co-existing licensed primary transmissions and to protect them from interference. This paper focuses on filter-bank-based sensing and provides a solid theoretical background for the design of these detectors. Optimum detectors based on the Neyman-Pearson theorem are developed for uniform discrete Fourier transform (DFT) and modified DFT filter banks with root-Nyquist filters. The proposed sensing framework does not require frequency alignment between the filter bank of the sensor and the primary signal. Each wideband primary channel is spanned and monitored by several sensor subchannels that analyse it in narrowband signals. Filter-bank-based sensing is proved to be robust and efficient under coloured noise. Moreover, the performance of the weighted energy detector as a sensing technique is evaluated. Finally, based on the Locally Most Powerful and the Generalized Likelihood Ratio test, real-world sensing algorithms that do not require a priori knowledge are proposed and tested.

A torque balance measurement of anisotropy of the magnetic susceptibility in white matter.

PubMed

van Gelderen, Peter; Mandelkow, Hendrik; de Zwart, Jacco A; Duyn, Jeff H

2015-11-01

Recent MRI studies have suggested that the magnetic susceptibility of white matter (WM) in the human brain is anisotropic, providing a new contrast mechanism for the visualization of fiber bundles and allowing the extraction of cellular compartment-specific information. This study provides an independent confirmation and quantification of this anisotropy. Anisotropic magnetic susceptibility results in a torque exerted on WM when placed in a uniform magnetic field, tending to align the WM fibers with the field. To quantify the effect, excised spinal cord samples were placed in a torque balance inside the magnet of a 7 T MRI system and the magnetic torque was measured as function of orientation. All tissue samples (n = 5) showed orienting effects, confirming the presence of anisotropic susceptibility. Analysis of the magnetic torque resulted in reproducible values for the WM volume anisotropy that ranged from 13.6 to 19.2 ppb. The independently determined anisotropy values confirm estimates inferred from MRI experiments and validate the use of anisotropy to extract novel information about brain fiber structure and myelination. © 2014 Wiley Periodicals, Inc.

Primary Care and Public Health Activities in Select US Health Centers: Documenting Successes, Barriers, and Lessons Learned

PubMed Central

Shi, Leiyu; Chowdhury, Joya; Sripipatana, Alek; Zhu, Jinsheng; Sharma, Ravi; Hayashi, A. Seiji; Daly, Charles A.; Tomoyasu, Naomi; Nair, Suma; Ngo-Metzger, Quyen

2012-01-01

Objectives. We examined primary care and public health activities among federally funded health centers, to better understand their successes, the barriers encountered, and the lessons learned. Methods. We used qualitative and quantitative methods to collect data from 9 health centers, stratified by administrative division, urban–rural location, and race/ethnicity of patients served. Descriptive data on patient and institutional characteristics came from the Uniform Data System, which collects data from all health centers annually. We administered questionnaires and conducted phone interviews with key informants. Results. Health centers performed well on primary care coordination and community orientation scales and reported conducting many essential public health activities. We identified specific needs for integrating primary care and public health: (1) more funding for collaborations and for addressing the social determinants of health, (2) strong leadership to champion collaborations, (3) trust building among partners, with shared missions and clear expectations of responsibilities, and (4) alignment and standardization of data collection, analysis, and exchange. Conclusions. Lessons learned from health centers should inform strategies to better integrate public health with primary care. PMID:22690975

Local structure order in Pd 78Cu 6Si 16 liquid

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

Yue, G. Q.; Zhang, Y.; Sun, Y.

2015-02-05

The short-range order (SRO) in Pd 78Cu 6Si 16 liquid was studied by high energy x-ray diffraction and ab initio molecular dynamics (MD) simulations. The calculated pair correlation functions at different temperatures agree well with the experimental results. The partial pair correlation functions from ab intio MD simulations indicate that Si atoms prefer to be uniformly distributed while Cu atoms tend to aggregate. By performing structure analysis using Honeycutt-Andersen index, Voronoi tessellation, and atomic cluster alignment method, we show that the icosahedron and face-centered cubic SRO increase upon cooling. The dominant SRO is the Pd-centered Pd 9Si 2 motif, namelymore » the structure of which motif is similar to the structure of Pd-centered clusters in the Pd 9Si 2 crystal. The study further confirms the existence of trigonal prism capped with three half-octahedra that is reported as a structural unit in Pd-based amorphous alloys. The majority of Cu-centered clusters are icosahedra, suggesting that the presence of Cu is benefit to promote the glass forming ability.« less

Electric fields in Earth orbital space

NASA Astrophysics Data System (ADS)

Olson, W. P.; Pfitzer, K. A.; Scotti, S. J.

1982-05-01

This is a report of progress during the past year. The work was performed in three areas with a long term goal understanding the formation and maintenance of electrostatic fields in the earth's magnetosphere. The entry of low energy charged particles into a magnetically closed magnetosphere has been examined in some detail. Entry is permitted because of the non-uniform nature of the magnetic field over the magnetopause surface. Electrostatic fields may be formed across the tail of the magnetosphere because fo the different 'entry efficiencies ' of protons and electrons. The consequences of this particle entry mechanism for the plasma sheet, plasma mantle, and boundary plasmas in the magnetosphere are examined. The mathematics of particle entry was investigated in a one-dimensional boundary using both kinetic theory and bulk MHD parameters. From our participation in the 6th Coordinated Data Analysis Workshop, we have determined that at least during disturbed magnetic conditions, currents persist near geosynchronous orbit in the nightime region which are presently not included in our dynamic magnetic field models. These currents are probably associated with the field aligned currents which close in the ionosphere near auroral latitudes.

The EMBL-EBI bioinformatics web and programmatic tools framework.

PubMed

Li, Weizhong; Cowley, Andrew; Uludag, Mahmut; Gur, Tamer; McWilliam, Hamish; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Lopez, Rodrigo

2015-07-01

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Molecular characterization and phylogenetic analysis of infectious bursal disease viruses isolated from chicken in South China in 2011.

PubMed

Liu, Di; Zhang, Xiang-Bin; Yan, Zhuan-Qiang; Chen, Feng; Ji, Jun; Qin, Jian-Ping; Li, Hai-Yan; Lu, Jun-Peng; Xue, Yu; Liu, Jia-Jia; Xie, Qing-Mei; Ma, Jing-Yun; Xue, Chun-Yi; Bee, Ying-Zuo

2013-06-01

Infectious bursal disease virus (IBDV) is a double-stranded RNA virus that causes immunosuppressive disease in young chickens. Thousands of cases of IBDV infection are reported each year in South China, and these infections can result in considerable economic losses to the poultry industry. To monitor variations of the virus during the outbreaks, 30 IBDVs were identified from vaccinated chicken flocks from nine provinces in South China in 2011. VP2 fragments from different virus strains were sequenced and analyzed by comparison with the published sequences of IBDV strains from China and around the world. Phylogenetic analysis of hypervariable regions of the VP2 (vVP2) gene showed that 29 of the isolates were very virulent (vv) IBDVs, and were closely related to vvIBDV strains from Europe and Asia. Alignment analysis of the deduced amino acid (aa) sequences of vVP2 showed the 29 vv isolates had high uniformity, indicated low variability and slow evolution of the virus. The non-vvIBDV isolate JX2-11 was associated with higher than expected mortality, and had high deduced aa sequence similarity (99.2 %) with the attenuated vaccine strain B87 (BJ). The present study has demonstrated the continued circulation of IBDV strains in South China, and emphasizes the importance of reinforcing IBDV surveillance.

Some aspects of SR beamline alignment

NASA Astrophysics Data System (ADS)

Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

2011-09-01

Based on the Synchrotron Radiation (SR) beamline optical element-by-element alignment with analysis of the alignment results an optimized beamline alignment algorithm has been designed and developed. The alignment procedures have been designed and developed for the MAX-lab I911-4 fixed energy beamline. It has been shown that the intermediate information received during the monochromator alignment stage can be used for the correction of both monochromator and mirror without the next stages of alignment of mirror, slits, sample holder, etc. Such an optimization of the beamline alignment procedures decreases the time necessary for the alignment and becomes useful and helpful in the case of any instability of the beamline optical elements, storage ring electron orbit or the wiggler insertion device, which could result in the instability of angular and positional parameters of the SR beam. A general purpose software package for manual, semi-automatic and automatic SR beamline alignment has been designed and developed using the developed algorithm. The TANGO control system is used as the middle-ware between the stand-alone beamline control applications BLTools, BPMonitor and the beamline equipment.

Vertically Aligned Carbon Nanotube Arrays as Efficient Supports for Faradaic Capacitive Electrodes

NASA Astrophysics Data System (ADS)

Oguntoye, Moses; Holleran, Mary-Kate; Roberts, Katherine; Pesika, Noshir

Supercapacitors are notable for their ability to deliver energy at higher power (compared to batteries) and store energy at higher density (compared to capacitors) as well as exhibit a long cycle life. In our efforts to further the development of supercapacitors, our focus is on using vertically aligned carbon nanotubes (VACNT) as supports for faradaic capacitive electrode materials. The objective is to develop electrodes functioning in an inexpensive aqueous environment with small potential windows, that store energy at a higher density than carbon materials alone. We describe the different approaches explored to overcome the challenges of non-uniform deposition, poor wetting and array collapse. Materials that are electrochemically anchored to VACNT supports include NiCo2O4, VOx, Fe2O3 and Co-Mn mixed oxides. In each case, the specific capacitance obtained using the VACNT arrays as supports is significantly more than that obtained by direct deposition onto current collectors or by using VACNT alone. The ease of VACNT growth and the degree of coating control achievable using electrodeposition means there is much potential in exploring them as supports for capacitive electrode materials.

The fabrication of vertically aligned and periodically distributed carbon nanotube bundles and periodically porous carbon nanotube films through a combination of laser interference ablation and metal-catalyzed chemical vapor deposition.

PubMed

Yuan, Dajun; Lin, Wei; Guo, Rui; Wong, C P; Das, Suman

2012-06-01

Scalable fabrication of carbon nanotube (CNT) bundles is essential to future advances in several applications. Here, we report on the development of a simple, two-step method for fabricating vertically aligned and periodically distributed CNT bundles and periodically porous CNT films at the sub-micron scale. The method involves laser interference ablation (LIA) of an iron film followed by CNT growth via iron-catalyzed chemical vapor deposition. CNT bundles with square widths ranging from 0.5 to 1.5 µm in width, and 50-200 µm in length, are grown atop the patterned catalyst over areas spanning 8 cm(2). The CNT bundles exhibit a high degree of control over square width, orientation, uniformity, and periodicity. This simple scalable method of producing well-placed and oriented CNT bundles demonstrates a high application potential for wafer-scale integration of CNT structures into various device applications, including IC interconnects, field emitters, sensors, batteries, and optoelectronics, etc.

Synthesis of subnanometer-diameter vertically aligned single-walled carbon nanotubes with copper-anchored cobalt catalysts.

PubMed

Cui, Kehang; Kumamoto, Akihito; Xiang, Rong; An, Hua; Wang, Benjamin; Inoue, Taiki; Chiashi, Shohei; Ikuhara, Yuichi; Maruyama, Shigeo

2016-01-21

We synthesize vertically aligned single-walled carbon nanotubes (VA-SWNTs) with subnanometer diameters on quartz (and SiO2/Si) substrates by alcohol CVD using Cu-anchored Co catalysts. The uniform VA-SWNTs with a nanotube diameter of 1 nm are synthesized at a CVD temperature of 800 °C and have a thickness of several tens of μm. The diameter of SWNTs was reduced to 0.75 nm at 650 °C with the G/D ratio maintained above 24. Scanning transmission electron microscopy energy-dispersive X-ray spectroscopy (EDS-STEM) and high angle annular dark field (HAADF-STEM) imaging of the Co/Cu bimetallic catalyst system showed that Co catalysts were captured and anchored by adjacent Cu nanoparticles, and thus were prevented from coalescing into a larger size, which contributed to the small diameter of SWNTs. The correlation between the catalyst size and the SWNT diameter was experimentally clarified. The subnanometer-diameter and high-quality SWNTs are expected to pave the way to replace silicon for next-generation optoelectronic and photovoltaic devices.

High-Resolution Inkjet-Printed Oxide Thin-Film Transistors with a Self-Aligned Fine Channel Bank Structure.

PubMed

Zhang, Qing; Shao, Shuangshuang; Chen, Zheng; Pecunia, Vincenzo; Xia, Kai; Zhao, Jianwen; Cui, Zheng

2018-05-09

A self-aligned inkjet printing process has been developed to construct small channel metal oxide (a-IGZO) thin-film transistors (TFTs) with independent bottom gates on transparent glass substrates. Poly(methylsilsesquioxane) was used to pattern hydrophobic banks on the transparent substrate instead of commonly used self-assembled octadecyltrichlorosilane. Photolithographic exposure from backside using bottom-gate electrodes as mask formed hydrophilic channel areas for the TFTs. IGZO ink was selectively deposited by an inkjet printer in the hydrophilic channel region and confined by the hydrophobic bank structure, resulting in the precise deposition of semiconductor layers just above the gate electrodes. Inkjet-printed IGZO TFTs with independent gate electrodes of 10 μm width have been demonstrated, avoiding completely printed channel beyond the broad of the gate electrodes. The TFTs showed on/off ratios of 10 8 , maximum mobility of 3.3 cm 2 V -1 s -1 , negligible hysteresis, and good uniformity. This method is conductive to minimizing the area of printed TFTs so as to the development of high-resolution printing displays.

Preparation of CNTs rope by electrostatic and airflow field carding with high speed rotor spinning

NASA Astrophysics Data System (ADS)

Dai, J. F.; Liu, J. F.; Zou, J. T.; Dai, Y. L.

2015-12-01

The large-scale preparation of disorderly CNTs with a length larger than 3 mm using CVD method were aligned in polymer monomer airflow fields in a quartz tube with an internal diameter of 200 μm and a length of 1.5 m. The airflow aligned CNTs at the output end of the pipe connects to a copper nozzle with an electrostatic field of applied voltage 5x105 V/m and space length of 0.03 m, which were further realigned using via electrostatic spinning. End to end spray into the high speed rotor twisted single-stranded carbon nanotubes threads via rotor spinning technology. The essential component of this technique was the use of carbon nanotubes at a high rotory speed (200000 r/min) combined with the double twisting of filaments that were twisted together to increase the radial friction of the entire section. SEM micrography showed that carbon nanotube thread has a uniform diameter of approximately 200 μm. Its tensile strength was tested up to 2.7 Gpa, with a length of several meters.

