Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

PubMed Central

Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

2013-01-01

Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

High yield growth of patterned vertically aligned carbon nanotubes using inkjet-printed catalyst.

PubMed

Beard, James D; Stringer, Jonathan; Ghita, Oana R; Smith, Patrick J

2013-10-09

This study reports on the fabrication of vertically aligned carbon nanotubes localized at specific sites on a growth substrate by deposition of a nanoparticle suspension using inkjet printing. Carbon nanotubes were grown with high yield as vertically aligned forests to a length of approximately 400 μm. The use of inkjet printing for catalyst fabrication considerably improves the production rate of vertically aligned patterned nanotube forests compared with conventional patterning techniques, for example, electron beam lithography or photolithography.

Plan, Save, Succeed! Financial Literacy Poster/Teaching Guide. Expect the Unexpected with Math[R

ERIC Educational Resources Information Center

Actuarial Foundation, 2013

2013-01-01

"Plan, Save, Succeed!" is a new program aligned with Jumpstart Coalition National Standards in K-12 Personal Finance Education, National Council of Teachers of Mathematics (NCTM) Standards, and Common Core Standards for Mathematical Practice. "Plan, Save, Succeed!" is designed to help students understand key financial literacy topics including…

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

PubMed

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

2014-07-15

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

Fabrication Process for Large Size Mold and Alignment Method for Nanoimprint System

NASA Astrophysics Data System (ADS)

Ishibashi, Kentaro; Kokubo, Mitsunori; Goto, Hiroshi; Mizuno, Jun; Shoji, Shuichi

Nanoimprint technology is considered one of the mass production methods of the display for cellular phone or notebook computer, with Anti-Reflection Structures (ARS) pattern and so on. In this case, the large size mold with nanometer order pattern is very important. Then, we describe the fabrication process for large size mold, and the alignment method for UV nanoimprint system. We developed the original mold fabrication process using nanoimprint method and etching techniques. In 66 × 45 mm2 area, 200nm period seamless patterns were formed using this process. And, we constructed original alignment system that consists of the CCD-camera system, X-Y-θ table, method of moiré fringe, and image processing system, because the accuracy of pattern connection depends on the alignment method. This alignment system accuracy was within 20nm.

Solving the Unknown with Algebra: Poster/Teaching Guide for Pre-Algebra Students. Expect the Unexpected with Math[R

ERIC Educational Resources Information Center

Actuarial Foundation, 2013

2013-01-01

"Solving the Unknown with Algebra" is a new math program aligned with the National Council of Teachers of Mathematics (NCTM) standards and designed to help students practice pre-algebra skills including using formulas, solving for unknowns, and manipulating equations. Developed by The Actuarial Foundation with Scholastic, this program provides…

The Power of Probability: Poster/Teaching Guide for Grades 6-8. Expect the Unexpected with Math[R

ERIC Educational Resources Information Center

Actuarial Foundation, 2013

2013-01-01

"The Power of Probability" is a new math program aligned with the National Council of Teachers of Mathematics (NCTM) and Common Core State Standards, which gives students opportunities to practice their skills and knowledge of the mathematics of probability. Developed by The Actuarial Foundation, the program's lessons and worksheets motivate…

Self-assembly and hierarchical patterning of aligned organic nanowire arrays by solvent evaporation on substrates with patterned wettability.

PubMed

Bao, Rong-Rong; Zhang, Cheng-Yi; Zhang, Xiu-Juan; Ou, Xue-Mei; Lee, Chun-Sing; Jie, Jian-Sheng; Zhang, Xiao-Hong

2013-06-26

The controlled growth and alignment of one-dimensional organic nanostructures at well-defined locations considerably hinders the integration of nanostructures for electronic and optoelectronic applications. Here, we demonstrate a simple process to achieve the growth, alignment, and hierarchical patterning of organic nanowires on substrates with controlled patterns of surface wettability. The first-level pattern is confined by the substrate patterns of wettability. Organic nanostructures are preferentially grown on solvent wettable regions. The second-level pattern is the patterning of aligned organic nanowires deposited by controlling the shape and movement of the solution contact lines during evaporation on the wettable regions. This process is controlled by the cover-hat-controlled method or vertical evaportation method. Therefore, various new patterns of organic nanostructures can be obtained by combing these two levels of patterns. This simple method proves to be a general approach that can be applied to other organic nanostructure systems. Using the as-prepared patterned nanowire arrays, an optoelectronic device (photodetector) is easily fabricated. Hence, the proposed simple, large-scale, low-cost method of preparing patterns of highly ordered organic nanostructures has high potential applications in various electronic and optoelectronic devices.

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.

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

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

PubMed Central

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

2013-01-01

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

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.

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.

Laser-Beam-Alignment Controller

NASA Technical Reports Server (NTRS)

Krasowski, M. J.; Dickens, D. E.

1995-01-01

In laser-beam-alignment controller, images from video camera compared to reference patterns by fuzzy-logic pattern comparator. Results processed by fuzzy-logic microcontroller, which sends control signals to motor driver adjusting lens and pinhole in spatial filter.

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

PubMed

Höhl, Michael; Ragan, Mark A

2007-04-01

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

Fabrication of Three-Dimensional Imprint Lithography Templates by Colloidal Dispersions

DTIC Science & Technology

2011-03-06

Dispersions A. Marcia Almanza-Workman, Taussig P. Carl, Albert H. Jeans, Robert L. Cobene HP Laboratories HPL-2011-32 Flexible displays, Self aligned...imprint lithography, stamps, fluorothermoplastics, latex Self -aligned imprint lithography (SAIL) enables patterning and alignment of submicron-sized...features on flexible substrates in the roll-to roll (R2R) environment. Soft molds made of elastomers have been used as stamps to pattern three

A Method for Functional Task Alignment Analysis of an Arthrocentesis Simulator.

PubMed

Adams, Reid A; Gilbert, Gregory E; Buckley, Lisa A; Nino Fong, Rodolfo; Fuentealba, I Carmen; Little, Erika L

2018-05-16

During simulation-based education, simulators are subjected to procedures composed of a variety of tasks and processes. Simulators should functionally represent a patient in response to the physical action of these tasks. The aim of this work was to describe a method for determining whether a simulator does or does not have sufficient functional task alignment (FTA) to be used in a simulation. Potential performance checklist items were gathered from published arthrocentesis guidelines and aggregated into a performance checklist using Lawshe's method. An expert panel used this performance checklist and an FTA analysis questionnaire to evaluate a simulator's ability to respond to the physical actions required by the performance checklist. Thirteen items, from a pool of 39, were included on the performance checklist. Experts had mixed reviews of the simulator's FTA and its suitability for use in simulation. Unexpectedly, some positive FTA was found for several tasks where the simulator lacked functionality. By developing a detailed list of specific tasks required to complete a clinical procedure, and surveying experts on the simulator's response to those actions, educators can gain insight into the simulator's clinical accuracy and suitability. Unexpected of positive FTA ratings of function deficits suggest that further revision of the survey method is required.

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

PubMed

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

2011-06-07

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

Information Compression, Multiple Alignment, and the Representation and Processing of Knowledge in the Brain.

PubMed

Wolff, J Gerard

2016-01-01

The SP theory of intelligence , with its realization in the SP computer model , aims to simplify and integrate observations and concepts across artificial intelligence, mainstream computing, mathematics, and human perception and cognition, with information compression as a unifying theme. This paper describes how abstract structures and processes in the theory may be realized in terms of neurons, their interconnections, and the transmission of signals between neurons. This part of the SP theory- SP-neural -is a tentative and partial model for the representation and processing of knowledge in the brain. Empirical support for the SP theory-outlined in the paper-provides indirect support for SP-neural. In the abstract part of the SP theory (SP-abstract), all kinds of knowledge are represented with patterns , where a pattern is an array of atomic symbols in one or two dimensions. In SP-neural, the concept of a "pattern" is realized as an array of neurons called a pattern assembly , similar to Hebb's concept of a "cell assembly" but with important differences. Central to the processing of information in SP-abstract is information compression via the matching and unification of patterns (ICMUP) and, more specifically, information compression via the powerful concept of multiple alignment , borrowed and adapted from bioinformatics. Processes such as pattern recognition, reasoning and problem solving are achieved via the building of multiple alignments, while unsupervised learning is achieved by creating patterns from sensory information and also by creating patterns from multiple alignments in which there is a partial match between one pattern and another. It is envisaged that, in SP-neural, short-lived neural structures equivalent to multiple alignments will be created via an inter-play of excitatory and inhibitory neural signals. It is also envisaged that unsupervised learning will be achieved by the creation of pattern assemblies from sensory information and from the neural equivalents of multiple alignments, much as in the non-neural SP theory-and significantly different from the "Hebbian" kinds of learning which are widely used in the kinds of artificial neural network that are popular in computer science. The paper discusses several associated issues, with relevant empirical evidence.

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

NASA Technical Reports Server (NTRS)

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

1985-01-01

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

Tile Patterns with LOGO--Part II: Tile Patterns from Rep Tiles Using LOGO.

ERIC Educational Resources Information Center

Clason, Robert G.

1991-01-01

Described is a recursive LOGO method for dissecting polygons into congruent parts (rep tiles) similar to the original polygon, thereby producing unexpected patterns. A list of descriptions for such dissections is included along with suggestions for modifications that allow extended student explorations into tile patterns. (JJK)

Control of fast elbow movement: a study of electromyographic patterns during movements against unexpectedly decreased inertial load.

PubMed

Latash, M L

1994-01-01

Predictions of three models of single-joint motor control were compared with experimental observations of the changes in electromyographic (EMG) patterns during fast voluntary movements against an unexpectedly reduced inertial load. The subjects performed elbow flexions over 40 degrees "as fast as possible" in two series. During the first series, an approximately 40% decrease in inertia, simulated by a torque-motor, might occur unpredictably on half of the trials (unloaded trials). During the second series, all the trials were unloaded. The major findings are: (1) no differences in the antagonist burst latency in unexpectedly unloaded and unperturbed trials; (2) a decrease in the antagonist latency during expected unloadings; (3) a small, statistically non significant decrease in the first agonist burst EMG integral; and (4) a larger, statistically significant increase in the antagonist burst EMG integral in unexpectedly unloaded trials as compared to unperturbed trials. The data are in good correspondence with a version of the equilibrium-point hypothesis that assumes central programming of the beginning of the antagonist burst and incorporates the possibility of reflex-induced changes in EMG amplitudes.

Unexpected inhibition of CO 2 gas hydrate formation in dilute TBAB solutions and the critical role of interfacial water structure

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

Nguyen, Ngoc N.; Nguyen, Anh V.; Nguyen, Khoi T.

Gas hydrates formed under moderated conditions open up novel approaches to tackling issues related to energy supply, gas separation, and CO 2 sequestration. Several additives like tetra-n-butylammonium bromide (TBAB) have been empirically developed and used to promote gas hydrate formation. Here we report unexpected experimental results which show that TBAB inhibits CO 2 gas hydrate formation when used at minuscule concentration. We also used spectroscopic techniques and molecular dynamics simulation to gain further insights and explain the experimental results. They have revealed the critical role of water alignment at the gas-water interface induced by surface adsorption of tetra-n-butylammonium cation (TBAmore » +) which gives rise to the unexpected inhibition of dilute TBAB solution. The water perturbation by TBA + in the bulk is attributed to the promotion effect of high TBAB concentration on gas hydrate formation. We explain our finding using the concept of activation energy of gas hydrate formation. Our results provide a step toward to mastering the control of gas hydrate formation.« less

Massive ordering and alignment of cylindrical micro-objects by photovoltaic optoelectronic tweezers.

PubMed

Elvira, Iris; Muñoz-Martínez, Juan F; Barroso, Álvaro; Denz, Cornelia; Ramiro, José B; García-Cabañes, Angel; Agulló-López, Fernando; Carrascosa, Mercedes

2018-01-01

Optical tools for manipulation and trapping of micro- and nano-objects are a fundamental issue for many applications in nano- and biotechnology. This work reports on the use of one such method, known as photovoltaic optoelectronics tweezers, to orientate and organize cylindrical microcrystals, specifically elongated zeolite L, on the surface of Fe-doped LiNbO 3 crystal plates. Patterns of aligned zeolites have been achieved through the forces and torques generated by the bulk photovoltaic effect. The alignment patterns with zeolites parallel or perpendicular to the substrate surface are highly dependent on the features of light distribution and crystal configuration. Moreover, dielectrophoretic chains of zeolites with lengths up to 100 μm have often been observed. The experimental results of zeolite trapping and alignment have been discussed and compared together with theoretical simulations of the evanescent photovoltaic electric field and the dielectrophoretic potential. They demonstrate the remarkable capabilities of the optoelectronic photovoltaic method to orientate and pattern anisotropic microcrystals. The combined action of patterning and alignment offers a unique tool to prepare functional nanostructures with potential applications in a variety of fields such as nonlinear optics or plasmonics.

Patterned Cell Alignment in Response to Macroscale Curvature

NASA Astrophysics Data System (ADS)

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

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

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

NASA Astrophysics Data System (ADS)

Huang, Shaoming

2003-06-01

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

An anisotropically and heterogeneously aligned patterned electrospun scaffold with tailored mechanical property and improved bioactivity for vascular tissue engineering.

PubMed

Xu, He; Li, Haiyan; Ke, Qinfei; Chang, Jiang

2015-04-29

The development of vascular scaffolds with controlled mechanical properties and stimulatory effects on biological activities of endothelial cells still remains a significant challenge to vascular tissue engineering. In this work, we reported an innovative approach to prepare a new type of vascular scaffolds with anisotropically and heterogeneously aligned patterns using electrospinning technique with unique wire spring templates, and further investigated the structural effects of the patterned electrospun scaffolds on mechanical properties and angiogenic differentiation of human umbilical vein endothelial cells (HUVECs). Results showed that anisotropically aligned patterned nanofibrous structure was obtained by depositing nanofibers on template in a structurally different manner, one part of nanofibers densely deposited on the embossments of wire spring and formed cylindrical-like structures in the transverse direction, while others loosely suspended and aligned along the longitudinal direction, forming a three-dimensional porous microstructure. We further found that such structures could efficiently control the mechanical properties of electrospun vascular scaffolds in both longitudinal and transverse directions by altering the interval distances between the embossments of patterned scaffolds. When HUVECs were cultured on scaffolds with different microstructures, the patterned scaffolds distinctively promoted adhesion of HUVECs at early stage and proliferation during the culture period. Most importantly, cells experienced a large shape change associated with cell cytoskeleton and nuclei remodeling, leading to a stimulatory effect on angiogenesis differentiation of HUVECs by the patterned microstructures of electrospun scaffolds, and the scaffolds with larger distances of intervals showed a higher stimulatory effect. These results suggest that electrospun scaffolds with the anisotropically and heterogeneously aligned patterns, which could efficiently control the mechanical properties and bioactivities of the scaffolds, might have great potential in vascular tissue engineering application.

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

PubMed

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

2011-09-07

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

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

PubMed Central

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

2011-01-01

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

Physiological modules for generating discrete and rhythmic movements: component analysis of EMG signals.

PubMed

Bengoetxea, Ana; Leurs, Françoise; Hoellinger, Thomas; Cebolla, Ana Maria; Dan, Bernard; Cheron, Guy; McIntyre, Joseph

2014-01-01

A central question in Neuroscience is that of how the nervous system generates the spatiotemporal commands needed to realize complex gestures, such as handwriting. A key postulate is that the central nervous system (CNS) builds up complex movements from a set of simpler motor primitives or control modules. In this study we examined the control modules underlying the generation of muscle activations when performing different types of movement: discrete, point-to-point movements in eight different directions and continuous figure-eight movements in both the normal, upright orientation and rotated 90°. To test for the effects of biomechanical constraints, movements were performed in the frontal-parallel or sagittal planes, corresponding to two different nominal flexion/abduction postures of the shoulder. In all cases we measured limb kinematics and surface electromyographic activity (EMG) signals for seven different muscles acting around the shoulder. We first performed principal component analysis (PCA) of the EMG signals on a movement-by-movement basis. We found a surprisingly consistent pattern of muscle groupings across movement types and movement planes, although we could detect systematic differences between the PCs derived from movements performed in each shoulder posture and between the principal components associated with the different orientations of the figure. Unexpectedly we found no systematic differences between the figure eights and the point-to-point movements. The first three principal components could be associated with a general co-contraction of all seven muscles plus two patterns of reciprocal activation. From these results, we surmise that both "discrete-rhythmic movements" such as the figure eight, and discrete point-to-point movement may be constructed from three different fundamental modules, one regulating the impedance of the limb over the time span of the movement and two others operating to generate movement, one aligned with the vertical and the other aligned with the horizontal.

Physiological modules for generating discrete and rhythmic movements: component analysis of EMG signals

PubMed Central

Bengoetxea, Ana; Leurs, Françoise; Hoellinger, Thomas; Cebolla, Ana Maria; Dan, Bernard; Cheron, Guy; McIntyre, Joseph

2015-01-01

A central question in Neuroscience is that of how the nervous system generates the spatiotemporal commands needed to realize complex gestures, such as handwriting. A key postulate is that the central nervous system (CNS) builds up complex movements from a set of simpler motor primitives or control modules. In this study we examined the control modules underlying the generation of muscle activations when performing different types of movement: discrete, point-to-point movements in eight different directions and continuous figure-eight movements in both the normal, upright orientation and rotated 90°. To test for the effects of biomechanical constraints, movements were performed in the frontal-parallel or sagittal planes, corresponding to two different nominal flexion/abduction postures of the shoulder. In all cases we measured limb kinematics and surface electromyographic activity (EMG) signals for seven different muscles acting around the shoulder. We first performed principal component analysis (PCA) of the EMG signals on a movement-by-movement basis. We found a surprisingly consistent pattern of muscle groupings across movement types and movement planes, although we could detect systematic differences between the PCs derived from movements performed in each shoulder posture and between the principal components associated with the different orientations of the figure. Unexpectedly we found no systematic differences between the figure eights and the point-to-point movements. The first three principal components could be associated with a general co-contraction of all seven muscles plus two patterns of reciprocal activation. From these results, we surmise that both “discrete-rhythmic movements” such as the figure eight, and discrete point-to-point movement may be constructed from three different fundamental modules, one regulating the impedance of the limb over the time span of the movement and two others operating to generate movement, one aligned with the vertical and the other aligned with the horizontal. PMID:25620928

Impact of materials engineering on edge placement error (Conference Presentation)

NASA Astrophysics Data System (ADS)

Freed, Regina; Mitra, Uday; Zhang, Ying

2017-04-01

Transistor scaling has transitioned from wavelength scaling to multi-patterning techniques, due to the resolution limits of immersion of immersion lithography. Deposition and etch have enabled scaling in the by means of SADP and SAQP. Spacer based patterning enables extremely small linewidths, sufficient for several future generations of transistors. However, aligning layers in Z-direction, as well as aligning cut and via patterning layers, is becoming a road-block due to global and local feature variation and fidelity. This presentation will highlight the impact of deposition and etch on this feature alignment (EPE) and illustrate potential paths toward lowering EPE using material engineering.

Information Compression, Multiple Alignment, and the Representation and Processing of Knowledge in the Brain

PubMed Central

Wolff, J. Gerard

2016-01-01

The SP theory of intelligence, with its realization in the SP computer model, aims to simplify and integrate observations and concepts across artificial intelligence, mainstream computing, mathematics, and human perception and cognition, with information compression as a unifying theme. This paper describes how abstract structures and processes in the theory may be realized in terms of neurons, their interconnections, and the transmission of signals between neurons. This part of the SP theory—SP-neural—is a tentative and partial model for the representation and processing of knowledge in the brain. Empirical support for the SP theory—outlined in the paper—provides indirect support for SP-neural. In the abstract part of the SP theory (SP-abstract), all kinds of knowledge are represented with patterns, where a pattern is an array of atomic symbols in one or two dimensions. In SP-neural, the concept of a “pattern” is realized as an array of neurons called a pattern assembly, similar to Hebb's concept of a “cell assembly” but with important differences. Central to the processing of information in SP-abstract is information compression via the matching and unification of patterns (ICMUP) and, more specifically, information compression via the powerful concept of multiple alignment, borrowed and adapted from bioinformatics. Processes such as pattern recognition, reasoning and problem solving are achieved via the building of multiple alignments, while unsupervised learning is achieved by creating patterns from sensory information and also by creating patterns from multiple alignments in which there is a partial match between one pattern and another. It is envisaged that, in SP-neural, short-lived neural structures equivalent to multiple alignments will be created via an inter-play of excitatory and inhibitory neural signals. It is also envisaged that unsupervised learning will be achieved by the creation of pattern assemblies from sensory information and from the neural equivalents of multiple alignments, much as in the non-neural SP theory—and significantly different from the “Hebbian” kinds of learning which are widely used in the kinds of artificial neural network that are popular in computer science. The paper discusses several associated issues, with relevant empirical evidence. PMID:27857695

Unexpected Patterns in Snow and Dirt

ERIC Educational Resources Information Center

Ackerson, Bruce J.

2018-01-01

For more than 30 years, Albert A. Bartlett published "Thermal patterns in the snow" in this journal. These are patterns produced by heat sources underneath the snow. Bartlett's articles encouraged me to pay attention to patterns in snow and to understanding them. At winter's end the last snow becomes dirty and is heaped into piles. This…

In Situ alignment system for phase-shifting point-diffraction interferometry

DOEpatents

Goldberg, Kenneth Alan; Naulleau, Patrick P.

2000-01-01

A device and method to facilitate the gross alignment of patterned object- and image-plane masks in optical systems such as the phase-shifting point diffraction interferometer are provided. When an array of similar pinholes or discreet mask fields is used, confusion can occur over the alignment of the focused beams within the field. Adding to the mask pattern a circumscribed or inscribed set of symbols that are identifiable in situ facilitates the unambiguous gross alignment of the object- and/or image-plane masks. Alternatively, a system of markings can be encoded directly into the window shape to accomplish this same task.

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

PubMed

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

2016-10-01

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

High-mobility, aligned crystalline domains of TIPS-pentacene with metastable polymorphs through lateral confinement of crystal growth.

PubMed

Giri, Gaurav; Park, Steve; Vosgueritchian, Michael; Shulaker, Max Marcel; Bao, Zhenan

2014-01-22

Patterns composed of solvent wetting and dewetting regions promote lateral confinement of solution-sheared and lattice-strained TIPS-pentacene crystals. This lateral confinement causes aligned crystal growth, and the smallest patterns of 0.5 μm wide solvent wetting regions promotes formation of highly strained, aligned, and single-crystalline TIPS-pentacene regions with mobility as high as 2.7 cm(2) V(-1) s(-1) . © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

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

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

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

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

PubMed

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

2012-09-25

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

Topologically Micropatterned Collagen and Poly(ε-caprolactone) Struts Fabricated Using the Poly(vinyl alcohol) Fibrillation/Leaching Process To Develop Efficiently Engineered Skeletal Muscle Tissue.

PubMed

Kim, Minseong; Kim, WonJin; Kim, GeunHyung

2017-12-20

Optimally designed three-dimensional (3D) biomedical scaffolds for skeletal muscle tissue regeneration pose significant research challenges. Currently, most studies on scaffolds focus on the two-dimensional (2D) surface structures that are patterned in the micro-/nanoscales with various repeating sizes and shapes to induce the alignment of myoblasts and myotube formation. The 2D patterned surface clearly provides effective analytical results of pattern size and shape of the myoblast alignment and differentiation. However, it is inconvenient in terms of the direct application for clinical usage due to the limited thickness and 3D shapeability. Hence, the present study suggests an innovative hydrogel or synthetic structure that consists of uniaxially surface-patterned cylindrical struts for skeleton muscle regeneration. The alignment of the pattern on the hydrogel (collagen) and poly(ε-caprolactone) struts was attained with the fibrillation of poly(vinyl alcohol) and the leaching process. Various cell culture results indicate that the C2C12 cells on the micropatterned collagen structure were fully aligned, and that a significantly high level of myotube formation was achieved when compared to the collagen structures that were not treated with the micropatterning process.

Mask-to-wafer alignment system

DOEpatents

Sweatt, William C.; Tichenor, Daniel A.; Haney, Steven J.

2003-11-04

A modified beam splitter that has a hole pattern that is symmetric in one axis and anti-symmetric in the other can be employed in a mask-to-wafer alignment device. The device is particularly suited for rough alignment using visible light. The modified beam splitter transmits and reflects light from a source of electromagnetic radiation and it includes a substrate that has a first surface facing the source of electromagnetic radiation and second surface that is reflective of said electromagnetic radiation. The substrate defines a hole pattern about a central line of the substrate. In operation, an input beam from a camera is directed toward the modified beam splitter and the light from the camera that passes through the holes illuminates the reticle on the wafer. The light beam from the camera also projects an image of a corresponding reticle pattern that is formed on the mask surface of the that is positioned downstream from the camera. Alignment can be accomplished by detecting the radiation that is reflected from the second surface of the modified beam splitter since the reflected radiation contains both the image of the pattern from the mask and a corresponding pattern on the wafer.

Theory of mind for processing unexpected events across contexts.

PubMed

Dungan, James A; Stepanovic, Michael; Young, Liane

2016-08-01

Theory of mind, or mental state reasoning, may be particularly useful for making sense of unexpected events. Here, we investigated unexpected behavior across both social and non-social contexts in order to characterize the precise role of theory of mind in processing unexpected events. We used functional magnetic resonance imaging to examine how people respond to unexpected outcomes when initial expectations were based on (i) an object's prior behavior, (ii) an agent's prior behavior and (iii) an agent's mental states. Consistent with prior work, brain regions for theory of mind were preferentially recruited when people first formed expectations about social agents vs non-social objects. Critically, unexpected vs expected outcomes elicited greater activity in dorsomedial prefrontal cortex, which also discriminated in its spatial pattern of activity between unexpected and expected outcomes for social events. In contrast, social vs non-social events elicited greater activity in precuneus across both expected and unexpected outcomes. Finally, given prior information about an agent's behavior, unexpected vs expected outcomes elicited an especially robust response in right temporoparietal junction, and the magnitude of this difference across participants correlated negatively with autistic-like traits. Together, these findings illuminate the distinct contributions of brain regions for theory of mind for processing unexpected events across contexts. © The Author (2016). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Self-aligned grating couplers on template-stripped metal pyramids via nanostencil lithography

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

Klemme, Daniel J.; Johnson, Timothy W.; Mohr, Daniel A.

2016-05-23

We combine nanostencil lithography and template stripping to create self-aligned patterns about the apex of ultrasmooth metal pyramids with high throughput. Three-dimensional patterns such as spiral and asymmetric linear gratings, which can couple incident light into a hot spot at the tip, are presented as examples of this fabrication method. Computer simulations demonstrate that spiral and linear diffraction grating patterns are both effective at coupling light to the tip. The self-aligned stencil lithography technique can be useful for integrating plasmonic couplers with sharp metallic tips for applications such as near-field optical spectroscopy, tip-based optical trapping, plasmonic sensing, and heat-assisted magneticmore » recording.« less

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

PubMed

Taylor, James; Tyekucheva, Svitlana; King, David C; Hardison, Ross C; Miller, Webb; Chiaromonte, Francesca

2006-12-01

Genomic sequence signals - such as base composition, presence of particular motifs, or evolutionary constraint - have been used effectively to identify functional elements. However, approaches based only on specific signals known to correlate with function can be quite limiting. When training data are available, application of computational learning algorithms to multispecies alignments has the potential to capture broader and more informative sequence and evolutionary patterns that better characterize a class of elements. However, effective exploitation of patterns in multispecies alignments is impeded by the vast number of possible alignment columns and by a limited understanding of which particular strings of columns may characterize a given class. We have developed a computational method, called ESPERR (evolutionary and sequence pattern extraction through reduced representations), which uses training examples to learn encodings of multispecies alignments into reduced forms tailored for the prediction of chosen classes of functional elements. ESPERR produces a greatly improved Regulatory Potential score, which can discriminate regulatory regions from neutral sites with excellent accuracy ( approximately 94%). This score captures strong signals (GC content and conservation), as well as subtler signals (with small contributions from many different alignment patterns) that characterize the regulatory elements in our training set. ESPERR is also effective for predicting other classes of functional elements, as we show for DNaseI hypersensitive sites and highly conserved regions with developmental enhancer activity. Our software, training data, and genome-wide predictions are available from our Web site (http://www.bx.psu.edu/projects/esperr).

Automatic target alignment of the Helios laser system

NASA Astrophysics Data System (ADS)

Liberman, I.; Viswanathan, V. K.; Klein, M.; Seery, B. D.

1980-05-01

An automatic target-alignment technique for the Helios laser facility is reported and verified experimentally. The desired alignment condition is completely described by an autocollimation test. A computer program examines the autocollimated return pattern from the surrogate target and correctly describes any changes required in mirror orientation to yield optimum target alignment with either aberrated or misaligned beams. Automated on-line target alignment is thus shown to be feasible.