Temperature-triggered chemical switching growth of in-plane and vertically stacked graphene-boron nitride heterostructures

PubMed Central

Gao, Teng; Song, Xiuju; Du, Huiwen; Nie, Yufeng; Chen, Yubin; Ji, Qingqing; Sun, Jingyu; Yang, Yanlian; Zhang, Yanfeng; Liu, Zhongfan

2015-01-01

In-plane and vertically stacked heterostructures of graphene and hexagonal boron nitride (h-BN-G and G/h-BN, respectively) are both recent focuses of graphene research. However, targeted synthesis of either heterostructure remains a challenge. Here, via chemical vapour deposition and using benzoic acid precursor, we have achieved the selective growth of h-BN-G and G/h-BN through a temperature-triggered switching reaction. The perfect in-plane h-BN-G is characterized by scanning tunnelling microscopy (STM), showing atomically patched graphene and h-BN with typical zigzag edges. In contrast, the vertical alignment of G/h-BN is confirmed by unique lattice-mismatch-induced moiré patterns in high-resolution STM images, and two sets of aligned selected area electron diffraction spots, both suggesting a van der Waals epitaxial mechanism. The present work demonstrates the chemical designability of growth process for controlled synthesis of graphene and h-BN heterostructures. With practical scalability, high uniformity and quality, our approach will promote the development of graphene-based electronics and optoelectronics. PMID:25869236

Failure of Anisotropic Unstructured Mesh Adaption Based on Multidimensional Residual Minimization

NASA Technical Reports Server (NTRS)

Wood, William A.; Kleb, William L.

2003-01-01

An automated anisotropic unstructured mesh adaptation strategy is proposed, implemented, and assessed for the discretization of viscous flows. The adaption criteria is based upon the minimization of the residual fluctuations of a multidimensional upwind viscous flow solver. For scalar advection, this adaption strategy has been shown to use fewer grid points than gradient based adaption, naturally aligning mesh edges with discontinuities and characteristic lines. The adaption utilizes a compact stencil and is local in scope, with four fundamental operations: point insertion, point deletion, edge swapping, and nodal displacement. Evaluation of the solution-adaptive strategy is performed for a two-dimensional blunt body laminar wind tunnel case at Mach 10. The results demonstrate that the strategy suffers from a lack of robustness, particularly with regard to alignment of the bow shock in the vicinity of the stagnation streamline. In general, constraining the adaption to such a degree as to maintain robustness results in negligible improvement to the solution. Because the present method fails to consistently or significantly improve the flow solution, it is rejected in favor of simple uniform mesh refinement.

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

PubMed

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

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

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

PubMed Central

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

2016-01-01

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

Pitch contour matching and interactional alignment across turns: an acoustic investigation.

PubMed

Gorisch, Jan; Wells, Bill; Brown, Guy J

2012-03-01

In order to explore the influence of context on the phonetic design of talk-in-interaction, we investigated the pitch characteristics of short turns (insertions) that are produced by one speaker between turns from another speaker. We investigated the hypothesis that the speaker of the insertion designs her turn as a pitch match to the prior turn in order to align with the previous speaker's agenda, whereas non-matching displays that the speaker of the insertion is non-aligning, for example to initiate a new action. Data were taken from the AMI meeting corpus, focusing on the spontaneous talk of first-language English participants. Using sequential analysis, 177 insertions were classified as either aligning or non-aligning in accordance with definitions of these terms in the Conversation Analysis literature. The degree of similarity between the pitch contour of the insertion and that of the prior speaker's turn was measured, using a new technique that integrates normalized F0 and intensity information. The results showed that aligning insertions were significantly more similar to the immediately preceding turn, in terms of pitch contour, than were non-aligning insertions. This supports the view that choice of pitch contour is managed locally, rather than by reference to an intonational lexicon.

Cryo-EM Image Alignment Based on Nonuniform Fast Fourier Transform

PubMed Central

Yang, Zhengfan; Penczek, Pawel A.

2008-01-01

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

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.

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

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

Kumar, Rishi, E-mail: kkraina@gmail.com; Sood, Srishti, E-mail: kkraina@gmail.com; Raina, K. K., E-mail: kkraina@gmail.com

2014-04-24

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

An Analysis of Strategies for Teaching Standards-Based Lesson Plan Alignment to Preservice Teachers

ERIC Educational Resources Information Center

Drost, Bryan R.; Levine, Anita C.

2015-01-01

Research consistently shows that well-aligned lesson plans lead to better student learning outcomes. The development of these plans challenges both preservice teachers and the teacher educators who instruct them. This exploratory study examined strategies for teaching lesson plan alignment utilized by 87 teacher educators in the United States.…

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

ERIC Educational Resources Information Center

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

2012-01-01

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

Distance education through the Internet: the GNA-VSNS biocomputing course.

PubMed

de la Vega, F M; Giegerich, R; Fuellen, G

1996-01-01

A prototype course on biocomputing was delivered via international computer networks in early summer 1995. The course lasted 11 weeks, and was offered free of charge. It was organized by the BioComputing Division of the Virtual School of Natural Sciences, which is a member school of the Globewide Network Academy. It brought together 34 students and 7 instructors from all over the world, and covered the basics of sequence analysis. Five authors from Germany and USA prepared a hypertext book which was discussed in weekly study sessions that took place in a virtual classroom at the BioMOO electronic conferencing system. The course aimed at students with backgrounds in molecular biology, biomedicine or computer science, complementing and extending their skills with an interdisciplinary curriculum. Special emphasis was placed on the use of Internet resources, and the development of new teaching tools. The hypertext book includes direct links to sequence analysis and databank search services on the Internet. A tool for the interactive visualization of unit-cost pairwise sequence alignment was developed for the course. All course material will stay accessible at the World Wide Web address (Uniform Resource Locator) http://+www.techfak.uni-bielefeld.de/bcd/welcome .html. This paper describes the aims and organization of the course, and gives a preliminary account of this novel experience in distance education.

Global Trophic Position Comparison of Two Dominant Mesopelagic Fish Families (Myctophidae, Stomiidae) Using Amino Acid Nitrogen Isotopic Analyses

PubMed Central

Choy, C. Anela; Davison, Peter C.; Drazen, Jeffrey C.; Flynn, Adrian; Gier, Elizabeth J.; Hoffman, Joel C.; McClain-Counts, Jennifer P.; Miller, Todd W.; Popp, Brian N.; Ross, Steve W.; Sutton, Tracey T.

2012-01-01

The δ15N values of organisms are commonly used across diverse ecosystems to estimate trophic position and infer trophic connectivity. We undertook a novel cross-basin comparison of trophic position in two ecologically well-characterized and different groups of dominant mid-water fish consumers using amino acid nitrogen isotope compositions. We found that trophic positions estimated from the δ15N values of individual amino acids are nearly uniform within both families of these fishes across five global regions despite great variability in bulk tissue δ15N values. Regional differences in the δ15N values of phenylalanine confirmed that bulk tissue δ15N values reflect region-specific water mass biogeochemistry controlling δ15N values at the base of the food web. Trophic positions calculated from amino acid isotopic analyses (AA-TP) for lanternfishes (family Myctophidae) (AA-TP ∼2.9) largely align with expectations from stomach content studies (TP ∼3.2), while AA-TPs for dragonfishes (family Stomiidae) (AA-TP ∼3.2) were lower than TPs derived from stomach content studies (TP∼4.1). We demonstrate that amino acid nitrogen isotope analysis can overcome shortcomings of bulk tissue isotope analysis across biogeochemically distinct systems to provide globally comparative information regarding marine food web structure. PMID:23209656

Global trophic position comparison of two dominant mesopelagic fish families (Myctophidae, Stomiidae) using amino acid nitrogen isotopic analyses

USGS Publications Warehouse

Choy, C. Anela; Davison, Peter C.; Drazen, Jeffrey C.; Flynn, Adrian; Gier, Elizabeth J.; Hoffman, Joel C.; McClain-Counts, Jennifer P.; Miller, Todd W.; Popp, Brian N.; Ross, Steve W.; Sutton, Tracey T.

2012-01-01

The δ15N values of organisms are commonly used across diverse ecosystems to estimate trophic position and infer trophic connectivity. We undertook a novel cross-basin comparison of trophic position in two ecologically well-characterized and different groups of dominant mid-water fish consumers using amino acid nitrogen isotope compositions. We found that trophic positions estimated from the δ15N values of individual amino acids are nearly uniform within both families of these fishes across five global regions despite great variability in bulk tissue δ15N values. Regional differences in the δ15N values of phenylalanine confirmed that bulk tissue δ15N values reflect region-specific water mass biogeochemistry controlling δ15N values at the base of the food web. Trophic positions calculated from amino acid isotopic analyses (AA-TP) for lanternfishes (family Myctophidae) (AA-TP ~2.9) largely align with expectations from stomach content studies (TP ~3.2), while AA-TPs for dragonfishes (family Stomiidae) (AA-TP ~3.2) were lower than TPs derived from stomach content studies (TP~4.1). We demonstrate that amino acid nitrogen isotope analysis can overcome shortcomings of bulk tissue isotope analysis across biogeochemically distinct systems to provide globally comparative information regarding marine food web structure.

Solid-state NMR detection of 14N-13C dipolar couplings between amino acid side groups provides constraints on amyloid fibril architecture.

PubMed

Middleton, David A

2011-02-01

Solid-state nuclear magnetic resonance (SSNMR) is a powerful technique for the structural analysis of amyloid fibrils. With suitable isotope labelling patterns, SSNMR can provide constraints on the secondary structure, alignment and registration of β-strands within amyloid fibrils and identify the tertiary and quaternary contacts defining the packing of the β-sheet layers. Detection of (14)N-(13)C dipolar couplings may provide potentially useful additional structural constraints on β-sheet packing within amyloid fibrils but has not until now been exploited for this purpose. Here a frequency-selective, transfer of population in double resonance SSNMR experiment is used to detect a weak (14)N-(13)C dipolar coupling in amyloid-like fibrils of the peptide H(2)N-SNNFGAILSS-COOH, which was uniformly (13)C and (15)N labelled across the four C-terminal amino acids. The (14)N-(13)C interatomic distance between leucine and asparagine side groups is constrained between 2.4 and 3.8 Å, which allows current structural models of the β-spine arrangement within the fibrils to be refined. This procedure could be useful for the general structural analysis of other proteins in condensed phases and environments, such as biological membranes. Copyright © 2011 John Wiley & Sons, Ltd.

Feature Based Retention Time Alignment for Improved HDX MS Analysis

NASA Astrophysics Data System (ADS)

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

2013-04-01

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

Reverse Kinematic Analysis and Uncertainty Analysis of the Space Shuttle AFT Propulsion System (APS) POD Lifting Fixture

NASA Technical Reports Server (NTRS)

Brink, Jeffrey S.

2005-01-01

The space shuttle Aft Propulsion System (APS) pod requires precision alignment to be installed onto the orbiter deck. The Ground Support Equipment (GSE) used to perform this task cannot be manipulated along a single Cartesian axis without causing motion along the other Cartesian axes. As a result, manipulations required to achieve a desired motion are not intuitive. My study calculated the joint angles required to align the APS pod, using reverse kinematic analysis techniques. Knowledge of these joint angles will allow the ground support team to align the APS pod more safely and efficiently. An uncertainty analysis was also performed to estimate the accuracy associated with this approach and to determine whether any inexpensive modifications can be made to further improve accuracy.

Smectic A Filled Birefringent Elements and Fast Switching Twisted Dual Frequency Nematic Cells Used for Digital Light Deflection

NASA Technical Reports Server (NTRS)

Pishnyak, Oleg; Golovin, Andrii; Kreminskia, Liubov; Pouch, John J.; Miranda, Felix A.; Winker, Bruce K.; Lavrentovich, Oleg D.

2006-01-01

We describe the application of smectic A (SmA) liquid crystals for beam deflection. SmA materials can be used in digital beam deflectors (DBDs) as fillers for passive birefringent prisms. SmA prisms have high birefringence and can be constructed in a variety of shapes, including single prisms and prismatic blazed gratings of different angles and profiles. We address the challenges of uniform alignment of SmA, such as elimination of focal conic domains. Fast rotation of the incident light polarization in DBDs is achieved by an electrically switched 90 twisted nematic (TN) cell.

Electric and magnetic target polarization in quantum radar

NASA Astrophysics Data System (ADS)

Brandsema, Matthew J.; Narayanan, Ram M.; Lanzagorta, Marco

2017-05-01

In this paper, we discuss the effect that photon polarization has on the quantum radar cross section (QRCS) during the special case scenario of when the target is enveloped in either a uniform electric field or magnetic field and all of its atomic electric/magnetic dipole moments become aligned (target polarization). This target polarization causes the coupling between the photon and the matter to change and alter the scattering characteristics of the target. Most notably, it causes scattering to be very near zero at a specified angle. We also investigate the relationship between electric and magnetic types of coupling and find that the electric contribution dominates the QRCS response.

Breakdown voltage reduction by field emission in multi-walled carbon nanotubes based ionization gas sensor

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

Saheed, M. Shuaib M.; Muti Mohamed, Norani; Arif Burhanudin, Zainal, E-mail: zainabh@petronas.com.my

2014-03-24

Ionization gas sensors using vertically aligned multi-wall carbon nanotubes (MWCNT) are demonstrated. The sharp tips of the nanotubes generate large non-uniform electric fields at relatively low applied voltage. The enhancement of the electric field results in field emission of electrons that dominates the breakdown mechanism in gas sensor with gap spacing below 14 μm. More than 90% reduction in breakdown voltage is observed for sensors with MWCNT and 7 μm gap spacing. Transition of breakdown mechanism, dominated by avalanche electrons to field emission electrons, as decreasing gap spacing is also observed and discussed.

Electron performance measurements with the ATLAS detector using the 2010 LHC proton-proton collision data

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2012-03-09

Here, detailed measurements of the electron performance of the ATLAS detector at the LHC are reported, using decays of the Z, W and J/ψ particles. Data collected in 2010 at √s = 7 TeV are used, corresponding to an integrated luminosity of almost 40 pb -1. The inter-alignment of the inner detector and the electromagnetic calorimeter, the determination of the electron energy scale and resolution, and the performance in terms of response uniformity and linearity are discussed. The electron identification, reconstruction and trigger efficiencies, as well as the charge misidentification probability, are also presented.

Atomistic cluster alignment method for local order mining in liquids and glasses

NASA Astrophysics Data System (ADS)

Fang, X. W.; Wang, C. Z.; Yao, Y. X.; Ding, Z. J.; Ho, K. M.

2010-11-01

An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the “order mining” idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65 , and Zr36Ni64 ). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

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

PubMed

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

2012-09-01

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

Uniform Sampling Table Method and its Applications II--Evaluating the Uniform Sampling by Experiment.

PubMed

Chen, Yibin; Chen, Jiaxi; Chen, Xuan; Wang, Min; Wang, Wei

2015-01-01

A new method of uniform sampling is evaluated in this paper. The items and indexes were adopted to evaluate the rationality of the uniform sampling. The evaluation items included convenience of operation, uniformity of sampling site distribution, and accuracy and precision of measured results. The evaluation indexes included operational complexity, occupation rate of sampling site in a row and column, relative accuracy of pill weight, and relative deviation of pill weight. They were obtained from three kinds of drugs with different shape and size by four kinds of sampling methods. Gray correlation analysis was adopted to make the comprehensive evaluation by comparing it with the standard method. The experimental results showed that the convenience of uniform sampling method was 1 (100%), odds ratio of occupation rate in a row and column was infinity, relative accuracy was 99.50-99.89%, reproducibility RSD was 0.45-0.89%, and weighted incidence degree exceeded the standard method. Hence, the uniform sampling method was easy to operate, and the selected samples were distributed uniformly. The experimental results demonstrated that the uniform sampling method has good accuracy and reproducibility, which can be put into use in drugs analysis.

Application of Raman spectroscopy for on-line monitoring of low dose blend uniformity.

PubMed

Hausman, Debra S; Cambron, R Thomas; Sakr, Adel

2005-07-14

On-line Raman spectroscopy was used to evaluate the effect of blending time on low dose, 1%, blend uniformity of azimilide dihydrochloride. An 8 qt blender was used for the experiments and instrumented with a Raman probe through the I-bar port. The blender was slowed to 6.75 rpm to better illustrate the blending process (normal speed is 25 rpm). Uniformity was reached after 20 min of blending at 6.75 rpm (135 revolutions or 5.4 min at 25 rpm). On-line Raman analysis of blend uniformity provided more benefits than traditional thief sampling and off-line analysis. On-line Raman spectroscopy enabled generating data rich blend profiles, due to the ability to collect a large number of samples during the blending process (sampling every 20s). In addition, the Raman blend profile was rapidly generated, compared to the lengthy time to complete a blend profile with thief sampling and off-line analysis. The on-line Raman blend uniformity results were also significantly correlated (p-value < 0.05) to the HPLC uniformity results of thief samples.

Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards

PubMed Central

Tsai, Tsung-Heng; Tadesse, Mahlet G.; Di Poto, Cristina; Pannell, Lewis K.; Mechref, Yehia; Wang, Yue; Ressom, Habtom W.

2013-01-01

Motivation: Liquid chromatography-mass spectrometry (LC-MS) has been widely used for profiling expression levels of biomolecules in various ‘-omic’ studies including proteomics, metabolomics and glycomics. Appropriate LC-MS data preprocessing steps are needed to detect true differences between biological groups. Retention time (RT) alignment, which is required to ensure that ion intensity measurements among multiple LC-MS runs are comparable, is one of the most important yet challenging preprocessing steps. Current alignment approaches estimate RT variability using either single chromatograms or detected peaks, but do not simultaneously take into account the complementary information embedded in the entire LC-MS data. Results: We propose a Bayesian alignment model for LC-MS data analysis. The alignment model provides estimates of the RT variability along with uncertainty measures. The model enables integration of multiple sources of information including internal standards and clustered chromatograms in a mathematically rigorous framework. We apply the model to LC-MS metabolomic, proteomic and glycomic data. The performance of the model is evaluated based on ground-truth data, by measuring correlation of variation, RT difference across runs and peak-matching performance. We demonstrate that Bayesian alignment model improves significantly the RT alignment performance through appropriate integration of relevant information. Availability and implementation: MATLAB code, raw and preprocessed LC-MS data are available at http://omics.georgetown.edu/alignLCMS.html Contact: hwr@georgetown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24013927

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

PubMed

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

2016-09-01

Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics data sets.

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

PubMed

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

2015-02-01

Acoustic particle manipulation is an emerging technology that uses ultrasonic standing waves to position objects with pressure gradients and acoustic radiation forces. To produce strong standing waves, the transducer and the reflector must be aligned properly such that they are parallel to each other. This can be a difficult process due to the need to visualise the ultrasound waves and as higher frequencies are introduced, this alignment requires higher accuracy. In this paper, we present a method for aligning acoustic resonators with cepstral analysis. This is a simple signal processing technique that requires only the electrical impedance measurement data of the resonator, which is usually recorded during the fabrication process of the device. We first introduce the mathematical basis of cepstral analysis and then demonstrate and validate it using a computer simulation of an acoustic resonator. Finally, the technique is demonstrated experimentally to create many parallel linear traps for 10 μm fluorescent beads inside an acoustic resonator. Copyright © 2014 Elsevier B.V. All rights reserved.

A basic analysis toolkit for biological sequences

PubMed Central

Giancarlo, Raffaele; Siragusa, Alessandro; Siragusa, Enrico; Utro, Filippo

2007-01-01

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at under the GNU GPL. PMID:17877802

MaxAlign: maximizing usable data in an alignment.

PubMed

Gouveia-Oliveira, Rodrigo; Sackett, Peter W; Pedersen, Anders G

2007-08-28

The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

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

PubMed

Bonham-Carter, Oliver; Steele, Joe; Bastola, Dhundy

2014-11-01

Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base-base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel-Ziv techniques from data compression. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Phylogenetic inference under varying proportions of indel-induced alignment gaps

PubMed Central

Dwivedi, Bhakti; Gadagkar, Sudhindra R

2009-01-01

Background The effect of alignment gaps on phylogenetic accuracy has been the subject of numerous studies. In this study, we investigated the relationship between the total number of gapped sites and phylogenetic accuracy, when the gaps were introduced (by means of computer simulation) to reflect indel (insertion/deletion) events during the evolution of DNA sequences. The resulting (true) alignments were subjected to commonly used gap treatment and phylogenetic inference methods. Results (1) In general, there was a strong – almost deterministic – relationship between the amount of gap in the data and the level of phylogenetic accuracy when the alignments were very "gappy", (2) gaps resulting from deletions (as opposed to insertions) contributed more to the inaccuracy of phylogenetic inference, (3) the probabilistic methods (Bayesian, PhyML & "MLε, " a method implemented in DNAML in PHYLIP) performed better at most levels of gap percentage when compared to parsimony (MP) and distance (NJ) methods, with Bayesian analysis being clearly the best, (4) methods that treat gapped sites as missing data yielded less accurate trees when compared to those that attribute phylogenetic signal to the gapped sites (by coding them as binary character data – presence/absence, or as in the MLε method), and (5) in general, the accuracy of phylogenetic inference depended upon the amount of available data when the gaps resulted from mainly deletion events, and the amount of missing data when insertion events were equally likely to have caused the alignment gaps. Conclusion When gaps in an alignment are a consequence of indel events in the evolution of the sequences, the accuracy of phylogenetic analysis is likely to improve if: (1) alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis, (2) the evolutionary signal provided by indels is harnessed in the phylogenetic analysis, and (3) methods that utilize the phylogenetic signal in indels are developed for distance methods too. When the true homology is known and the amount of gaps is 20 percent of the alignment length or less, the methods used in this study are likely to yield trees with 90–100 percent accuracy. PMID:19698168

Effects of dialysate to serum sodium (Na+) alignment in chronic hemodialysis (HD) patients: retrospective cohort study from a quality improvement project.

PubMed

Raimann, Jochen G; Ficociello, Linda H; Usvyat, Len A; Zhang, Hanjie; Pacelli, Lisa; Moore, Sandi; Sheppard, Penny; Xiao, Qingqing; Wang, Yuedong; Mullon, Claudy; Balter, Paul; Sullivan, Terry; Kotanko, Peter

2018-04-02

Evidence indicates favorable effects of dialysate (DNa + ) to serum sodium concentration (SNa + ) alignment, however, results from larger sample populations are needed. For this reason, we conducted a retrospective propensity score-matched cohort study from a quality improvement project to investigate the effects of alignment on population of maintenance hemodialysis patients. At 4 participating hemodialysis (HD) clinics, patients with SNa + lower than the standard DNa + of 137 mEq/L who received HD with DNa + aligned to the average of the last 4 SNa + measurements were evaluated (clinicaltrials.gov # NCT01825590 ). In this retrospective data analysis, an intention-to-treat (primary) and an as-treated "intervention" (secondary) cohort were created. "Aligned" patients from both cohorts (N = 163 for the primary and N = 137 for the secondary) were then propensity-score matched in a 1:1 fashion to "unaligned" patients from the Renal Research Institute database. The propensity score was generated based on age, gender, white race, Hispanic ethnicity, absence or presence of diabetes, hemodialysis vintage, interdialytic weight gain (IDWG; as a percentage of postdialysis body weight), catheter as primary dialysis access, predialysis systolic blood pressure, serum sodium concentration, hospitalization count during baseline. T-Test was employed for group comparisons of changes to the primary (volume-related and hemodynamic parameters) and tertiary outcomes. All-cause and fluid overload-related hospitalization admission rates were compared using Wilcoxon Rank Sum test and Cox regression analysis for repeated events. In the primary analysis, aligned and unaligned subjects showed comparable demographics at baseline. Treatment effects were significant for IDWG [-0.12 (95% CI -0.24 to 0) L] and showed decreasing non-significant trends for pre-dialysis hemodynamic parameters. Count comparison and Cox regression analysis showed no clear advantage of alignment in terms of all-cause and fluid overload-related hospitalization. Results from the largest sodium alignment program to date suggest positive treatment effects on volume-related and hemodynamic parameters, but no clear effect on risk of hospitalization. Well-matched control patients minimized confounding effects. Small effects and lack of significant differences may be explained by a low baseline DNa + limiting the interventional change.

MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer.

PubMed

Gauthier, Nicholas Paul; Reznik, Ed; Gao, Jianjiong; Sumer, Selcuk Onur; Schultz, Nikolaus; Sander, Chris; Miller, Martin L

2016-01-04

The MutationAligner web resource, available at http://www.mutationaligner.org, enables discovery and exploration of somatic mutation hotspots identified in protein domains in currently (mid-2015) more than 5000 cancer patient samples across 22 different tumor types. Using multiple sequence alignments of protein domains in the human genome, we extend the principle of recurrence analysis by aggregating mutations in homologous positions across sets of paralogous genes. Protein domain analysis enhances the statistical power to detect cancer-relevant mutations and links mutations to the specific biological functions encoded in domains. We illustrate how the MutationAligner database and interactive web tool can be used to explore, visualize and analyze mutation hotspots in protein domains across genes and tumor types. We believe that MutationAligner will be an important resource for the cancer research community by providing detailed clues for the functional importance of particular mutations, as well as for the design of functional genomics experiments and for decision support in precision medicine. MutationAligner is slated to be periodically updated to incorporate additional analyses and new data from cancer genomics projects. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

PubMed

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

2007-07-27

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

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.

PubMed

Roca, Alberto I

2014-01-01

The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org.

The effectiveness of position- and composition-specific gap costs for protein similarity searches.

PubMed

Stojmirović, Aleksandar; Gertz, E Michael; Altschul, Stephen F; Yu, Yi-Kuo

2008-07-01

The flexibility in gap cost enjoyed by hidden Markov models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs). We attempt to quantify the effect of more general gap parameters by separately examining the influence of position- and composition-specific gap scores, as well as by comparing the retrieval accuracy of the PSSMs constructed using an iterative procedure to that of the HMMs provided by Pfam and SUPERFAMILY, curated ensembles of multiple alignments. We found that position-specific gap penalties have an advantage over uniform gap costs. We did not explore optimizing distinct uniform gap costs for each query. For Pfam, PSSMs iteratively constructed from seeds based on HMM consensus sequences perform equivalently to HMMs that were adjusted to have constant gap transition probabilities, albeit with much greater variance. We observed no effect of composition-specific gap costs on retrieval performance. These results suggest possible improvements to the PSI-BLAST protein database search program. The scripts for performing evaluations are available upon request from the authors.

Electrohydrodynamics of drops in strong uniform dc electric fields

NASA Astrophysics Data System (ADS)

Salipante, Paul F.; Vlahovska, Petia M.

2010-11-01

Drop deformation in an uniform dc electric field is a classic problem. The pioneering work of Taylor demonstrated that for weakly conducting media, the drop fluid undergoes a toroidal flow and the drop adopts a prolate or oblate spheroidal shape, the flow and shape being axisymmetrically aligned with the applied field. However, recent studies have revealed a nonaxisymmetric rotational flow in strong fields, similar to the rotation of solid dielectric particles observed by Quincke in the 19th century. We present a systematic experimental study of this phenomenon, which highlights the importance of charge convection along the drop surface. The critical electric field, drop inclination angle, and rate of rotation are measured. We find that for small, high viscosity drops, the threshold field strength is well approximated by the Quincke rotation criterion. Reducing the viscosity ratio shifts the onset for rotation to stronger fields. The drop inclination angle increases with field strength. The rotation rate is approximately given by the inverse Maxwell-Wagner polarization time. Novel features are also observed such as a hysteresis in the tilt angle for large low-viscosity drops.

Deformation and Rotation of a Drop in a Uniform Electric Field

NASA Astrophysics Data System (ADS)

Salipante, Paul; Hanna, James; Vlahovska, Petia

2009-11-01

Drop deformation in uniform electric fields is a classic problem. The pioneering work of G.I.Taylor demonstrated that for weakly conducting media, the drop fluid undergoes a toroidal flow and the drop adopts a prolate or oblate spheroidal shape, the flow and shape being axisymmetrically aligned with the applied field. However, recent studies have revealed a nonaxisymmetric rotational mode for drops of lower conductivity than the surrounding medium, similar to the rotation of solid dielectric particles observed by Quincke in the 19th century. We will present an experimental and theoretical study of this phenomenon in DC fields. The critical electric field, drop inclination angle, and rate of rotation are measured. For small, high viscosity drops, the threshold field strength is well approximated by the Quincke rotation criterion. Reducing the viscosity ratio shifts the onset for rotation to stronger fields. The drop inclination angle increases with field strength. The rotation rate is approximately given by the inverse Maxwell-Wagner polarization time. We also observe a hysteresis in the tilt angle for low-viscosity drops. The effects of AC fields and surfactants are also explored.

Comminution process to produce precision wood particles of uniform size and shape with disrupted grain structure from wood chips

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

Dooley, James H.; Lanning, David N.