Setting the Stage with Geometry: Lessons & Worksheets to Build Skills in Measuring Perimeter, Area, Surface Area, and Volume. Poster/Teaching Guide. Expect the Unexpected with Math[R

ERIC Educational Resources Information Center

Actuarial Foundation, 2013

2013-01-01

"Setting the Stage with Geometry" is a new math program aligned with the National Council of Teachers of Mathematics (NCTM) standards that is designed to help students in grades 6-8 build and reinforce basic geometry skills for measuring 2D and 3D shapes. Developed by The Actuarial Foundation, this program seeks to provide skill-building math…

Align-and-shine photolithography

NASA Astrophysics Data System (ADS)

Petrusis, Audrius; Rector, Jan H.; Smith, Kristen; de Man, Sven; Iannuzzi, Davide

2009-10-01

At the beginning of 2009, our group has introduced a new technique that allows fabrication of photolithographic patterns on the cleaved end of an optical fibre: the align-and-shine photolithography technique (see A. Petrušis et al., "The align-and-shine technique for series production of photolithography patterns on optical fibres", J. Micromech. Microeng. 19, 047001, 2009). Align-and-shine photolithography combines standard optical lithography with imagebased active fibre alignment processes. The technique adapts well to series production, opening the way to batch fabrication of fibre-top devices (D. Iannuzzi et al., "Monolithic fibre-top cantilever for critical environments and standard applications", Appl. Phys. Lett. 88, 053501, 2006) and all other devices that rely on suitable machining of engineered parts on the tip of a fibre. In this paper we review our results and briefly discuss its potential applications.

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

ERIC Educational Resources Information Center

Fusaroli, Riccardo; Tylén, Kristian

2016-01-01

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

That note sounds wrong! Age-related effects in processing of musical expectation.

PubMed

Halpern, Andrea R; Zioga, Ioanna; Shankleman, Martin; Lindsen, Job; Pearce, Marcus T; Bhattacharya, Joydeep

2017-04-01

Part of musical understanding and enjoyment stems from the ability to accurately predict what note (or one of a small set of notes) is likely to follow after hearing the first part of a melody. Selective violation of expectations can add to aesthetic response but radical or frequent violations are likely to be disliked or not comprehended. In this study we investigated whether a lifetime of exposure to music among untrained older adults would enhance their reaction to unexpected endings of unfamiliar melodies. Older and younger adults listened to melodies that had expected or unexpected ending notes, according to Western music theory. Ratings of goodness-of-fit were similar in the groups, as was ERP response to the note onset (N1). However, in later time windows (P200 and Late Positive Component), the amplitude of a response to unexpected and expected endings was both larger in older adults, corresponding to greater sensitivity, and more widespread in locus, consistent with a dedifferentiation pattern. Lateralization patterns also differed. We conclude that older adults refine their understanding of this important aspect of music throughout life, with the ability supported by changing patterns of neural activity. Copyright © 2017 Elsevier Inc. All rights reserved.

Self-aligned blocking integration demonstration for critical sub-40nm pitch Mx level patterning

NASA Astrophysics Data System (ADS)

Raley, Angélique; Mohanty, Nihar; Sun, Xinghua; Farrell, Richard A.; Smith, Jeffrey T.; Ko, Akiteru; Metz, Andrew W.; Biolsi, Peter; Devilliers, Anton

2017-04-01

Multipatterning has enabled continued scaling of chip technology at the 28nm node and beyond. Selfaligned double patterning (SADP) and self-aligned quadruple patterning (SAQP) as well as Litho- Etch/Litho-Etch (LELE) iterations are widely used in the semiconductor industry to enable patterning at sub 193 immersion lithography resolutions for layers such as FIN, Gate and critical Metal lines. Multipatterning requires the use of multiple masks which is costly and increases process complexity as well as edge placement error variation driven mostly by overlay. To mitigate the strict overlay requirements for advanced technology nodes (7nm and below), a self-aligned blocking integration is desirable. This integration trades off the overlay requirement for an etch selectivity requirement and enables the cut mask overlay tolerance to be relaxed from half pitch to three times half pitch. Selfalignement has become the latest trend to enable scaling and self-aligned integrations are being pursued and investigated for various critical layers such as contact, via, metal patterning. In this paper we propose and demonstrate a low cost flexible self-aligned blocking strategy for critical metal layer patterning for 7nm and beyond from mask assembly to low -K dielectric etch. The integration is based on a 40nm pitch SADP flow with 2 cut masks compatible with either cut or block integration and employs dielectric films widely used in the back end of the line. As a consequence this approach is compatible with traditional etch, deposition and cleans tools that are optimized for dielectric etches. We will review the critical steps and selectivities required to enable this integration along with bench-marking of each integration option (cut vs. block).

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

PubMed

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

2018-05-09

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

Patterned forests of vertically-aligned multiwalled carbon nanotubes using metal salt catalyst solutions.

PubMed

Garrett, David J; Flavel, Benjamin S; Baronian, Keith H R; Downard, Alison J

2013-01-01

A simple method for producing patterned forests of multiwalled carbon nanotubes (MWCNTs) is described. An aqueous metal salt solution is spin-coated onto a substrate patterned with photoresist by standard methods. The photoresist is removed by acetone washing leaving the acetone-insoluble catalyst pattern on the substrate. Dense forests of vertically aligned (VA) MWCNTs are grown on the patterned catalyst layers by chemical vapour deposition. The procedures have been demonstrated by growing MWCNT forests on two substrates: silicon and conducting graphitic carbon films. The forests adhere strongly to the substrates and when grown directly on carbon film, offer a simple method of preparing MWCNT electrodes.

Field-aligned current associated with a distorted two-cell convection pattern during northward interplanetary magnetic field

NASA Technical Reports Server (NTRS)

Zhu, L.; Schunk, R. W.; Sojka, J. J.

1991-01-01

The influence of the ionospheric conductance on the field-aligned current associated with a distorted two-cell convection pattern during northward IMF was investigated using the Heppner-Maynard (1987) convection model and the Utah State University conductivity model described by Rasmussen and Schunk (1987). Results show that the variation of the ionospheric conductivity distribution can significantly affect the features of the field-aligned current for northward IMF, where matching or mismatching between the conductance gradient and the convection electric field plays a key role. It was found that the increase of the field-aligned current in the polar cap observed during summer is mainly due to the increasing contribution from the Pedersen current, and that the increase of the field-aligned current in both the oval region and the evening-midnight sector during the active aurora period is mainly due to the increasing contribution from the Hall current.

Spatiotemporal alignment of in utero BOLD-MRI series.

PubMed

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

2017-08-01

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

A Semi-Automatic Alignment Method for Math Educational Standards Using the MP (Materialization Pattern) Model

ERIC Educational Resources Information Center

Choi, Namyoun

2010-01-01

Educational standards alignment, which matches similar or equivalent concepts of educational standards, is a necessary task for educational resource discovery and retrieval. Automated or semi-automated alignment systems for educational standards have been recently available. However, existing systems frequently result in inconsistency in…

Remotely controlled spray gun

NASA Technical Reports Server (NTRS)

Cunningham, William C. (Inventor)

1987-01-01

A remotely controlled spray gun is described in which a nozzle and orifice plate are held in precise axial alignment by an alignment member, which in turn is held in alignment with the general outlet of the spray gun by insert. By this arrangement, the precise repeatability of spray patterns is insured.

Interactive Alignment: A Teaching-Friendly View of Second Language Pronunciation Learning

ERIC Educational Resources Information Center

Trofimovich, Pavel

2016-01-01

Interactive alignment is a phenomenon whereby interlocutors adopt and re-use each other's language patterns in the course of authentic interaction. According to the interactive alignment model, originally proposed by Pickering & Garrod (2004), this linguistic coordination is one way in which interlocutors achieve understanding in dialogue,…

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…

Pattern formation of frictional fingers in a gravitational potential

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Changes in Head Stability Control in Response to a Lateral Perturbation while Walking in Older Adults

NASA Technical Reports Server (NTRS)

Buccello, Regina R.; Cromwell, Ronita L.; Bloomberg, Jacob J.

2008-01-01

Falling is a main contributor of injury in older adults. The decline in sensory systems associated with aging limits information needed to successfully compensate for unexpected perturbations. Therefore, sensory changes result in older adults having problems maintaining balance stability when experiencing an unexpected lateral perturbation (e.g. slip) in the environment. The goal of this study was to determine head stability movement strategies used by older adults when experiencing an unexpected lateral perturbation during walking. A total of 16 healthy adults, aged 66-81 years, walked across a foam pathway 6 times. One piece of the foam pathway covered a movable platform that translated to the left when the subject stepped on the foam. Three trials were randomized in which the platform shifted. Angular rate sensors were placed on the center of mass for the head and trunk segments to collect head and trunk movement in all three planes of motion. The predominant movement strategies for maintaining head stability were determined from the results of the cross-correlation analyses between the head and trunk segments. The Chi square test of independence was used to evaluate the movement pattern distributions of head-trunk coordination during perturbed and non-perturbed walking. When perturbed, head stabilization was significantly challenged in the yaw and roll planes of motion. Subjects demonstrated a movement pattern of the head leading the trunk in an effort to stabilize the head. The older adult subjects used this head stabilization movement pattern to compensate for sensory changes when experiencing the unexpected lateral perturbation.

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

PubMed

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

2016-01-01

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

Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation

PubMed Central

Noirot-Gros, Marie-Francoise; Shinde, Shalaka; Larsen, Peter E.; Zerbs, Sarah; Korajczyk, Peter J.; Kemner, Kenneth M.; Noirot, Philippe H.

2018-01-01

Rhizosphere-associated Pseudomonas fluorescens are known plant growth promoting (PGP) and mycorrhizal helper bacteria (MHB) of many plants and ectomycorrhizal fungi. We investigated the spatial and temporal dynamics of colonization of mycorrhizal and non-mycorrhizal Aspen seedlings roots by the P. fluorescens strains SBW25, WH6, Pf0-1, and the P. protegens strain Pf-5. Seedlings were grown in laboratory vertical plates systems, inoculated with a fluorescently labeled Pseudomonas strain, and root colonization was monitored over a period of 5 weeks. We observed unexpected diversity of bacterial assemblies on seedling roots that changed over time and were strongly affected by root mycorrhization. P. fluorescens SBW25 and WH6 stains developed highly structured biofilms with internal void spaces forming channels. On mycorrhizal roots bacteria appeared encased in a mucilaginous substance in which they aligned side by side in parallel arrangements. The different phenotypic classes of bacterial assemblies observed for the four Pseudomonas strains were summarized in a single model describing transitions between phenotypic classes. Our findings also reveal that bacterial assembly phenotypes are driven by interactions with mucilaginous materials present at roots. PMID:29774013

The effect of irregular breathing patterns on internal target volumes in four-dimensional CT and cone-beam CT images in the context of stereotactic lung radiotherapy

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

Clements, N.; Kron, T.; Roxby, P.

2013-02-15

Purpose: Stereotactic lung radiotherapy is complicated by tumor motion from patient respiration. Four-dimensional CT (4DCT) imaging is a motion compensation method used in treatment planning to generate a maximum intensity projection (MIP) internal target volume (ITV). Image guided radiotherapy during treatment may involve acquiring a volumetric cone-beam CT (CBCT) image and visually aligning the tumor to the planning 4DCT MIP ITV contour. Moving targets imaged with CBCT can appear blurred and currently there are no studies reporting on the effect that irregular breathing patterns have on CBCT volumes and their alignment to 4DCT MIP ITV contours. The objective of thismore » work was therefore to image a phantom moving with irregular breathing patterns to determine whether any configurations resulted in errors in volume contouring or alignment. Methods: A Perspex thorax phantom was used to simulate a patient. Three wooden 'lung' inserts with embedded Perspex 'lesions' were moved up to 4 cm with computer-generated motion patterns, and up to 1 cm with patient-specific breathing patterns. The phantom was imaged on 4DCT and CBCT with the same acquisition settings used for stereotactic lung patients in the clinic and the volumes on all phantom images were contoured. This project assessed the volumes for qualitative and quantitative changes including volume, length of the volume, and errors in alignment between CBCT volumes and 4DCT MIP ITV contours. Results: When motion was introduced 4DCT and CBCT volumes were reduced by up to 20% and 30% and shortened by up to 7 and 11 mm, respectively, indicating that volume was being under-represented at the extremes of motion. Banding artifacts were present in 4DCT MIP images, while CBCT volumes were largely reduced in contrast. When variable amplitudes from patient traces were used and CBCT ITVs were compared to 4DCT MIP ITVs there was a distinct trend in reduced ITV with increasing amplitude that was not seen when compared to true ITVs. Breathing patterns with a rest period following expiration resulted in well-defined superior edges and were better aligned using an edge-to-edge alignment technique. In most cases, sinusoidal motion patterns resulted in the closest agreements to true values and the smallest misalignments. Conclusions: Strategies are needed to compensate for volume losses at the extremes of motion for both 4DCT MIP and CBCT images for larger and varied amplitudes, and for patterns with rest periods following expiration. Lesions moving greater than 2 cm would warrant larger treatment margins added to the 4DCT MIP ITV to account for the volume being under-represented at the extremes of motion. Lesions moving with a rest period following expiration would be better aligned using an edge-to-edge alignment technique. Sinusoidal patterns represented the ideal clinical scenario, reinforcing the importance of investigating clinically relevant motions and their effects on 4DCT MIP and CBCT volumes. Since most patients do not breathe sinusoidally this may lead to misinterpretation of previous studies using only sinusoidal motion.« less

The effect of irregular breathing patterns on internal target volumes in four-dimensional CT and cone-beam CT images in the context of stereotactic lung radiotherapy.

PubMed

Clements, N; Kron, T; Franich, R; Dunn, L; Roxby, P; Aarons, Y; Chesson, B; Siva, S; Duplan, D; Ball, D

2013-02-01

Stereotactic lung radiotherapy is complicated by tumor motion from patient respiration. Four-dimensional CT (4DCT) imaging is a motion compensation method used in treatment planning to generate a maximum intensity projection (MIP) internal target volume (ITV). Image guided radiotherapy during treatment may involve acquiring a volumetric cone-beam CT (CBCT) image and visually aligning the tumor to the planning 4DCT MIP ITV contour. Moving targets imaged with CBCT can appear blurred and currently there are no studies reporting on the effect that irregular breathing patterns have on CBCT volumes and their alignment to 4DCT MIP ITV contours. The objective of this work was therefore to image a phantom moving with irregular breathing patterns to determine whether any configurations resulted in errors in volume contouring or alignment. A Perspex thorax phantom was used to simulate a patient. Three wooden "lung" inserts with embedded Perspex "lesions" were moved up to 4 cm with computer-generated motion patterns, and up to 1 cm with patient-specific breathing patterns. The phantom was imaged on 4DCT and CBCT with the same acquisition settings used for stereotactic lung patients in the clinic and the volumes on all phantom images were contoured. This project assessed the volumes for qualitative and quantitative changes including volume, length of the volume, and errors in alignment between CBCT volumes and 4DCT MIP ITV contours. When motion was introduced 4DCT and CBCT volumes were reduced by up to 20% and 30% and shortened by up to 7 and 11 mm, respectively, indicating that volume was being under-represented at the extremes of motion. Banding artifacts were present in 4DCT MIP images, while CBCT volumes were largely reduced in contrast. When variable amplitudes from patient traces were used and CBCT ITVs were compared to 4DCT MIP ITVs there was a distinct trend in reduced ITV with increasing amplitude that was not seen when compared to true ITVs. Breathing patterns with a rest period following expiration resulted in well-defined superior edges and were better aligned using an edge-to-edge alignment technique. In most cases, sinusoidal motion patterns resulted in the closest agreements to true values and the smallest misalignments. Strategies are needed to compensate for volume losses at the extremes of motion for both 4DCT MIP and CBCT images for larger and varied amplitudes, and for patterns with rest periods following expiration. Lesions moving greater than 2 cm would warrant larger treatment margins added to the 4DCT MIP ITV to account for the volume being under-represented at the extremes of motion. Lesions moving with a rest period following expiration would be better aligned using an edge-to-edge alignment technique. Sinusoidal patterns represented the ideal clinical scenario, reinforcing the importance of investigating clinically relevant motions and their effects on 4DCT MIP and CBCT volumes. Since most patients do not breathe sinusoidally this may lead to misinterpretation of previous studies using only sinusoidal motion.

Expression of secreted Wnt pathway components reveals unexpected complexity of the planarian amputation response.

PubMed

Gurley, Kyle A; Elliott, Sarah A; Simakov, Oleg; Schmidt, Heiko A; Holstein, Thomas W; Sánchez Alvarado, Alejandro

2010-11-01

Regeneration is widespread throughout the animal kingdom, but our molecular understanding of this process in adult animals remains poorly understood. Wnt/β-catenin signaling plays crucial roles throughout animal life from early development to adulthood. In intact and regenerating planarians, the regulation of Wnt/β-catenin signaling functions to maintain and specify anterior/posterior (A/P) identity. Here, we explore the expression kinetics and RNAi phenotypes for secreted members of the Wnt signaling pathway in the planarian Schmidtea mediterranea. Smed-wnt and sFRP expression during regeneration is surprisingly dynamic and reveals fundamental aspects of planarian biology that have been previously unappreciated. We show that after amputation, a wounding response precedes rapid re-organization of the A/P axis. Furthermore, cells throughout the body plan can mount this response and reassess their new A/P location in the complete absence of stem cells. While initial stages of the amputation response are stem cell independent, tissue remodeling and the integration of a new A/P address with anatomy are stem cell dependent. We also show that WNT5 functions in a reciprocal manner with SLIT to pattern the planarian mediolateral axis, while WNT11-2 patterns the posterior midline. Moreover, we perform an extensive phylogenetic analysis on the Smed-wnt genes using a method that combines and integrates both sequence and structural alignments, enabling us to place all nine genes into Wnt subfamilies for the first time. Copyright © 2010 Elsevier Inc. All rights reserved.

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

PubMed

Zwickl, Derrick J; Stein, Joshua C; Wing, Rod A; Ware, Doreen; Sanderson, Michael J

2014-09-01

We describe new methods for characterizing gene tree discordance in phylogenomic data sets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short arm of chromosome 3 in Oryza (rice) species, we applied these methods to identify the causes and consequences of differing patterns of discordance in the sets of gene trees inferred using a panel of 20 distinct analysis pipelines. We found that discordance patterns were strongly affected by aspects of data selection, alignment, and alignment masking. Unusual patterns of discordance evident when using certain pipelines were reduced or eliminated by using alternative pipelines, suggesting that they were the product of methodological biases rather than evolutionary processes. In some cases, once such biases were eliminated, evolutionary processes such as introgression could be implicated. Additionally, patterns of gene tree discordance had significant downstream impacts on species tree inference. For example, inference from supermatrices was positively misleading when pipelines that led to biased gene trees were used. Several results may generalize to other data sets: we found that gene tree and species tree inference gave more reasonable results when intron sequence was included during sequence alignment and tree inference, the alignment software PRANK was used, and detectable "block-shift" alignment artifacts were removed. We discuss our findings in the context of well-established relationships in Oryza and continuing controversies regarding the domestication history of O. sativa. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Consistency functional map propagation for repetitive patterns

NASA Astrophysics Data System (ADS)

Wang, Hao

2017-09-01

Repetitive patterns appear frequently in both man-made and natural environments. Automatically and robustly detecting such patterns from an image is a challenging problem. We study repetitive pattern alignment by embedding segmentation cue with a functional map model. However, this model cannot tackle the repetitive patterns directly due to the large photometric and geometric variations. Thus, a consistency functional map propagation (CFMP) algorithm that extends the functional map with dynamic propagation is proposed to address this issue. This propagation model is acquired in two steps. The first one aligns the patterns from a local region, transferring segmentation functions among patterns. It can be cast as an L norm optimization problem. The latter step updates the template segmentation for the next round of pattern discovery by merging the transferred segmentation functions. Extensive experiments and comparative analyses have demonstrated an encouraging performance of the proposed algorithm in detection and segmentation of repetitive patterns.

Self-aligned quadruple patterning using spacer on spacer integration optimization for N5

NASA Astrophysics Data System (ADS)

Thibaut, Sophie; Raley, Angélique; Mohanty, Nihar; Kal, Subhadeep; Liu, Eric; Ko, Akiteru; O'Meara, David; Tapily, Kandabara; Biolsi, Peter

2017-04-01

To meet scaling requirements, the semiconductor industry has extended 193nm immersion lithography beyond its minimum pitch limitation using multiple patterning schemes such as self-aligned double patterning, self-aligned quadruple patterning and litho-etch / litho etch iterations. Those techniques have been declined in numerous options in the last few years. Spacer on spacer pitch splitting integration has been proven to show multiple advantages compared to conventional pitch splitting approach. Reducing the number of pattern transfer steps associated with sacrificial layers resulted in significant decrease of cost and an overall simplification of the double pitch split technique. While demonstrating attractive aspects, SAQP spacer on spacer flow brings challenges of its own. Namely, material set selections and etch chemistry development for adequate selectivities, mandrel shape and spacer shape engineering to improve edge placement error (EPE). In this paper we follow up and extend upon our previous learning and proceed into more details on the robustness of the integration in regards to final pattern transfer and full wafer critical dimension uniformity. Furthermore, since the number of intermediate steps is reduced, one will expect improved uniformity and pitch walking control. This assertion will be verified through a thorough pitch walking analysis.

Target volume geometric change and/or deviation from the cranium during fractionated stereotactic radiotherapy for brain metastases: potential pitfalls in image guidance based on bony anatomy alignment.

PubMed

Ohtakara, Kazuhiro; Hoshi, Hiroaki

2014-12-01

This study sought to evaluate the potential geometrical change and/or displacement of the target relative to the cranium during fractionated stereotactic radiotherapy (FSRT) for treating newly developed brain metastases. For 16 patients with 21 lesions treated with image-guided frameless FSRT in 5 or 10 fractions using a 6-degree-of-freedom image guidance system-integrated platform, the unenhanced computed tomography or T2-weighted magnetic resonance images acquired until the completion of FSRT were fused to the planning image datasets for comparison. Significant change was defined as ≥3-mm change in the tumour diameter or displacement of the tumour centroid. FSRT was started 1 day after planning image acquisition. Tumour shrinkage, deviation and both were observed in 2, 1 and 1 of the 21 lesions, respectively, over a period of 7-13 days. Tumour shrinkage or deviation resulted in an increase or decrease in the marginal dose to the tumour, respectively, and a substantial increase in the irradiated volume for the surrounding tissue irrespective of the pattern of alteration. No obvious differences in the clinical and treatment characteristics were noted among the populations with or without significant changes in tumour volume or position. Target deformity and/or deviation can unexpectedly occur even during relatively short-course FSRT, inevitably leading to a gradual discrepancy between the planned and actually delivered doses to the tumour and surrounding tissue. To appropriately weigh the treatment outcome against the planned dose distribution, target deformity and/or deviation should also be considered in addition to the immobilisation accuracy, as image guidance with bony anatomy alignment does not necessarily guarantee accurate target localisation until completion of FSRT. © 2014 The Royal Australian and New Zealand College of Radiologists.

Pattern optimizing verification of self-align quadruple patterning

NASA Astrophysics Data System (ADS)

Yamato, Masatoshi; Yamada, Kazuki; Oyama, Kenichi; Hara, Arisa; Natori, Sakurako; Yamauchi, Shouhei; Koike, Kyohei; Yaegashi, Hidetami

2017-03-01

Lithographic scaling continues to advance by extending the life of 193nm immersion technology, and spacer-type multi-patterning is undeniably the driving force behind this trend. Multi-patterning techniques such as self-aligned double patterning (SADP) and self-aligned quadruple patterning (SAQP) have come to be used in memory devices, and they have also been adopted in logic devices to create constituent patterns in the formation of 1D layout designs. Multi-patterning has consequently become an indispensible technology in the fabrication of all advanced devices. In general, items that must be managed when using multi-patterning include critical dimension uniformity (CDU), line edge roughness (LER), and line width roughness (LWR). Recently, moreover, there has been increasing focus on judging and managing pattern resolution performance from a more detailed perspective and on making a right/wrong judgment from the perspective of edge placement error (EPE). To begin with, pattern resolution performance in spacer-type multi-patterning is affected by the process accuracy of the core (mandrel) pattern. Improving the controllability of CD and LER of the mandrel is most important, and to reduce LER, an appropriate smoothing technique should be carefully selected. In addition, the atomic layer deposition (ALD) technique is generally used to meet the need for high accuracy in forming the spacer film. Advances in scaling are accompanied by stricter requirements in the controllability of fine processing. In this paper, we first describe our efforts in improving controllability by selecting the most appropriate materials for the mandrel pattern and spacer film. Then, based on the materials selected, we present experimental results on a technique for improving etching selectivity.

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

PubMed

Neuwald, Andrew F

2009-08-01

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

Vertical Alignment of Single-Walled Carbon Nanotubes on Nanostructure Fabricated by Atomic Force Microscope

DTIC Science & Technology

2007-03-30

Langmuir - Blodgett and self-assembly methods, WNTs are patterned selectively onto various substrates [3,4]. hou et al. assembled SWNTs into aligned...dispersion usually decreases with increasing ionic concentration, it is suggested that chloride ions are produced by dissociating from acid chloride groups...patterns can be attributed to the Marangoni effect and diffusion-limited aggregation (DLA) in the liquid film during droplet evaporation t different

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.

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

PubMed

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

2010-02-23

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

Robust passive dynamics of the musculoskeletal system compensate for unexpected surface changes during human hopping

PubMed Central

van der Krogt, Marjolein M.; de Graaf, Wendy W.; Farley, Claire T.; Moritz, Chet T.; Richard Casius, L. J.; Bobbert, Maarten F.

2009-01-01

When human hoppers are surprised by a change in surface stiffness, they adapt almost instantly by changing leg stiffness, implying that neural feedback is not necessary. The goal of this simulation study was first to investigate whether leg stiffness can change without neural control adjustment when landing on an unexpected hard or unexpected compliant (soft) surface, and second to determine what underlying mechanisms are responsible for this change in leg stiffness. The muscle stimulation pattern of a forward dynamic musculoskeletal model was optimized to make the model match experimental hopping kinematics on hard and soft surfaces. Next, only surface stiffness was changed to determine how the mechanical interaction of the musculoskeletal model with the unexpected surface affected leg stiffness. It was found that leg stiffness adapted passively to both unexpected surfaces. On the unexpected hard surface, leg stiffness was lower than on the soft surface, resulting in close-to-normal center of mass displacement. This reduction in leg stiffness was a result of reduced joint stiffness caused by lower effective muscle stiffness. Faster flexion of the joints due to the interaction with the hard surface led to larger changes in muscle length, while the prescribed increase in active state and resulting muscle force remained nearly constant in time. Opposite effects were found on the unexpected soft surface, demonstrating the bidirectional stabilizing properties of passive dynamics. These passive adaptations to unexpected surfaces may be critical when negotiating disturbances during locomotion across variable terrain. PMID:19589956

Method for nanoscale spatial registration of scanning probes with substrates and surfaces

NASA Technical Reports Server (NTRS)

Wade, Lawrence A. (Inventor)

2010-01-01

Embodiments in accordance with the present invention relate to methods and apparatuses for aligning a scanning probe used to pattern a substrate, by comparing the position of the probe to a reference location or spot on the substrate. A first light beam is focused on a surface of the substrate as a spatial reference point. A second light beam then illuminates the scanning probe being used for patterning. An optical microscope images both the focused light beam, and a diffraction pattern, shadow, or light backscattered by the illuminated scanning probe tip of a scanning probe microscope (SPM), which is typically the tip of the scanning probe on an atomic force microscope (AFM). Alignment of the scanning probe tip relative to the mark is then determined by visual observation of the microscope image. This alignment process may be repeated to allow for modification or changing of the scanning probe microscope tip.

Three-dimensional direct cell patterning in collagen hydrogels with near-infrared femtosecond laser

PubMed Central

Hribar, Kolin C.; Meggs, Kyle; Liu, Justin; Zhu, Wei; Qu, Xin; Chen, Shaochen

2015-01-01

We report a methodology for three-dimensional (3D) cell patterning in a hydrogel in situ. Gold nanorods within a cell-encapsulating collagen hydrogel absorb a focused near-infrared femtosecond laser beam, locally denaturing the collagen and forming channels, into which cells migrate, proliferate, and align in 3D. Importantly, pattern resolution is tunable based on writing speed and laser power, and high cell viability (>90%) is achieved using higher writing speeds and lower laser intensities. Overall, this patterning technique presents a flexible direct-write method that is applicable in tissue engineering systems where 3D alignment is critical (such as vascular, neural, cardiac, and muscle tissue). PMID:26603915

Alignment of nematic liquid crystals by inhomogeneous surfaces

NASA Astrophysics Data System (ADS)

Ong, Hiap Liew; Hurd, Alan J.; Meyer, Robert B.

1985-01-01

Variable oblique alignment of nematic liquid crystals has been achieved on microscopically inhomogeneous surfaces. The surfaces consist of small patches favoring vertical (homeotropic) alignment surrounded by a matrix favoring a planar alignment. The construction of these surfaces employs randomly distributed microscopic metal islands formed by certain metals as vapor-deposited films. Larger scale periodic patterns were made as well to verify the techniques. The results are interpreted in terms of a continuum elasticity theory and azimuthal degeneracy is also discussed.

Concentration solar power optimization system and method of using the same

DOEpatents

Andraka, Charles E

2014-03-18

A system and method for optimizing at least one mirror of at least one CSP system is provided. The system has a screen for displaying light patterns for reflection by the mirror, a camera for receiving a reflection of the light patterns from the mirror, and a solar characterization tool. The solar characterization tool has a characterizing unit for determining at least one mirror parameter of the mirror based on an initial position of the camera and the screen, and a refinement unit for refining the determined parameter(s) based on an adjusted position of the camera and screen whereby the mirror is characterized. The system may also be provided with a solar alignment tool for comparing at least one mirror parameter of the mirror to a design geometry whereby an alignment error is defined, and at least one alignment unit for adjusting the mirror to reduce the alignment error.