A process of comminution of wood chips (C) having a grain direction to produce a mixture of wood particles (P), wherein the wood chips are characterized by an average length dimension (L.sub.C) as measured substantially parallel to the grain, an average width dimension (W.sub.C) as measured normal to L.sub.C and aligned cross grain, and an average height dimension (H.sub.C) as measured normal to W.sub.C and L.sub.C, wherein W.sub.C>L.sub.C, and wherein the comminution process comprises the step of feeding the wood chips in a direction of travel substantially randomly to the grain direction through a counter rotating pair of intermeshing arraysmore » of cutting discs (D) arrayed axially perpendicular to the direction of wood chip travel, wherein the cutting discs have a uniform thickness (T.sub.D), and wherein at least one of L.sub.C, W.sub.C, and H.sub.C is less than T.sub.D.« less

Electromagnet Design for an Experimental Search for CP Violation in Positronium Decay

NASA Astrophysics Data System (ADS)

Petersburg, Ryan; Henning, Reyco; Bartram, Chelsea

2015-04-01

The 3-photon decay of spin-aligned triplet positronium could be used to search for a charge conjugation and parity (CP) symmetry violation. This CP violation would manifest as a nonzero angular correlation (S-> .k1 -->) (S-> .k1 --> ×k2 -->) between the three decay photons' momentum vectors (|k1 --> | > |k2 --> | > |k3 --> |) and the triplet positronium spin (S->). Current limits on this correlation are at the ~10-3 level; therefore, we propose an experiment to improve this limit. In our experiment, the positronium is spin-polarized by a uniform magnetic field from a conventional electromagnet, and the photons are detected by a segmented NaI gamma detector array with large angular acceptance. This talk discusses the design of this unique electromagnet, which requires good field uniformity for the positronium source and a novel yoke design to minimize fringe field effects for the NaI array's PMTs. This project was supported by the Gillian T. Cell Senior Thesis Research Award in the College of Arts & Sciences, administered by Honors Carolina.

Highly oriented NdFeCoB nanocrystalline magnets from partially disproportionated compacts by reactive deformation under low pressure

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

Zheng, Qing; Li, Jun; Liu, Ying, E-mail: liuying5536@163.com

2014-05-07

In the present investigation, we take advantage of the ultrafine grain size of NdFeCoB partially hydrogen-disproportionated phases, and prepare anisotropic nanocrystalline magnets with full density and homogenous microstructure and texture by reactive deformation under low pressure. Our results suggest that the pressure could properly promote an occurrence of desorption-recombination reaction due to a shorter-range rearrangement of the atoms, and the newly recombined Nd{sub 2}Fe{sub 14}B grains with fine grain size could undergo deformation immediately after the phase transformation, and then an obvious anisotropy and uniform alignment would be obtained. The maximum magnetic properties, (BH){sub max} = 25.8 MGOe, Br = 11.8 kG, H{sub cj} = 5.5more » kOe, were obtained after being treated for 5 min at 820 °C in vacuum. The present study highlights the feasibility to prepare anisotropic nanocrystalline magnets with homogeneous microstructure and a strong (00l) texture of uniform grain size under low pressure.« less

Guided Lithium Metal Deposition and Improved Lithium Coulombic Efficiency through Synergistic Effects of LiAsF 6 and Cyclic Carbonate Additives

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

Ren, Xiaodi; Zhang, Yaohui; Engelhard, Mark H.

Spatial and morphology control over lithium (Li) metal nucleation/growth, as well as improving Li Coulombic efficiency (CE) are of the most challenging issues for rechargeable Li metal batteries. Here, we report that LiAsF6 and vinylene carbonate (VC) can work synergistically to address these challenges. It is revealed that AsF6- can be reduced to Li3As and LiF, which can act as seeds for Li growth and form a robust solid electrolyte interphase (SEI) layer, respectively. The addition of VC is critical because it not only enables uniform AsF6- reduction by passivating the defect sites on Cu substrate, but also improves themore » SEI layer flexibility during the reductive polymerization process. As a result, highly compact, uniform and dendrite-free Li film with vertically aligned columns structure can be obtained with greatly increased Li CE, and the Li metal batteries using the electrolyte with both LiAsF6 and VC additives can have much improved cycle life.« less

Extending a CAD-Based Cartesian Mesh Generator for the Lattice Boltzmann Method

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

Cantrell, J Nathan; Inclan, Eric J; Joshi, Abhijit S

2012-01-01

This paper describes the development of a custom preprocessor for the PaRAllel Thermal Hydraulics simulations using Advanced Mesoscopic methods (PRATHAM) code based on an open-source mesh generator, CartGen [1]. PRATHAM is a three-dimensional (3D) lattice Boltzmann method (LBM) based parallel flow simulation software currently under development at the Oak Ridge National Laboratory. The LBM algorithm in PRATHAM requires a uniform, coordinate system-aligned, non-body-fitted structured mesh for its computational domain. CartGen [1], which is a GNU-licensed open source code, already comes with some of the above needed functionalities. However, it needs to be further extended to fully support the LBM specificmore » preprocessing requirements. Therefore, CartGen is being modified to (i) be compiler independent while converting a neutral-format STL (Stereolithography) CAD geometry to a uniform structured Cartesian mesh, (ii) provide a mechanism for PRATHAM to import the mesh and identify the fluid/solid domains, and (iii) provide a mechanism to visually identify and tag the domain boundaries on which to apply different boundary conditions.« less

Fabrication of needle-like ZnO nanorods arrays by a low-temperature seed-layer growth approach in solution

NASA Astrophysics Data System (ADS)

Zhang, Haimin; Quan, Xie; Chen, Shuo; Zhao, Huimin

2007-11-01

Uniform, large-scale, and well-aligned needle-like ZnO nanorods with good photoluminescence and photocatalysis properties on Zn substrates, have been successfully fabricated using a simple low-temperature seed-layer growth approach in solution (50 °C). The formation of ZnO seed-layer by the anodic oxidation technique (AOT) plays an important role in the subsequent growth of highly oriented ZnO nanorods arrays. Temperature also proved to be a significant factor in the growth of ZnO nanorods and had a great effect on their optical properties. X-ray diffraction (XRD) analysis, selected-area electron diffraction (SAED) pattern and high-resolution TEM (HRTEM) indicated that the needle-like ZnO nanorods were single crystal in nature and that they had grown up preferentially along the [0001] direction. The well-aligned ZnO nanorods arrays on Zn substrates exhibited strong UV emission at around 380 nm at room temperature. To investigate their potential as photocatalysts, degradation of pentachlorophenol (PCP) in aqueous solution was carried out using photocatalytic processes, with comparison to direct photolysis. After 1 h, the degradation efficiencies of PCP by direct photolysis and photocatalytic processes achieved 57% and 76% under given experimental conditions, respectively. This improved degradation efficiency of PCP illustrates that ZnO nanorods arrays on Zn substrates have good photocatalytic activity. This simple low-temperature seed-layer growth approach in solution resulted in the development of an effective and low-cost fabrication process for high-quality ZnO nanorods arrays with good optical and photocatalytic properties that can be applicable in many fields such as photocatalysis, photovoltaic cells, luminescent sensors, and photoconductive sensors.

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

PubMed

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

2015-08-01

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

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

ERIC Educational Resources Information Center

Vanfretti, L.; Milano, F.

2012-01-01

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

Performance Reports: Mirror alignment system performance prediction comparison between SAO and EKC

NASA Technical Reports Server (NTRS)

Tananbaum, H. D.; Zhang, J. P.

1994-01-01

The objective of this study is to perform an independent analysis of the residual high resolution mirror assembly (HRMA) mirror distortions caused by force and moment errors in the mirror alignment system (MAS) to statistically predict the HRMA performance. These performance predictions are then compared with those performed by Kodak to verify their analysis results.

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

ERIC Educational Resources Information Center

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

2015-01-01

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

An Image-Guided Study of Setup Reproducibility of Postmastectomy Breast Cancer Patients Treated With Inverse-Planned Intensity Modulated Radiation Therapy

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

Feng, Christine H.; Gerry, Emily; Chmura, Steven J.

2015-01-01

Purpose: To calculate planning target volume (PTV) margins for chest wall and regional nodal targets using daily orthogonal kilovolt (kV) imaging and to study residual setup error after kV alignment using volumetric cone-beam computed tomography (CBCT). Methods and Materials: Twenty-one postmastectomy patients were treated with intensity modulated radiation therapy with 7-mm PTV margins. Population-based PTV margins were calculated from translational shifts after daily kV positioning and/or weekly CBCT data for each of 8 patients, whose surgical clips were used as surrogates for target volumes. Errors from kV and CBCT data were mathematically combined to generate PTV margins for 3 simulatedmore » alignment workflows: (1) skin marks alone; (2) weekly kV imaging; and (3) daily kV imaging. Results: The kV data from 613 treatment fractions indicated that a 7-mm uniform margin would account for 95% of daily shifts if patients were positioned using only skin marks. Total setup errors incorporating both kV and CBCT data were larger than those from kV alone, yielding PTV expansions of 7 mm anterior–posterior, 9 mm left–right, and 9 mm superior–inferior. Required PTV margins after weekly kV imaging were similar in magnitude as alignment to skin marks, but rotational adjustments of patients were required in 32% ± 17% of treatments. These rotations would have remained uncorrected without the use of daily kV imaging. Despite the use of daily kV imaging, CBCT data taken at the treatment position indicate that an anisotropic PTV margin of 6 mm anterior–posterior, 4 mm left–right, and 8 mm superior–inferior must be retained to account for residual errors. Conclusions: Cone-beam CT provides additional information on 3-dimensional reproducibility of treatment setup for chest wall targets. Three-dimensional data indicate that a uniform 7-mm PTV margin is insufficient in the absence of daily IGRT. Interfraction movement is greater than suggested by 2-dimensional imaging, thus a margin of at least 4 to 8 mm must be retained despite the use of daily IGRT.« less

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies.

PubMed

Kim, Jiwoong; Kim, Min Soo; Koh, Andrew Y; Xie, Yang; Zhan, Xiaowei

2016-10-10

Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets. Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline). FMAP performs alignment, gene family abundance calculations, and statistical analysis (three levels of analyses are provided: differentially-abundant genes, operons and pathways). The resulting output can be easily visualized with heatmaps and functional pathway diagrams. FMAP functional predictions are consistent with currently available functional analysis pipelines. FMAP is a comprehensive tool for providing functional analysis of metagenomic/metatranscriptomic sequencing data. With the added features of integrated alignment, operon-level analysis, and the ability to process large datasets, FMAP will be a valuable addition to the currently available functional analysis toolbox. We believe that this software will be of great value to the wider biology and bioinformatics communities.

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

PubMed

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

2017-01-12

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

Simulation-based comprehensive benchmarking of RNA-seq aligners

PubMed Central

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

2018-01-01

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

Gate-tunable resonant tunneling in double bilayer graphene heterostructures.

PubMed

Fallahazad, Babak; Lee, Kayoung; Kang, Sangwoo; Xue, Jiamin; Larentis, Stefano; Corbet, Christopher; Kim, Kyounghwan; Movva, Hema C P; Taniguchi, Takashi; Watanabe, Kenji; Register, Leonard F; Banerjee, Sanjay K; Tutuc, Emanuel

2015-01-14

We demonstrate gate-tunable resonant tunneling and negative differential resistance in the interlayer current-voltage characteristics of rotationally aligned double bilayer graphene heterostructures separated by hexagonal boron nitride (hBN) dielectric. An analysis of the heterostructure band alignment using individual layer densities, along with experimentally determined layer chemical potentials indicates that the resonance occurs when the energy bands of the two bilayer graphene are aligned. We discuss the tunneling resistance dependence on the interlayer hBN thickness, as well as the resonance width dependence on mobility and rotational alignment.

Projected alignment of non-sphericities of stellar, gas, and dark matter distributions in galaxy clusters: analysis of the Horizon-AGN simulation

NASA Astrophysics Data System (ADS)

Okabe, Taizo; Nishimichi, Takahiro; Oguri, Masamune; Peirani, Sébastien; Kitayama, Tetsu; Sasaki, Shin; Suto, Yasushi

2018-04-01

While various observations measured ellipticities of galaxy clusters and alignments between orientations of the brightest cluster galaxies and their host clusters, there are only a handful of numerical simulations that implement realistic baryon physics to allow direct comparisons with those observations. Here we investigate ellipticities of galaxy clusters and alignments between various components of them and the central galaxies in the state-of-the-art cosmological hydrodynamical simulation Horizon-AGN, which contains dark matter, stellar, and gas components in a large simulation box of (100h-1 Mpc)3 with high spatial resolution (˜1 kpc). We estimate ellipticities of total matter, dark matter, stellar, gas surface mass density distributions, X-ray surface brightness, and the Compton y-parameter of the Sunyaev-Zel'dovich effect, as well as alignments between these components and the central galaxies for 120 projected images of galaxy clusters with masses M200 > 5 × 1013M⊙. Our results indicate that the distributions of these components are well aligned with the major-axes of the central galaxies, with the root mean square value of differences of their position angles of ˜20°, which vary little from inner to the outer regions. We also estimate alignments of these various components with total matter distributions, and find tighter alignments than those for central galaxies with the root mean square value of ˜15°. We compare our results with previous observations of ellipticities and position angle alignments and find reasonable agreements. The comprehensive analysis presented in this paper provides useful prior information for analyzing stacked lensing signals as well as designing future observations to study ellipticities and alignments of galaxy clusters.

Projected alignment of non-sphericities of stellar, gas, and dark matter distributions in galaxy clusters: analysis of the Horizon-AGN simulation

NASA Astrophysics Data System (ADS)

Okabe, Taizo; Nishimichi, Takahiro; Oguri, Masamune; Peirani, Sébastien; Kitayama, Tetsu; Sasaki, Shin; Suto, Yasushi

2018-07-01

While various observations measured ellipticities of galaxy clusters and alignments between orientations of the brightest cluster galaxies and their host clusters, there are only a handful of numerical simulations that implement realistic baryon physics to allow direct comparisons with those observations. Here, we investigate ellipticities of galaxy clusters and alignments between various components of them and the central galaxies in the state-of-the-art cosmological hydrodynamical simulation Horizon-AGN, which contains dark matter, stellar, and gas components in a large simulation box of (100h-1 Mpc)3 with high spatial resolution (˜1 kpc). We estimate ellipticities of total matter, dark matter, stellar, gas surface mass density distributions, X-ray surface brightness, and the Compton y-parameter of the Sunyaev-Zel'dovich effect, as well as alignments between these components and the central galaxies for 120 projected images of galaxy clusters with masses M200 > 5 × 1013 M⊙. Our results indicate that the distributions of these components are well aligned with the major axes of the central galaxies, with the root-mean-square value of differences of their position angles of ˜20°, which vary little from inner to the outer regions. We also estimate alignments of these various components with total matter distributions, and find tighter alignments than those for central galaxies with the root-mean-square value of ˜15°. We compare our results with previous observations of ellipticities and position angle alignments and find reasonable agreements. The comprehensive analysis presented in this paper provides useful prior information for analysing stacked lensing signals as well as designing future observations to study ellipticities and alignments of galaxy clusters.

A Python object-oriented framework for the CMS alignment and calibration data

NASA Astrophysics Data System (ADS)

Dawes, Joshua H.; CMS Collaboration

2017-10-01

The Alignment, Calibrations and Databases group at the CMS Experiment delivers Alignment and Calibration Conditions Data to a large set of workflows which process recorded event data and produce simulated events. The current infrastructure for releasing and consuming Conditions Data was designed in the two years of the first LHC long shutdown to respond to use cases from the preceding data-taking period. During the second run of the LHC, new use cases were defined. For the consumption of Conditions Metadata, no common interface existed for the detector experts to use in Python-based custom scripts, resulting in many different querying and transaction management patterns. A new framework has been built to address such use cases: a simple object-oriented tool that detector experts can use to read and write Conditions Metadata when using Oracle and SQLite databases, that provides a homogeneous method of querying across all services. The tool provides mechanisms for segmenting large sets of conditions while releasing them to the production database, allows for uniform error reporting to the client-side from the server-side and optimizes the data transfer to the server. The architecture of the new service has been developed exploiting many of the features made available by the metadata consumption framework to implement the required improvements. This paper presents the details of the design and implementation of the new metadata consumption and data upload framework, as well as analyses of the new upload service’s performance as the server-side state varies.

Biological length scale topography enhances cell-substratum adhesion of human corneal epithelial cells

PubMed Central

Karuri, Nancy W.; Liliensiek, Sara; Teixeira, Ana I.; Abrams, George; Campbell, Sean; Nealey, Paul F.; Murphy, Christopher J.

2006-01-01

Summary The basement membrane possesses a rich 3-dimensional nanoscale topography that provides a physical stimulus, which may modulate cell-substratum adhesion. We have investigated the strength of cell-substratum adhesion on nanoscale topographic features of a similar scale to that of the native basement membrane. SV40 human corneal epithelial cells were challenged by well-defined fluid shear, and cell detachment was monitored. We created silicon substrata with uniform grooves and ridges having pitch dimensions of 400-4000 nm using X-ray lithography. F-actin labeling of cells that had been incubated for 24 hours revealed that the percentage of aligned and elongated cells on the patterned surfaces was the same regardless of pitch dimension. In contrast, at the highest fluid shear, a biphasic trend in cell adhesion was observed with cells being most adherent to the smaller features. The 400 nm pitch had the highest percentage of adherent cells at the end of the adhesion assay. The effect of substratum topography was lost for the largest features evaluated, the 4000 nm pitch. Qualitative and quantitative analyses of the cells during and after flow indicated that the aligned and elongated cells on the 400 nm pitch were more tightly adhered compared to aligned cells on the larger patterns. Selected experiments with primary cultured human corneal epithelial cells produced similar results to the SV40 human corneal epithelial cells. These findings have relevance to interpretation of cell-biomaterial interactions in tissue engineering and prosthetic design. PMID:15226393

Motor mechanisms of vertical fusion in individuals with superior oblique paresis.

PubMed

Mudgil, Ananth V; Walker, Mark; Steffen, Heimo; Guyton, David L; Zee, David S

2002-06-01

We wanted to determine the mechanisms of motor vertical fusion in patients with superior oblique paresis and to correlate these mechanisms with surgical outcomes. Ten patients with superior oblique paresis underwent 3-axis, bilateral, scleral search coil eye movement recordings. Eye movements associated with fusion were analyzed. Six patients had decompensated congenital superior oblique paresis and 4 had acquired superior oblique paresis. All patients with acquired superior oblique paresis relied predominantly on the vertical rectus muscles for motor fusion. Patients with congenital superior oblique paresis were less uniform in their mechanisms for motor fusion: 2 patients used predominantly the oblique muscles, 2 patients used predominantly the vertical recti, and 2 patients used predominantly the superior oblique in the hyperdeviated eye and the superior rectus in the hypodeviated eye. The last 2 patients developed the largest changes in torsional eye alignment relative to changes in vertical eye alignment and were the only patients to develop symptomatic surgical overcorrections. There are 3 different mechanisms for vertical fusion in individuals with superior oblique paresis, with the predominant mechanism being the vertical recti. A subset of patients with superior oblique paresis uses predominantly the superior oblique muscle in the hyperdeviated paretic eye and the superior rectus muscle in the fellow eye for fusion. This results in intorsion of both eyes, causing a large change in torsional alignment. The consequent cyclodisparity, in addition to the existing vertical deviation, may make fusion difficult. The differing patterns of vertical fusional vergence may have implications for surgical treatment.

Manning’s equation and two-dimensional flow analogs

NASA Astrophysics Data System (ADS)

Hromadka, T. V., II; Whitley, R. J.; Jordan, N.; Meyer, T.

2010-07-01

SummaryTwo-dimensional (2D) flow models based on the well-known governing 2D flow equations are applied to floodplain analysis purposes. These 2D models numerically solve the governing flow equations simultaneously or explicitly on a discretization of the floodplain using grid tiles or similar tile cell geometry, called "elements". By use of automated information systems such as digital terrain modeling, digital elevation models, and GIS, large-scale topographic floodplain maps can be readily discretized into thousands of elements that densely cover the floodplain in an edge-to-edge form. However, the assumed principal flow directions of the flow model analog, as applied across an array of elements, typically do not align with the floodplain flow streamlines. This paper examines the mathematical underpinnings of a four-direction flow analog using an array of square elements with respect to floodplain flow streamlines that are not in alignment with the analog's principal flow directions. It is determined that application of Manning's equation to estimate the friction slope terms of the governing flow equations, in directions that are not coincident with the flow streamlines, may introduce a bias in modeling results, in the form of slight underestimation of flow depths. It is also determined that the maximum theoretical bias, occurs when a single square element is rotated by about 13°, and not 45° as would be intuitively thought. The bias as a function of rotation angle for an array of square elements follows approximately the bias for a single square element. For both the theoretical single square element and an array of square elements, the bias as a function of alignment angle follows a relatively constant value from about 5° to about 85°, centered at about 45°. This bias was first noted about a decade prior to the present paper, and the magnitude of this bias was estimated then to be about 20% at about 10° misalignment. An adjustment of Manning's n is investigated based on a considered steady state uniform flow problem, but the magnitude of the adjustment (about 20%) is on the order of the magnitude of the accepted ranges of friction factors. For usual cases where random streamline trajectory variability within the floodplain flow is greater than a few degrees from perfect alignment, the apparent bias appears to be implicitly included in the Manning's n values. It can be concluded that the array of square elements may be applied over the digital terrain model without respect to topographic flow directions.

AGILE: Autonomous Global Integrated Language Exploitation

DTIC Science & Technology

2009-12-01

combination, including METEOR-based alignment (with stemming and WordNet synonym matching) and GIZA ++ based alignment. So far, we have not seen any...parse trees and a detailed analysis of how function words operate in translation. This program lets us fix alignment errors that systems like GIZA ...correlates better with Pyramid than with Responsiveness scoring (i.e., it is a more precise, careful, measure) • BE generally outperforms ROUGE

Aligning Curriculum Materials with the Australian Curriculum: What Is Happening in the Field and What Needs to Be Done?

ERIC Educational Resources Information Center

Watt, Michael

2016-01-01

The purpose of this study was to inform the deliberations of a policymakers' working group by investigating what key actors in the materials' marketplace are doing to align digital and print-based materials with the Australian Curriculum and what steps need to be taken to deliver aligned materials to schools. Content analysis method was used to…

An analysis of the New York State Earth Science Curriculum with respect to standards, classroom practices, and the Regents Examination

NASA Astrophysics Data System (ADS)

Contino, Julie Anna

In a standards-based system, it is important for all components of the system to align in order to achieve the intended goals. In New York State, standards are provided to the teachers who then create individual curricula that will lead to student success on the state assessment. This mixed methods study presents an analysis of the alignment between the National Science Education Standards (NSES), New York State Physical Setting/Earth Science Core Curriculum (Core Curriculum), and New York State Earth Science Regents Examination (Regents)---the sources teachers use for creating Earth Science curricula in New York State. The NSES were found to have a 49% overlap with the Core Curriculum and a 27% overlap with the Regents. The Core Curriculum and Regents, represented by matrices consisting of performance indicators and cognitive demands, were compared using the Porter alignment index. The alignment was 0.35, categorized as slightly aligned, due to the different emphases on cognitive levels (the Core Curriculum focused on Understand and Apply while the Regents focused on Apply followed by Understand and Remember). Additionally, a purposeful sample of experienced and innovative teachers were surveyed and interviewed to gain insight on how NYS Earth Science teachers organize their scope and sequences, align their lessons with the Core Curriculum, establish internal lesson coherence, and prepare their students for the Regents Exam. Teachers' scope and sequences were well-aligned with the Core Curriculum and Regents but misalignment was found between their lessons and the Core Curriculum as well as between the stated objectives for their students and evaluation of those objectives. Based on the findings, it is suggested that the NSES be revised and the Core Curriculum updated to include quantifiable emphasis on the major understandings such as percentage of time, as well as an emphasis on alignment principles. Teacher professional development focused on alignment issues relative to the state standards and enhancing internal lesson coherence should also be provided. The insights gained from this analysis of the NYS system may be helpful to other states as they move toward standards-based systems.

Measurement and statistical analysis of single-molecule current-voltage characteristics, transition voltage spectroscopy, and tunneling barrier height.

PubMed

Guo, Shaoyin; Hihath, Joshua; Díez-Pérez, Ismael; Tao, Nongjian

2011-11-30

We report on the measurement and statistical study of thousands of current-voltage characteristics and transition voltage spectra (TVS) of single-molecule junctions with different contact geometries that are rapidly acquired using a new break junction method at room temperature. This capability allows one to obtain current-voltage, conductance voltage, and transition voltage histograms, thus adding a new dimension to the previous conductance histogram analysis at a fixed low-bias voltage for single molecules. This method confirms the low-bias conductance values of alkanedithiols and biphenyldithiol reported in literature. However, at high biases the current shows large nonlinearity and asymmetry, and TVS allows for the determination of a critically important parameter, the tunneling barrier height or energy level alignment between the molecule and the electrodes of single-molecule junctions. The energy level alignment is found to depend on the molecule and also on the contact geometry, revealing the role of contact geometry in both the contact resistance and energy level alignment of a molecular junction. Detailed statistical analysis further reveals that, despite the dependence of the energy level alignment on contact geometry, the variation in single-molecule conductance is primarily due to contact resistance rather than variations in the energy level alignment.

Isospectrals of non-uniform Rayleigh beams with respect to their uniform counterparts

PubMed Central

Ganguli, Ranjan

2018-01-01

In this paper, we look for non-uniform Rayleigh beams isospectral to a given uniform Rayleigh beam. Isospectral systems are those that have the same spectral properties, i.e. the same free vibration natural frequencies for a given boundary condition. A transformation is proposed that converts the fourth-order governing differential equation of non-uniform Rayleigh beam into a uniform Rayleigh beam. If the coefficients of the transformed equation match with those of the uniform beam equation, then the non-uniform beam is isospectral to the given uniform beam. The boundary-condition configuration should be preserved under this transformation. We present the constraints under which the boundary configurations will remain unchanged. Frequency equivalence of the non-uniform beams and the uniform beam is confirmed by the finite-element method. For the considered cases, examples of beams having a rectangular cross section are presented to show the application of our analysis. PMID:29515879

Use of Bayesian Methods to Analyze and Visualize Content Uniformity Capability Versus United States Pharmacopeia and ASTM Standards.

PubMed

Hofer, Jeffrey D; Rauk, Adam P

2017-02-01

The purpose of this work was to develop a straightforward and robust approach to analyze and summarize the ability of content uniformity data to meet different criteria. A robust Bayesian statistical analysis methodology is presented which provides a concise and easily interpretable visual summary of the content uniformity analysis results. The visualization displays individual batch analysis results and shows whether there is high confidence that different content uniformity criteria could be met a high percentage of the time in the future. The 3 tests assessed are as follows: (a) United States Pharmacopeia Uniformity of Dosage Units <905>, (b) a specific ASTM E2810 Sampling Plan 1 criterion to potentially be used for routine release testing, and (c) another specific ASTM E2810 Sampling Plan 2 criterion to potentially be used for process validation. The approach shown here could readily be used to create similar result summaries for other potential criteria. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

PubMed

Padial, José M; Grant, Taran; Frost, Darrel R

2014-06-26

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments. Our results also provide a clear empirical demonstration of the different effects of wildcard taxa produced by missing data in parsimony and maximum likelihood analyses. Specifically, maximum likelihood analyses consistently (81% bootstrap frequency) provided spurious resolution despite a lack of evidence, whereas parsimony correctly depicted the ambiguity due to missing data by collapsing unsupported nodes. We provide a new taxonomy for the group that retains previously recognized Linnaean taxa except for Ceuthomantidae, Strabomantidae, and Strabomantinae. A phenotypically diagnosable superfamily is recognized formally as Brachycephaloidea, with the informal, unranked name terrarana retained as the standard common name for these frogs. We recognize three families within Brachycephaloidea that are currently diagnosable solely on molecular grounds (Brachycephalidae, Craugastoridae, and Eleutherodactylidae), as well as five subfamilies (Craugastorinae, Eleutherodactylinae, Holoadeninae, Phyzelaphryninae, and Pristimantinae) corresponding in large part to previous families and subfamilies. Our analyses upheld the monophyly of all tested genera, but we found numerous subgeneric taxa to be non-monophyletic and modified the taxonomy accordingly.