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.

Size Effects in Dye-Sensitized TiO2 Clusters

NASA Astrophysics Data System (ADS)

Marom, Noa; Körzdörfer, Thomas; Ren, Xinguo; Tkatchenko, Alexandre; Chelikowsky, James

2014-03-01

The development of solar cells is driven by the need for clean and sustainable energy. Organic and dye sensitized cells are considered as promising technologies, particularly for large area, low cost applications. However, the efficiency of such cells is still far from the theoretical limit. Ab initio simulations may be used for computer-aided design of new materials and nano-structures for more efficient solar cells. It is essential to obtain an accurate description of the electronic structure, including the fundamental gaps and energy level alignment at the interfaces in the device active region. This requires going beyond ground-state DFT to the GW approximation. A recently developed GW method [PRB 86, 041110R (2012)] is applied to dye-sensitized TiO2 clusters [PRB 84, 245115 (2011)]. The effect of cluster size on the energy level alignment at the dye-TiO2 interface is discussed. With the increase in the TiO2 cluster size its gap narrows. The gap of the molecule attached to the cluster subsequently narrows due to screening. As a result, the energy level alignment at the interface changes in an unexpected way [Marom, Körzdörfer, Ren, Tkatchenko, Chelikowsky, to be published].

Self-aligning and compressed autosophy video databases

NASA Astrophysics Data System (ADS)

Holtz, Klaus E.

1993-04-01

Autosophy, an emerging new science, explains `self-assembling structures,' such as crystals or living trees, in mathematical terms. This research provides a new mathematical theory of `learning' and a new `information theory' which permits the growing of self-assembling data network in a computer memory similar to the growing of `data crystals' or `data trees' without data processing or programming. Autosophy databases are educated very much like a human child to organize their own internal data storage. Input patterns, such as written questions or images, are converted to points in a mathematical omni dimensional hyperspace. The input patterns are then associated with output patterns, such as written answers or images. Omni dimensional information storage will result in enormous data compression because each pattern fragment is only stored once. Pattern recognition in the text or image files is greatly simplified by the peculiar omni dimensional storage method. Video databases will absorb input images from a TV camera and associate them with textual information. The `black box' operations are totally self-aligning where the input data will determine their own hyperspace storage locations. Self-aligning autosophy databases may lead to a new generation of brain-like devices.

CodonLogo: a sequence logo-based viewer for codon patterns.

PubMed

Sharma, Virag; Murphy, David P; Provan, Gregory; Baranov, Pavel V

2012-07-15

Conserved patterns across a multiple sequence alignment can be visualized by generating sequence logos. Sequence logos show each column in the alignment as stacks of symbol(s) where the height of a stack is proportional to its informational content, whereas the height of each symbol within the stack is proportional to its frequency in the column. Sequence logos use symbols of either nucleotide or amino acid alphabets. However, certain regulatory signals in messenger RNA (mRNA) act as combinations of codons. Yet no tool is available for visualization of conserved codon patterns. We present the first application which allows visualization of conserved regions in a multiple sequence alignment in the context of codons. CodonLogo is based on WebLogo3 and uses the same heuristics but treats codons as inseparable units of a 64-letter alphabet. CodonLogo can discriminate patterns of codon conservation from patterns of nucleotide conservation that appear indistinguishable in standard sequence logos. The CodonLogo source code and its implementation (in a local version of the Galaxy Browser) are available at http://recode.ucc.ie/CodonLogo and through the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/.

Neural Responses to Electrical Stimulation on Patterned Silk Films

PubMed Central

Hronik-Tupaj, Marie; Raja, Waseem Khan; Tang-Schomer, Min; Omenetto, Fiorenzo G.; Kaplan, David L.

2013-01-01

Peripheral nerve injury is a critical issue for trauma patients. Following injury, incomplete axon regeneration or misguided axon innervation into tissue will result in loss of sensory and motor functions. The objective of this study was to examine axon outgrowth and axon alignment in response to surface patterning and electrical stimulation. To accomplish our objective, metal electrodes with dimensions of 1.5 mm × 4 cm, were sputter coated onto micropatterned silk protein films, with surface grooves 3.5 μm wide × 500 nm deep. P19 neurons were seeded on the patterned electronic silk films and stimulated at 120 mV, 1 kHz, for 45 minutes each day for 7 days. Responses were compared to neurons on flat electronic silk films, patterned silk films without stimulation, and flat silk films without stimulation. Significant alignment was found on the patterned film groups compared to the flat film groups. Axon outgrowth was greater (p < 0.05) on electronic films on day 5 and day 7 compared to the unstimulated groups. In conclusion, electrical stimulation, at 120 mV, 1 kHz, for 45 minutes daily, in addition to surface patterning, of 3.5 μm wide × 500 nm deep grooves, offered control of nerve axon outgrowth and alignment. PMID:23401351

Advanced electric-field scanning probe lithography on molecular resist using active cantilever

NASA Astrophysics Data System (ADS)

Kaestner, Marcus; Aydogan, Cemal; Ivanov, Tzvetan; Ahmad, Ahmad; Angelov, Tihomir; Reum, Alexander; Ishchuk, Valentyn; Krivoshapkina, Yana; Hofer, Manuel; Lenk, Steve; Atanasov, Ivaylo; Holz, Mathias; Rangelow, Ivo W.

2015-07-01

The routine "on demand" fabrication of features smaller than 10 nm opens up new possibilities for the realization of many devices. Driven by the thermally actuated piezoresistive cantilever technology, we have developed a prototype of a scanning probe lithography (SPL) platform which is able to image, inspect, align, and pattern features down to the single digit nanoregime. Here, we present examples of practical applications of the previously published electric-field based current-controlled scanning probe lithography. In particular, individual patterning tests are carried out on calixarene by using our developed table-top SPL system. We have demonstrated the application of a step-and-repeat SPL method including optical as well as atomic force microscopy-based navigation and alignment. The closed-loop lithography scheme was applied to sequentially write positive and negative tone features. Due to the integrated unique combination of read-write cycling, each single feature is aligned separately with the highest precision and inspected after patterning. This routine was applied to create a pattern step by step. Finally, we have demonstrated the patterning over larger areas, over existing topography, and the practical applicability of the SPL processes for lithography down to 13-nm pitch patterns. To enhance the throughput capability variable beam diameter electric field, current-controlled SPL is briefly discussed.

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

PubMed

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

2017-06-01

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

Optical Alignment of the Global Precipitation Measurement (GPM) Star Trackers

NASA Technical Reports Server (NTRS)

Hetherington, Samuel; Osgood, Dean; McMann, Joe; Roberts, Viki; Gill, James; Mclean, Kyle

2013-01-01

The optical alignment of the star trackers on the Global Precipitation Measurement (GPM) core spacecraft at NASA Goddard Space Flight Center (GSFC) was challenging due to the layout and structural design of the GPM Lower Bus Structure (LBS) in which the star trackers are mounted as well as the presence of the star tracker shades that blocked line-of-sight to the primary star tracker optical references. The initial solution was to negotiate minor changes in the original LBS design to allow for the installation of a removable item of ground support equipment (GSE) that could be installed whenever measurements of the star tracker optical references were needed. However, this GSE could only be used to measure secondary optical reference cube faces not used by the star tracker vendor to obtain the relationship information and matrix transformations necessary to determine star tracker alignment. Unfortunately, due to unexpectedly large orthogonality errors between the measured secondary adjacent cube faces and the lack of cube calibration data, we required a method that could be used to measure the same reference cube faces as originally measured by the vendor. We describe an alternative technique to theodolite auto-collimation for measurement of an optical reference mirror pointing direction when normal incidence measurements are not possible. This technique was used to successfully align the GPM star trackers and has been used on a number of other NASA flight projects. We also discuss alignment theory as well as a GSFC-developed theodolite data analysis package used to analyze angular metrology data.

Retinoic acid regulates size, pattern and alignment of tissues at the head-trunk transition.

PubMed

Lee, Keun; Skromne, Isaac

2014-11-01

At the head-trunk transition, hindbrain and spinal cord alignment to occipital and vertebral bones is crucial for coherent neural and skeletal system organization. Changes in neural or mesodermal tissue configuration arising from defects in the specification, patterning or relative axial placement of territories can severely compromise their integration and function. Here, we show that coordination of neural and mesodermal tissue at the zebrafish head-trunk transition crucially depends on two novel activities of the signaling factor retinoic acid (RA): one specifying the size and the other specifying the axial position relative to mesodermal structures of the hindbrain territory. These activities are each independent but coordinated with the well-established function of RA in hindbrain patterning. Using neural and mesodermal landmarks we demonstrate that the functions of RA in aligning neural and mesodermal tissues temporally precede the specification of hindbrain and spinal cord territories and the activation of hox transcription. Using cell transplantation assays we show that RA activity in the neuroepithelium regulates hindbrain patterning directly and territory size specification indirectly. This indirect function is partially dependent on Wnts but independent of FGFs. Importantly, RA specifies and patterns the hindbrain territory by antagonizing the activity of the spinal cord specification gene cdx4; loss of Cdx4 rescues the defects associated with the loss of RA, including the reduction in hindbrain size and the loss of posterior rhombomeres. We propose that at the head-trunk transition, RA coordinates specification, patterning and alignment of neural and mesodermal tissues that are essential for the organization and function of the neural and skeletal systems. © 2014. Published by The Company of Biologists Ltd.

Multicolor microcontact printing of proteins on nanoporous surface for patterned immunoassay

NASA Astrophysics Data System (ADS)

Ng, Elaine; Gopal, Ashwini; Hoshino, Kazunori; Zhang, Xiaojing

2011-07-01

The large scale patterning of therapeutic proteins is a key to the efficient design, characterization, and production of biologics for cost effective, high throughput, and point-of-care detection and analysis system. We demonstrate an efficient method for protein deposition and adsorption on nanoporous silica substrates in specific patterns using a method called "micro-contact printing". Multiple color-tagged proteins can be printed through sequential application of such micro-patterning technique. Two groups of experiments were performed. In the first group, the protein stamp was aligned precisely with the printing sites, where the stamp was applied multiple times. Optimal conditions were identified for protein transfer and adsorption using the pore size of 4 nm and thickness of 30 nm porous silica thin film. In the second group, we demonstrate the patterning of two-color rabbit immunoglobin labeled with fluorescein isothiocyanate and tetramethyl rhodamine iso-thiocyanate on porous silica substrates that have a pore size 4 nm, porosity 57% and thickness of the porous layer 30 nm. A pair of protein stamps, with corresponding alignment markings and coupled patterns, were aligned and used to produce a two-colored stamp pattern of proteins on porous silica. Different colored proteins can be applied to exemplify the diverse protein composition within a sample. This method of multicolor microcontact printing can be used to perform a fluorescence-based patterned enzyme-linked immunosorbent assay to detect the presence of various proteins within a sample.

Film patterned retarder for stereoscopic three-dimensional display using ink-jet printing method.

PubMed

Lim, Young Jin; Yu, Ji Hoon; Song, Ki Hoon; Lee, Myong-Hoon; Ren, Hongwen; Mun, Byung-June; Lee, Gi-Dong; Lee, Seung Hee

2014-09-22

We propose a film patterned retarder (FPR) for stereoscopic three-dimensional display with polarization glasses using ink-jet printing method. Conventional FPR process requires coating of photo-alignment and then UV exposure using wire-grid mask, which is very expensive and difficult. The proposed novel fabrication method utilizes a plastic substrate made of polyether sulfone and an alignment layer, poly (4, 4' - (9, 9 -fluorenyl) diphenylene cyclobutanyltetracarboximide) (9FDA/CBDA) in which the former and the latter aligns reactive mesogen along and perpendicular to the rubbing direction, respectively. The ink-jet printing of 9FDA/CBDA line by line allows fabricating the cost effective FPR which can be widely applied for 3D display applications.

Self-aligned spatial filtering using laser optical tweezers.

PubMed

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

2006-09-01

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

Growth of high-aspect ratio horizontally-aligned ZnO nanowire arrays.

PubMed

Soman, Pranav; Darnell, Max; Feldman, Marc D; Chen, Shaochen

2011-08-01

A method of fabricating horizontally-aligned zinc-oxide (ZnO) nanowire (NW) arrays with full control over the width and length is demonstrated. SEM images reveal the hexagonal structure typical of zinc oxide NWs. Arrays of high-aspect ratio horizontal ZnO NWs are fabricated by making use of the lateral overgrowth from dot patterns created by electron beam lithography (EBL). An array of patterned wires are lifted off and transferred to a flexible PDMS substrate with possible applications in several key nanotechnology areas.

Fourier-transform and global contrast interferometer alignment methods

DOEpatents

Goldberg, Kenneth A.

2001-01-01

Interferometric methods are presented to facilitate alignment of image-plane components within an interferometer and for the magnified viewing of interferometer masks in situ. Fourier-transforms are performed on intensity patterns that are detected with the interferometer and are used to calculate pseudo-images of the electric field in the image plane of the test optic where the critical alignment of various components is being performed. Fine alignment is aided by the introduction and optimization of a global contrast parameter that is easily calculated from the Fourier-transform.

Wet-spinning fabrication of shear-patterned alginate hydrogel microfibers and the guidance of cell alignment

PubMed Central

Yang, You; Sun, Jing; Liu, Xiaolu; Guo, Zhenzhen; He, Yunhu; Wei, Dan; Zhong, Meiling; Guo, Likun; Zhang, Xingdong

2017-01-01

Abstract Native tissue is naturally comprised of highly-ordered cell-matrix assemblies in a multi-hierarchical way, and the nano/submicron alignment of fibrous matrix is found to be significant in supporting cellular functionalization. In this study, a self-designed wet-spinning device appended with a rotary receiving pool was used to continuously produce shear-patterned hydrogel microfibers with aligned submicron topography. The process that the flow-induced shear force reshapes the surface of hydrogel fiber into aligned submicron topography was systematically analysed. Afterwards, the effect of fiber topography on cellular longitudinal spread and elongation was investigated by culturing rat neuron-like PC12 cells and human osteosarcoma MG63 cells with the spun hydrogel microfibers, respectively. The results suggested that the stronger shear flow force would lead to more distinct aligned submicron topography on fiber surface, which could induce cell orientation along with fiber axis and therefore form the cell-matrix dual-alignment. Finally, a multi-hierarchical tissue-like structure constructed by dual-oriented cell-matrix assemblies was fabricated based on this wet-spinning method. This work is believed to be a potentially novel biofabrication scheme for bottom-up constructing of engineered linear tissue, such as nerve bundle, cortical bone, muscle and hepatic cord. PMID:29026644

Dual-color STED microscopy reveals a sandwich structure of Bassoon and Piccolo in active zones of adult and aged mice.

PubMed

Nishimune, Hiroshi; Badawi, Yomna; Mori, Shuuichi; Shigemoto, Kazuhiro

2016-06-20

Presynaptic active zones play a pivotal role as synaptic vesicle release sites for synaptic transmission, but the molecular architecture of active zones in mammalian neuromuscular junctions (NMJs) at sub-diffraction limited resolution remains unknown. Bassoon and Piccolo are active zone specific cytosolic proteins essential for active zone assembly in NMJs, ribbon synapses, and brain synapses. These proteins are thought to colocalize and share some functions at active zones. Here, we report an unexpected finding of non-overlapping localization of these two proteins in mouse NMJs revealed using dual-color stimulated emission depletion (STED) super resolution microscopy. Piccolo puncta sandwiched Bassoon puncta and aligned in a Piccolo-Bassoon-Piccolo structure in adult NMJs. P/Q-type voltage-gated calcium channel (VGCC) puncta colocalized with Bassoon puncta. The P/Q-type VGCC and Bassoon protein levels decreased significantly in NMJs from aged mouse. In contrast, the Piccolo levels in NMJs from aged mice were comparable to levels in adult mice. This study revealed the molecular architecture of active zones in mouse NMJs at sub-diffraction limited resolution, and described the selective degeneration mechanism of active zone proteins in NMJs from aged mice. Interestingly, the localization pattern of active zone proteins described herein is similar to active zone structures described using electron microscope tomography.

Pythagoras Meets Fibonacci.

ERIC Educational Resources Information Center

Boulger, William

1989-01-01

Patterns and relationships are shown between the Pythagorean theorem, Fibonacci sequences, and the golden ratio. Historical references also include the works of Euclid and Euler. These unexpected relationships can be used to motivate secondary students. (DC)

Fabrication of Vertically Aligned Carbon Nanotube or Zinc Oxide Nanorod Arrays for Optical Diffraction Gratings.

PubMed

Kim, Jeong; Kim, Sun Il; Cho, Seong-Ho; Hwang, Sungwoo; Lee, Young Hee; Hur, Jaehyun

2015-11-01

We report on new fabrication methods for a transparent, hierarchical, and patterned electrode comprised of either carbon nanotubes or zinc oxide nanorods. Vertically aligned carbon nanotubes or zinc oxide nanorod arrays were fabricated by either chemical vapor deposition or hydrothermal growth, in combination with photolithography. A transparent conductive graphene layer or zinc oxide seed layer was employed as the transparent electrode. On the patterned surface defined using photoresist, the vertically grown carbon nanotubes or zinc oxides could produce a concentrated electric field under applied DC voltage. This periodic electric field was used to align liquid crystal molecules in localized areas within the optical cell, effectively modulating the refractive index. Depending on the material and morphology of these patterned electrodes, the diffraction efficiency presented different behavior. From this study, we established the relationship between the hierarchical structure of the different electrodes and their efficiency for modulating the refractive index. We believe that this study will pave a new path for future optoelectronic applications.

Response of human corneal fibroblasts on silk film surface patterns.

PubMed

Gil, Eun Seok; Park, Sang-Hyug; Marchant, Jeff; Omenetto, Fiorenzo; Kaplan, David L

2010-06-11

Transparent, biodegradable, mechanically robust, and surface-patterned silk films were evaluated for the effect of surface morphology on human corneal fibroblast (hCF) cell proliferation, orientation, and ECM deposition and alignment. A series of dimensionally different surface groove patterns were prepared from optically graded glass substrates followed by casting poly(dimethylsiloxane) (PDMS) replica molds. The features on the patterned silk films showed an array of asymmetric triangles and displayed 37-342 nm depths and 445-3 582 nm widths. hCF DNA content on all patterned films were not significantly different from that on flat silk films after 4 d in culture. However, the depth and width of the grooves influenced cell alignment, while the depth differences affected cell orientation; overall, deeper and narrower grooves induced more hCF orientation. Over 14 d in culture, cell layers and actin filament organization demonstrated that confluent hCFs and their cytoskeletal filaments were oriented along the direction of the silk film patterned groove axis. Collagen type V and proteoglycans (decorin and biglycan), important markers of corneal stromal tissue, were highly expressed with alignment. Understanding corneal stromal fibroblast responses to surface features on a protein-based biomaterial applicable in vivo for corneal repair potential suggests options to improve corneal tissue mimics. Further, the approaches provide fundamental biomaterial designs useful for bioengineering oriented tissue layers, an endemic feature in most biological tissue structures that lead to critical tissue functions.

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

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

sc-PDB-Frag: a database of protein-ligand interaction patterns for Bioisosteric replacements.

PubMed

Desaphy, Jérémy; Rognan, Didier

2014-07-28

Bioisosteric replacement plays an important role in medicinal chemistry by keeping the biological activity of a molecule while changing either its core scaffold or substituents, thereby facilitating lead optimization and patenting. Bioisosteres are classically chosen in order to keep the main pharmacophoric moieties of the substructure to replace. However, notably when changing a scaffold, no attention is usually paid as whether all atoms of the reference scaffold are equally important for binding to the desired target. We herewith propose a novel database for bioisosteric replacement (scPDBFrag), capitalizing on our recently published structure-based approach to scaffold hopping, focusing on interaction pattern graphs. Protein-bound ligands are first fragmented and the interaction of the corresponding fragments with their protein environment computed-on-the-fly. Using an in-house developed graph alignment tool, interaction patterns graphs can be compared, aligned, and sorted by decreasing similarity to any reference. In the herein presented sc-PDB-Frag database ( http://bioinfo-pharma.u-strasbg.fr/scPDBFrag ), fragments, interaction patterns, alignments, and pairwise similarity scores have been extracted from the sc-PDB database of 8077 druggable protein-ligand complexes and further stored in a relational database. We herewith present the database, its Web implementation, and procedures for identifying true bioisosteric replacements based on conserved interaction patterns.

Relation between film character and wafer alignment: critical alignment issues on HV device for VLSI manufacturing

NASA Astrophysics Data System (ADS)

Lo, Yi-Chuan; Lee, Chih-Hsiung; Lin, Hsun-Peng; Peng, Chiou-Shian

1998-06-01

Several continuous splits for wafer alignment target topography conditions to improve epitaxy film alignment were applied. The alignment evaluation among former layer pad oxide thickness (250 angstrom - 500 angstrom), drive oxide thickness (6000 angstrom - 10000 angstrom), nitride film thickness (600 angstrom - 1500 angstrom), initial oxide etch (fully wet etch, fully dry etch and dry plus wet etch) will be split to this experiment. Also various epitaxy deposition recipe such as: epitaxy source (SiHCl2 or SiCHCl3) and growth rate (1.3 micrometer/min approximately 2.0 micrometer/min) will be used to optimize the process window for alignment issue. All the reflectance signal and cross section photography of alignment target during NIKON stepper alignment process will be examined. Experimental results show epitaxy recipe plays an important role to wafer alignment. Low growth rate with good performance conformity epitaxy lead to alignment target avoid washout, pattern shift and distortion. All the results (signal monitor and film character) combined with NIKON's stepper standard laser scanning alignment system will be discussed in this paper.

Self-aligned blocking integration demonstration for critical sub-30nm pitch Mx level patterning with EUV self-aligned double patterning

NASA Astrophysics Data System (ADS)

Raley, Angélique; Lee, Joe; Smith, Jeffrey T.; Sun, Xinghua; Farrell, Richard A.; Shearer, Jeffrey; Xu, Yongan; Ko, Akiteru; Metz, Andrew W.; Biolsi, Peter; Devilliers, Anton; Arnold, John; Felix, Nelson

2018-04-01

We report a sub-30nm pitch self-aligned double patterning (SADP) integration scheme with EUV lithography coupled with self-aligned block technology (SAB) targeting the back end of line (BEOL) metal line patterning applications for logic nodes beyond 5nm. The integration demonstration is a validation of the scalability of a previously reported flow, which used 193nm immersion SADP targeting a 40nm pitch with the same material sets (Si3N4 mandrel, SiO2 spacer, Spin on carbon, spin on glass). The multi-color integration approach is successfully demonstrated and provides a valuable method to address overlay concerns and more generally edge placement error (EPE) as a whole for advanced process nodes. Unbiased LER/LWR analysis comparison between EUV SADP and 193nm immersion SADP shows that both integrations follow the same trend throughout the process steps. While EUV SADP shows increased LER after mandrel pull, metal hardmask open and dielectric etch compared to 193nm immersion SADP, the final process performance is matched in terms of LWR (1.08nm 3 sigma unbiased) and is only 6% higher than 193nm immersion SADP for average unbiased LER. Using EUV SADP enables almost doubling the line density while keeping most of the remaining processes and films unchanged, and provides a compelling alternative to other multipatterning integrations, which present their own sets of challenges.

Detection of Polarized Infrared Emission by Polycyclic Aromatic Hydrocarbons in the MWC 1080 Nebula

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

Zhang, Han; Telesco, Charles M.; Pantin, Eric

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in astrophysical environments, as revealed by their pronounced emission features at 3.3, 6.2, 7.7, 8.6, 11.3, and 12.7 μ m commonly ascribed to the C–H and C–C vibrational modes. Although these features have long been predicted to be polarized, previous searches for PAH polarization led to null or, at best, tentative detections. Here we report the definite detection of polarized PAH emission at 11.3 μ m in the nebula associated with the Herbig Be star MWC 1080. We measure a polarization degree of 1.9% ± 0.2%, which is unexpectedly high compared to models. Thismore » poses a challenge in the current understanding of the alignment of PAHs, which is required to polarize the PAH emission but thought to be substantially suppressed. PAH alignment with a magnetic field via a resonance paramagnetic relaxation process may account for such a high level of polarization.« less

Parallel and Perpendicular Alignment of Anisotropic Particles in Free Liquid Microjets and Emerging Microdroplets.

PubMed

Schlenk, Mathias; Hofmann, Eddie; Seibt, Susanne; Rosenfeldt, Sabine; Schrack, Lukas; Drechsler, Markus; Rothkirch, Andre; Ohm, Wiebke; Breu, Josef; Gekle, Stephan; Förster, Stephan

2018-04-24

Liquid microjets play a key role in fiber spinning, inkjet printing, and coating processes. In all of these applications, the liquid jets carry dispersed particles whose spatial and orientational distributions within the jet critically influence the properties of the fabricated structures. Despite its importance, there is currently no knowledge about the orientational distribution of particles within microjets and droplets. Here, we demonstrate a microfluidic device that allows to determine the local particle distribution and orientation by X-ray scattering. Using this methodology, we discovered unexpected changes in the particle orientation upon exiting the nozzle to form a free jet, and upon jet break-up into droplets, causing an unusual biaxial particle orientation. We show how flow and aspect ratio determine the flow orientation of anisotropic particles. Furthermore, we demonstrate that the observed phenomena are a general characteristic of anisotropic particles. Our findings greatly enhance our understanding of particle orientation in free jets and droplets and provide a rationale for controlling particle alignment in liquid jet-based fabrication methodologies.

Detection of Polarized Infrared Emission by Polycyclic Aromatic Hydrocarbons in the MWC 1080 Nebula

NASA Astrophysics Data System (ADS)

Zhang, Han; Telesco, Charles M.; Hoang, Thiem; Li, Aigen; Pantin, Eric; Wright, Christopher M.; Li, Dan; Barnes, Peter

2017-07-01

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in astrophysical environments, as revealed by their pronounced emission features at 3.3, 6.2, 7.7, 8.6, 11.3, and 12.7 μm commonly ascribed to the C-H and C-C vibrational modes. Although these features have long been predicted to be polarized, previous searches for PAH polarization led to null or, at best, tentative detections. Here we report the definite detection of polarized PAH emission at 11.3 μm in the nebula associated with the Herbig Be star MWC 1080. We measure a polarization degree of 1.9% ± 0.2%, which is unexpectedly high compared to models. This poses a challenge in the current understanding of the alignment of PAHs, which is required to polarize the PAH emission but thought to be substantially suppressed. PAH alignment with a magnetic field via a resonance paramagnetic relaxation process may account for such a high level of polarization.

An Advanced Electrospinning Method of Fabricating Nanofibrous Patterned Architectures with Controlled Deposition and Desired Alignment

NASA Astrophysics Data System (ADS)

Rasel, Sheikh Md

We introduce a versatile advanced method of electrospinning for fabricating various kinds of nanofibrous patterns along with desired alignment, controlled amount of deposition and locally variable density into the architectures. In this method, we employed multiple electrodes whose potentials have been altered in milliseconds with the help of microprocessor based control system. Therefore, key success of this method was that the electrical field as well as charge carrying fibers could be switched shortly from one electrode's location to another, as a result, electrospun fibers could be deposited on the designated areas with desired alignment. A wide range of nanofibrous patterned architectures were constructed using proper arrangement of multiple electrodes. By controlling the concurrent activation time of two adjacent electrodes, we demonstrated that amount of fibers going into the pattern can be adjusted and desired alignment in electrospun fibers can be obtained. We also revealed that the deposition density of electrospun fibers in different areas of patterned architectures can be varied. We showed that by controlling the deposition time between two adjacent electrodes, a number of functionally graded patterns can be generated with uniaxial alignment. We also demonstrated that this handy method was capable of producing random, aligned, and multidirectional nanofibrous mats by engaging a number of electrodes and switching them in desired patterns. A comprehensive study using finite element method was carried out to understand the effects of electrical field. Simulation results revealed that electrical field strength alters shortly based on electrode control switch patterns. Nanofibrous polyvinyl alcohol (PVA) scaffolds and its composite reinforced with wollastonite and wood flour were fabricated using rotating drum electrospinning technique. Morphological, mechanical, and thermal, properties were characterized on PVA/wollastonite and PVA/wood flour nanocomposites containing 0, 5, 10, and 20 wt % of fillers. Morphological analyses carried out by digital optical microscope, scanning electron microscopy, x-ray computed tomography, and Fourier transform infrared spectroscopy, confirmed the presence and well dispersion of fillers in the composites. In addition, improvement of mechanical properties with increased filler content further emphasized the adhesion between matrix and reinforcement. PVA with 20 wt % wollastonite composite exhibited the highest tensile strength (11.99 MPa) and tensile module (198 MPa) as compared to pure PVA (3.92 MPa and 83 MPa, respectively). Moreover, the thermal tests demonstrated that there is no major deviation in the thermal stability due to the addition of wollastonite in PVA scaffolds. Almost similar trend was observed in PVA/wood flour nanocomposites where tensile strength improved by 228 % for 20 wt % of reinforcement. The PVA/wollastonite and PVA/wood flour fibrous nanocomposite which poses higher mechanical properties might be potentially suitable for many advanced applications such as filtration, tissue engineering, and food processing. We believe this study will contribute to further scientific understanding of the patterning mechanism of electrospun nanofibers and to allow for variety of design of specific patterned nanofibrous architectures with desired functional properties. Therefore, this improved scheme of electrospinning can have significant impact in a broad range of applications including tissue engineering scaffolds, filtrations, and nanoelectronics.

Customization and design of directed self-assembly using hybrid prepatterns

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Alignment of smectic mesogens over engineered surfaces

NASA Astrophysics Data System (ADS)

Chandran, Achu; Joshi, Tilak; Khanna, P. K.; Mehta, Dalip. S.; Haranath, D.; Biradar, Ashok M.

2017-07-01

The alignment of smectic C* liquid crystals (LCs) has been manipulated over and near different surfaces such as bare glass, indium tin oxide (ITO) coated glass, patterned glass, and near spacers. The LC sample cell is made of one ITO coated glass plate and other having striped ITO with a Mylar spacer maintaining a finite cell gap between them. Laser scribing is used to make striped ITO, while the scribed area results in the formation of the patterned glass surface. The geometry of the cell is such that overlapped ITO lie in the middle and spacers are placed in the two extreme corners of the cell. The alignment of LC is found to be homeotropic over the ITO coated glass, while it is planar near the spacer. Interestingly, a transition from homeotropic to planar is observed while moving away from the middle towards either corner of the cell. The origin of both types of alignment in the same cell has been explained by considering the difference in the surface energy of different surfaces. This work renders new advancement towards the manipulation of LC alignment using different surfaces and interfaces for advanced electro-optical and photonic devices based on LCs.

3D patterned substrates for bioartificial blood vessels - The effect of hydrogels on aligned cells on a biomaterial surface.

PubMed

Zhao, Xinxin; Irvine, Scott Alexander; Agrawal, Animesh; Cao, Ye; Lim, Pei Qi; Tan, Si Ying; Venkatraman, Subbu S

2015-10-01

The optimal bio-artificial blood vessel construct is one that has a compliant tubular core with circumferentially aligned smooth muscle cells (SMCs). Obtaining this well-aligned pattern of SMCs on a scaffold is highly beneficial as this cellular orientation preserves the SMC contractile phenotype. We used 3D patterning to create channels on a polycaprolactone (PCL) scaffold; SMCs were then found to be aligned within the microchannels. To preserve this alignment, and to provide a protective coating that could further incorporate cells, we evaluated the use of two hydrogels, one based on poly(ethylene glycol) diacrylate (PEGDA) and the other based on gelatin. Hydrogels were either physically coated on the PCL surfaces or covalently linked via suitable surface modification of PCL. For covalent immobilization of PEGDA hydrogel, alkene groups were introduced on PCL, while for gelatin covalent linkage, serum proteins were introduced. It is, however, crucial that the hydrogel coating does not disrupt the cellular patterning and distribution. We show in this work that both the process of coating as well as the nature of the coating are critical to preservation of the aligned SMCs. The covalent coating methods involving the crosslinking of hydrogels with the surface of PCL films promoted hydrogel retention time on the film as compared with physical deposition. Furthermore, subsequent hydrogel degradation is affected by the components of the cell culture medium, hinting at a possible route to in vivo biodegradation. Surface features control cellular orientation and subsequently influence their functionality, a useful effect for cellularized biomedical devices. Such devices also can benefit from protective and cell friendly hydrogel coatings. However, literature is lacking on the fate of cells that have endured hydrogel coating whilst orientated on a biomaterial surface. In particular, elucidation of the cells ability to remain adherent and orientated post hydrogel addition. Coating requires two procedures that may be deleterious to the orientated cells: the surface pretreatment for gel binding and the hydrogel crosslinking reaction. We compare transglutaminase gelatin crosslinking and UV initiated PEGDA crosslinking, coated onto smooth muscle cells orientated on patterned PCL surfaces. This original study will be of considerable use to the wider biomaterials community. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Unidirectionally aligned line patterns driven by entropic effects on faceted surfaces

PubMed Central

Hong, Sung Woo; Huh, June; Gu, Xiaodan; Lee, Dong Hyun; Jo, Won Ho; Park, Soojin; Xu, Ting; Russell, Thomas P.

2012-01-01

A simple, versatile approach to the directed self-assembly of block copolymers into a macroscopic array of unidirectionally aligned cylindrical microdomains on reconstructed faceted single crystal surfaces or on flexible, inexpensive polymeric replicas was discovered. High fidelity transfer of the line pattern generated from the microdomains to a master mold is also shown. A single-grained line patterns over arbitrarily large surface areas without the use of top-down techniques is demonstrated, which has an order parameter typically in excess of 0.97 and a slope error of 1.1 deg. This degree of perfection, produced in a short time period, has yet to be achieved by any other methods. The exceptional alignment arises from entropic penalties of chain packing in the facets coupled with the bending modulus of the cylindrical microdomains. This is shown, theoretically, to be the lowest energy state. The atomic crystalline ordering of the substrate is transferred, over multiple length scales, to the block copolymer microdomains, opening avenues to large-scale roll-to-roll type and nanoimprint processing of perfectly patterned surfaces and as templates and scaffolds for magnetic storage media, polarizing devices, and nanowire arrays. PMID:22307591

Spontaneous Magnetic Alignment by Yearling Snapping Turtles: Rapid Association of Radio Frequency Dependent Pattern of Magnetic Input with Novel Surroundings

PubMed Central

Landler, Lukas; Painter, Michael S.; Youmans, Paul W.; Hopkins, William A.; Phillips, John B.

2015-01-01

We investigated spontaneous magnetic alignment (SMA) by juvenile snapping turtles using exposure to low-level radio frequency (RF) fields at the Larmor frequency to help characterize the underlying sensory mechanism. Turtles, first introduced to the testing environment without the presence of RF aligned consistently towards magnetic north when subsequent magnetic testing conditions were also free of RF (‘RF off → RF off’), but were disoriented when subsequently exposed to RF (‘RF off → RF on’). In contrast, animals initially introduced to the testing environment with RF present were disoriented when tested without RF (‘RF on → RF off’), but aligned towards magnetic south when tested with RF (‘RF on → RF on’). Sensitivity of the SMA response of yearling turtles to RF is consistent with the involvement of a radical pair mechanism. Furthermore, the effect of RF appears to result from a change in the pattern of magnetic input, rather than elimination of magnetic input altogether, as proposed to explain similar effects in other systems/organisms. The findings show that turtles first exposed to a novel environment form a lasting association between the pattern of magnetic input and their surroundings. However, under natural conditions turtles would never experience a change in the pattern of magnetic input. Therefore, if turtles form a similar association of magnetic cues with the surroundings each time they encounter unfamiliar habitat, as seems likely, the same pattern of magnetic input would be associated with multiple sites/localities. This would be expected from a sensory input that functions as a global reference frame, helping to place multiple locales (i.e., multiple local landmark arrays) into register to form a global map of familiar space. PMID:25978736

Spontaneous magnetic alignment by yearling snapping turtles: rapid association of radio frequency dependent pattern of magnetic input with novel surroundings.

PubMed

Landler, Lukas; Painter, Michael S; Youmans, Paul W; Hopkins, William A; Phillips, John B

2015-01-01

We investigated spontaneous magnetic alignment (SMA) by juvenile snapping turtles using exposure to low-level radio frequency (RF) fields at the Larmor frequency to help characterize the underlying sensory mechanism. Turtles, first introduced to the testing environment without the presence of RF aligned consistently towards magnetic north when subsequent magnetic testing conditions were also free of RF ('RF off → RF off'), but were disoriented when subsequently exposed to RF ('RF off → RF on'). In contrast, animals initially introduced to the testing environment with RF present were disoriented when tested without RF ('RF on → RF off'), but aligned towards magnetic south when tested with RF ('RF on → RF on'). Sensitivity of the SMA response of yearling turtles to RF is consistent with the involvement of a radical pair mechanism. Furthermore, the effect of RF appears to result from a change in the pattern of magnetic input, rather than elimination of magnetic input altogether, as proposed to explain similar effects in other systems/organisms. The findings show that turtles first exposed to a novel environment form a lasting association between the pattern of magnetic input and their surroundings. However, under natural conditions turtles would never experience a change in the pattern of magnetic input. Therefore, if turtles form a similar association of magnetic cues with the surroundings each time they encounter unfamiliar habitat, as seems likely, the same pattern of magnetic input would be associated with multiple sites/localities. This would be expected from a sensory input that functions as a global reference frame, helping to place multiple locales (i.e., multiple local landmark arrays) into register to form a global map of familiar space.

Exploring EUV and SAQP pattering schemes at 5nm technology node

NASA Astrophysics Data System (ADS)

Hamed Fatehy, Ahmed; Kotb, Rehab; Lafferty, Neal; Jiang, Fan; Word, James

2018-03-01

For years, Moore's law keeps driving the semiconductors industry towards smaller dimensions and higher density chips with more devices. Earlier, the correlation between exposure source's wave length and the smallest resolvable dimension, mandated the usage of Deep Ultra-Violent (DUV) optical lithography system which has been used for decades to sustain Moore's law, especially when immersion lithography was introduced with 193nm ArF laser sources. As dimensions of devices get smaller beyond Deep Ultra-Violent (DUV) optical resolution limits, the need for Extremely Ultra-Violent (EUV) optical lithography systems was a must. However, EUV systems were still under development at that time for the mass-production in semiconductors industry. Theretofore, Multi-Patterning (MP) technologies was introduced to swirl about DUV optical lithography limitations in advanced nodes beyond minimum dimension (CD) of 20nm. MP can be classified into two main categories; the first one is to split the target itself across multiple masks that give the original target patterns when they are printed. This category includes Double, Triple and Quadruple patterning (DP, TP, and QP). The second category is the Self-Aligned Patterning (SAP) where the target is divided into Mandrel patterns and non-Mandrel patterns. The Mandrel patterns get printed first, then a self-aligned sidewalls are grown around these printed patterns drawing the other non-Mandrel targets, afterword, a cut mask(s) is used to define target's line-ends. This approach contains Self-Aligned-Double Pattering (SADP) and Self-Aligned- Quadruple-Pattering (SAQP). DUV and MP along together paved the way for the industry down to 7nm. However, with the start of development at the 5nm node and the readiness of EUV, the differentiation question is aroused again, which pattering approach should be selected, direct printing using EUV or DUV with MP, or a hybrid flow that contains both DUV-MP and EUV. In this work we are comparing two potential pattering techniques for Back End Of Line (BEOL) metal layers in the 5nm technology node, the first technique is Single Exposure EUV (SE-EUV) with a Direct Patterning EUV lithography process, and the second one is Self-Aligned Quadruple Patterning (SAQP) with a hybrid lithography processes, where the drawn metal target layer is decomposed into a Mandrel mask and Blocks/Cut mask, Mandrel mask is printed using DUV 193i lithography process, while Block/Cut Mask is printed using SE-EUV lithography process. The pros and cons of each technique are quantified based on Edge-Placement-Error (EPE) and Process Variation Band (PVBand) measured at 1D and 2D edges. The layout used in this comparison is a candidate layout for Foundries 5nm process node.

Prosody and Alignment: A Sequential Perspective

ERIC Educational Resources Information Center

Reed, Beatrice Szczepek

2010-01-01

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…

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.

Fusion bonding and alignment fixture

DOEpatents

Ackler, Harold D.; Swierkowski, Stefan P.; Tarte, Lisa A.; Hicks, Randall K.

2000-01-01

An improved vacuum fusion bonding structure and process for aligned bonding of large area glass plates, patterned with microchannels and access holes and slots, for elevated glass fusion temperatures. Vacuum pumpout of all the components is through the bottom platform which yields an untouched, defect free top surface which greatly improves optical access through this smooth surface. Also, a completely non-adherent interlayer, such as graphite, with alignment and location features is located between the main steel platform and the glass plate pair, which makes large improvements in quality, yield, and ease of use, and enables aligned bonding of very large glass structures.

The mechanical life of magnetotactic bacteria inside sediments: implications for paleo- and environmental magnetism

NASA Astrophysics Data System (ADS)

Egli, Ramon; Mao, Xuegang

2015-04-01

Magnetotactic bacteria (MTB) are responsible for up to almost 100% of the magnetic signature of certain sediments through fossil reminders called magnetofossils. Besides being stable carriers of useful paleomagnetic signals, magnetofossils provide interesting environmental proxies that reflect MTB abundance variations due to nutrient supply and/or dilution by detrital/aeolian inputs. Unfortunately factors affecting MTB abundances in sediment are poorly known and based at best on extrapolations of observations on pure cultures. For example, MTB displacement models have been always based on the assumption that full alignment with the Earth magnetic field is possible, as observed in water. However, we recently found that the alignment of living MTB does not exceed few % inside sediments. This observation raises questions on the true nature of the biologic advantage of such bacteria over other motile organisms, and, ultimatively, on what is controlling their abundance in sediment. Here we report experiments that demonstrate the role of the Earth magnetic field in directing MTB to optimal living depths with the observed poor magnetic alignment. These exerments explain the apparent useless abundance of magnetosomes in certain MTB strains (e.g. M. Bavaricum) and reveal unexpected differences between strains with respect to their ability to cope with chemical signals and absent or reversed magnetic fields.

A fast, robust pattern recognition asystem for low light level image registration and its application to retinal imaging

NASA Astrophysics Data System (ADS)

Wade, Alex Robert; Fitzke, Frederick W.

1998-08-01

We describe an image processing system which we have developed to align autofluorescence and high-magnification images taken with a laser scanning ophthalmoscope. The low signal to noise ratio of these images makes pattern recognition a non-trivial task. However, once n images are aligned and averaged, the noise levels drop by a factor of n and the image quality is improved. We include examples of autofluorescence images and images of the cone photoreceptor mosaic obtained using this system.

Role of Symmetry in the Mirror-Image Confusions of Preschoolers.

ERIC Educational Resources Information Center

Vogel, Juliet M.; Loughlin, Kathleen A.

1978-01-01

Preschool children copied peg locations with standardized comparison pegboards aligned horizontally and diagonally and with three levels of pegboard complexity. Error patterns varied with type of alignment and display complexity. Results failed to support Bryant's hypothesis that mirror image confusions are no more frequent than other in-line…

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

PubMed Central

Hasson, Uri; Frith, Chris D.

2016-01-01

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

Photolithography-Based Patterning of Liquid Metal Interconnects for Monolithically Integrated Stretchable Circuits.

PubMed

Park, Chan Woo; Moon, Yu Gyeong; Seong, Hyejeong; Jung, Soon Won; Oh, Ji-Young; Na, Bock Soon; Park, Nae-Man; Lee, Sang Seok; Im, Sung Gap; Koo, Jae Bon

2016-06-22

We demonstrate a new patterning technique for gallium-based liquid metals on flat substrates, which can provide both high pattern resolution (∼20 μm) and alignment precision as required for highly integrated circuits. In a very similar manner as in the patterning of solid metal films by photolithography and lift-off processes, the liquid metal layer painted over the whole substrate area can be selectively removed by dissolving the underlying photoresist layer, leaving behind robust liquid patterns as defined by the photolithography. This quick and simple method makes it possible to integrate fine-scale interconnects with preformed devices precisely, which is indispensable for realizing monolithically integrated stretchable circuits. As a way for constructing stretchable integrated circuits, we propose a hybrid configuration composed of rigid device regions and liquid interconnects, which is constructed on a rigid substrate first but highly stretchable after being transferred onto an elastomeric substrate. This new method can be useful in various applications requiring both high-resolution and precisely aligned patterning of gallium-based liquid metals.

Layout decomposition of self-aligned double patterning for 2D random logic patterning

NASA Astrophysics Data System (ADS)

Ban, Yongchan; Miloslavsky, Alex; Lucas, Kevin; Choi, Soo-Han; Park, Chul-Hong; Pan, David Z.

2011-04-01

Self-aligned double pattering (SADP) has been adapted as a promising solution for sub-30nm technology nodes due to its lower overlay problem and better process tolerance. SADP is in production use for 1D dense patterns with good pitch control such as NAND Flash memory applications, but it is still challenging to apply SADP to 2D random logic patterns. The favored type of SADP for complex logic interconnects is a two mask approach using a core mask and a trim mask. In this paper, we first describe layout decomposition methods of spacer-type double patterning lithography, then report a type of SADP compliant layouts, and finally report SADP applications on Samsung 22nm SRAM layout. For SADP decomposition, we propose several SADP-aware layout coloring algorithms and a method of generating lithography-friendly core mask patterns. Experimental results on 22nm node designs show that our proposed layout decomposition for SADP effectively decomposes any given layouts.

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

PubMed

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

2010-07-01

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

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.

Improving scanner wafer alignment performance by target optimization

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

Using ProMED-Mail and MedWorm blogs for cross-domain pattern analysis in epidemic intelligence.

PubMed

Stewart, Avaré; Denecke, Kerstin

2010-01-01

In this work we motivate the use of medical blog user generated content for gathering facts about disease reporting events to support biosurveillance investigation. Given the characteristics of blogs, the extraction of such events is made more difficult due to noise and data abundance. We address the problem of automatically inferring disease reporting event extraction patterns in this more noisy setting. The sublanguage used in outbreak reports is exploited to align with the sequences of disease reporting sentences in blogs. Based our Cross Domain Pattern Analysis Framework, experimental results show that Phase-Level sequences tend to produce more overlap across the domains than Word-Level sequences. The cross domain alignment process is effective at filtering noisy sequences from blogs and extracting good candidate sequence patterns from an abundance of text.

Electrocardiographic features of sudden unexpected death in epilepsy.

PubMed

Chyou, Janice Y; Friedman, Daniel; Cerrone, Marina; Slater, William; Guo, Yu; Taupin, Daniel; O'Rourke, Sean; Priori, Silvia G; Devinsky, Orrin

2016-07-01

Sudden unexpected death in epilepsy (SUDEP) is the most common cause of epilepsy-related mortality. We hypothesized that electrocardiography (ECG) features may distinguish SUDEP cases from living subjects with epilepsy. Using a matched case-control design, we compared ECG studies of 12 consecutive cases of SUDEP over 10 years and 22 epilepsy controls matched for age, sex, epilepsy type (focal, generalized, or unknown/mixed type), concomitant antiepileptic, and psychotropic drug classes. Conduction intervals and prevalence of abnormal ventricular conduction diagnosis (QRS ≥110 msec), abnormal ventricular conduction pattern (QRS <110 msec, morphology of incomplete right or left bundle branch block or intraventricular conduction delay), early repolarization, and features of inherited cardiac channelopathies were assessed. Abnormal ventricular conduction diagnosis and pattern distinguished SUDEP cases from matched controls. Abnormal ventricular conduction diagnosis was present in two cases and no controls. Abnormal ventricular conduction pattern was more common in cases than controls (58% vs. 18%, p = 0.04). Early repolarization was similarly prevalent in cases and controls, but the overall prevalence exceeded that of published community-based cohorts. Wiley Periodicals, Inc. © 2016 International League Against Epilepsy.

The role of trauma scoring in developing trauma clinical governance in the Defence Medical Services

PubMed Central

Russell, R. J.; Hodgetts, T. J.; McLeod, J.; Starkey, K.; Mahoney, P.; Harrison, K.; Bell, E.

2011-01-01

This paper discusses mathematical models of expressing severity of injury and probability of survival following trauma and their use in establishing clinical governance of a trauma system. There are five sections: (i) Historical overview of scoring systems—anatomical, physiological and combined systems and the advantages and disadvantages of each. (ii) Definitions used in official statistics—definitions of ‘killed in action’ and other categories and the importance of casualty reporting rates and comparison across conflicts and nationalities. (iii) Current scoring systems and clinical governance—clinical governance of the trauma system in the Defence Medical Services (DMS) by using trauma scoring models to analyse injury and clinical patterns. (iv) Unexpected outcomes—unexpected outcomes focus clinical governance tools. Unexpected survivors signify good practice to be promulgated. Unexpected deaths pick up areas of weakness to be addressed. Seventy-five clinically validated unexpected survivors were identified over 2 years during contemporary combat operations. (v) Future developments—can the trauma scoring methods be improved? Trauma scoring systems use linear approaches and have significant weaknesses. Trauma and its treatment is a complex system. Nonlinear methods need to be investigated to determine whether these will produce a better approach to the analysis of the survival from major trauma. PMID:21149354

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.

PubMed

Muth, Thilo; García-Martín, Juan A; Rausell, Antonio; Juan, David; Valencia, Alfonso; Pazos, Florencio

2012-02-15

We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.

Using Patterns of Summed Scores in Paper-and-Pencil Tests and Computer-Adaptive Tests to Detect Misfitting Item Score Patterns

ERIC Educational Resources Information Center

Meijer, Rob R.

2004-01-01

Two new methods have been proposed to determine unexpected sum scores on sub-tests (testlets) both for paper-and-pencil tests and computer adaptive tests. A method based on a conservative bound using the hypergeometric distribution, denoted p, was compared with a method where the probability for each score combination was calculated using a…

Spectral optical coherence tomography vs. fluorescein pattern for rigid gas-permeable lens fit.

PubMed

Piotrowiak, Ilona; Kaluzny, Bartłomiej Jan; Danek, Beata; Chwiędacz, Adam; Sikorski, Bartosz Lukasz; Malukiewicz, Grażyna

2014-07-04

This study aimed to evaluate anterior segment spectral optical coherence tomography (AS SOCT) for assessing the lens-to-cornea fit of rigid gas-permeable (RGP) lenses. The results were verified with the fluorescein pattern method, considered the criterion standard for RGP lens alignment evaluations. Twenty-six eyes of 14 patients were enrolled in the study. Initial base curve radius (BCR) of each RGP lens was determined on the basis of keratometry readings. The fluorescein pattern and AS SOCT tomograms were evaluated, starting with an alignment fit, and subsequently, with BCR reductions in increments of 0.1 mm, up to 3 consecutive changes. AS SOCT examination was performed with the use of RTVue (Optovue, California, USA). The average BCR for alignment fits, defined according to the fluorescein pattern, was 7.8 mm (SD=0.26). Repeatability of the measurements was 18.2%. BCR reductions of 0.1, 0.2, and 0.3 mm resulted in average apical clearances detected with AS SOCT of 12.38 (SD=9.91, p<0.05), 28.79 (SD=15.39, p<0.05), and 33.25 (SD=10.60, p>0.05), respectively. BCR steepening of 0.1 mm or more led to measurable changes in lens-to-cornea fits. Although AS SOCT represents a new method of assessing lens-to-cornea fit, apical clearance detection with current commercial technology showed lower sensitivity than the fluorescein pattern assessment.

Liquid crystal devices based on photoalignment and photopatterning materials

NASA Astrophysics Data System (ADS)

Chigrinov, Vladimir

2014-02-01

Liquid crystal (LC) display and photonics devices based on photo-alignment and photo-patterning LC cells are developed. A fast switchable grating based on ferroelectric liquid crystals and orthogonal planar alignment by means of photo alignments. Both 1D and 2D gratings have been constructed. The proposed diffracting element provides fast response time of around 20 μs, contrast of 7000:1 and high diffraction efficiency, at the electric field of 6V/μm. A switchable LC Fresnel zone lens was also developed with the efficiency of ~42% that can be further improved, and the switching time for the 3 μm thick cell is ~6.7 ms which is relatively fast in comparison of existing devices. Thus, because of the photoalignment technology the fabrication of Fresnel lens became considerably simpler than others. A thin high spatial resolution, photo-patterned micropolarizer array for complementary metal-oxide-semiconductor (CMOS) image sensors was implemented for the complete optical visualization of so called "invisible" objects, which are completely transparent (reflective) and colorless. Four Stokes parameters, which fully characterized the reflected light beam can be simultaneously detected using the array of photo-patterned polarizers on CMOS sensor plate. The cheap, high resolution photo-patterned LC matrix sensor was developed to be able successfully compete with the expensive and low reliable wire grid polarizer patterned arrays currently used for the purpose.

Esophageal Cancer Metastases to Unexpected Sites: A Systematic Review

PubMed Central

2017-01-01

The most common pattern of esophageal cancer metastases (ECM) is to the lymph nodes, lung, liver, bones, adrenal glands, and brain. On the other hand, unexpected metastasis (UM) spread to uncommon sites has increasingly reported and consequently affected the pathway of diagnosis, staging, and management. Using the PubMed database, a systematic search of the following headings “Esophageal” and “Metastasis” or “Metastases” was performed, 10049 articles were identified, and the articles were included if they demonstrated unexpected ECM. 84% of cases were men with an average age of 60.7 years. EC was located in the lower third in 65%. Two-thirds of the UM originated from the lower esophagus, and the two major histological types were adenocarcinoma 40% and squamous cell carcinoma 60%. Metastases were disseminated toward five main anatomical sites: the head and neck (42%), thoracic (17%), abdomen and pelvis (25%), extremities (9%), and multiple skin and muscle metastases (7%). The EC metastases were found to be synchronous 42% and metachronous 58%, isolated in 53.5% and multiple in 46.5%. The overall survival rate was 10.2 months. Since distant metastases are responsible for most EC-related deaths, understanding of ECM dissemination patterns needs more extensive studies. These critical data are the cornerstone of optimal cancer approach and treatment. PMID:28659974

Construction, alignment, and implementation of an acousto-optical deflector-based system for patterned uncaging with ultraviolet light.

PubMed

Civillico, Eugene F; Shoham, Shy; O'Connor, Daniel H; Sarkisov, Dmitry V; Wang, Samuel S-H

2012-08-01

The method of patterned photoactivation is a natural fit for the study of neuronal dendritic integration. Photoactivatable molecules that influence a wide range of extracellular and intracellular neurophysiological functions are available. The choice of photosensitive molecules depends on the research question and will influence the design of the experimental apparatus. An acousto-optical deflector (AOD)-based system can be used for rapid ultraviolet (UV) photolysis in arbitrary spatial and temporal patterns. Photolysis-activated "caged" diffusible molecules or newer light-sensitive membrane proteins can be used in this system. This protocol describes the addition of a UV beam for uncaging to a homebuilt two-photon microscope. The goal is to get UV light from the light source (laser) to the approximate center of the objective's back aperture, passing through a pair of perpendicularly oriented AODs along the way. The protocol also describes the fine alignment of the UV beam and the implementation of AOD-based beam steering. Performing the final alignment with the beam passing through the AODs will ensure that the system is optimized for the idiosyncrasies of the crystals.

Statistical modeling of SRAM yield performance and circuit variability

NASA Astrophysics Data System (ADS)

Cheng, Qi; Chen, Yijian

2015-03-01

In this paper, we develop statistical models to investigate SRAM yield performance and circuit variability in the presence of self-aligned multiple patterning (SAMP) process. It is assumed that SRAM fins are fabricated by a positivetone (spacer is line) self-aligned sextuple patterning (SASP) process which accommodates two types of spacers, while gates are fabricated by a more pitch-relaxed self-aligned quadruple patterning (SAQP) process which only allows one type of spacer. A number of possible inverter and SRAM structures are identified and the related circuit multi-modality is studied using the developed failure-probability and yield models. It is shown that SRAM circuit yield is significantly impacted by the multi-modality of fins' spatial variations in a SRAM cell. The sensitivity of 6-transistor SRAM read/write failure probability to SASP process variations is calculated and the specific circuit type with the highest probability to fail in the reading/writing operation is identified. Our study suggests that the 6-transistor SRAM configuration may not be scalable to 7-nm half pitch and more robust SRAM circuit design needs to be researched.

Graphene electron cannon: High-current edge emission from aligned graphene sheets

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

Liu, Jianlong; Li, Nannan; Guo, Jing

2014-01-13

High-current field emitters are made by graphene paper consist of aligned graphene sheets. Field emission luminance pattern shows that their electron beams can be controlled by rolling the graphene paper from sheet to cylinder. These specific electron beams would be useful to vacuum devices and electron beam lithograph. To get high-current emission, the graphene paper is rolled to array and form graphene cannon. Due to aligned emission array, graphene cannon have high emission current. Besides high emission current, the graphene cannon is also tolerable with excellent emission stability. With good field emission properties, these aligned graphene emitters bring application insight.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

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

PubMed

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

2009-03-01

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

Instance-Based Ontology Matching for Open and Distance Learning Materials

ERIC Educational Resources Information Center

Cerón-Figueroa, Sergio; López-Yáñez, Itzamá; Villuendas-Rey, Yenny; Camacho-Nieto, Oscar; Aldape-Pérez, Mario; Yáñez-Márquez, Cornelio

2017-01-01

The present work describes an original associative model of pattern classification and its application to align different ontologies containing Learning Objects (LOs), which are in turn related to Open and Distance Learning (ODL) educative content. The problem of aligning ontologies is known as Ontology Matching Problem (OMP), whose solution is…

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

PubMed

Domagalska-Szopa, Małgorzata; Szopa, Andrzej

2017-11-01

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

Applications of alignment-free methods in epigenomics.

PubMed

Pinello, Luca; Lo Bosco, Giosuè; Yuan, Guo-Cheng

2014-05-01

Epigenetic mechanisms play an important role in the regulation of cell type-specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have supported a role of DNA sequences in recruitment of epigenetic regulators. Alignment-free methods have been applied to identify distinct sequence features that are associated with epigenetic patterns and to predict epigenomic profiles. Here, we review recent advances in such applications, including the methods to map DNA sequence to feature space, sequence comparison and prediction models. Computational studies using these methods have provided important insights into the epigenetic regulatory mechanisms.