A method for real time detecting of non-uniform magnetic field

NASA Astrophysics Data System (ADS)

Marusenkov, Andriy

2015-04-01

The principle of measuring magnetic signatures for observing diverse objects is widely used in Near Surface work (unexploded ordnance (UXO); engineering & environmental; archaeology) and security and vehicle detection systems as well. As a rule, the magnitude of the signals to be measured is much lower than that of the quasi-uniform Earth magnetic field. Usually magnetometers for these purposes contain two or more spatially separated sensors to estimate the full tensor gradient of the magnetic field or, more frequently, only partial gradient components. The both types (scalar and vector) of magnetic sensors could be used. The identity of the scale factors and proper alignment of the sensitivity axes of the vector sensors are very important for deep suppression of the ambient field and detection of weak target signals. As a rule, the periodical calibration procedure is used to keep matching sensors' parameters as close as possible. In the present report we propose the technique for detection magnetic anomalies, which is almost insensitive to imperfect matching of the sensors. This method based on the idea that the difference signals between two sensors are considerably different when the instrument is rotated or moved in uniform and non-uniform fields. Due to the misfit of calibration parameters the difference signal observed at the rotation in the uniform field is similar to the total signal - the sum of the signals of both sensors. Zero change of the difference and total signals is expected, if the instrument moves in the uniform field along a straight line. In contrast, the same move in the non-uniform field produces some response of each of the sensors. In case one measures dB/dx and moves along x direction, the sensors signals is shifted in time with the lag proportional to the distance between sensors and the speed of move. It means that the difference signal looks like derivative of the total signal at move in the non-uniform field. So, using quite simple electronic schematic it is possible to detect the lag between the total and difference signals and to trigger alarms, when the instrument passes near a magnetized object. The proposed method was successfully applied in the two instruments: the low-power search coil magnetometer for vehicle detection system and the low-noise flux-gate magnetometer for magnetocardiograph. Author believes that this approach could be also useful for the fast inspection of the area during the engineering, archaeology, UXO surveys.

Consensus-Based Course Design and Implementation of Constructive Alignment Theory in a Power System Analysis Course

ERIC Educational Resources Information Center

Vanfretti, Luigi; Farrokhabadi, Mostafa

2015-01-01

This article presents the implementation of the constructive alignment theory (CAT) in a power system analysis course through a consensus-based course design process. The consensus-based design process involves both the instructor and graduate-level students and it aims to develop the CAT framework in a holistic manner with the goal of including…

Sharp Morphological Transitions from Nanoscale Mixed-Anchoring Patterns in Confined Nematic Liquid Crystals

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

Armas-Pérez, Julio C.; Li, Xiao; Martínez-González, José A.

Liquid crystals are known to be particularly sensitive to orientational cues provided at surfaces or interfaces. In this work, we explore theoretically, computationally, and experimentally the behavior of liquid crystals on isolated nanoscale patterns with controlled anchoring characteristics at small length scales. The orientation of the liquid crystal is controlled through the use of chemically patterned polymer brushes that are tethered to a surface. This system can be engineered with remarkable precision, and the central question addressed here is whether a characteristic length scale exists at which information encoded on a surface is no longer registered by a liquid crystal.more » To do so, we adopt a tensorial description of the free energy of the hybrid liquidcrystal surface system, and we investigate its morphology in a systematic manner. For long and narrow surface stripes, it is found that the liquid crystal follows the instructions provided by the pattern down to 100 nm widths. This is accomplished through the creation of line defects that travel along the sides of the stripes. We show that a "sharp" morphological transition occurs from a uniform undistorted alignment to a dual uniform/splay-bend morphology. The theoretical and numerical predictions advanced here are confirmed by experimental observations. Our combined analysis suggests that nanoscale patterns can be used to manipulate the orientation of liquid crystals at a fraction of the energetic cost that is involved in traditional liquid crystal-based devices. The insights presented in this work have the potential to provide a new fabrication platform to assemble low power bistable devices, which could be reconfigured upon application of small external fields.« less

Fertigation uniformity under sprinkler irrigation: evaluation and analysis

USDA-ARS?s Scientific Manuscript database

n modern farming systems, fertigation is widely practiced as a cost effective and convenient method for applying soluble fertilizers to crops. Along with efficiency and adequacy, uniformity is an important fertigation performance evaluation criterion. Fertigation uniformity is defined here as a comp...

Atmospheric lidar co-alignment sensor: flight model electro-optical characterization campaign

NASA Astrophysics Data System (ADS)

Valverde Guijarro, Ángel Luis; Belenguer Dávila, Tomás.; Laguna Hernandez, Hugo; Ramos Zapata, Gonzalo

2017-10-01

Due to the difficulty in studying the upper layer of the troposphere by using ground-based instrumentation, the conception of a space-orbit atmospheric LIDAR (ATLID) becomes necessary. ATLID born in the ESA's EarthCare Programme framework as one of its payloads, being the first instrument of this kind that will be in the Space. ATLID will provide vertical profiles of aerosols and thin clouds, separating the relative contribution of aerosol and molecular scattering to know aerosol optical depth. It operates at a wavelength of 355 nm and has a high spectral resolution receiver and depolarization channel with a vertical resolution up to 100m from ground to an altitude of 20 km and, and up to 500m from 20km to 40km. ATLID measurements will be done from a sun-synchronous orbit at 393 km altitude, and an alignment (co-alignment) sensor (CAS) is revealed as crucial due to the way in which LIDAR analyses the troposphere. As in previous models, INTA has been in charge of part of the ATLID instrument co-alignment sensor (ATLID-CAS) electro-optical characterization campaign. CAS includes a set of optical elements to take part of the useful signal, to direct it onto the memory CCD matrix (MCCD) used for the co-alignment determination, and to focus the selected signal on the MCCD. Several tests have been carried out for a proper electro-optical characterization: CAS line of sight (LoS) determination and stability, point spread function (PSF), absolute response (AbsRes), pixel response non uniformity (PRNU), response linearity (ResLin) and spectral response. In the following lines, a resume of the flight model electrooptical characterization campaign is reported on. In fact, results concerning the protoflight model (CAS PFM) will be summarized. PFM requires flight-level characterization, so most of the previously mentioned tests must be carried out under simulated working conditions, i.e., the vacuum level (around 10-5 mbar) and temperature range (between 50°C and -30°C) that are expected during ATLID Space operation.

Alignment of learning objectives and assessments in therapeutics courses to foster higher-order thinking.

PubMed

FitzPatrick, Beverly; Hawboldt, John; Doyle, Daniel; Genge, Terri

2015-02-17

To determine whether national educational outcomes, course objectives, and classroom assessments for 2 therapeutics courses were aligned for curricular content and cognitive processes, and if they included higher-order thinking. Document analysis and student focus groups were used. Outcomes, objectives, and assessment tasks were matched for specific therapeutics content and cognitive processes. Anderson and Krathwohl's Taxonomy was used to define higher-order thinking. Students discussed whether assessments tested objectives and described their thinking when responding to assessments. There were 7 outcomes, 31 objectives, and 412 assessment tasks. The alignment for content and cognitive processes was not satisfactory. Twelve students participated in the focus groups. Students thought more short-answer questions than multiple choice questions matched the objectives for content and required higher-order thinking. The alignment analysis provided data that could be used to reveal and strengthen the enacted curriculum and improve student learning.

Galactic cosmic ray gradients, field-aligned and latitudinal, among Voyagers 1/2 and IMP-8

NASA Technical Reports Server (NTRS)

Roelof, E. C.; Decker, R. B.; Krimigis, S. M.; Venkatesan, D.; Lazarus, A. J.

1982-01-01

The present investigation represents a summary of a comprehensive analysis of the same subject conducted by Roelof et al. (1981). It is pointed out that the tandem earth-Jupiter trajectories of the Voyager 1/2 spacecraft, combined with baseline measurements from the earth-orbiting IMP 7/8 spacecraft, provide the first opportunity for unambiguously separating latitude from radial or field-aligned effects in galactic cosmic ray gradients. Attention is given to the method of data analysis, and the separation of field-aligned and latitudinal gradients. It is found that latitudinal gradients approximately equal to or greater than 1 percent per deg in the cosmic ray intensity were a common feature of the interplanetary medium between 1 and 5 AU in 1977-78. Except in the most disturbed periods, cosmic ray intensities are well-ordered in field-aligned structures.

GATA: A graphic alignment tool for comparative sequenceanalysis

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

Nix, David A.; Eisen, Michael B.

2005-01-01

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

Prosody and alignment: a sequential perspective

NASA Astrophysics Data System (ADS)

Szczepek Reed, Beatrice

2010-12-01

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

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

A distributed system for fast alignment of next-generation sequencing data.

PubMed

Srimani, Jaydeep K; Wu, Po-Yen; Phan, John H; Wang, May D

2010-12-01

We developed a scalable distributed computing system using the Berkeley Open Interface for Network Computing (BOINC) to align next-generation sequencing (NGS) data quickly and accurately. NGS technology is emerging as a promising platform for gene expression analysis due to its high sensitivity compared to traditional genomic microarray technology. However, despite the benefits, NGS datasets can be prohibitively large, requiring significant computing resources to obtain sequence alignment results. Moreover, as the data and alignment algorithms become more prevalent, it will become necessary to examine the effect of the multitude of alignment parameters on various NGS systems. We validate the distributed software system by (1) computing simple timing results to show the speed-up gained by using multiple computers, (2) optimizing alignment parameters using simulated NGS data, and (3) computing NGS expression levels for a single biological sample using optimal parameters and comparing these expression levels to that of a microarray sample. Results indicate that the distributed alignment system achieves approximately a linear speed-up and correctly distributes sequence data to and gathers alignment results from multiple compute clients.

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.

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos

PubMed Central

2014-01-01

Background The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. Results The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. Conclusions The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org. PMID:25237393

Optimal Parameter Design of Coarse Alignment for Fiber Optic Gyro Inertial Navigation System.

PubMed

Lu, Baofeng; Wang, Qiuying; Yu, Chunmei; Gao, Wei

2015-06-25

Two different coarse alignment algorithms for Fiber Optic Gyro (FOG) Inertial Navigation System (INS) based on inertial reference frame are discussed in this paper. Both of them are based on gravity vector integration, therefore, the performance of these algorithms is determined by integration time. In previous works, integration time is selected by experience. In order to give a criterion for the selection process, and make the selection of the integration time more accurate, optimal parameter design of these algorithms for FOG INS is performed in this paper. The design process is accomplished based on the analysis of the error characteristics of these two coarse alignment algorithms. Moreover, this analysis and optimal parameter design allow us to make an adequate selection of the most accurate algorithm for FOG INS according to the actual operational conditions. The analysis and simulation results show that the parameter provided by this work is the optimal value, and indicate that in different operational conditions, the coarse alignment algorithms adopted for FOG INS are different in order to achieve better performance. Lastly, the experiment results validate the effectiveness of the proposed algorithm.

HSA: a heuristic splice alignment tool.

PubMed

Bu, Jingde; Chi, Xuebin; Jin, Zhong

2013-01-01

RNA-Seq methodology is a revolutionary transcriptomics sequencing technology, which is the representative of Next generation Sequencing (NGS). With the high throughput sequencing of RNA-Seq, we can acquire much more information like differential expression and novel splice variants from deep sequence analysis and data mining. But the short read length brings a great challenge to alignment, especially when the reads span two or more exons. A two steps heuristic splice alignment tool is generated in this investigation. First, map raw reads to reference with unspliced aligner--BWA; second, split initial unmapped reads into three equal short reads (seeds), align each seed to the reference, filter hits, search possible split position of read and extend hits to a complete match. Compare with other splice alignment tools like SOAPsplice and Tophat2, HSA has a better performance in call rate and efficiency, but its results do not as accurate as the other software to some extent. HSA is an effective spliced aligner of RNA-Seq reads mapping, which is available at https://github.com/vlcc/HSA.

Clustalnet: the joining of Clustal and CORBA.

PubMed

Campagne, F

2000-07-01

Performing sequence alignment operations from a different program than the original sequence alignment code, and/or through a network connection, is often required. Interactive alignment editors and large-scale biological data analysis are common examples where such a flexibility is important. Interoperability between the alignment engine and the client should be obtained regardless of the architectures and programming languages of the server and client. Clustalnet, a Clustal alignment CORBA server is described, which was developed on the basis of Clustalw. This server brings the robustness of the algorithms and implementations of Clustal to a new level of reuse. A Clustalnet server object can be accessed from a program, transparently through the network. We present interfaces to perform the alignment operations and to control these operations via immutable contexts. The interfaces that select the contexts do not depend on the nature of the operation to be performed, making the design modular. The IDL interfaces presented here are not specific to Clustal and can be implemented on top of different sequence alignment algorithm implementations.

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

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

PubMed Central

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

2009-01-01

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

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

PubMed

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

2009-08-28

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

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

PubMed Central

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

2010-01-01

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

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

PubMed

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

2017-07-01

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

Silicon photonics and challenges for fabrication

NASA Astrophysics Data System (ADS)

Feilchenfeld, N. B.; Nummy, K.; Barwicz, T.; Gill, D.; Kiewra, E.; Leidy, R.; Orcutt, J. S.; Rosenberg, J.; Stricker, A. D.; Whiting, C.; Ayala, J.; Cucci, B.; Dang, D.; Doan, T.; Ghosal, M.; Khater, M.; McLean, K.; Porth, B.; Sowinski, Z.; Willets, C.; Xiong, C.; Yu, C.; Yum, S.; Giewont, K.; Green, W. M. J.

2017-03-01

Silicon photonics is rapidly becoming the key enabler for meeting the future data speed and volume required by the Internet of Things. A stable manufacturing process is needed to deliver cost and yield expectations to the technology marketplace. We present the key challenges and technical results from both 200mm and 300mm facilities for a silicon photonics fabrication process which includes monolithic integration with CMOS. This includes waveguide patterning, optical proximity correction for photonic devices, silicon thickness uniformity and thick material patterning for passive fiber to waveguide alignment. The device and process metrics show that the transfer of the silicon photonics process from 200mm to 300mm will provide a stable high volume manufacturing platform for silicon photonics designs.

VETA x ray data acquisition and control system

NASA Technical Reports Server (NTRS)

Brissenden, Roger J. V.; Jones, Mark T.; Ljungberg, Malin; Nguyen, Dan T.; Roll, John B., Jr.

1992-01-01

We describe the X-ray Data Acquisition and Control System (XDACS) used together with the X-ray Detection System (XDS) to characterize the X-ray image during testing of the AXAF P1/H1 mirror pair at the MSFC X-ray Calibration Facility. A variety of X-ray data were acquired, analyzed and archived during the testing including: mirror alignment, encircled energy, effective area, point spread function, system housekeeping and proportional counter window uniformity data. The system architecture is presented with emphasis placed on key features that include a layered UNIX tool approach, dedicated subsystem controllers, real-time X-window displays, flexibility in combining tools, network connectivity and system extensibility. The VETA test data archive is also described.

Forces between permanent magnets: experiments and model

NASA Astrophysics Data System (ADS)

González, Manuel I.

2017-03-01

This work describes a very simple, low-cost experimental setup designed for measuring the force between permanent magnets. The experiment consists of placing one of the magnets on a balance, attaching the other magnet to a vertical height gauge, aligning carefully both magnets and measuring the load on the balance as a function of the gauge reading. A theoretical model is proposed to compute the force, assuming uniform magnetisation and based on laws and techniques accessible to undergraduate students. A comparison between the model and the experimental results is made, and good agreement is found at all distances investigated. In particular, it is also found that the force behaves as r -4 at large distances, as expected.