Fast switchable ferroelectric liquid crystal gratings with two electro-optical modes

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

Ma, Ying; Srivastava, A. K., E-mail: abhishek-srivastava-lu@yahoo.co.in; Chigrinov, V. G.

In this article, we reveal a theoretical and experimental illustration of the Ferroelectric liquid crystal (FLC) grating fabricated by mean of patterned alignment based on photo-alignment. The complexity related to the mismatching of the predefined alignment domains on the top and bottom substrate has been avoided by incorporating only one side photo aligned substrate while the other substrate does not have any alignment layer. Depending on the easy axis in the said alignment domains and the azimuth plane of the impinging polarized light, the diffracting element can be tuned in two modes i.e. DIFF/OFF switchable and DIFF/TRANS switchable modes, whichmore » can be applied to different applications. The diffraction profile has been illustrated theoretically that fits well with the experimental finding and thus the proposed diffraction elements with fast response time and high diffraction efficiency could find application in many modern devices.« less

Modular and configurable optimal sequence alignment software: Cola.

PubMed

Zamani, Neda; Sundström, Görel; Höppner, Marc P; Grabherr, Manfred G

2014-01-01

The fundamental challenge in optimally aligning homologous sequences is to define a scoring scheme that best reflects the underlying biological processes. Maximising the overall number of matches in the alignment does not always reflect the patterns by which nucleotides mutate. Efficiently implemented algorithms that can be parameterised to accommodate more complex non-linear scoring schemes are thus desirable. We present Cola, alignment software that implements different optimal alignment algorithms, also allowing for scoring contiguous matches of nucleotides in a nonlinear manner. The latter places more emphasis on short, highly conserved motifs, and less on the surrounding nucleotides, which can be more diverged. To illustrate the differences, we report results from aligning 14,100 sequences from 3' untranslated regions of human genes to 25 of their mammalian counterparts, where we found that a nonlinear scoring scheme is more consistent than a linear scheme in detecting short, conserved motifs. Cola is freely available under LPGL from https://github.com/nedaz/cola.

Understanding the critical challenges of self-aligned octuple patterning

NASA Astrophysics Data System (ADS)

Yu, Ji; Xiao, Wei; Kang, Weiling; Chen, Yijian

2014-03-01

In this paper, we present a thorough investigation of self-aligned octuple patterning (SAOP) process characteristics, cost structure, integration challenges, and layout decomposition. The statistical characteristics of SAOP CD variations such as multi-modality are analyzed and contributions from various features to CDU and MTT (mean-to-target) budgets are estimated. The gap space is found to have the worst CDU+MTT performance and is used to determine the required overlay accuracy to ensure a satisfactory edge-placement yield of a cut process. Moreover, we propose a 5-mask positive-tone SAOP (pSAOP) process for memory FEOL patterning and a 3-mask negative-tone SAOP (nSAOP) process for logic BEOL patterning. The potential challenges of 2-D SAOP layout decomposition for BEOL applications are identified. Possible decomposition approaches are explored and the functionality of several developed algorithm is verified using 2-D layout examples from Open Cell Library.

Genetic drift and collective dispersal can result in chaotic genetic patchiness.

PubMed

Broquet, Thomas; Viard, Frédérique; Yearsley, Jonathan M

2013-06-01

Chaotic genetic patchiness denotes unexpected patterns of genetic differentiation that are observed at a fine scale and are not stable in time. These patterns have been described in marine species with free-living larvae, but are unexpected because they occur at a scale below the dispersal range of pelagic larvae. At the scale where most larvae are immigrants, theory predicts spatially homogeneous, temporally stable genetic variation. Empirical studies have suggested that genetic drift interacts with complex dispersal patterns to create chaotic genetic patchiness. Here we use a co-ancestry model and individual-based simulations to test this idea. We found that chaotic genetic patterns (qualified by global FST and spatio-temporal variation in FST's between pairs of samples) arise from the combined effects of (1) genetic drift created by the small local effective population sizes of the sessile phase and variance in contribution among breeding groups and (2) collective dispersal of related individuals in the larval phase. Simulations show that patchiness levels qualitatively comparable to empirical results can be produced by a combination of strong variance in reproductive success and mild collective dispersal. These results call for empirical studies of the effective number of breeders producing larval cohorts, and population genetics at the larval stage. © 2012 The Author(s). Evolution © 2012 The Society for the Study of Evolution.

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

DOE PAGES

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

2014-01-01

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

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model.

PubMed

Hellweger, Ferdi L; van Sebille, Erik; Fredrick, Neil D

2014-09-12

A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection. Copyright © 2014, American Association for the Advancement of Science.

How genome complexity can explain the difficulty of aligning reads to genomes.

PubMed

Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

2015-01-01

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

Influence of the narrow {111} planes on axial and planar ion channeling.

PubMed

Motapothula, M; Dang, Z Y; Venkatesan, T; Breese, M B H; Rana, M A; Osman, A

2012-05-11

We report channeling patterns where clearly resolved effects of the narrow {111} planes are observed in axial and planar alignments for 2 MeV protons passing through a 55 nm [001] silicon membrane. At certain axes, such as <213> and <314>, the offset in atomic rows forming the narrow {111} planes results in shielding from the large potential at the wide {111} planes, producing a region of shallow, asymmetric potential from which axial channeling patterns have no plane of symmetry. At small tilts from such axes, different behavior is observed from the wide and narrow {111} planes. At planar alignment, distinctive channeling effects due to the narrow planes are observed. As a consequence of the shallow potential well at the narrow planes, incident protons suffer dechanneled trajectories which are excluded from channeling within the wide planes, resulting in an anomalously large scattered beam at {111} alignment.

INTERNAL DOSE AND RESPONSE IN REAL-TIME.

EPA Science Inventory

Abstract: Rapid temporal fluctuations in exposure may occur in a number of situations such as accidents or other unexpected acute releases of airborne substances. Often risk assessments overlook temporal exposure patterns under simplifying assumptions such as the use of time-wei...

An Accurate Scalable Template-based Alignment Algorithm

PubMed Central

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

2013-01-01

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

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

Demographic modelling reveals a history of divergence with gene flow for a glacially tied stonefly in a changing post-Pleistocene landscape

USGS Publications Warehouse

Hotaling, Scott; Muhlfeld, Clint C.; Giersch, J. Joseph; Ali, Omar; Jordan, Steve; Miller, Michael R.; Luikart, Gordon; Weisrock, David W.

2018-01-01

AimClimate warming is causing extensive loss of glaciers in mountainous regions, yet our understanding of how glacial recession influences evolutionary processes and genetic diversity is limited. Linking genetic structure with the influences shaping it can improve understanding of how species respond to environmental change. Here, we used genome-scale data and demographic modelling to resolve the evolutionary history of Lednia tumana, a rare, aquatic insect endemic to alpine streams. We also employed a range of widely used data filtering approaches to quantify how they influenced population structure results.LocationAlpine streams in the Rocky Mountains of Glacier National Park, Montana, USA.TaxonLednia tumana, a stonefly (Order Plecoptera) in the family Nemouridae.MethodsWe generated single nucleotide polymorphism data through restriction-site associated DNA sequencing to assess contemporary patterns of genetic structure for 11 L. tumana populations. Using identified clusters, we assessed demographic history through model selection and parameter estimation in a coalescent framework. During population structure analyses, we filtered our data to assess the influence of singletons, missing data and total number of markers on results.ResultsContemporary patterns of population structure indicate that L. tumana exhibits a pattern of isolation-by-distance among populations within three genetic clusters that align with geography. Mean pairwise genetic differentiation (FST) among populations was 0.033. Coalescent-based demographic modelling supported divergence with gene flow among genetic clusters since the end of the Pleistocene (~13-17 kya), likely reflecting the south-to-north recession of ice sheets that accumulated during the Wisconsin glaciation.Main conclusionsWe identified a link between glacial retreat, evolutionary history and patterns of genetic diversity for a range-restricted stonefly imperiled by climate change. This finding included a history of divergence with gene flow, an unexpected conclusion for a mountaintop species. Beyond L. tumana, this study demonstrates the complexity of assessing genetic structure for weakly differentiated species, shows the degree to which rare alleles and missing data may influence results, and highlights the usefulness of genome-scale data to extend population genetic inquiry in non-model species.

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

PubMed

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

2015-06-01

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

The evolution from long-range magnetic order to spin-glass behaviour in PrAu2(Si1- xGex)2

NASA Astrophysics Data System (ADS)

Krimmel, A.; Hemberger, J.; Kegler, C.; Nicklas, M.; Engelmayer, A.; Knebel, G.; Fritsch, V.; Reehuis, M.; Brando, M.; Loidl, A.

1999-09-01

We have studied the magnetic behaviour of PrAu2(Si1-xGex)2 by means of magnetic susceptibility, resistivity, and heat capacity measurements, and x-ray and neutron powder diffraction. All compounds are isostructural and crystallize in the well known ThCr2Si2-type structure. PrAu2Si2 shows the characteristic features of a canonical spin glass with a freezing temperature of TF = 3 K. Completely unexpectedly, on introducing/increasing the atomic disorder by alloying with Ge, the spin-glass transition is suppressed as is first evident from a slight decrease of the freezing temperature TF up to x = 0.10. Long-range magnetic order sets in for xicons/Journals/Common/ge" ALT="ge" ALIGN="TOP"/>0.12. Within the range 0.15icons/Journals/Common/le" ALT="le" ALIGN="TOP"/> xicons/Journals/Common/le" ALT="le" ALIGN="TOP"/>1, all compounds show the same simple AF-I-type antiferromagnetic structure with a monotonic increase of both the Néel temperature and the ordered magnetic moment for increasing Ge concentration. The magnetic phase diagram of PrAu2(Si1-xGex)2 is explained by the presence of weak disorder at a constant level at the Au sites. Clear indications of crystal-field effects have been observed.

Inkjet printing of aligned single-walled carbon-nanotube thin films

NASA Astrophysics Data System (ADS)

Takagi, Yuki; Nobusa, Yuki; Gocho, Shota; Kudou, Hikaru; Yanagi, Kazuhiro; Kataura, Hiromichi; Takenobu, Taishi

2013-04-01

We report a method for the inkjet printing of aligned single-walled carbon-nanotube (SWCNT) films by combining inkjet technology with the strong wettability contrast between hydrophobic and hydrophilic areas based on the patterning of self-assembled monolayers. Both the drying process control using the strong wettability boundary and the coffee-stain effect strongly promote the aggregation of SWCNTs along the contact line of a SWCNT ink droplet, thereby demonstrating our achievement of inkjet-printed aligned SWCNT films. This method could open routes for developing high-performance and environmentally friendly SWCNT printed electronics.

Step-by-step growth of epitaxially aligned polythiophene by surface-confined reaction

PubMed Central

Lipton-Duffin, J. A.; Miwa, J. A.; Kondratenko, M.; Cicoira, F.; Sumpter, B. G.; Meunier, V.; Perepichka, D. F.; Rosei, F.

2010-01-01

One of the great challenges in surface chemistry is to assemble aromatic building blocks into ordered structures that are mechanically robust and electronically interlinked—i.e., are held together by covalent bonds. We demonstrate the surface-confined growth of ordered arrays of poly(3,4-ethylenedioxythiophene) (PEDOT) chains, by using the substrate (the 110 facet of copper) simultaneously as template and catalyst for polymerization. Copper acts as promoter for the Ullmann coupling reaction, whereas the inherent anisotropy of the fcc 110 facet confines growth to a single dimension. High resolution scanning tunneling microscopy performed under ultrahigh vacuum conditions allows us to simultaneously image PEDOT oligomers and the copper lattice with atomic resolution. Density functional theory calculations confirm an unexpected adsorption geometry of the PEDOT oligomers, which stand on the sulfur atom of the thiophene ring rather than lying flat. This polymerization approach can be extended to many other halogen-terminated molecules to produce epitaxially aligned conjugated polymers. Such systems might be of central importance to develop future electronic and optoelectronic devices with high quality active materials, besides representing model systems for basic science investigations. PMID:20534511

Pirate Stealth or Inattentional Blindness? The Effects of Target Relevance and Sustained Attention on Security Monitoring for Experienced and Naïve Operators

PubMed Central

Näsholm, Erika; Rohlfing, Sarah; Sauer, James D.

2014-01-01

Closed Circuit Television (CCTV) operators are responsible for maintaining security in various applied settings. However, research has largely ignored human factors that may contribute to CCTV operator error. One important source of error is inattentional blindness – the failure to detect unexpected but clearly visible stimuli when attending to a scene. We compared inattentional blindness rates for experienced (84 infantry personnel) and naïve (87 civilians) operators in a CCTV monitoring task. The task-relevance of the unexpected stimulus and the length of the monitoring period were manipulated between participants. Inattentional blindness rates were measured using typical post-event questionnaires, and participants' real-time descriptions of the monitored event. Based on the post-event measure, 66% of the participants failed to detect salient, ongoing stimuli appearing in the spatial field of their attentional focus. The unexpected task-irrelevant stimulus was significantly more likely to go undetected (79%) than the unexpected task-relevant stimulus (55%). Prior task experience did not inoculate operators against inattentional blindness effects. Participants' real-time descriptions revealed similar patterns, ruling out inattentional amnesia accounts. PMID:24465932

Shear induced alignment of short nanofibers in 3D printed polymer composites.

PubMed

Yunus, Doruk Erdem; Shi, Wentao; Sohrabi, Salman; Liu, Yaling

2016-12-09

3D printing of composite materials offers an opportunity to combine the desired properties of composite materials with the flexibility of additive manufacturing in geometric shape and complexity. In this paper, the shear-induced alignment of aluminum oxide nanowires during stereolithography printing was utilized to fabricate a nanowire reinforced polymer composite. To align the fibers, a lateral oscillation mechanism was implemented and combined with wall pattern printing technique to generate shear flow in both vertical and horizontal directions. A series of specimens were fabricated for testing the composite material's tensile strength. The results showed that mechanical properties of the composite were improved by reinforcement of nanofibers through shear induced alignment. The improvement of tensile strength was approximately ∼28% by aligning the nanowires at 5 wt% (∼1.5% volume fraction) loading of aluminum oxide nanowires.

Helium beam shadowing for high spatial resolution patterning of antibodies on microstructured diagnostic surfaces

PubMed Central

Cacao, Eliedonna; Sherlock, Tim; Nasrullah, Azeem; Kemper, Steven; Knoop, Jennifer; Kourentzi, Katerina; Ruchhoeft, Paul; Stein, Gila E; Atmar, Robert L; Willson, Richard C

2013-01-01

Abstract We have developed a technique for the high-resolution, self-aligning, and high-throughput patterning of antibody binding functionality on surfaces by selectively changing the reactivity of protein-coated surfaces in specific regions of a workpiece with a beam of energetic helium particles. The exposed areas are passivated with bovine serum albumin (BSA) and no longer bind the antigen. We demonstrate that patterns can be formed (1) by using a stencil mask with etched openings that forms a patterned exposure, or (2) by using angled exposure to cast shadows of existing raised microstructures on the surface to form self-aligned patterns. We demonstrate the efficacy of this process through the patterning of anti-lysozyme, anti-Norwalk virus, and anti-Escherichia coli antibodies and the subsequent detection of each of their targets by the enzyme-mediated formation of colored or silver deposits, and also by binding of gold nanoparticles. The process allows for the patterning of three-dimensional structures by inclining the sample relative to the beam so that the shadowed regions remain unaltered. We demonstrate that the resolution of the patterning process is of the order of hundreds of nanometers, and that the approach is well-suited for high throughput patterning. PMID:24706125

Shear Alignment of Diblock Copolymers for Patterning Nanowire Meshes

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

Gustafson, Kyle T.

2016-09-08

Metallic nanowire meshes are useful as cheap, flexible alternatives to indium tin oxide – an expensive, brittle material used in transparent conductive electrodes. We have fabricated nanowire meshes over areas up to 2.5 cm 2 by: 1) mechanically aligning parallel rows of diblock copolymer (diBCP) microdomains; 2) selectively infiltrating those domains with metallic ions; 3) etching away the diBCP template; 4) sintering to reduce ions to metal nanowires; and, 5) repeating steps 1 – 4 on the same sample at a 90° offset. We aligned parallel rows of polystyrene-b-poly(2-vinylpyridine) [PS(48.5 kDa)-b-P2VP(14.5 kDa)] microdomains by heating above its glass transition temperaturemore » (T g ≈ 100°C), applying mechanical shear pressure (33 kPa) and normal force (13.7 N), and cooling below T g. DiBCP samples were submerged in aqueous solutions of metallic ions (15 – 40 mM ions; 0.1 – 0.5 M HCl) for 30 – 90 minutes, which coordinate to nitrogen in P2VP. Subsequent ozone-etching and sintering steps yielded parallel nanowires. We aimed to optimize alignment parameters (e.g. shear and normal pressures, alignment duration, and PDMS thickness) to improve the quality, reproducibility, and scalability of meshes. We also investigated metals other than Pt and Au that may be patterned using this technique (Cu, Ag).« less

Analogical processes in children's understanding of spatial representations.

PubMed

Yuan, Lei; Uttal, David; Gentner, Dedre

2017-06-01

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

Does Funding for Arctic Research Align with Research Priorities and Policy Needs? Trends in the USA, Canada and Europe

NASA Astrophysics Data System (ADS)

Murray, M. S.; Ibarguchi, G.; Rajdev, V.

2015-12-01

Over the past twenty years, increasing awareness and understanding of changes in the Arctic system, the stated desires of Arctic Peoples to be engaged in the research process, and a growing international interest in the region's resources have informed various stakeholders to undertake many Arctic science planning activities. Some examples of science planning include priority-setting for research, knowledge translation, stakeholder engagement, improved coordination, and international collaboration. The International Study of Arctic Change recently initiated an analysis of the extent to which alignment exists among stated science priorities, recognized societal needs, and funding patterns of the major North American and European agencies. In this paper, we present a decade of data on international funding patterns and data on two decades of science planning. We discuss whether funding patterns reflect the priority research questions and identified needs for information that are articulated in a myriad of Arctic research planning documents. The alignment in many areas remains poor, bringing into question the purpose of large-scale science planning if it does not lead to funding of those priorities identified by Arctic stakeholder communities (scientists, Arctic Peoples, planners, policy makers, the private sector, and others).

Pattern masking: the importance of remote spatial frequencies and their phase alignment.

PubMed

Huang, Pi-Chun; Maehara, Goro; May, Keith A; Hess, Robert F

2012-02-16

To assess the effects of spatial frequency and phase alignment of mask components in pattern masking, target threshold vs. mask contrast (TvC) functions for a sine-wave grating (S) target were measured for five types of mask: a sine-wave grating (S), a square-wave grating (Q), a missing fundamental square-wave grating (M), harmonic complexes consisting of phase-scrambled harmonics of a square wave (Qp), and harmonic complexes consisting of phase-scrambled harmonics of a missing fundamental square wave (Mp). Target and masks had the same fundamental frequency (0.46 cpd) and the target was added in phase with the fundamental frequency component of the mask. Under monocular viewing conditions, the strength of masking depends on phase relationships among mask spatial frequencies far removed from that of the target, at least 3 times the target frequency, only when there are common target and mask spatial frequencies. Under dichoptic viewing conditions, S and Q masks produced similar masking to each other and the phase-scrambled masks (Qp and Mp) produced less masking. The results suggest that pattern masking is spatial frequency broadband in nature and sensitive to the phase alignments of spatial components.

Unexpected Patterns in Snow and Dirt

NASA Astrophysics Data System (ADS)

Ackerson, Bruce J.

2018-01-01

For more than 30 years, Albert A. Bartlett published "Thermal patterns in the snow" in this journal. These are patterns produced by heat sources underneath the snow. Bartlett's articles encouraged me to pay attention to patterns in snow and to understanding them. At winter's end the last snow becomes dirty and is heaped into piles. This snow comes from the final clearing of sidewalks and driveways. The patterns observed in these piles defied my intuition. This melting snow develops edges where dirt accumulates, in contrast to ice cubes, which lose sharp edges and become more spherical upon melting. Furthermore, dirt absorbs more radiation than snow and yet doesn't melt and round the sharp edges of snow, where dirt accumulates.

The Alignment of the Informal and Formal Organizational Supports for Reform: Implications for Improving Teaching in Schools

ERIC Educational Resources Information Center

Penuel, William R.; Riel, Margaret; Joshi, Aasha; Pearlman, Leslie; Kim, Chong Min; Frank, Kenneth A.

2010-01-01

Previous qualitative studies show that when the formal organization of a school and patterns of informal interaction are aligned, faculty and leaders in a school are better able to coordinate instructional change. This article combines social network analysis with interview data to analyze how well the formal and informal aspects of a school's…

Sleep, circadian rhythm and body weight: parallel developments.

PubMed

Westerterp-Plantenga, Margriet S

2016-11-01

Circadian alignment is crucial for body-weight management, and for metabolic health. In this context, circadian alignment consists of alignment of sleep, meal patterns and physical activity. During puberty a significant reduction in sleep duration occurs, and pubertal status is inversely associated with sleep duration. A consistent inverse association between habitual sleep duration and body-weight development occurs, independent of possible confounders. Research on misalignment reveals that circadian misalignment affects sleep-architecture and subsequently disturbs glucose-insulin metabolism, substrate oxidation, leptin- and ghrelin concentrations, appetite, food reward, hypothalamic-pituitary-adrenal-axis activity and gut-peptide concentrations enhancing positive energy balance and metabolic disturbance. Not only aligning meals and sleep in a circadian way is crucial, also regular physical activity during the day strongly promotes the stability and amplitude of circadian rhythm, and thus may serve as an instrument to restore poor circadian rhythms. Endogenicity may play a role in interaction of these environmental variables with a genetic predisposition. In conclusion, notwithstanding the separate favourable effects of sufficient daily physical activity, regular meal patterns, sufficient sleep duration and quality sleep on energy balance, the overall effect of the amplitude and stability of the circadian rhythm, perhaps including genetic predisposition, may integrate the separate effects in an additive way.

Microfluidic impact printer with interchangeable cartridges for versatile non-contact multiplexed micropatterning

PubMed Central

Ding, Yuzhe; Huang, Eric; Lam, Kit S.; Pan, Tingrui

2015-01-01

Biopatterning has been increasingly used for well-defined cellular microenvironment, patterned surface topology, and guided biological cues; however, it meets additional challenges on biocompatibility, temperature and chemical sensitivity and limited reagent volume. In this paper, we target at combining the desired features from the non-contact inkjet printing and the dot-matrix impact printing to establish a versatile multiplexed micropatterning platform, referred to as Microfluidic Impact Printer (MI-Printer), for emerging biomedical applications. Using this platform, we can achieve the distinct features of no cross-contamination, minute volume manipulation with minimal dead volume, high-throughput and biocompatible printing process, multiplexed patterning with automatic alignment, printing availability for complex medium (cell suspension or colloidal solutions), interchangeable/disposable microfluidic cartridge design with out-of-cleanroom microfabrication, simple printing system assembly and configuration, all highly desirable towards biological applications. Specifically, the printing resolution of the MI-printer platform has been experimentally characterized and theoretically analyzed. Printed droplets with 80µm in diameter have been repeatedly obtained. Furthermore, two unique features of MI-printer platform, multiplexed printing and self-alignment printing, have been successfully experimentally demonstrated (less than 10µm misalignment). In addition, combinatorial patterning and biological patterning, which utilizes the multiplexed and self-alignment printing nature of the MI-printer, have been devised to demonstrate the applicability of this robust printing technique for emerging biomedical applications. PMID:23525299

Time-Dependent Trapping of Pollinators Driven by the Alignment of Floral Phenology with Insect Circadian Rhythms

PubMed Central

Lau, Jenny Y. Y.; Guo, Xing; Pang, Chun-Chiu; Tang, Chin Cheung; Thomas, Daniel C.; Saunders, Richard M. K.

2017-01-01

Several evolutionary lineages in the early divergent angiosperm family Annonaceae possess flowers with a distinctive pollinator trapping mechanism, in which floral phenological events are very precisely timed in relation with pollinator activity patterns. This contrasts with previously described angiosperm pollinator traps, which predominantly function as pitfall traps. We assess the circadian rhythms of pollinators independently of their interactions with flowers, and correlate these data with detailed assessments of floral phenology. We reveal a close temporal alignment between patterns of pollinator activity and the floral phenology driving the trapping mechanism (termed ‘circadian trapping’ here). Non-trapping species with anthesis of standard duration (c. 48 h) cannot be pollinated effectively by pollinators with a morning-unimodal activity pattern; non-trapping species with abbreviated anthesis (23–27 h) face limitations in utilizing pollinators with a bimodal circadian activity; whereas species that trap pollinators (all with short anthesis) can utilize a broader range of potential pollinators, including those with both unimodal and bimodal circadian rhythms. In addition to broadening the range of potential pollinators based on their activity patterns, circadian trapping endows other selective advantages, including the possibility of an extended staminate phase to promote pollen deposition, and enhanced interfloral movement of pollinators. The relevance of the alignment of floral phenological changes with peaks in pollinator activity is furthermore evaluated for pitfall trap pollination systems. PMID:28713403

Multiscale Currents Observed by MMS in the Flow Braking Region

NASA Astrophysics Data System (ADS)

Nakamura, Rumi; Varsani, Ali; Genestreti, Kevin J.; Le Contel, Olivier; Nakamura, Takuma; Baumjohann, Wolfgang; Nagai, Tsugunobu; Artemyev, Anton; Birn, Joachim; Sergeev, Victor A.; Apatenkov, Sergey; Ergun, Robert E.; Fuselier, Stephen A.; Gershman, Daniel J.; Giles, Barbara J.; Khotyaintsev, Yuri V.; Lindqvist, Per-Arne; Magnes, Werner; Mauk, Barry; Petrukovich, Anatoli; Russell, Christopher T.; Stawarz, Julia; Strangeway, Robert J.; Anderson, Brian; Burch, James L.; Bromund, Ken R.; Cohen, Ian; Fischer, David; Jaynes, Allison; Kepko, Laurence; Le, Guan; Plaschke, Ferdinand; Reeves, Geoff; Singer, Howard J.; Slavin, James A.; Torbert, Roy B.; Turner, Drew L.

2018-02-01

We present characteristics of current layers in the off-equatorial near-Earth plasma sheet boundary observed with high time-resolution measurements from the Magnetospheric Multiscale mission during an intense substorm associated with multiple dipolarizations. The four Magnetospheric Multiscale spacecraft, separated by distances of about 50 km, were located in the southern hemisphere in the dusk portion of a substorm current wedge. They observed fast flow disturbances (up to about 500 km/s), most intense in the dawn-dusk direction. Field-aligned currents were observed initially within the expanding plasma sheet, where the flow and field disturbances showed the distinct pattern expected in the braking region of localized flows. Subsequently, intense thin field-aligned current layers were detected at the inner boundary of equatorward moving flux tubes together with Earthward streaming hot ions. Intense Hall current layers were found adjacent to the field-aligned currents. In particular, we found a Hall current structure in the vicinity of the Earthward streaming ion jet that consisted of mixed ion components, that is, hot unmagnetized ions, cold E × B drifting ions, and magnetized electrons. Our observations show that both the near-Earth plasma jet diversion and the thin Hall current layers formed around the reconnection jet boundary are the sites where diversion of the perpendicular currents take place that contribute to the observed field-aligned current pattern as predicted by simulations of reconnection jets. Hence, multiscale structure of flow braking is preserved in the field-aligned currents in the off-equatorial plasma sheet and is also translated to ionosphere to become a part of the substorm field-aligned current system.

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

The Classical Vacuum.

ERIC Educational Resources Information Center

Boyer, Timothy H.

1985-01-01

The classical vacuum of physics is not empty, but contains a distinctive pattern of electromagnetic fields. Discovery of the vacuum, thermal spectrum, classical electron theory, zero-point spectrum, and effects of acceleration are discussed. Connection between thermal radiation and the classical vacuum reveals unexpected unity in the laws of…

Jobs in Unexpected Places--A Pattern for the 80s.

ERIC Educational Resources Information Center

Samuels, Jack B.

1983-01-01

Opportunities now await the leisure service professional in several employment areas not traditionally occupied by people with training or experience in the recreation or leisure service profession. Areas include theme parks, auditorium and arena management, themed restaurants, shopping centers, and resort management. (CJ)

The inhibition of methane hydrate formation by water alignment underneath surface adsorption of surfactants

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

Nguyen, Ngoc N.; Nguyen, Anh V.; Dang, Liem X.

Sodium dodecyl sulfate (SDS) has been widely shown to strongly promote the formation of methane hydrate. Here we show that SDS displays an extraordinary inhibition effect on methane hydrate formation when the surfactant is used in sub-millimolar concentration (around 0.3 mM). We have also employed Sum Frequency Generation vibrational spectroscopy (SFG) and molecular dynamics simulation (MDS) to elucidate the molecular mechanism of this inhibition. The SFG and MDS results revealed a strong alignment of water molecules underneath surface adsorption of SDS in its sub-millimolar solution. Interestingly, both the alignment of water and the inhibition effect (in 0.3 mM SDS solution)more » went vanishing when an oppositely-charged surfactant (tetra-n-butylammonium bromide, TBAB) was suitably added to produce a mixed solution of 0.3 mM SDS and 3.6 mM TBAB. Combining structural and kinetic results, we pointed out that the alignment of water underneath surface adsorption of dodecyl sulfate (DS-) anions gave rise to the unexpected inhibition of methane hydration formation in sub-millimolar solution of SDS. The adoption of TBAB mitigated the SDS-induced electrostatic field at the solution’s surface and, therefore, weakened the alignment of interfacial water which, in turn, erased the inhibition effect. We discussed this finding using the concept of activation energy of the interfacial formation of gas hydrate. The main finding of this work is to reveal the interplay of interfacial water in governing gas hydrate formation which sheds light on a universal molecular-scale understanding of the influence of surfactants on gas hydrate formation. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

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

PubMed

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

2011-06-02

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

Manufacturing Methods and Technology Program Accomplishments

DTIC Science & Technology

1981-10-01

ALIGNMENT USING CHARACTERISTIC X-RADIATION •KOSSEL PATTERNS KOSSEL PATTERN SHOWING EXPECTED EFFECT OF 1% HYDROSTATIC STRAIN >THE KOSSEL METHOD WAS...Chemical Demilitarization & Restoration, Attn: DRCPM-DR PM, Smoke/Obscurant3 (SMOKE), Attn: DRCPM- SMK Cdr, Attn: STEAP*MT-M, Mr. J. L. Sanders

Periodic dielectric structure for production of photonic band gap and method for fabricating the same

DOEpatents

Ozbay, Ekmel; Tuttle, Gary; Michel, Erick; Ho, Kai-Ming; Biswas, Rana; Chan, Che-Ting; Soukoulis, Costas

1995-01-01

A method for fabricating a periodic dielectric structure which exhibits a photonic band gap. Alignment holes are formed in a wafer of dielectric material having a given crystal orientation. A planar layer of elongate rods is then formed in a section of the wafer. The formation of the rods includes the step of selectively removing the dielectric material of the wafer between the rods. The formation of alignment holes and layers of elongate rods and wafers is then repeated to form a plurality of patterned wafers. A stack of patterned wafers is then formed by rotating each successive wafer with respect to the next-previous wafer, and then placing the successive wafer on the stack. This stacking results in a stack of patterned wafers having a four-layer periodicity exhibiting a photonic band gap.

Cell behavior on surface modified polydimethylsiloxane (PDMS).

PubMed

Stanton, Morgan M; Rankenberg, Johanna M; Park, Byung-Wook; McGimpsey, W Grant; Malcuit, Christopher; Lambert, Christopher R

2014-07-01

Designing complex tissue culture systems requires cell alignment and directed extracellular matrix (ECM) and gene expression. Here, a micro-rough, polydimethylsiloxane (PDMS) surface, that also integrates a micro-pattern of 50 µm wide lines of fibronectin (FN) separated by 60 µm wide lines of bovine serum albumin (BSA), is developed. Human fibroblasts cultured on the rough, patterned substrate have aligned growth and a significant change in morphology when compared to cells on a flat, patterned surface. The rough PDMS topography significantly decreases cell area and induces the upregulation of several ECM related genes by two-fold when compared to cells cultured on flat PDMS. This study describes a simple surface engineering procedure for creating surface architecture for scaffolds to design and control the cell-surface interface. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Signal quality improvement using cylindrical confinement for laser induced breakdown spectroscopy.

PubMed

Hou, Zongyu; Wang, Zhe; Liu, Jianmin; Ni, Weidou; Li, Zheng

2013-07-01

In our previous work, we found that there was great potential to improve the pulse-to-pulse signal repeatability using a moderate cylindrical cavity confinement. However, the improvement was achieved only with certain experimental parameters; while under other conditions, there was no improvement or even worse repeatability. In the present work, the experimental configuration was redesigned and unexpected uncertainty from the variation of the laser and cavity alignment and the laser ablated aerosols were avoided. With these two improvements, we demonstrated that the cavity can always increase the signal repeatability. In addition, image taken by ICCD verified that the confinement improved the stability of the plasma morphology as expected.

System for inspecting large size structural components

DOEpatents

Birks, Albert S.; Skorpik, James R.

1990-01-01

The present invention relates to a system for inspecting large scale structural components such as concrete walls or the like. The system includes a mobile gamma radiation source and a mobile gamma radiation detector. The source and detector are constructed and arranged for simultaneous movement along parallel paths in alignment with one another on opposite sides of a structural component being inspected. A control system provides signals which coordinate the movements of the source and detector and receives and records the radiation level data developed by the detector as a function of source and detector positions. The radiation level data is then analyzed to identify areas containing defects corresponding to unexpected variations in the radiation levels detected.

Optical alignment using a CGH and an autostigmatic microscope

NASA Astrophysics Data System (ADS)

Parks, Robert E.

2017-08-01

We show how custom computer generated holograms (CGH) are used along with an autostigmatic microscope (ASM) to align both optical and mechanical components relative to the CGH. The patterns in the CGHs define points and lines in space when interrogated with the focus of the ASM. Once the ASM is aligned to the CGH, an optical or mechanical component such as a lens, a well-polished ball or a cylinder can be aligned to the ASM in 3 or 4 degrees of freedom and thus to the CGH. In this case we show how a CGH is used to make a fixture for cementing a doublet lens without the need for a rotary table or a precision vertical stage.

Guided growth of large-scale, horizontally aligned arrays of single-walled carbon nanotubes and their use in thin-film transistors.

PubMed

Kocabas, Coskun; Hur, Seung-Hyun; Gaur, Anshu; Meitl, Matthew A; Shim, Moonsub; Rogers, John A

2005-11-01

A convenient process for generating large-scale, horizontally aligned arrays of pristine, single-walled carbon nanotubes (SWNTs) is described. The approach uses guided growth, by chemical vapor deposition (CVD), of SWNTs on miscut single-crystal quartz substrates. Studies of the growth reveal important relationships between the density and alignment of the tubes, the CVD conditions, and the morphology of the quartz. Electrodes and dielectrics patterned on top of these arrays yield thin-film transistors that use the SWNTs as effective thin-film semiconductors. The ability to build high-performance devices of this type suggests significant promise for large-scale aligned arrays of SWNTs in electronics, sensors, and other applications.

Large-Scale Patterns in a Minimal Cognitive Flocking Model: Incidental Leaders, Nematic Patterns, and Aggregates

NASA Astrophysics Data System (ADS)

Barberis, Lucas; Peruani, Fernando

2016-12-01

We study a minimal cognitive flocking model, which assumes that the moving entities navigate using the available instantaneous visual information exclusively. The model consists of active particles, with no memory, that interact by a short-ranged, position-based, attractive force, which acts inside a vision cone (VC), and lack velocity-velocity alignment. We show that this active system can exhibit—due to the VC that breaks Newton's third law—various complex, large-scale, self-organized patterns. Depending on parameter values, we observe the emergence of aggregates or millinglike patterns, the formation of moving—locally polar—files with particles at the front of these structures acting as effective leaders, and the self-organization of particles into macroscopic nematic structures leading to long-ranged nematic order. Combining simulations and nonlinear field equations, we show that position-based active models, as the one analyzed here, represent a new class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems. The reported results are of prime importance in the study, interpretation, and modeling of collective motion patterns in living and nonliving active systems.

Large-Scale Patterns in a Minimal Cognitive Flocking Model: Incidental Leaders, Nematic Patterns, and Aggregates.

PubMed

Barberis, Lucas; Peruani, Fernando

2016-12-09

We study a minimal cognitive flocking model, which assumes that the moving entities navigate using the available instantaneous visual information exclusively. The model consists of active particles, with no memory, that interact by a short-ranged, position-based, attractive force, which acts inside a vision cone (VC), and lack velocity-velocity alignment. We show that this active system can exhibit-due to the VC that breaks Newton's third law-various complex, large-scale, self-organized patterns. Depending on parameter values, we observe the emergence of aggregates or millinglike patterns, the formation of moving-locally polar-files with particles at the front of these structures acting as effective leaders, and the self-organization of particles into macroscopic nematic structures leading to long-ranged nematic order. Combining simulations and nonlinear field equations, we show that position-based active models, as the one analyzed here, represent a new class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems. The reported results are of prime importance in the study, interpretation, and modeling of collective motion patterns in living and nonliving active systems.

Beneath the Surface: Understanding Patterns of Intra-Domain Orientational Order

NASA Astrophysics Data System (ADS)

Prasad, Ishan; Seo, Youngmi; Hall, Lisa; Grason, Gregory

Block copolymers (BCP) self assemble into a rich spectrum of ordered phases due to asymmetry in copolymer architecture. Despite extensive study of spatially-ordered composition patterns of BCP, knowledge of orientational order of chain segments that underlie these spatial patterns is evidently missing. We show using self consistent field (SCF) theory and coarse-grained molecular dynamics (MD) simulations that, even without explicit orientational interactions between segments, BCP exhibit generic patterns of intra-domain segment orientation, which vary both within a given morphology and from morphology to morphology. We find that segment alignment is usually both normal and parallel to the interface within different local regions of a BCP sub-domain. We describe principles that control relative strength and directionality of alignment in different morphologies and report a surprising yet generic emergence of biaxial segment order in morphologies with anisotropic curved interfaces, such as cylinders and gyroid phases. Finally, we focus our study on cholesteric textures that pervade mesochiral BCP morphologies, specifically alternating double gyroid (aDG) and helical cylinder (H*) phases, and analyze patterns of twisted (nematic and polar) segment order within these domains.

Study for new hardmask process scheme

NASA Astrophysics Data System (ADS)

Lee, Daeyoup; Tatti, Phillip; Lee, Richard; Chang, Jack; Cho, Winston; Bae, Sanggil

2017-03-01

Hardmask processes are a key technique to enable low-k semiconductors, but they can have an impact on patterning control, influencing defectivity, alignment, and overlay. Specifically, amorphous carbon layer (ACL) hardmask schemes can negatively affect overlay by creating distorted alignment signals. A new scheme needs to be developed that can be inserted where amorphous carbon is used but provide better alignment performance. Typical spin-on carbon (SOC) materials used in other hardmask schemes have issues with DCD-FCD skew. In this paper we will evaluate new spin-on carbon material with a higher carbon content that could be a candidate to replace amorphous carbon.

Fine alignment of a large segmented mirror

NASA Technical Reports Server (NTRS)

Dey, Thomas William (Inventor)

2010-01-01

A system for aligning a segmented mirror includes a source of radiation directed along a first axis to the segmented mirror and a beamsplitter removably inserted along the first axis for redirecting radiation from the first axis to a second axis, substantially perpendicular to the first axis. An imaging array is positioned along the second axis for imaging the redirected radiation, and a knife-edge configured for cutting the redirected radiation is serially positioned to occlude and not occlude the redirected radiation, effectively providing a variable radiation pattern detected by the imaging array for aligning the segmented mirror.

Method for vacuum fusion bonding

DOEpatents

Ackler, Harold D.; Swierkowski, Stefan P.; Tarte, Lisa A.; Hicks, Randall K.

2001-01-01

An improved vacuum fusion bonding structure and process for aligned bonding of large area glass plates, patterned with microchannels and access holes and slots, for elevated glass fusion temperatures. Vacuum pumpout of all components is through the bottom platform which yields an untouched, defect free top surface which greatly improves optical access through this smooth surface. Also, a completely non-adherent interlayer, such as graphite, with alignment and location features is located between the main steel platform and the glass plate pair, which makes large improvements in quality, yield, and ease of use, and enables aligned bonding of very large glass structures.

Surface tension-driven self-alignment.

PubMed

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

2017-01-04

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

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

PubMed

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

2011-01-01

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

Soft X-ray holographic grating beam splitter including a double frequency grating for interferometer pre-alignment.

PubMed

Liu, Ying; Tan, Xin; Liu, Zhengkun; Xu, Xiangdong; Hong, Yilin; Fu, Shaojun

2008-09-15

Grating beam splitters have been fabricated for soft X-ray Mach- Zehnder interferometer using holographic interference lithography. The grating beam splitter consists of two gratings, one works at X-ray laser wavelength of 13.9 nm with the spatial frequency of 1000 lines/mm as the operation grating, the other works at visible wavelength of 632.8 nm for pre-aligning the X-ray interferometer with the spatial frequency of 22 lines/mm as the pre-alignment grating. The two gratings lie vertically on the same substrate. The main feature of the beam splitter is the use of low-spatial- frequency beat grating of a holographic double frequency grating as the pre-alignment grating of the X-ray interferometer. The grating line parallelism between the two gratings can be judged by observing the diffraction patterns of the pre-alignment grating directly.

Cardiac and electro-cortical concomitants of social feedback processing in women

PubMed Central

van der Molen, Melle J. W.; Gunther Moor, Bregtje; van der Veen, Frederik M.; van der Molen, Maurits W.

2015-01-01

This study provides a joint analysis of the cardiac and electro-cortical—early and late P3 and feedback-related negativity (FRN)—responses to social acceptance and rejection feedback. Twenty-five female participants performed on a social- and age-judgment control task, in which they received feedback with respect to their liking and age judgments, respectively. Consistent with previous reports, results revealed transient cardiac slowing to be selectively prolonged to unexpected social rejection feedback. Late P3 amplitude was more pronounced to unexpected relative to expected feedback. Both early and late P3 amplitudes were shown to be context dependent, in that they were more pronounced to social as compared with non-social feedback. FRN amplitudes were more pronounced to unexpected relative to expected feedback, irrespective of context and feedback valence. This pattern of findings indicates that social acceptance and rejection feedback have widespread effects on bodily state and brain function, which are modulated by prior expectancies. PMID:25870439

Multiple effects of sentential constraint on word processing

PubMed Central

Federmeier, Kara D.; Wlotko, Edward W.; De Ochoa-Dewald, Esmeralda; Kutas, Marta

2009-01-01

Behavioral and electrophysiological studies have uncovered different patterns of constraint effects on the processing of words in sentences. Whereas response time measures have indicated a reduced scope of facilitation from strongly constraining contexts, event-related brain potential (ERP) measures have instead revealed enhanced facilitation for semantically related endings in such sentences. Given this disparity, and the concomitant possibility of functionally separable stages of context effects, the current study jointly examined expectancy (cloze probability) and constraint effects on the ERP response to words. Expected and unexpected (but plausible) words completed strongly and weakly constraining sentences; unexpected items were matched for contextual fit across the two levels of constraint and were semantically unrelated to the most expected endings. N400 amplitudes were graded by expectancy but unaffected by constraint and seemed to index the benefit of contextual information. However, a later effect, in the form of increased frontal positivity from 500 to 900 ms post-stimulus-onset, indicated a possible cost associated with the processing of unexpected words in strongly constraining contexts. PMID:16901469

Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

PubMed Central

Shih, Arthur Chun-Chieh; Lee, DT; Peng, Chin-Lin; Wu, Yu-Wei

2007-01-01

Background When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. Results A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. Conclusion With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL . PMID:17319966

An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences.

PubMed

Ye, Kai; Kosters, Walter A; Ijzerman, Adriaan P

2007-03-15

Pattern discovery in protein sequences is often based on multiple sequence alignments (MSA). The procedure can be computationally intensive and often requires manual adjustment, which may be particularly difficult for a set of deviating sequences. In contrast, two algorithms, PRATT2 (http//www.ebi.ac.uk/pratt/) and TEIRESIAS (http://cbcsrv.watson.ibm.com/) are used to directly identify frequent patterns from unaligned biological sequences without an attempt to align them. Here we propose a new algorithm with more efficiency and more functionality than both PRATT2 and TEIRESIAS, and discuss some of its applications to G protein-coupled receptors, a protein family of important drug targets. In this study, we designed and implemented six algorithms to mine three different pattern types from either one or two datasets using a pattern growth approach. We compared our approach to PRATT2 and TEIRESIAS in efficiency, completeness and the diversity of pattern types. Compared to PRATT2, our approach is faster, capable of processing large datasets and able to identify the so-called type III patterns. Our approach is comparable to TEIRESIAS in the discovery of the so-called type I patterns but has additional functionality such as mining the so-called type II and type III patterns and finding discriminating patterns between two datasets. The source code for pattern growth algorithms and their pseudo-code are available at http://www.liacs.nl/home/kosters/pg/.

Improving Spectral Results Using Row-by-Row Fourier Transform of Spatial Heterodyne Raman Spectrometer Interferogram.

PubMed

Barnett, Patrick D; Strange, K Alicia; Angel, S Michael

2017-06-01

This work describes a method of applying the Fourier transform to the two-dimensional Fizeau fringe patterns generated by the spatial heterodyne Raman spectrometer (SHRS), a dispersive interferometer, to correct the effects of certain types of optical alignment errors. In the SHRS, certain types of optical misalignments result in wavelength-dependent and wavelength-independent rotations of the fringe pattern on the detector. We describe here a simple correction technique that can be used in post-processing, by applying the Fourier transform in a row-by-row manner. This allows the user to be more forgiving of fringe alignment and allows for a reduction in the mechanical complexity of the SHRS.

Alignment of Ge nanoislands on Si(111) by Ga-induced substrate self-patterning.

PubMed

Schmidt, Th; Flege, J I; Gangopadhyay, S; Clausen, T; Locatelli, A; Heun, S; Falta, J

2007-02-09

A novel mechanism is described which enables the selective formation of three-dimensional Ge islands. Submonolayer adsorption of Ga on Si(111) at high temperature leads to a self-organized two-dimensional pattern formation by separation of the 7 x 7 substrate and Ga/Si(111)-(square root[3] x square root[3])-R30 degrees domains. The latter evolve at step edges and domain boundaries of the initial substrate reconstruction. Subsequent Ge deposition results in the growth of 3D islands which are aligned at the boundaries between bare and Ga-covered domains. This result is explained in terms of preferential nucleation conditions due to a modulation of the surface chemical potential.

The Surprising Persistence of Biglan's Classification Scheme

ERIC Educational Resources Information Center

Simpson, Adrian

2017-01-01

Within higher education systems, different institutions deliver different patterns of disciplines. A simple analysis of the structure of that pattern of disciplines across institutions in one higher education system uncovers a surprising relationship. That is, the key dimensions which describe that structure align nearly perfectly with dimensions…

A diagnostic technique used to obtain cross range radiation centers from antenna patterns

NASA Technical Reports Server (NTRS)

Lee, T. H.; Burnside, W. D.

1988-01-01

A diagnostic technique to obtain cross range radiation centers based on antenna radiation patterns is presented. This method is similar to the synthetic aperture processing of scattered fields in the radar application. Coherent processing of the radiated fields is used to determine the various radiation centers associated with the far-zone pattern of an antenna for a given radiation direction. This technique can be used to identify an unexpected radiation center that creates an undesired effect in a pattern; on the other hand, it can improve a numerical simulation of the pattern by identifying other significant mechanisms. Cross range results for two 8' reflector antennas are presented to illustrate as well as validate that technique.

New colored optical security elements using Rolic's LPP/LCP technology: devices for first- to third-level inspection

NASA Astrophysics Data System (ADS)

Moia, Franco

2002-04-01

With linear photo-polymerization (LPP) ROLIC has invented a photo-patternable technology enabling to align not only conventional liquid crystals but also liquid crystals polymers (LCP). ROLIC's optical security device technology derives from its LPP/LCP technology. LPP/LCP security devices are created by structured photo-alignment of an LPP layer through phot-masks, thus generating a high resolution, photo-patterned aligning layer which carries the aligning information of the image to be created. The subsequent LCP layer transforms the aligning information into an optical phase image with low and/or very high information content, such as invisible photographic pictures. The building block capability of the LPP/LCP technology allows the manufacturing of cholesteric and non-cholesteric LPP/LCP devices which cover 1st and/or 2nd level applications. Apart from black/white security devices colored information zones can be integrated. Moreover, we have developed an LPP/LCP security device which covers all three- 1st, 2nd and 3rd- inspection levels in one and the same authentication device: besides a color shift by tilting the device (1st level) and the detection of normally hidden information by use of a simple sheet polarizer (2nd level) the new device contains encrypted hidden information which can be visualized only by superimposing an LPP/LCP inspection tool (key) for decryption (3rd level). This optical key is also based on the LPP/LCP technology and is itself a 3rd level security device.

Debugging from the Student Perspective

ERIC Educational Resources Information Center

Fitzgerald, S.; McCauley, R.; Hanks, B.; Murphy, L.; Simon, B.; Zander, C.

2010-01-01

Learning to debug is a difficult, yet essential, aspect of learning to program. Students in this multi-institutional study report that finding bugs is harder than fixing them. They use a wide variety of debugging strategies, some of them unexpected. Time spent on understanding the problem can be effective. Pattern matching, particularly at the…

Gene dosage induction of silencing directed against an Arabidopsis Myb transgene in tobacco

USDA-ARS?s Scientific Manuscript database

An unexpected reduction in petal pigmentation on petunia plants genetically engineered for enhanced flower color was one of the first experimental demonstrations of the natural process of RNA-associated gene silencing. The obvious visual nature of such alterations to pigment patterns of transgenic ...

Multiscale Currents Observed by MMS in the Flow Braking Region.

PubMed

Nakamura, Rumi; Varsani, Ali; Genestreti, Kevin J; Le Contel, Olivier; Nakamura, Takuma; Baumjohann, Wolfgang; Nagai, Tsugunobu; Artemyev, Anton; Birn, Joachim; Sergeev, Victor A; Apatenkov, Sergey; Ergun, Robert E; Fuselier, Stephen A; Gershman, Daniel J; Giles, Barbara J; Khotyaintsev, Yuri V; Lindqvist, Per-Arne; Magnes, Werner; Mauk, Barry; Petrukovich, Anatoli; Russell, Christopher T; Stawarz, Julia; Strangeway, Robert J; Anderson, Brian; Burch, James L; Bromund, Ken R; Cohen, Ian; Fischer, David; Jaynes, Allison; Kepko, Laurence; Le, Guan; Plaschke, Ferdinand; Reeves, Geoff; Singer, Howard J; Slavin, James A; Torbert, Roy B; Turner, Drew L

2018-02-01

We present characteristics of current layers in the off-equatorial near-Earth plasma sheet boundary observed with high time-resolution measurements from the Magnetospheric Multiscale mission during an intense substorm associated with multiple dipolarizations. The four Magnetospheric Multiscale spacecraft, separated by distances of about 50 km, were located in the southern hemisphere in the dusk portion of a substorm current wedge. They observed fast flow disturbances (up to about 500 km/s), most intense in the dawn-dusk direction. Field-aligned currents were observed initially within the expanding plasma sheet, where the flow and field disturbances showed the distinct pattern expected in the braking region of localized flows. Subsequently, intense thin field-aligned current layers were detected at the inner boundary of equatorward moving flux tubes together with Earthward streaming hot ions. Intense Hall current layers were found adjacent to the field-aligned currents. In particular, we found a Hall current structure in the vicinity of the Earthward streaming ion jet that consisted of mixed ion components, that is, hot unmagnetized ions, cold E × B drifting ions, and magnetized electrons. Our observations show that both the near-Earth plasma jet diversion and the thin Hall current layers formed around the reconnection jet boundary are the sites where diversion of the perpendicular currents take place that contribute to the observed field-aligned current pattern as predicted by simulations of reconnection jets. Hence, multiscale structure of flow braking is preserved in the field-aligned currents in the off-equatorial plasma sheet and is also translated to ionosphere to become a part of the substorm field-aligned current system.

'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.

Redundant via insertion in self-aligned double patterning

NASA Astrophysics Data System (ADS)

Song, Youngsoo; Jung, Jinwook; Shin, Youngsoo

2017-03-01

Redundant via (RV) insertion is employed to enhance via manufacturability, and has been extensively studied. Self-aligned double patterning (SADP) process, brings a new challenge to RV insertion since newly created cut for each RV insertion has to be taken care of. Specifically, when a cut for RV, which we simply call RV-cut, is formed, cut conflict may occur with nearby line-end cuts, which results in a decrease in RV candidates. We introduce cut merging to reduce the number of cut conflicts; merged cuts are processed with stitch using litho-etch-litho-etch (LELE) multi-patterning method. In this paper, we propose a new RV insertion method with cut merging in SADP for the first time. In our experiments, a simple RV insertion yields 55.3% vias to receives RVs; our proposed method that considers cut merging increases that number to 69.6% on average of test circuits.

Periodic dielectric structure for production of photonic band gap and method for fabricating the same

DOEpatents

Ozbay, E.; Tuttle, G.; Michel, E.; Ho, K.M.; Biswas, R.; Chan, C.T.; Soukoulis, C.

1995-04-11

A method is disclosed for fabricating a periodic dielectric structure which exhibits a photonic band gap. Alignment holes are formed in a wafer of dielectric material having a given crystal orientation. A planar layer of elongate rods is then formed in a section of the wafer. The formation of the rods includes the step of selectively removing the dielectric material of the wafer between the rods. The formation of alignment holes and layers of elongate rods and wafers is then repeated to form a plurality of patterned wafers. A stack of patterned wafers is then formed by rotating each successive wafer with respect to the next-previous wafer, and then placing the successive wafer on the stack. This stacking results in a stack of patterned wafers having a four-layer periodicity exhibiting a photonic band gap. 42 figures.

Self-aligned quadruple patterning-compliant placement

NASA Astrophysics Data System (ADS)

Nakajima, Fumiharu; Kodama, Chikaaki; Nakayama, Koichi; Nojima, Shigeki; Kotani, Toshiya

2015-03-01

Self-Aligned Quadruple Patterning (SAQP) will be one of the leading candidates for sub-14nm node and beyond. However, compared with triple patterning, making a feasible standard cell placement has following problems. (1) When coloring conflicts occur between two adjoining cells, they may not be solved easily since SAQP layout has stronger coloring constraints. (2) SAQP layout cannot use stitch to solve coloring conflict. In this paper, we present a framework of SAQP-aware standard cell placement considering the above problems. When standard cell is placed, the proposed method tries to solve coloring conflicts between two cells by exchanging two of three colors. If some conflicts remain between adjoining cells, dummy space will be inserted to keep coloring constraints of SAQP. We show some examples to confirm effectiveness of the proposed framework. To our best knowledge, this is the first framework of SAQP-aware standard cell placement.

Photopolymerized materials and patterning for improved performance of neural prosthetics

NASA Astrophysics Data System (ADS)

Tuft, Bradley William

Neural prosthetics are used to replace or substantially augment remaining motor and sensory functions of neural pathways that were lost or damaged due to physical trauma, disease, or genetics. However, due to poor spatial signal resolution, neural prostheses fail to recapitulate the intimate, precise interactions inherent to neural networks. Designing materials and interfaces that direct de novo nerve growth to spatially specific stimulating elements is, therefore, a promising method to enhance signal specificity and performance of prostheses such as the successful cochlear implant (CI) and the developing retinal implant. In this work, the spatial and temporal reaction control inherent to photopolymerization was used to develop methods to generate micro and nanopatterned materials that direct neurite growth from prosthesis relevant neurons. In particular, neurite growth and directionality has been investigated in response to physical, mechanical, and chemical cues on photopolymerized surfaces. Spiral ganglion neurons (SGNs) serve as the primary neuronal model as they are the principal target for CI stimulation. The objective of the research is to rationally design materials that spatially direct neurite growth and to translate fundamental understanding of nerve cell-material interactions into methods of nerve regeneration that improve neural prosthetic performance. A rapid, single-step photopolymerization method was developed to fabricate micro and nanopatterned physical cues on methacrylate surfaces by selectively blocking light with photomasks. Feature height is readily tuned by modulating parameters of the photopolymerizaiton including initiator concentration and species, light intensity, separation distance from the photomask, and radiation exposure time. Alignment of neural elements increases significantly with increasing feature amplitude and constant periodicity, as well as with decreasing periodicity and constant amplitude. SGN neurite alignment strongly correlates with the maximum feature slope. Neurite alignment is compared on unpatterned, unidirectional, and multidirectional photopolymerized micropatterns. The effect of substrate rigidity on neurite alignment to physical cues was determined by maintaining equivalent pattern microfeatures, afforded by the reaction control of photopolymerization, while concomitantly altering the composition of several copolymer platforms to tune matrix stiffness. For each platform, neurite alignment to unidirectional patterns increases with increasing substrate rigidity. Interestingly, SGN neurites respond to material stiffness cues that are orders of magnitude higher (GPa) than what is typically ascribed to neural environments (kPa). Finally, neurite behavior at bioactive borders of various adhesion modulating molecules was evaluated on micropatterned materials to determine which cues took precedence in establishing neurite directionality. At low microfeatures aspect ratios, neurites align to the pattern direction but are then caused to turn and repel from or turn and align to bioactive borders. Conversely, physical cues dominate neurite path-finding as pattern feature slope increases, i.e. aspect ratio of sloping photopolymerized features increases, causing neurites to readily cross bioactive borders. The photopolymerization method developed in this work to generate micro and nanopatterned materials serves as an additional surface engineering tool that enables investigation of cell-material interactions including directed de novo neurite growth. The results of this interdisciplinary effort contribute substantially to polymer neural regeneration technology and will lead to development of advanced biomaterials that improve neural prosthetic tissue integration and performance by spatially directing nerve growth.