Self-sustaining charging of identical colliding particles

NASA Astrophysics Data System (ADS)

Siu, Theo; Cotton, Jake; Mattson, Gregory; Shinbrot, Troy

2014-05-01

Recent experiments have demonstrated that identical material samples can charge one another after being brought into symmetric contact. The mechanism for this charging is not known. In this article, we use a simplified one-dimensional lattice model to analyze charging in the context of agitated particles. We find that the electric field from a single weakly polarized grain can feed back on itself by polarizing its neighbors, leading to an exponential growth in polarization. We show that, by incorporating partial neutralization between neighboring polarized particles, either uniform alignment of dipoles or complex charge and polarization waves can be produced. We reproduce a polarized state experimentally using identical colliding particles and raise several issues for future study.

Production of atmospheric pressure microwave plasma with dielectric half-mirror resonator and its application to polymer surface treatment

NASA Astrophysics Data System (ADS)

Sasai, Kensuke; Keyamura, Kazuki; Suzuki, Haruka; Toyoda, Hirotaka

2018-06-01

For the surface treatment of a polymer tube, a ring-shaped atmospheric pressure microwave plasma (APMP) using a coaxial waveguide is studied. In this APMP, a dielectric plate is used not only as a partial mirror for cavity resonation but also for the precise alignment of the discharge gap for ring-shaped plasma production. The optimum position of the dielectric plate is investigated by electromagnetic wave simulation. On the basis of simulation results, a ring-shaped plasma with good uniformity along the ring is produced. The coaxial APMP is applied to the surface treatment of ethylene tetrafluoroethylene. A very fast surface modification within 3 s is observed.

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

PubMed

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

2016-01-01

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

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

PubMed

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

2017-05-01

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

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

PubMed

Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

2016-01-01

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

gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances

PubMed Central

Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav

2016-01-01

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

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

ERIC Educational Resources Information Center

Council of Chief State School Officers, 2009

2009-01-01

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

Warp-averaging event-related potentials.

PubMed

Wang, K; Begleiter, H; Porjesz, B

2001-10-01

To align the repeated single trials of the event-related potential (ERP) in order to get an improved estimate of the ERP. A new implementation of the dynamic time warping is applied to compute a warp-average of the single trials. The trilinear modeling method is applied to filter the single trials prior to alignment. Alignment is based on normalized signals and their estimated derivatives. These features reduce the misalignment due to aligning the random alpha waves, explaining amplitude differences in latency differences, or the seemingly small amplitudes of some components. Simulations and applications to visually evoked potentials show significant improvement over some commonly used methods. The new implementation of the dynamic time warping can be used to align the major components (P1, N1, P2, N2, P3) of the repeated single trials. The average of the aligned single trials is an improved estimate of the ERP. This could lead to more accurate results in subsequent analysis.

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

Iterative refinement of structure-based sequence alignments by Seed Extension

PubMed Central

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

2009-01-01

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

Synthesis of stiffened shells of revolution

NASA Technical Reports Server (NTRS)

Thornton, W. A.

1974-01-01

Computer programs for the synthesis of shells of various configurations were developed. The conditions considered are: (1) uniform shells (mainly cones) using a membrane buckling analysis, (2) completely uniform shells (cones, spheres, toroidal segments) using linear bending prebuckling analysis, and (3) revision of second design process to reduce the number of design variables to about 30 by considering piecewise uniform designs. A perturbation formula was derived and this allows exact derivatives of the general buckling load to be computed with little additional computer time.

Mobile Gait Analysis System for Lower Limb Amputee High-Level Activity Rehabilitation

DTIC Science & Technology

2012-09-01

take this data and give the clinician information they can use immediately to get more insight into existing prosthesis fit or alignment issues, help...Modification of Smart Pylon for prosthesis fit, alignment and gait training purposes – 20 In May the larger, more rugged trans-tibial (TT) Smart Pylon...data to determine metrics to indicate positive patient biomechanics factors and indicate successful prosthesis fit and alignment This will be

Dry-plasma-free chemical etch technique for variability reduction in multi-patterning (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kal, Subhadeep; Mohanty, Nihar; Farrell, Richard A.; Franke, Elliott; Raley, Angelique; Thibaut, Sophie; Pereira, Cheryl; Pillai, Karthik; Ko, Akiteru; Mosden, Aelan; Biolsi, Peter

2017-04-01

Scaling beyond the 7nm technology node demands significant control over the variability down to a few angstroms, in order to achieve reasonable yield. For example, to meet the current scaling targets it is highly desirable to achieve sub 30nm pitch line/space features at back-end of the line (BEOL) or front end of line (FEOL); uniform and precise contact/hole patterning at middle of line (MOL). One of the quintessential requirements for such precise and possibly self-aligned patterning strategies is superior etch selectivity between the target films while other masks/films are exposed. The need to achieve high etch selectivity becomes more evident for unit process development at MOL and BEOL, as a result of low density films choices (compared to FEOL film choices) due to lower temperature budget. Low etch selectivity with conventional plasma and wet chemical etch techniques, causes significant gouging (un-intended etching of etch stop layer, as shown in Fig 1), high line edge roughness (LER)/line width roughness (LWR), non-uniformity, etc. In certain circumstances this may lead to added downstream process stochastics. Furthermore, conventional plasma etches may also have the added disadvantage of plasma VUV damage and corner rounding (Fig. 1). Finally, the above mentioned factors can potentially compromise edge placement error (EPE) and/or yield. Therefore a process flow enabled with extremely high selective etches inherent to film properties and/or etch chemistries is a significant advantage. To improve this etch selectivity for certain etch steps during a process flow, we have to implement alternate highly selective, plasma free techniques in conjunction with conventional plasma etches (Fig 2.). In this article, we will present our plasma free, chemical gas phase etch technique using chemistries that have high selectivity towards a spectrum of films owing to the reaction mechanism ( as shown Fig 1). Gas phase etches also help eliminate plasma damage to the features during the etch process. Herein we will also demonstrate a test case on how a combination or plasma assisted and plasma free etch techniques has the potential to improve process performance of a 193nm immersion based self aligned quandruple patterning (SAQP) for BEOL compliant films (an example shown in Fig 2). In addition, we will also present on the application of gas etches for (1) profile improvement, (2) selective mandrel pull (3) critical dimension trim of mandrels, with an analysis of advantages over conventional techniques in terms of LER and EPE.

Aspects of the Fracture Toughness of Carbon Nanotube Modified Epoxy Polymer Composites

NASA Astrophysics Data System (ADS)

Mirjalili, Vahid

Epoxy resins used in fibre reinforced composites exhibit a brittle fracture behaviour, because they show no sign of damage prior to a catastrophic failure. Rubbery materials and micro-particles have been added to epoxy resins to improve their fracture toughness, which reduces strength and elastic properties. In this research, carbon nanotubes (CNTs) are investigated as a potential toughening agent for epoxy resins and carbon fibre reinforced composites, which can also enhance strength and elastic properties. More specifically, the toughening mechanisms of CNTs are investigated theoretically and experimentally. The effect of aligned and randomly oriented carbon nanotubes (CNTs) on the fracture toughness of polymers was modelled using Elastic Plastic Fracture Mechanics. Toughening from CNT pull-out and rupture were considered, depending on the CNTs critical length. The model was used to identify the effect of CNTs geometrical and mechanical properties on the fracture toughness of CNT-modified epoxies. The modelling results showed that a uniform dispersion and alignment of a high volume fraction of CNTs normal to the crack growth plane would lead to the maximum fracture toughness enhancement. To achieve a uniform dispersion, the effect of processing on the dispersion of single walled and multi walled CNTs in epoxy resins was investigated. An instrumented optical microscope with a hot stage was used to quantify the evolution of the CNT dispersion during cure. The results showed that the reduction of the resin viscosity at temperatures greater than 100 °C caused an irreversible re-agglomeration of the CNTs in the matrix. The dispersion quality was then directly correlated to the fracture toughness of the modified resin. It was shown that the fine tuning of the ratio of epoxy resin, curing agent and CNT content was paramount to the improvement of the base resin fracture toughness. For the epoxy resin (MY0510 from Hexcel), an improvement of 38% was achieved with 0.3 wt.% of Single Walled CNT (SWNT). Finally, the CNT-modified epoxy resin was used to manufacture carbon fibre laminates by resin film infusion and prepreg technologies. The Mode I and Mode II delamination properties of the CNT-modified composite increased by 140% and 127%, respectively. In contrast, this improvement was not observed for the base CNT-modified polymers, used to manufacture the composite laminates. A qualitative analysis of the fractured surface using a Scanning Electron Microscope revealed a good dispersion in the composites samples, confirming the importance of processing to harness the full potential of carbon nanotubes for toughening polymer composites.

The impact of visual layout factors on performance in Web pages: a cross-language study.

PubMed

Parush, Avi; Shwarts, Yonit; Shtub, Avy; Chandra, M Jeya

2005-01-01

Visual layout has a strong impact on performance and is a critical factor in the design of graphical user interfaces (GUIs) and Web pages. Many design guidelines employed in Web page design were inherited from human performance literature and GUI design studies and practices. However, few studies have investigated the more specific patterns of performance with Web pages that may reflect some differences between Web page and GUI design. We investigated interactions among four visual layout factors in Web page design (quantity of links, alignment, grouping indications, and density) in two experiments: one with pages in Hebrew, entailing right-to-left reading, and the other with English pages, entailing left-to-right reading. Some performance patterns (measured by search times and eye movements) were similar between languages. Performance was particularly poor in pages with many links and variable densities, but it improved with the presence of uniform density. Alignment was not shown to be a performance-enhancing factor. The findings are discussed in terms of the similarities and differences in the impact of layout factors between GUIs and Web pages. Actual or potential applications of this research include specific guidelines for Web page design.

Graphene-and-Copper Artificial Nacre Fabricated by a Preform Impregnation Process: Bioinspired Strategy for Strengthening-Toughening of Metal Matrix Composite.

PubMed

Xiong, Ding-Bang; Cao, Mu; Guo, Qiang; Tan, Zhanqiu; Fan, Genlian; Li, Zhiqiang; Zhang, Di

2015-07-28

Metals can be strengthened by adding hard reinforcements, but such strategy usually compromises ductility and toughness. Natural nacre consists of hard and soft phases organized in a regular "brick-and-mortar" structure and exhibits a superior combination of mechanical strength and toughness, which is an attractive model for strengthening and toughening artificial composites, but such bioinspired metal matrix composite has yet to be made. Here we prepared nacre-like reduced graphene oxide (RGrO) reinforced Cu matrix composite based on a preform impregnation process, by which two-dimensional RGrO was used as "brick" and inserted into "□-and-mortar" ordered porous Cu preform (the symbol "□" means the absence of "brick"), followed by compacting. This process realized uniform dispersion and alignment of RGrO in Cu matrix simultaneously. The RGrO-and-Cu artificial nacres exhibited simultaneous enhancement on yield strength and ductility as well as increased modulus, attributed to RGrO strengthening, effective crack deflection and a possible combined failure mode of RGrO. The artificial nacres also showed significantly higher strengthening efficiency than other conventional Cu matrix composites, which might be related to the alignment of RGrO.

How jet lag impairs Major League Baseball performance.

PubMed

Song, Alex; Severini, Thomas; Allada, Ravi

2017-02-07

Laboratory studies have demonstrated that circadian clocks align physiology and behavior to 24-h environmental cycles. Examination of athletic performance has been used to discern the functions of these clocks in humans outside of controlled settings. Here, we examined the effects of jet lag, that is, travel that shifts the alignment of 24-h environmental cycles relative to the endogenous circadian clock, on specific performance metrics in Major League Baseball. Accounting for potential differences in home and away performance, travel direction, and team confounding variables, we observed that jet-lag effects were largely evident after eastward travel with very limited effects after westward travel, consistent with the >24-h period length of the human circadian clock. Surprisingly, we found that jet lag impaired major parameters of home-team offensive performance, for example, slugging percentage, but did not similarly affect away-team offensive performance. On the other hand, jet lag impacted both home and away defensive performance. Remarkably, the vast majority of these effects for both home and away teams could be explained by a single measure, home runs allowed. Rather than uniform effects, these results reveal surprisingly specific effects of circadian misalignment on athletic performance under natural conditions.

How jet lag impairs Major League Baseball performance

PubMed Central

Song, Alex; Severini, Thomas; Allada, Ravi

2017-01-01

Laboratory studies have demonstrated that circadian clocks align physiology and behavior to 24-h environmental cycles. Examination of athletic performance has been used to discern the functions of these clocks in humans outside of controlled settings. Here, we examined the effects of jet lag, that is, travel that shifts the alignment of 24-h environmental cycles relative to the endogenous circadian clock, on specific performance metrics in Major League Baseball. Accounting for potential differences in home and away performance, travel direction, and team confounding variables, we observed that jet-lag effects were largely evident after eastward travel with very limited effects after westward travel, consistent with the >24-h period length of the human circadian clock. Surprisingly, we found that jet lag impaired major parameters of home-team offensive performance, for example, slugging percentage, but did not similarly affect away-team offensive performance. On the other hand, jet lag impacted both home and away defensive performance. Remarkably, the vast majority of these effects for both home and away teams could be explained by a single measure, home runs allowed. Rather than uniform effects, these results reveal surprisingly specific effects of circadian misalignment on athletic performance under natural conditions. PMID:28115724

Continuous-flow system and monitoring tools for the dielectrophoretic integration of nanowires in light sensor arrays.

PubMed

Marín, A García; Núñez, C García; Rodríguez, P; Shen, G; Kim, S M; Kung, P; Piqueras, J; Pau, J L

2015-03-20

Although nanowires (NWs) may improve the performance of many optoelectronic devices such as light emitters and photodetectors, the mass commercialization of these devices is limited by the difficult task of finding reliable and reproducible methods to integrate the NWs on foreign substrates. This work shows the fabrication of zinc oxide NWs photodetectors on conventional glass using transparent conductive electrodes to effectively integrate the NWs at specific locations by dielectrophoresis (DEP). The paper describes the careful preparation of NW dispersions by sedimentation and the dielectrophoretic alignment of NWs in a home-made system. This system includes an impedance technique for the assessment of the alignment quality in real time. Following this procedure, ultraviolet photodetectors based on the electrical contacts formed by the DEP process on the transparent electrodes are fabricated. This cost-effective mean of contacting NWs enables front-and back-illumination operation modes, the latter eliminating shadowing effects caused by the deposition of metals. The electro-optical characterization of the devices shows uniform responsivities in the order of 106 A W(-1) below 390 nm under both modes, as well as, time responses of a few seconds.