Electrical comparison of iN7 EUV hybrid and EUV single patterning BEOL metal layers

NASA Astrophysics Data System (ADS)

Larivière, Stéphane; Wilson, Christopher J.; Kutrzeba Kotowska, Bogumila; Versluijs, Janko; Decoster, Stefan; Mao, Ming; van der Veen, Marleen H.; Jourdan, Nicolas; El-Mekki, Zaid; Heylen, Nancy; Kesters, Els; Verdonck, Patrick; Béral, Christophe; Van den Heuvel, Dieter; De Bisschop, Peter; Bekaert, Joost; Blanco, Victor; Ciofi, Ivan; Wan, Danny; Briggs, Basoene; Mallik, Arindam; Hendrickx, Eric; Kim, Ryoung-han; McIntyre, Greg; Ronse, Kurt; Bömmels, Jürgen; Tőkei, Zsolt; Mocuta, Dan

2018-03-01

The semiconductor scaling roadmap shows the continuous node to node scaling to push Moore's law down to the next generations. In that context, the foundry N5 node requires 32nm metal pitch interconnects for the advanced logic Back- End of Line (BEoL). 193immersion usage now requires self-aligned and/or multiple patterning technique combinations to enable such critical dimension. On the other hand, EUV insertion investigation shows that 32nm metal pitch is still a challenge but, related to process flow complexity, presents some clear motivations. Imec has already evaluated on test chip vehicles with different patterning approaches: 193i SAQP (Self-Aligned Quadruple Patterning), LE3 (triple patterning Litho Etch), tone inversion, EUV SE (Single Exposure) with SMO (Source-mask optimization). Following the run path in the technology development for EUV insertion, imec N7 platform (iN7, corresponding node to the foundry N5) is developed for those BEoL layers. In this paper, following technical motivation and development learning, a comparison between the iArF SAQP/EUV block hybrid integration scheme and a single patterning EUV flow is proposed. These two integration patterning options will be finally compared from current morphological and electrical criteria.

Trabecular architecture of the manual elements reflects locomotor patterns in primates.

PubMed

Matarazzo, Stacey A

2015-01-01

The morphology of trabecular bone has proven sensitive to loading patterns in the long bones and metacarpal heads of primates. It is expected that we should also see differences in the manual digits of primates that practice different methods of locomotion. Primate proximal and middle phalanges are load-bearing elements that are held in different postures and experience different mechanical strains during suspension, quadrupedalism, and knuckle walking. Micro CT scans of the middle phalanx, proximal phalanx and the metacarpal head of the third ray were used to examine the pattern of trabecular orientation in Pan, Gorilla, Pongo, Hylobates and Macaca. Several zones, i.e., the proximal ends of both phalanges and the metacarpal heads, were capable of distinguishing between knuckle-walking, quadrupedal, and suspensory primates. Orientation and shape seem to be the primary distinguishing factors but differences in bone volume, isotropy index, and degree of anisotropy were seen across included taxa. Suspensory primates show primarily proximodistal alignment in all zones, and quadrupeds more palmar-dorsal orientation in several zones. Knuckle walkers are characterized by having proximodistal alignment in the proximal ends of the phalanges and a palmar-dorsal alignment in the distal ends and metacarpal heads. These structural differences may be used to infer locmotor propensities of extinct primate taxa.

Correlation between the graft-host junction of penetrating keratoplasty by anterior segment-optical coherence tomography and the magnitude of postoperative astigmatism.

PubMed

Nassar, Ghada Azab; Arfeen, Shaimaa Abd El Salam

2017-07-01

This study aimed to evaluate the alignment pattern of the graft-host junction after penetrating keratoplasty (PK) by anterior segment-optical coherence tomography (AS-OCT) and to correlate this pattern with the magnitude of postoperative astigmatism. This retrospective observational study was carried out on forty patients who underwent PK from February 2013 to August 2014. AS-OCT was performed, and the graft-host junctions were classified into well-apposed junction, malapposed junction, and equally apposed junction. Mal-apposition is subdivided into gap and protrusion. The correlations between clinical characteristics, wound profiles from the AS-OCT, and the magnitude of postoperative astigmatism by Sirius camera (Costruzione Strumenti Oftalmici [CSO], Florence, Italy (CSO, Sirius), were analyzed. Graft-host junctions from forty patients were analyzed; 18 eyes had well-apposed junctions, ten eyes had malapposed junctions, and 12 had equally apposed junctions. The mean cylinder was -9.44 ± -4.00D in well-apposed group, -13.40 ± -5.01D in malapposed group, and -4.67 ± -0.94D in equally apposed group. Alignment pattern of the graft-host junction correlated significantly with the magnitude of astigmatism (P = 0.034). Preoperative corneal diseases did not have an effect on the magnitude of astigmatism (P = 0.123). The alignment pattern of the graft-host junction by AS-OCT can explain the postoperative astigmatism after PK where it correlates significantly with the magnitude of astigmatism.

Digital polarization holography advancing geometrical phase optics.

PubMed

De Sio, Luciano; Roberts, David E; Liao, Zhi; Nersisyan, Sarik; Uskova, Olena; Wickboldt, Lloyd; Tabiryan, Nelson; Steeves, Diane M; Kimball, Brian R

2016-08-08

Geometrical phase or the fourth generation (4G) optics enables realization of optical components (lenses, prisms, gratings, spiral phase plates, etc.) by patterning the optical axis orientation in the plane of thin anisotropic films. Such components exhibit near 100% diffraction efficiency over a broadband of wavelengths. The films are obtained by coating liquid crystalline (LC) materials over substrates with patterned alignment conditions. Photo-anisotropic materials are used for producing desired alignment conditions at the substrate surface. We present and discuss here an opportunity of producing the widest variety of "free-form" 4G optical components with arbitrary spatial patterns of the optical anisotropy axis orientation with the aid of a digital spatial light polarization converter (DSLPC). The DSLPC is based on a reflective, high resolution spatial light modulator (SLM) combined with an "ad hoc" optical setup. The most attractive feature of the use of a DSLPC for photoalignment of nanometer thin photo-anisotropic coatings is that the orientation of the alignment layer, and therefore of the fabricated LC or LC polymer (LCP) components can be specified on a pixel-by-pixel basis with high spatial resolution. By varying the optical magnification or de-magnification the spatial resolution of the photoaligned layer can be adjusted to an optimum for each application. With a simple "click" it is possible to record different optical components as well as arbitrary patterns ranging from lenses to invisible labels and other transparent labels that reveal different images depending on the side from which they are viewed.

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

PubMed

Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

2016-06-15

Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Age-related changes in posture response under a continuous and unexpected perturbation.

PubMed

Tsai, Yi-Ching; Hsieh, Lin-Fen; Yang, Saiwei

2014-01-22

Aging is a critical factor to influence the functional performance during daily life. Without an appropriate posture control response when experiencing an unexpected external perturbation, fall may occur. A novel six-degree-of freedom platform with motion control protocol was designed to provide a real-life simulation of unexpected disturbance in order to discriminate the age-related changes of the balance control and the recovery ability. Twenty older adults and 20 healthy young adults participated in the study. The subjects stood barefoot on the novel movable platform, data of the center of mass (COM) excursion, joint rotation angle and electromyography (EMG) were recorded and compared. The results showed that the older adults had similar patterns of joint movement and COM excursion as the young adults during the balance reactive-recovery. However, larger proximal joint rotation in elderly group induced larger COM sway envelop and therefore loss of the compensatory strategy of posture recovery. The old adults also presented a lower muscle power. In order to keep an adequate joint stability preventing from falling, the EMG activity was increased, but the asymmetric pattern might be the key reason of unstable postural response. This novel design of moveable platform and test protocol comprised the computerized dynamic posturography (CDP) demonstrate its value to assess the possible sensory, motor, and central adaptive impairments to balance control and could be the training tool for posture inability person. © 2013 Elsevier Ltd. All rights reserved.

Planes of satellite galaxies and the cosmic web

NASA Astrophysics Data System (ADS)

Libeskind, Noam I.; Hoffman, Yehuda; Tully, R. Brent; Courtois, Helene M.; Pomarède, Daniel; Gottlöber, Stefan; Steinmetz, Matthias

2015-09-01

Recent observational studies have demonstrated that the majority of satellite galaxies tend to orbit their hosts on highly flattened, vast, possibly corotating planes. Two nearly parallel planes of satellites have been confirmed around the M31 galaxy and around the Centaurus A galaxy, while the Milky Way also sports a plane of satellites. It has been argued that such an alignment of satellites on vast planes is unexpected in the standard Λ cold dark matter (ΛCDM) model of cosmology if not even in contradiction to its generic predictions. Guided by ΛCDM numerical simulations, which suggest that satellites are channelled towards hosts along the axis of the slowest collapse as dictated by the ambient velocity shear tensor, we re-examine the planes of local satellites systems within the framework of the local shear tensor derived from the Cosmicflows-2 data set. The analysis reveals that the Local Group and Centaurus A reside in a filament stretched by the Virgo cluster and compressed by the expansion of the Local Void. Four out of five thin planes of satellite galaxies are indeed closely aligned with the axis of compression induced by the Local Void. Being the less massive system, the moderate misalignment of the Milky Way's satellite plane can likely be ascribed to its greater susceptibility to tidal torques, as suggested by numerical simulations. The alignment of satellite systems in the local Universe with the ambient shear field is thus in general agreement with predictions of the ΛCDM model.

Diagnosis and treatment of movement system impairment syndromes.

PubMed

Sahrmann, Shirley; Azevedo, Daniel C; Dillen, Linda Van

Diagnoses and treatments based on movement system impairment syndromes were developed to guide physical therapy treatment. This masterclass aims to describe the concepts on that are the basis of the syndromes and treatment and to provide the current research on movement system impairment syndromes. The conceptual basis of the movement system impairment syndromes is that sustained alignment in a non-ideal position and repeated movements in a specific direction are thought to be associated with several musculoskeletal conditions. Classification into movement system impairment syndromes and treatment has been described for all body regions. The classification involves interpreting data from standardized tests of alignments and movements. Treatment is based on correcting the impaired alignment and movement patterns as well as correcting the tissue adaptations associated with the impaired alignment and movement patterns. The reliability and validity of movement system impairment syndromes have been partially tested. Although several case reports involving treatment using the movement system impairment syndromes concept have been published, efficacy of treatment based on movement system impairment syndromes has not been tested in randomized controlled trials, except in people with chronic low back pain. Copyright © 2017 Associação Brasileira de Pesquisa e Pós-Graduação em Fisioterapia. Publicado por Elsevier Editora Ltda. All rights reserved.

Quasi-parallel precession diffraction: Alignment method for scanning transmission electron microscopes.

PubMed

Plana-Ruiz, S; Portillo, J; Estradé, S; Peiró, F; Kolb, Ute; Nicolopoulos, S

2018-06-06

A general method to set illuminating conditions for selectable beam convergence and probe size is presented in this work for Transmission Electron Microscopes (TEM) fitted with µs/pixel fast beam scanning control, (S)TEM, and an annular dark field detector. The case of interest of beam convergence and probe size, which enables diffraction pattern indexation, is then used as a starting point in this work to add 100 Hz precession to the beam while imaging the specimen at a fast rate and keeping the projector system in diffraction mode. The described systematic alignment method for the adjustment of beam precession on the specimen plane while scanning at fast rates is mainly based on the sharpness of the precessed STEM image. The complete alignment method for parallel condition and precession, Quasi-Parallel PED-STEM, is presented in block diagram scheme, as it has been tested on a variety of instruments. The immediate application of this methodology is that it renders the TEM column ready for the acquisition of Precessed Electron Diffraction Tomographies (EDT) as well as for the acquisition of slow Precessed Scanning Nanometer Electron Diffraction (SNED). Examples of the quality of the Precessed Electron Diffraction (PED) patterns and PED-STEM alignment images are presented with corresponding probe sizes and convergence angles. Copyright © 2018. Published by Elsevier B.V.

A phase and frequency alignment protocol for 1H MRSI data of the prostate.

PubMed

Wright, Alan J; Buydens, Lutgarde M C; Heerschap, Arend

2012-05-01

(1)H MRSI of the prostate reveals relative metabolite levels that vary according to the presence or absence of tumour, providing a sensitive method for the identification of patients with cancer. Current interpretations of prostate data rely on quantification algorithms that fit model metabolite resonances to individual voxel spectra and calculate relative levels of metabolites, such as choline, creatine, citrate and polyamines. Statistical pattern recognition techniques can potentially improve the detection of prostate cancer, but these analyses are hampered by artefacts and sources of noise in the data, such as variations in phase and frequency of resonances. Phase and frequency variations may arise as a result of spatial field gradients or local physiological conditions affecting the frequency of resonances, in particular those of citrate. Thus, there are unique challenges in developing a peak alignment algorithm for these data. We have developed a frequency and phase correction algorithm for automatic alignment of the resonances in prostate MRSI spectra. We demonstrate, with a simulated dataset, that alignment can be achieved to a phase standard deviation of 0.095  rad and a frequency standard deviation of 0.68  Hz for the citrate resonances. Three parameters were used to assess the improvement in peak alignment in the MRSI data of five patients: the percentage of variance in all MRSI spectra explained by their first principal component; the signal-to-noise ratio of a spectrum formed by taking the median value of the entire set at each spectral point; and the mean cross-correlation between all pairs of spectra. These parameters showed a greater similarity between spectra in all five datasets and the simulated data, demonstrating improved alignment for phase and frequency in these spectra. This peak alignment program is expected to improve pattern recognition significantly, enabling accurate detection and localisation of prostate cancer with MRSI. Copyright © 2011 John Wiley & Sons, Ltd.

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

PubMed

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

2015-01-01

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

The Relationship between Distributed Leadership and Teachers' Academic Optimism

ERIC Educational Resources Information Center

Mascall, Blair; Leithwood, Kenneth; Straus, Tiiu; Sacks, Robin

2008-01-01

Purpose: The goal of this study was to examine the relationship between four patterns of distributed leadership and a modified version of a variable Hoy et al. have labeled "teachers' academic optimism." The distributed leadership patterns reflect the extent to which the performance of leadership functions is consciously aligned across…

"Change deafness" arising from inter-feature masking within a single auditory object.

PubMed

Barascud, Nicolas; Griffiths, Timothy D; McAlpine, David; Chait, Maria

2014-03-01

Our ability to detect prominent changes in complex acoustic scenes depends not only on the ear's sensitivity but also on the capacity of the brain to process competing incoming information. Here, employing a combination of psychophysics and magnetoencephalography (MEG), we investigate listeners' sensitivity in situations when two features belonging to the same auditory object change in close succession. The auditory object under investigation is a sequence of tone pips characterized by a regularly repeating frequency pattern. Signals consisted of an initial, regularly alternating sequence of three short (60 msec) pure tone pips (in the form ABCABC…) followed by a long pure tone with a frequency that is either expected based on the on-going regular pattern ("LONG expected"-i.e., "LONG-expected") or constitutes a pattern violation ("LONG-unexpected"). The change in LONG-expected is manifest as a change in duration (when the long pure tone exceeds the established duration of a tone pip), whereas the change in LONG-unexpected is manifest as a change in both the frequency pattern and a change in the duration. Our results reveal a form of "change deafness," in that although changes in both the frequency pattern and the expected duration appear to be processed effectively by the auditory system-cortical signatures of both changes are evident in the MEG data-listeners often fail to detect changes in the frequency pattern when that change is closely followed by a change in duration. By systematically manipulating the properties of the changing features and measuring behavioral and MEG responses, we demonstrate that feature changes within the same auditory object, which occur close together in time, appear to compete for perceptual resources.

Sparse alignment for robust tensor learning.

PubMed

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

2014-10-01

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

Micro-miniature gas chromatograph column disposed in silicon wafers

DOEpatents

Yu, Conrad M.

2000-01-01

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

Thermal characterization of magnetically aligned carbonyl iron/agar composites.

PubMed

Diaz-Bleis, D; Vales-Pinzón, C; Freile-Pelegrín, Y; Alvarado-Gil, J J

2014-01-01

Composites of magnetic particles into polymeric matrices have received increasing research interest due to their capacity to respond to external magnetic or electromagnetic fields. In this study, agar from Gelidium robustum has been chosen as natural biocompatible polymer to build the matrix of the magnetic carbonyl iron particles (CIP) for their uses in biomedical fields. Heat transfer behavior of the CIP-agar composites containing different concentrations (5, 10, 15, 20, 25 and 30% w/w) of magnetically aligned and non-aligned CIP in the agar matrix was studied using photothermal radiometry (PTR) in the back-propagation emission configuration. The morphology of the CIP-agar composites with aligned and non-aligned CIP under magnetic field was also evaluated by scanning electron microscopy (SEM). The results revealed a dominant effect of CIP concentration over the alignment patterns induced by the magnetic field, which agrees with the behavior of the thermal diffusivity and thermal conductivity. Agar served as a perfect matrix to be used with CIP, and CIP-agar composites magnetically aligned at 20% CIP concentration can be considered as promising 'smart' material for hyperthermia treatments in the biomedical field. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

PubMed

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

2012-01-01

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

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

DOE PAGES

Tian, Wenhong; Samatova, Nagiza F.

2013-01-01

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

Cell Alignment Required in Differentiation of Myxococcus xanthus

NASA Astrophysics Data System (ADS)

Kim, Seung K.; Kaiser, Dale

1990-08-01

During fruiting body morphogenesis of Myxococcus xanthus, cell movement is required for transmission of C-factor, a short range intercellular signaling protein necessary for sporulation and developmental gene expression. Nonmotile cells fail to sporulate and to express C-factor-dependent genes, but both defects were rescued by a simple manipulation of cell position that oriented the cells in aligned, parallel groups. A similar pattern of aligned cells normally results from coordinated recruitment of wild-type cells into multicellular aggregates, which later form mature fruiting bodies. It is proposed that directed cell movement establishes critical contacts between adjacent cells, which are required for efficient intercellular C-factor transmission.

Multi-port valve

DOEpatents

Lewin, Keith F.

1997-04-15

A multi-port valve for regulating, as a function of ambient air having varying wind velocity and wind direction in an open-field control area, the distribution of a fluid, particularly carbon dioxide (CO.sub.2) gas, in a fluid distribution system so that the control area remains generally at an elevated fluid concentration or level of said fluid. The multi-port valve generally includes a multi-port housing having a plurality of outlets therethrough disposed in a first pattern of outlets and at least one second pattern of outlets, and a movable plate having a plurality of apertures extending therethrough disposed in a first pattern of apertures and at least one second pattern of apertures. The first pattern of apertures being alignable with the first pattern of outlets and the at least one second pattern of apertures being alignable with the second pattern of outlets. The first pattern of apertures has a predetermined orientation with the at least one second pattern of apertures. For an open-field control area subject to ambient wind having a low velocity from any direction, the movable plate is positioned to equally distribute the supply of fluid in a fluid distribution system to the open-field control area. For an open-field control area subject to ambient wind having a high velocity from a given direction, the movable plate is positioned to generally distribute a supply of fluid in a fluid distribution system to that portion of the open-field control area located upwind.

Multi-port valve

DOEpatents

Lewin, K.F.

1997-04-15

A multi-port valve is described for regulating, as a function of ambient air having varying wind velocity and wind direction in an open-field control area, the distribution of a fluid, particularly carbon dioxide (CO{sub 2}) gas, in a fluid distribution system so that the control area remains generally at an elevated fluid concentration or level of said fluid. The multi-port valve generally includes a multi-port housing having a plurality of outlets there through disposed in a first pattern of outlets and at least one second pattern of outlets, and a movable plate having a plurality of apertures extending there through disposed in a first pattern of apertures and at least one second pattern of apertures. The first pattern of apertures being alignable with the first pattern of outlets and the at least one second pattern of apertures being alignable with the second pattern of outlets. The first pattern of apertures has a predetermined orientation with the at least one second pattern of apertures. For an open-field control area subject to ambient wind having a low velocity from any direction, the movable plate is positioned to equally distribute the supply of fluid in a fluid distribution system to the open-field control area. For an open-field control area subject to ambient wind having a high velocity from a given direction, the movable plate is positioned to generally distribute a supply of fluid in a fluid distribution system to that portion of the open-field control area located upwind. 7 figs.

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

NASA Astrophysics Data System (ADS)

Liu, Limin

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

Effects of Knee Alignments and Toe Clip on Frontal Plane Knee Biomechanics in Cycling

PubMed Central

Shen, Guangping; Zhang, Songning; Bennett, Hunter J.; Martin, James C.; Crouter, Scott E.; Fitzhugh, Eugene C.

2018-01-01

Effects of knee alignment on the internal knee abduction moment (KAM) in walking have been widely studied. The KAM is closely associated with the development of medial knee osteoarthritis. Despite the importance of knee alignment, no studies have explored its effects on knee frontal plane biomechanics during stationary cycling. The purpose of this study was to examine the effects of knee alignment and use of a toe clip on the knee frontal plane biomechanics during stationary cycling. A total of 32 participants (11 varus, 11 neutral, and 10 valgus alignment) performed five trials in each of six cycling conditions: pedaling at 80 rpm and 0.5 kg (40 Watts), 1.0 kg (78 Watts), and 1.5 kg (117 Watts) with and without a toe clip. A motion analysis system and a customized instrumented pedal were used to collect 3D kinematic and kinetic data. A 3 × 2 × 3 (group × toe clip × workload) mixed design ANOVA was used for statistical analysis (p < 0.05). There were two different knee frontal plane loading patterns, internal abduction and adduction moment, which were affected by knee alignment type. The knee adduction angle was 12.2° greater in the varus group compared to the valgus group (p = 0.001), yet no difference was found for KAM among groups. Wearing a toe clip increased the knee adduction angle by 0.95º (p = 0.005). The findings of this study indicate that stationary cycling may be a safe exercise prescription for people with knee malalignments. In addition, using a toe clip may not have any negative effects on knee joints during stationary cycling. Key points Varus or valgus alignment did not cause increased frontal-plane knee joint loading, suggesting stationary cycling is a safe exercise. This study supports that using a toe clip did not lead to abnormal frontal-plane knee loading during stationary cycling. Two different knee frontal plane loading patterns, knee abduction and adduction moment, were observed during stationary cycling, which are likely affected by the type of knee alignment. PMID:29769833

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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

Incremental Ontology-Based Extraction and Alignment in Semi-structured Documents

NASA Astrophysics Data System (ADS)

Thiam, Mouhamadou; Bennacer, Nacéra; Pernelle, Nathalie; Lô, Moussa

SHIRIis an ontology-based system for integration of semi-structured documents related to a specific domain. The system’s purpose is to allow users to access to relevant parts of documents as answers to their queries. SHIRI uses RDF/OWL for representation of resources and SPARQL for their querying. It relies on an automatic, unsupervised and ontology-driven approach for extraction, alignment and semantic annotation of tagged elements of documents. In this paper, we focus on the Extract-Align algorithm which exploits a set of named entity and term patterns to extract term candidates to be aligned with the ontology. It proceeds in an incremental manner in order to populate the ontology with terms describing instances of the domain and to reduce the access to extern resources such as Web. We experiment it on a HTML corpus related to call for papers in computer science and the results that we obtain are very promising. These results show how the incremental behaviour of Extract-Align algorithm enriches the ontology and the number of terms (or named entities) aligned directly with the ontology increases.

Compaction and sintering behaviors of a Nd-Fe-B permanent magnet alloy

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

Chin, T.; Hung, M.; Tsai, D.

1988-11-15

Extensive x-ray diffraction (XRD) and magnetic measurements were done on Nd/sub 15/ Fe/sub 77/ B/sub 8/ magnet alloy green compacts after cold isostatic pressing following a pulsed 2-T field (CIP) and die-pressing under a static 1.2-T perpendicular field (DP1) or parallel field (DP2), and on those after sintering. An alignment factor F, through the calculation of the integrated diffraction intensity ratio of the XRD patterns, was adopted as the effectiveness of magnetic alignment. At the green compact state, DP1 has the best alignment while CIP the worst. However, after sintering the alignment factor was such that CIP>DPI>DP2, the same ordermore » as the magnetic properties. Three mechanisms were proposed for the evolution of the alignment factor at different stages of sintering, i.e., that both the appearance of a liquid phase at low temperatures and preferred grain growth at high temperatures enhance F, while recrystallization at intermediate temperatures deteriorates F. CIP results in less-defect green compact, hence less recrystallization, leading to better resultant alignment« less

Transcription Factor Map Alignment of Promoter Regions

PubMed Central

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

2006-01-01

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

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.

Diffeomorphic functional brain surface alignment: Functional demons.

PubMed

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

2017-08-01

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

Study of infectious diseases in archaeological bone material - A dataset.

PubMed

Pucu, Elisa; Cascardo, Paula; Chame, Marcia; Felice, Gisele; Guidon, Niéde; Cleonice Vergne, Maria; Campos, Guadalupe; Roberto Machado-Silva, José; Leles, Daniela

2017-08-01

Bones of human and ground sloth remains were analyzed for presence of Trypanosoma cruzi by conventional PCR using primers TC, TC1 and TC2. Sequence results amplified a fragment with the same product size as the primers (300 and 350pb). Amplified PCR product was sequenced and analyzed on GenBank, using Blast. Although these sequences did not match with these parasites they showed high amplification with species of bacteria. This article presents the methodology used and the alignment of the sequences. The display of this dataset will allow further analysis of our results and discussion presented in the manuscript "Finding the unexpected: a critical view on molecular diagnosis of infectious diseases in archaeological samples" (Pucu et al. 2017) [1].

Analysis of the STS-126 Flow Control Valve Structural-Acoustic Coupling Failure

NASA Technical Reports Server (NTRS)

Jones, Trevor M.; Larko, Jeffrey M.; McNelis, Mark E.

2010-01-01

During the Space Transportation System mission STS-126, one of the main engine's flow control valves incurred an unexpected failure. A section of the valve broke off during liftoff. It is theorized that an acoustic mode of the flowing fuel, coupled with a structural mode of the valve, causing a high cycle fatigue failure. This report documents the analysis efforts conducted in an attempt to verify this theory. Hand calculations, computational fluid dynamics, and finite element methods are all implemented and analyses are performed using steady-state methods in addition to transient analysis methods. The conclusion of the analyses is that there is a critical acoustic mode that aligns with a structural mode of the valve

Patterned growth of carbon nanotubes on Si substrates without predeposition of metal catalysts

NASA Astrophysics Data System (ADS)

Chen, Y.; Yu, J.

2005-07-01

Aligned carbon nanotubes (CNTs) can be readily synthesized on quartz or silicon-oxide-coated Si substrates using a chemical vapor deposition method, but it is difficult to grow them on pure Si substrates without predeposition of metal catalysts. We report that aligned CNTs were grown by pyrolysis of iron phthalocyanine at 1000°C on the templates created on Si substrates with simple mechanical scratching. Scanning electron microscopy and x-ray energy spectroscopy analysis revealed that the trenches and patterns created on the surface of Si substrates were preferred nucleation sites for nanotube growth due to a high surface energy, metastable surface structure, and possible capillarity effect. A two-step pyrolysis process maintained Fe as an active catalyst.

Comparison of field-aligned currents at ionospheric and magnetospheric altitudes

NASA Technical Reports Server (NTRS)

Spence, H. E.; Kivelson, M. G.; Walker, R. J.

1988-01-01

Using the empirical terrestrial magnetospheric magnetic field models of Tsyganenko and Usmanov (1982) and Tsyganenko (1987) the average field-aligned currents (FACs) in the magnetosphere were determined as a function of the Kp index. Three major model FAC systems were identified, namely, the dayside region 1, the nightside region 1, and the nightside polar cap. The models provide information about the sources of the current systems. Mapped ionospheric model FACs are compared with low-altitude measurements obtained by the spacecraft. It is found that low-altitude data can reveal either classic region 1/2 or more highly structured FAC patterns. Therefore, statistical results either obtained from observations or inferred from models are expected to be averages over temporally and spatially shifting patterns.

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.

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

NASA Astrophysics Data System (ADS)

Bae, Junwan; Lee, I. J.

2015-05-01

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

Method of fabricating electrode catalyst layers with directionally oriented carbon support for proton exchange membrane fuel cell

DOEpatents

Liu, Di-Jia [Naperville, IL; Yang, Junbing [Bolingbrook, IL

2012-03-20

A membrane electrode assembly (MEA) of the invention comprises an anode and a cathode and a proton conductive membrane therebetween, the anode and the cathode each comprising a patterned sheet of longitudinally aligned transition metal-containing carbon nanotubes, wherein the carbon nanotubes are in contact with and are aligned generally perpendicular to the membrane, wherein a catalytically active transition metal is incorporated throughout the nanotubes.

Improved high power/high frequency inductor

NASA Technical Reports Server (NTRS)

Mclyman, W. T. (Inventor)

1990-01-01

A toroidal core is mounted on an alignment disc having uniformly distributed circumferential notches or holes therein. Wire is then wound about the toroidal core in a uniform pattern defined by the notches or holes. Prior to winding, the wire may be placed within shrink tubing. The shrink tubing is then wound about the alignment disc and core and then heat-shrunk to positively retain the wire in the uniform position on the toroidal core.