Visualizing molecular polar order in tissues via electromechanical coupling

PubMed Central

Denning, Denise; Alilat, Sofiane; Habelitz, Stefan; Fertala, Andrzej; Rodriguez, Brian J.

2015-01-01

Electron microscopy (EM) and atomic force microscopy (AFM) techniques have long been used to characterize collagen fibril ordering and alignment in connective tissues. These techniques, however, are unable to map collagen fibril polarity, i.e., the polar orientation that is directed from the amine to the carboxyl termini. Using a voltage modulated AFM-based technique called piezoresponse force microscopy (PFM), we show it is possible to visualize both the alignment of collagen fibrils within a tissue and the polar orientation of the fibrils with minimal sample preparation. We demonstrate the technique on rat tail tendon and porcine eye tissues in ambient conditions. In each sample, fibrils are arranged into domains whereby neighboring domains exhibit opposite polarizations, which in some cases extend to the individual fibrillar level. Uniform polarity has not been observed in any of the tissues studied. Evidence of anti-parallel ordering of the amine to carboxyl polarity in bundles of fibrils or in individual fibrils is found in all tissues, which has relevance for understanding mechanical and biofunctional properties and the formation of connective tissues. The technique can be applied to any biological material containing piezoelectric biopolymers or polysaccharides. PMID:22985991

PGDD: a database of gene and genome duplication in plants

PubMed Central

Lee, Tae-Ho; Tang, Haibao; Wang, Xiyin; Paterson, Andrew H.

2013-01-01

Genome duplication (GD) has permanently shaped the architecture and function of many higher eukaryotic genomes. The angiosperms (flowering plants) are outstanding models in which to elucidate consequences of GD for higher eukaryotes, owing to their propensity for chromosomal duplication or even triplication in a few cases. Duplicated genome structures often require both intra- and inter-genome alignments to unravel their evolutionary history, also providing the means to deduce both obvious and otherwise-cryptic orthology, paralogy and other relationships among genes. The burgeoning sets of angiosperm genome sequences provide the foundation for a host of investigations into the functional and evolutionary consequences of gene and GD. To provide genome alignments from a single resource based on uniform standards that have been validated by empirical studies, we built the Plant Genome Duplication Database (PGDD; freely available at http://chibba.agtec.uga.edu/duplication/), a web service providing synteny information in terms of colinearity between chromosomes. At present, PGDD contains data for 26 plants including bryophytes and chlorophyta, as well as angiosperms with draft genome sequences. In addition to the inclusion of new genomes as they become available, we are preparing new functions to enhance PGDD. PMID:23180799

Continuous-flow system and monitoring tools for the dielectrophoretic integration of nanowires in light sensor arrays

NASA Astrophysics Data System (ADS)

García Marín, A.; García Núñez, C.; Rodríguez, P.; Shen, G.; Kim, S. M.; Kung, P.; Piqueras, J.; Pau, J. L.

2015-03-01

Although nanowires (NWs) may improve the performance of many optoelectronic devices such as light emitters and photodetectors, the mass commercialization of these devices is limited by the difficult task of finding reliable and reproducible methods to integrate the NWs on foreign substrates. This work shows the fabrication of zinc oxide NWs photodetectors on conventional glass using transparent conductive electrodes to effectively integrate the NWs at specific locations by dielectrophoresis (DEP). The paper describes the careful preparation of NW dispersions by sedimentation and the dielectrophoretic alignment of NWs in a home-made system. This system includes an impedance technique for the assessment of the alignment quality in real time. Following this procedure, ultraviolet photodetectors based on the electrical contacts formed by the DEP process on the transparent electrodes are fabricated. This cost-effective mean of contacting NWs enables front-and back-illumination operation modes, the latter eliminating shadowing effects caused by the deposition of metals. The electro-optical characterization of the devices shows uniform responsivities in the order of 106 A W-1 below 390 nm under both modes, as well as, time responses of a few seconds.

Flow separation on flapping and rotating profiles with spanwise gradients.

PubMed

Wong, J G; laBastide, B P; Rival, D E

2017-02-15

The growth of leading-edge vortices (LEV) on analogous flapping and rotating profiles has been investigated experimentally. Three time-varying cases were considered: a two-dimensional reference case with a spanwise-uniform angle-of-attack variation α; a case with increasing α towards the profile tip (similar to flapping flyers); and a case with increasing α towards the profile root (similar to rotor blades experiencing an axial gust). It has been shown that the time-varying spanwise angle-of-attack gradient produces a vorticity gradient, which, in combination with spanwise flow, results in a redistribution of circulation along the profile. Specifically, when replicating the angle-of-attack gradient characteristic of a rotor experiencing an axial gust, the spanwise-vorticity gradient is aligned such that circulation increases within the measurement domain. This in turn increases the local LEV growth rate, which is suggestive of force augmentation on the blade. Reversing the relative alignment of the spanwise-vorticity gradient and spanwise flow, thereby replicating that arrangement found in a flapping flyer, was found to reduce local circulation. From this, we can conclude that spanwise flow can be arranged to vary LEV growth to prolong lift augmentation and reduce the unsteadiness of cyclic loads.

Vertically aligned CNT-Cu nano-composite material for stacked through-silicon-via interconnects.

PubMed

Sun, Shuangxi; Mu, Wei; Edwards, Michael; Mencarelli, Davide; Pierantoni, Luca; Fu, Yifeng; Jeppson, Kjell; Liu, Johan

2016-08-19

For future miniaturization of electronic systems using 3D chip stacking, new fine-pitch materials for through-silicon-via (TSV) applications are likely required. In this paper, we propose a novel carbon nanotube (CNT)/copper nanocomposite material consisting of high aspect ratio, vertically aligned CNT bundles coated with copper. These bundles, consisting of hundreds of tiny CNTs, were uniformly coated by copper through electroplating, and aspect ratios as high as 300:1 were obtained. The resistivity of this nanomaterial was found to be as low as ∼10(-8) Ω m, which is of the same order of magnitude as the resistivity of copper, and its temperature coefficient was found to be only half of that of pure copper. The main advantage of the composite TSV nanomaterial is that its coefficient of thermal expansion (CTE) is similar to that of silicon, a key reliability factor. A finite element model was set up to demonstrate the reliability of this composite material and thermal cycle simulations predicted very promising results. In conclusion, this composite nanomaterial appears to be a very promising material for future 3D TSV applications offering both a low resistivity and a low CTE similar to that of silicon.

Efficient alignment-free DNA barcode analytics.

PubMed

Kuksa, Pavel; Pavlovic, Vladimir

2009-11-10

In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding.

EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

PubMed Central

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

2006-01-01

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

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/ .

Reconstruction of interatomic vectors by principle component analysis of nuclear magnetic resonance data in multiple alignments

NASA Astrophysics Data System (ADS)

Hus, Jean-Christophe; Bruschweiler, Rafael

2002-07-01

A general method is presented for the reconstruction of interatomic vector orientations from nuclear magnetic resonance (NMR) spectroscopic data of tensor interactions of rank 2, such as dipolar coupling and chemical shielding anisotropy interactions, in solids and partially aligned liquid-state systems. The method, called PRIMA, is based on a principal component analysis of the covariance matrix of the NMR parameters collected for multiple alignments. The five nonzero eigenvalues and their eigenvectors efficiently allow the approximate reconstruction of the vector orientations of the underlying interactions. The method is demonstrated for an isotropic distribution of sample orientations as well as for finite sets of orientations and internuclear vectors encountered in protein systems.

Gravitational-Wave Data Analysis with Spinning Merger-Ringdown Waveforms

NASA Technical Reports Server (NTRS)

Kelly Bernard J.

2011-01-01

The recent availability of high-quality, gravitational merger-ringdown waveforms from spinning black-hole systems has made possible the development of multi-mode GW templates for use in data-analysis studies of current and proposed interferometric GW detectors. We report on recent work at NASA Goddard, analyzing the most significant modes from aligned-spin black-hole-binary mergers. From these, we have developed time-domain merger-ringdown GW templates covering the aligned-spin portion of parameter space. We also discuss how using the full information content of aligned-spin mergers can significantly reduce uncertainties in some parameters, emphasizing the significant gains possible in the last stages of merger, inaccessible to inspiral-only post-Newtonian templates.

The Influence Of Component Alignment On The Life Of Total Knee Prostheses

NASA Astrophysics Data System (ADS)

Bugariu, Delia; Bereteu, Liviu

2012-12-01

An arthritic knee affects the patient's life by causing pain and limiting movement. If the cartilage and the bone surfaces are severely affected, the natural joint is replaced with an artificial joint. The procedure is called total knee arthroplasty (TKA). Lately, the numbers of implanted total knee prostheses grow steadily. An important factor in TKA is the perfect alignment of the total knee prosthesis (TKP) components. Component misalignment can lead to the prosthesis loss by producing wear particles. The paper proposes a study on mechanical behaviors of a TKP based on numerical analysis, using ANSYS software. The numerical analysis is based on both the normal and the changed angle of the components alignment.

Experiment Pamir-3. Coplanar emission of high energy gamma-quanta at interaction of hadrons with nuclei of air atoms at energies above 10 to the 7th power GeV

NASA Technical Reports Server (NTRS)

Asatiani, T. L.; Genina, L. E.; Zatsepin, G. T.

1985-01-01

A systematic analysis of large gamma families, detected in X-ray emulsion chambers, cases of multicore halos have been observed, and among them five events in which the halo is divided into three of four separate cores with their alignment observed in the target diagram (coplanarity of axes of corresponding electron photon cascades). The halo alignment (tendency to the straight line) leads to the aximuthal asymmetry (thrust). The analysis of lateral and momentum distributions of particles in these families shows that they also have thrust that correlates with the direction of the halo core alignment.

Energy transfer in compressible magnetohydrodynamic turbulence for isothermal self-gravitating fluids

NASA Astrophysics Data System (ADS)

Banerjee, Supratik; Kritsuk, Alexei G.

2018-02-01

Three-dimensional, compressible, magnetohydrodynamic turbulence of an isothermal, self-gravitating fluid is analyzed using two-point statistics in the asymptotic limit of large Reynolds numbers (both kinetic and magnetic). Following an alternative formulation proposed by Banerjee and Galtier [Phys. Rev. E 93, 033120 (2016), 10.1103/PhysRevE.93.033120; J. Phys. A: Math. Theor. 50, 015501 (2017), 10.1088/1751-8113/50/1/015501], an exact relation has been derived for the total energy transfer. This approach results in a simpler relation expressed entirely in terms of mixed second-order structure functions. The kinetic, thermodynamic, magnetic, and gravitational contributions to the energy transfer rate can be easily separated in the present form. By construction, the new formalism includes such additional effects as global rotation, the Hall term in the induction equation, etc. The analysis shows that solid-body rotation cannot alter the energy flux rate of compressible turbulence. However, the contribution of a uniform background magnetic field to the flux is shown to be nontrivial unlike in the incompressible case. Finally, the compressible, turbulent energy flux rate does not vanish completely due to simple alignments, which leads to a zero turbulent energy flux rate in the incompressible case.

Ontology for Semantic Data Integration in the Domain of IT Benchmarking.

PubMed

Pfaff, Matthias; Neubig, Stefan; Krcmar, Helmut

2018-01-01

A domain-specific ontology for IT benchmarking has been developed to bridge the gap between a systematic characterization of IT services and their data-based valuation. Since information is generally collected during a benchmark exercise using questionnaires on a broad range of topics, such as employee costs, software licensing costs, and quantities of hardware, it is commonly stored as natural language text; thus, this information is stored in an intrinsically unstructured form. Although these data form the basis for identifying potentials for IT cost reductions, neither a uniform description of any measured parameters nor the relationship between such parameters exists. Hence, this work proposes an ontology for the domain of IT benchmarking, available at https://w3id.org/bmontology. The design of this ontology is based on requirements mainly elicited from a domain analysis, which considers analyzing documents and interviews with representatives from Small- and Medium-Sized Enterprises and Information and Communications Technology companies over the last eight years. The development of the ontology and its main concepts is described in detail (i.e., the conceptualization of benchmarking events, questionnaires, IT services, indicators and their values) together with its alignment with the DOLCE-UltraLite foundational ontology.

Macrosegregation During Re-melting and Holding of Directionally Solidified Al-7 wt.% Si Alloy in Microgravity

NASA Astrophysics Data System (ADS)

Lauer, M.; Ghods, M.; Angart, S. G.; Grugel, R. N.; Tewari, S. N.; Poirier, D. R.

2017-08-01

As-cast aluminum-7 wt.% ailicon alloy sample rods were re-melted and directionally solidified on Earth which resulted in uniform dendritically aligned arrays. These arrays were then partially back-melted through an imposed, and constant, temperature gradient in the microgravity environment aboard the International Space Station. The mushy zones that developed in the seed crystals were held for different periods prior to initiating directional solidification. Upon return, examination of the initial mushy-zone regions exhibited significant macrosegregation in terms of a solute-depleted zone that increased as a function of the holding time. The silicon (solute) content in these regions was measured on prepared longitudinal sections by electron microprobe analysis as well as by determining the fraction eutectic on several transverse sections. The silicon content was found to increase up the temperature gradient resulting in significant silicon concentration immediately ahead of the mushy-zone tips. The measured macrosegregation agrees well with calculations from a mathematical model developed to simulate the re-melting and holding process. The results, due to processing in a microgravity environment where buoyancy and thermosolutal convection are minimized, serve as benchmark solidification data.

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.

Numerical Analysis of Micromixers for Optimization of Mixing Action

NASA Astrophysics Data System (ADS)

Panta, Yogendra; Adhikari, Param

2011-03-01

Micro-bio/chemical applications often require rapid and uniform mixing of a number of fluid streams that carries bio/chemical species in the solution. At microscale, fluid flow is highly laminar with low Reynolds number, fluids mixing mechanism is primarily by diffusion and free from any turbulence. Demand for highly efficient micromixers for microfluidic networks is due to slower mixing process for larger bio-molecules such as peptides, proteins, and nucleic acids compared to micro-scale molecules. Passive and active mixers are two basic mixers that are currently in use for these applications. Passive mixers often require very long mixing channels where are most active mixers require bulky moving parts to stir the fluids. In this study, electroosmotic effects orthogonally aligned with the fluid flowstream are utilized for optimum mixing effect in various micromixers. Cross-dependencies among several geometrical, electrical, and fluid parameters and their significance are studied in order to achieve an optimum mixing effect. It has been planned to optimize the mixer by non-moving stirring actions provided by an external magnetic field. Acknowledgements to School of Graduate Studies and Research at YSU for URC Grant and RP Award 2009-2010.