Plasmonic Properties of Vertically Aligned Nanowire Arrays

DTIC Science & Technology

2012-01-01

scattering (SERS) applications. In this investigation, two types of vertical NW arrays were studied; those of ZnO NWs grown on nanosphere lithography...plasmonic nanowires to investigate this SERS effect. Here we used two types of vertical NWs, ZnO NWs, and Si NWs, respectively, to investigate SERS...successfully grow vertically aligned ZnO nanowires by the well-known VLS process. In this way, the ZnO NWs can be arranged in a repeatable hexagonal pattern

Effect of Prefrontal Cortex Damage on Resolving Lexical Ambiguity in Text

ERIC Educational Resources Information Center

Frattali, Carol; Hanna, Rebecca; McGinty, Anita Shukla; Gerber, Lynn; Wesley, Robert; Grafman, Jordan; Coelho, Carl

2007-01-01

The function of suppression of context-inappropriate meanings during lexical ambiguity resolution was examined in 25 adults with prefrontal cortex damage (PFCD) localized to the left (N = 8), right (N = 6), or bilaterally (N = 11); and 21 matched Controls. Results revealed unexpected inverse patterns of suppression between PFCD and Control groups,…

The Learning and Recall of Unexpected Information in Social Schemas.

ERIC Educational Resources Information Center

Glasnapp, Pamela M.

A study examined how people respond to violations of F. Heider's (1958) balance principle when learning patterns of sentiments among people in a group. Subjects, 90 students from introductory psychology and communication courses at the University of Kansas, participated in the experiment, and were randomly assigned to one of three schema…

Topological defects control collective dynamics in neural progenitor cell cultures

NASA Astrophysics Data System (ADS)

Kawaguchi, Kyogo; Kageyama, Ryoichiro; Sano, Masaki

2017-04-01

Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and of the macroscopic patterns resulting from cell-to-cell interactions remains largely qualitative. Here we report on the collective dynamics of cultured murine neural progenitor cells (NPCs), which are multipotent stem cells that give rise to cells in the central nervous system. At low densities, NPCs moved randomly in an amoeba-like fashion. However, NPCs at high density elongated and aligned their shapes with one another, gliding at relatively high velocities. Although the direction of motion of individual cells reversed stochastically along the axes of alignment, the cells were capable of forming an aligned pattern up to length scales similar to that of the migratory stream observed in the adult brain. The two-dimensional order of alignment within the culture showed a liquid-crystalline pattern containing interspersed topological defects with winding numbers of +1/2 and -1/2 (half-integer due to the nematic feature that arises from the head-tail symmetry of cell-to-cell interaction). We identified rapid cell accumulation at +1/2 defects and the formation of three-dimensional mounds. Imaging at the single-cell level around the defects allowed us to quantify the velocity field and the evolving cell density; cells not only concentrate at +1/2 defects, but also escape from -1/2 defects. We propose a generic mechanism for the instability in cell density around the defects that arises from the interplay between the anisotropic friction and the active force field.

Differences in pediatric vertical ground reaction force between planovalgus and neutrally aligned feet.

PubMed

Pauk, Jolanta; Szymul, Joanna

2014-01-01

Ground reaction forces (GRF) reflect the force history of human body contact with the ground. The purpose of this study was to explore human gait abnormalities due to planovalgus by comparing vertical GRF data between individuals with planovalgus and those with neutrally aligned feet. Second we estimated associations between various measurements and vertical GRF parameters in a pediatric population. Boys and girls between the ages of 4 and 18 years (72 planovalgus feet and 74 neutrally aligned feet) took part in this study. Ground reaction forces were recorded by two Kistler platforms and normalized to body weight. Comparison of vertical GRF between planovalgus and neutrally aligned feet suggests that the first and the second peaks of vertical force (Fz1, Fz2) are most affected by planovalgus. The results also indicate that neutrally aligned feet display a different ground reaction force pattern than planovalgus, and that differences between boys and girls may be observed. The shape of the vertical GRF curve can help in clinical interpretation of abnormal gait.

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

PubMed

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

2010-03-31

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

Directional cell elongation through filopodia-steered lamellipodial extension on patterned silk fibroin films.

PubMed

You, Renchuan; Li, Xiufang; Luo, Zuwei; Qu, Jing; Li, Mingzhong

2015-03-05

Micropatterned biomaterials have been used to direct cell alignment for specific tissue engineering applications. However, the understanding of how cells respond to guidance cues remains limited. Plasticity in protrusion formation has been proposed to enable cells to adapt their motility mode to microenvironment. In this study, the authors investigated the key role of protrusion response in cell guidance on patterned silk fibroin films. The results revealed that the ability to transform between filopodia and small lamellipodia played important roles in directional cell guidance. Filopodia did not show directional extension on patterned substrates prior to spreading, but they transduced topographical cues to the cell to trigger the formation of small lamellipodia along the direction of a microgrooved or parallel nanofiber pattern. The polar lamellipodia formation provided not only a path with directionality, but a driving force for directional cell elongation. Moreover, aligned nanofibers coating provided better mechanical support for the traction of filopodia and lamellipodia, promoting cell attachment, spreading, and migration. This study provides new insight into how cells respond to guidance cues and how filopodia and lamellipodia control cell contact guidance on micropatterned biomaterial surfaces.

Advanced electric-field scanning probe lithography on molecular resist using active cantilever

NASA Astrophysics Data System (ADS)

Kaestner, Marcus; Aydogan, Cemal; Lipowicz, Hubert-Seweryn; Ivanov, Tzvetan; Lenk, Steve; Ahmad, Ahmad; Angelov, Tihomir; Reum, Alexander; Ishchuk, Valentyn; Atanasov, Ivaylo; Krivoshapkina, Yana; Hofer, Manuel; Holz, Mathias; Rangelow, Ivo W.

2015-03-01

The routine "on demand" fabrication of features smaller than 10 nm opens up new possibilities for the realization of many novel nanoelectronic, NEMS, optical and bio-nanotechnology-based devices. Based on the thermally actuated, piezoresistive cantilever technology we have developed a first prototype of a scanning probe lithography (SPL) platform able to image, inspect, align and pattern features down to single digit nano regime. The direct, mask-less patterning of molecular resists using active scanning probes represents a promising path circumventing the problems in today's radiation-based lithography. Here, we present examples of practical applications of the previously published electric field based, current-controlled scanning probe lithography on molecular glass resist calixarene by using the developed tabletop SPL system. We demonstrate the application of a step-and-repeat scanning probe lithography scheme including optical as well as AFM based alignment and navigation. In addition, sequential read-write cycle patterning combining positive and negative tone lithography is shown. We are presenting patterning over larger areas (80 x 80 μm) and feature the practical applicability of the lithographic processes.

Language and theory of mind in autism spectrum disorder: the relationship between complement syntax and false belief task performance.

PubMed

Lind, Sophie E; Bowler, Dermot M

2009-06-01

This study aimed to test the hypothesis that children with autism spectrum disorder (ASD) use their knowledge of complement syntax as a means of "hacking out" solutions to false belief tasks, despite lacking a representational theory of mind (ToM). Participants completed a "memory for complements" task, a measure of receptive vocabulary, and traditional location change and unexpected contents false belief tasks. Consistent with predictions, the correlation between complement syntax score and location change task performance was significantly stronger within the ASD group than within the comparison group. However, contrary to predictions, complement syntax score was not significantly correlated with unexpected contents task performance within either group. Possible explanations for this pattern of results are considered.

Batchwise growth of silica cone patterns via self-assembly of aligned nanowires.

PubMed

Luo, Shudong; Zhou, Weiya; Chu, Weiguo; Shen, Jun; Zhang, Zengxing; Liu, Lifeng; Liu, Dongfang; Xiang, Yanjuan; Ma, Wenjun; Xie, Sishen

2007-03-01

Silica-cone patterns self-assembled from well-aligned nanowires are synthesized using gallium droplets as the catalyst and silicon wafers as the silicon source. The cones form a triangular pattern array radially on almost the whole surface of the molten Ga ball. Detailed field-emission scanning electron microscopy (SEM) analysis shows that the cone-pattern pieces frequently slide off and are detached from the molten Ga ball surface, which leads to the exposure of the catalyst surface and the growth of a new batch of silicon oxide nanowires as well as the cone patterns. The processes of growth and detachment alternate, giving rise to the formation of a volcano-like or a flower-like structure with bulk-quantity pieces of cone patterns piled up around the Ga ball. Consequently, the cone-patterned layer grows batch by batch until the reaction is terminated. Different to the conventional metal-catalyzed growth model, the batch-by-batch growth of the triangular cone patterns proceeds on the molten Ga balls via alternate growth on and detachment from the catalyst surface of the patterns; the Ga droplet can be used continuously and circularly as an effective catalyst for the growth of amorphous SiO(x) nanowires during the whole growth period. The intriguing batchwise growth phenomena may enrich our understanding of the vapour-liquid-solid (VLS) growth mechanism for the catalyst growth of nanowires or other nanostructures and may offer a different way of self-assembling novel silica nanostructures.

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

PubMed

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

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

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

PubMed Central

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

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

Wind selection and drift compensation optimize migratory pathways in a high-flying moth.

PubMed

Chapman, Jason W; Reynolds, Don R; Mouritsen, Henrik; Hill, Jane K; Riley, Joe R; Sivell, Duncan; Smith, Alan D; Woiwod, Ian P

2008-04-08

Numerous insect species undertake regular seasonal migrations in order to exploit temporary breeding habitats [1]. These migrations are often achieved by high-altitude windborne movement at night [2-6], facilitating rapid long-distance transport, but seemingly at the cost of frequent displacement in highly disadvantageous directions (the so-called "pied piper" phenomenon [7]). This has lead to uncertainty about the mechanisms migrant insects use to control their migratory directions [8, 9]. Here we show that, far from being at the mercy of the wind, nocturnal moths have unexpectedly complex behavioral mechanisms that guide their migratory flight paths in seasonally-favorable directions. Using entomological radar, we demonstrate that free-flying individuals of the migratory noctuid moth Autographa gamma actively select fast, high-altitude airstreams moving in a direction that is highly beneficial for their autumn migration. They also exhibit common orientation close to the downwind direction, thus maximizing the rectilinear distance traveled. Most unexpectedly, we find that when winds are not closely aligned with the moth's preferred heading (toward the SSW), they compensate for cross-wind drift, thus increasing the probability of reaching their overwintering range. We conclude that nocturnally migrating moths use a compass and an inherited preferred direction to optimize their migratory track.

CpG PatternFinder: a Windows-based utility program for easy and rapid identification of the CpG methylation status of DNA.

PubMed

Xu, Yi-Hua; Manoharan, Herbert T; Pitot, Henry C

2007-09-01

The bisulfite genomic sequencing technique is one of the most widely used techniques to study sequence-specific DNA methylation because of its unambiguous ability to reveal DNA methylation status to the order of a single nucleotide. One characteristic feature of the bisulfite genomic sequencing technique is that a number of sample sequence files will be produced from a single DNA sample. The PCR products of bisulfite-treated DNA samples cannot be sequenced directly because they are heterogeneous in nature; therefore they should be cloned into suitable plasmids and then sequenced. This procedure generates an enormous number of sample DNA sequence files as well as adding extra bases belonging to the plasmids to the sequence, which will cause problems in the final sequence comparison. Finding the methylation status for each CpG in each sample sequence is not an easy job. As a result CpG PatternFinder was developed for this purpose. The main functions of the CpG PatternFinder are: (i) to analyze the reference sequence to obtain CpG and non-CpG-C residue position information. (ii) To tailor sample sequence files (delete insertions and mark deletions from the sample sequence files) based on a configuration of ClustalW multiple alignment. (iii) To align sample sequence files with a reference file to obtain bisulfite conversion efficiency and CpG methylation status. And, (iv) to produce graphics, highlighted aligned sequence text and a summary report which can be easily exported to Microsoft Office suite. CpG PatternFinder is designed to operate cooperatively with BioEdit, a freeware on the internet. It can handle up to 100 files of sample DNA sequences simultaneously, and the total CpG pattern analysis process can be finished in minutes. CpG PatternFinder is an ideal software tool for DNA methylation studies to determine the differential methylation pattern in a large number of individuals in a population. Previously we developed the CpG Analyzer program; CpG PatternFinder is our further effort to create software tools for DNA methylation studies.

Bistable director alignments of nematic liquid crystals confined in frustrated substrates

NASA Astrophysics Data System (ADS)

Araki, Takeaki; Nagura, Jumpei

2017-01-01

We studied in-plane bistable alignments of nematic liquid crystals confined by two frustrated surfaces by means of Monte Carlo simulations of the Lebwohl-Lasher spin model. The surfaces are prepared with orientational checkerboard patterns, on which the director field is locally anchored to be planar yet orthogonal between the neighboring blocks. We found the director field in the bulk tends to be aligned along the diagonal axes of the checkerboard pattern, as reported experimentally [J.-H. Kim et al., Appl. Phys. Lett. 78, 3055 (2001), 10.1063/1.1371246]. The energy barrier between the two stable orientations is increased, when the system is brought to the isotropic-nematic transition temperature. Based on an elastic theory, we found that the bistability is attributed to the spatial modulation of the director field near the frustrated surfaces. As the block size is increased and/or the elastic modulus is reduced, the degree of the director inhomogeneity is increased, enlarging the energy barrier. We also found that the switching rate between the stable states is decreased when the block size is comparable to the cell thickness.

An efficient algorithm for pairwise local alignment of protein interaction networks

DOE PAGES

Chen, Wenbin; Schmidt, Matthew; Tian, Wenhong; ...

2015-04-01

Recently, researchers seeking to understand, modify, and create beneficial traits in organisms have looked for evolutionarily conserved patterns of protein interactions. Their conservation likely means that the proteins of these conserved functional modules are important to the trait's expression. In this paper, we formulate the problem of identifying these conserved patterns as a graph optimization problem, and develop a fast heuristic algorithm for this problem. We compare the performance of our network alignment algorithm to that of the MaWISh algorithm [Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A, Pairwise alignment of protein interaction networks, J Computmore » Biol 13(2): 182-199, 2006.], which bases its search algorithm on a related decision problem formulation. We find that our algorithm discovers conserved modules with a larger number of proteins in an order of magnitude less time. In conclusion, the protein sets found by our algorithm correspond to known conserved functional modules at comparable precision and recall rates as those produced by the MaWISh algorithm.« less

Complementary Speckle Patterns: Deterministic Interchange of Intrinsic Vortices and Maxima through Scattering Media.

PubMed

Gateau, Jérôme; Rigneault, Hervé; Guillon, Marc

2017-01-27

Intensity maxima and zeros of speckle patterns obtained behind a diffuser are experimentally interchanged by applying a spiral phase delay of charge ±1 to the impinging coherent beam. This transform arises from the expectation that tightly focused beams, which have a planar wave front around the focus, are so changed into vortex beams and vice versa. The statistics of extrema locations and the intensity distribution of the so-generated "complementary" patterns are characterized by numerical simulations. It is demonstrated experimentally that the incoherent superposition of the three "complementary speckle patterns" yield a synthetic speckle grain size enlarged by a factor of sqrt[3]. A cyclic permutation of optical vortices and intensity maxima is unexpectedly observed and discussed.

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.

Toward optimized light utilization in nanowire arrays using scalable nanosphere lithography and selected area growth.

PubMed

Madaria, Anuj R; Yao, Maoqing; Chi, Chunyung; Huang, Ningfeng; Lin, Chenxi; Li, Ruijuan; Povinelli, Michelle L; Dapkus, P Daniel; Zhou, Chongwu

2012-06-13

Vertically aligned, catalyst-free semiconducting nanowires hold great potential for photovoltaic applications, in which achieving scalable synthesis and optimized optical absorption simultaneously is critical. Here, we report combining nanosphere lithography (NSL) and selected area metal-organic chemical vapor deposition (SA-MOCVD) for the first time for scalable synthesis of vertically aligned gallium arsenide nanowire arrays, and surprisingly, we show that such nanowire arrays with patterning defects due to NSL can be as good as highly ordered nanowire arrays in terms of optical absorption and reflection. Wafer-scale patterning for nanowire synthesis was done using a polystyrene nanosphere template as a mask. Nanowires grown from substrates patterned by NSL show similar structural features to those patterned using electron beam lithography (EBL). Reflection of photons from the NSL-patterned nanowire array was used as a measure of the effect of defects present in the structure. Experimentally, we show that GaAs nanowires as short as 130 nm show reflection of <10% over the visible range of the solar spectrum. Our results indicate that a highly ordered nanowire structure is not necessary: despite the "defects" present in NSL-patterned nanowire arrays, their optical performance is similar to "defect-free" structures patterned by more costly, time-consuming EBL methods. Our scalable approach for synthesis of vertical semiconducting nanowires can have application in high-throughput and low-cost optoelectronic devices, including solar cells.

Knee Joint Loading during Gait in Healthy Controls and Individuals with Knee Osteoarthritis

PubMed Central

Kumar, Deepak; Manal, Kurt T.; Rudolph, Katherine S.

2013-01-01

Objective People with knee osteoarthritis (OA) are thought to walk with high loads at the knee which are yet to be quantfied using modeling techniques that account for subject specific EMG patterns, kinematics and kinetics. The objective was to estimate medial and lateral loading for people with knee OA and controls using an approach that is sensitive to subject specific muscle activation patterns. Methods 16 OA and 12 control (C) subjects walked while kinematic, kinetic and EMG data were collected. Muscle forces were calculated using an EMG-Driven model and loading was calculated by balancing the external moments with internal muscle and contact forces Results OA subjects walked slower and had greater laxity, static and dynamic varus alignment, less flexion and greater knee adduction moment (KAM). Loading (normalized to body weight) was no different between the groups but OA subjects had greater absolute medial load than controls and maintained a greater %total load on the medial compartment. These patterns were associated with body mass, sagittal and frontal plane moments, static alignment and close to signficance for dynamic alignment. Lateral compartment unloading during mid-late stance was observed in 50% of OA subjects. Conclusions Loading for control subjects was similar to data from instrumented prostheses. Knee OA subjects had high medial contact loads in early stance and half of the OA cohort demonstared lateral compartment lift-off. Results suggest that interventions aimed at reducing body weight and dynamic malalignment might be effective in reducing medial compartment loading and establishing normal medio-lateral load sharing patterns. PMID:23182814

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

PubMed

Sawyer, Travis W

2018-02-01

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

Carbon Nanotube-Based Structural Health Monitoring Sensors

NASA Technical Reports Server (NTRS)

Wincheski, Russell; Jordan, Jeffrey; Oglesby, Donald; Watkins, Anthony; Patry, JoAnne; Smits, Jan; Williams, Phillip

2011-01-01

Carbon nanotube (CNT)-based sensors for structural health monitoring (SHM) can be embedded in structures of all geometries to monitor conditions both inside and at the surface of the structure to continuously sense changes. These CNTs can be manipulated into specific orientations to create small, powerful, and flexible sensors. One of the sensors is a highly flexible sensor for crack growth detection and strain field mapping that features a very dense and highly ordered array of single-walled CNTs. CNT structural health sensors can be mass-produced, are inexpensive, can be packaged in small sizes (0.5 micron(sup 2)), require less power than electronic or piezoelectric transducers, and produce less waste heat per square centimeter than electronic or piezoelectric transducers. Chemically functionalized lithographic patterns are used to deposit and align the CNTs onto metallic electrodes. This method consistently produces aligned CNTs in the defined locations. Using photo- and electron-beam lithography, simple Cr/Au thin-film circuits are patterned onto oxidized silicon substrates. The samples are then re-patterned with a CNT-attracting, self-assembled monolayer of 3-aminopropyltriethoxysilane (APTES) to delineate the desired CNT locations between electrodes. During the deposition of the solution-suspended single- wall CNTs, the application of an electric field to the metallic contacts causes alignment of the CNTs along the field direction. This innovation is a prime candidate for smart skin technologies with applications ranging from military, to aerospace, to private industry.

Importance of orthotic subtalar alignment for development and gait of children with cerebral palsy.

PubMed

Carmick, Judy

2012-01-01

This case report addresses the assumption that ankle and foot orthoses assist children with cerebral palsy. Outcome research reports are not consistent. Clinical observations and research studies suggest that inappropriate fit and design of orthoses may contribute to poor outcomes. In particular, problems occur when the subtalar joint is out of alignment as children often compensate with unwanted movement patterns that affect progress, development, and function. Four cases are presented to demonstrate problems that can occur when ankle-foot or supramalleolar orthoses are not cast in subtalar neutral. Physical therapists can use their clinical observation skills to evaluate the proper fit and alignment of orthoses for children with cerebral palsy.

EFFECT OF PRE-ANNEALING TEMPERATURE ON THE GROWTH OF ALIGNED α-Fe2O3 NANOWIRES VIA A TWO-STEP THERMAL OXIDATION

NASA Astrophysics Data System (ADS)

Rashid, Norhana Mohamed; Kishi, Naoki; Soga, Tetsuo

2016-03-01

Pre-annealing as part of a two-step thermal oxidation process has a significant effect on the growth of hematite (α-Fe2O3) nanowires on Fe foil. High-density aligned nanowires were obtained on iron foils pre-annealed at 300∘C under a dry air flow for 30min. The X-ray diffraction (XRD) patterns indicate that the nanowires are transformed from the small α-Fe2O3 grains and uniquely grow in the (110) direction. The formation of a high-density of small grains by pre-annealing improved the alignment and density of the α-Fe2O3 nanowires.

Medium scale carbon nanotube thin film integrated circuits on flexible plastic substrates

DOEpatents

Rogers, John A; Cao, Qing; Alam, Muhammad; Pimparkar, Ninad

2015-02-03

The present invention provides device components geometries and fabrication strategies for enhancing the electronic performance of electronic devices based on thin films of randomly oriented or partially aligned semiconducting nanotubes. In certain aspects, devices and methods of the present invention incorporate a patterned layer of randomly oriented or partially aligned carbon nanotubes, such as one or more interconnected SWNT networks, providing a semiconductor channel exhibiting improved electronic properties relative to conventional nanotubes-based electronic systems.

Nanofabricated Racks of Aligned and Anchored DNA Substrates for Single-Molecule Imaging

PubMed Central

2009-01-01

Single-molecule studies of biological macromolecules can benefit from new experimental platforms that facilitate experimental design and data acquisition. Here we develop new strategies to construct curtains of DNA in which the molecules are aligned with respect to one another and maintained in an extended configuration by anchoring both ends of the DNA to the surface of a microfluidic sample chamber that is otherwise coated with an inert lipid bilayer. This “double-tethered” DNA substrate configuration is established through the use of nanofabricated rack patterns comprised of two distinct functional elements: linear barriers to lipid diffusion that align DNA molecules anchored by one end to the bilayer and antibody-coated pentagons that provide immobile anchor points for the opposite ends of the DNA. These devices enable the alignment and anchoring of thousands of individual DNA molecules, which can then be visualized using total internal reflection fluorescence microscopy under conditions that do not require continuous application of buffer flow to stretch the DNA. This unique strategy offers the potential for studying protein−DNA interactions on large DNA substrates without compromising measurements through application of hydrodynamic force. We provide a proof-of-principle demonstration that double-tethered DNA curtains made with nanofabricated rack patterns can be used in a one-dimensional diffusion assay that monitors the motion of quantum dot-tagged proteins along DNA. PMID:19736980

Nanofabricated racks of aligned and anchored DNA substrates for single-molecule imaging.

PubMed

Gorman, Jason; Fazio, Teresa; Wang, Feng; Wind, Shalom; Greene, Eric C

2010-01-19

Single-molecule studies of biological macromolecules can benefit from new experimental platforms that facilitate experimental design and data acquisition. Here we develop new strategies to construct curtains of DNA in which the molecules are aligned with respect to one another and maintained in an extended configuration by anchoring both ends of the DNA to the surface of a microfluidic sample chamber that is otherwise coated with an inert lipid bilayer. This "double-tethered" DNA substrate configuration is established through the use of nanofabricated rack patterns comprised of two distinct functional elements: linear barriers to lipid diffusion that align DNA molecules anchored by one end to the bilayer and antibody-coated pentagons that provide immobile anchor points for the opposite ends of the DNA. These devices enable the alignment and anchoring of thousands of individual DNA molecules, which can then be visualized using total internal reflection fluorescence microscopy under conditions that do not require continuous application of buffer flow to stretch the DNA. This unique strategy offers the potential for studying protein-DNA interactions on large DNA substrates without compromising measurements through application of hydrodynamic force. We provide a proof-of-principle demonstration that double-tethered DNA curtains made with nanofabricated rack patterns can be used in a one-dimensional diffusion assay that monitors the motion of quantum dot-tagged proteins along DNA.

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

PubMed

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

2017-06-01

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

Query-seeded iterative sequence similarity searching improves selectivity 5–20-fold

PubMed Central

Li, Weizhong; Lopez, Rodrigo

2017-01-01

Abstract Iterative similarity search programs, like psiblast, jackhmmer, and psisearch, are much more sensitive than pairwise similarity search methods like blast and ssearch because they build a position specific scoring model (a PSSM or HMM) that captures the pattern of sequence conservation characteristic to a protein family. But models are subject to contamination; once an unrelated sequence has been added to the model, homologs of the unrelated sequence will also produce high scores, and the model can diverge from the original protein family. Examination of alignment errors during psiblast PSSM contamination suggested a simple strategy for dramatically reducing PSSM contamination. psiblast PSSMs are built from the query-based multiple sequence alignment (MSA) implied by the pairwise alignments between the query model (PSSM, HMM) and the subject sequences in the library. When the original query sequence residues are inserted into gapped positions in the aligned subject sequence, the resulting PSSM rarely produces alignment over-extensions or alignments to unrelated sequences. This simple step, which tends to anchor the PSSM to the original query sequence and slightly increase target percent identity, can reduce the frequency of false-positive alignments more than 20-fold compared with psiblast and jackhmmer, with little loss in search sensitivity. PMID:27923999

Cellular self-organization by autocatalytic alignment feedback

PubMed Central

Junkin, Michael; Leung, Siu Ling; Whitman, Samantha; Gregorio, Carol C.; Wong, Pak Kin

2011-01-01

Myoblasts aggregate, differentiate and fuse to form skeletal muscle during both embryogenesis and tissue regeneration. For proper muscle function, long-range self-organization of myoblasts is required to create organized muscle architecture globally aligned to neighboring tissue. However, how the cells process geometric information over distances considerably longer than individual cells to self-organize into well-ordered, aligned and multinucleated myofibers remains a central question in developmental biology and regenerative medicine. Using plasma lithography micropatterning to create spatial cues for cell guidance, we show a physical mechanism by which orientation information can propagate for a long distance from a geometric boundary to guide development of muscle tissue. This long-range alignment occurs only in differentiating myoblasts, but not in non-fusing myoblasts perturbed by microfluidic disturbances or other non-fusing cell types. Computational cellular automata analysis of the spatiotemporal evolution of the self-organization process reveals that myogenic fusion in conjunction with rotational inertia functions in a self-reinforcing manner to enhance long-range propagation of alignment information. With this autocatalytic alignment feedback, well-ordered alignment of muscle could reinforce existing orientations and help promote proper arrangement with neighboring tissue and overall organization. Such physical self-enhancement might represent a fundamental mechanism for long-range pattern formation during tissue morphogenesis. PMID:22193956

Physics of self-aligned assembly at room temperature

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Mechanism of cell alignment in groups of Myxococcus xanthus bacteria

NASA Astrophysics Data System (ADS)

Balgam, Rajesh; Igoshin, Oleg

2015-03-01

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

Mumps resurgences in the United States: A historical perspective on unexpected elements.

PubMed

Barskey, Albert E; Glasser, John W; LeBaron, Charles W

2009-10-19

In 2006 the United States experienced the largest nationwide mumps epidemic in 20 years, primarily affecting college dormitory residents. Unexpected elements of the outbreak included very abrupt time course (75% of cases occurred within 90 days), geographic focality (85% of cases occurred in eight rural Midwestern states), rapid upward and downward shift in peak age-specific attack rate (5-9-year olds to 18-24-year olds, then back), and two-dose vaccine failure (63% of case-patients had received two doses). To construct a historical context in which to understand the recent outbreak, we reviewed US mumps surveillance data, vaccination coverage estimates, and relevant peer-reviewed literature for the period 1917-2008. Many of the unexpected features of the 2006 mumps outbreak had been reported several times previously in the US, e.g., the 1986-1987 mumps resurgence had extremely abrupt onset, rural geographic focality, and an upward-then-downward age shift. Evidence suggested recurrent mumps outbreak patterns were attributable to accumulation of susceptibles in dispersed situations where the risk of endemic disease exposure was low and were triggered when this susceptible population was brought together in crowded living conditions. The 2006 epidemic followed this pattern, with two unique variations: it was preceded by a period of very high vaccination rates and very low disease incidence and was characterized by two-dose failure rates among adults vaccinated in childhood. Data from the past 80 years suggest that preventing future mumps epidemics will depend on innovative measures to detect and eliminate build-up of susceptibles among highly vaccinated populations.

Line roughness improvements on self-aligned quadruple patterning by wafer stress engineering

NASA Astrophysics Data System (ADS)

Liu, Eric; Ko, Akiteru; Biolsi, Peter; Chae, Soo Doo; Hsieh, Chia-Yun; Kagaya, Munehito; Lee, Choongman; Moriya, Tsuyoshi; Tsujikawa, Shimpei; Suzuki, Yusuke; Okubo, Kazuya; Imai, Kiyotaka

2018-04-01

In integrated circuit and memory devices, size shrinkage has been the most effective method to reduce production cost and enable the steady increment of the number of transistors per unit area over the past few decades. In order to reduce the die size and feature size, it is necessary to minimize pattern formation in the advance node development. In the node of sub-10nm, extreme ultra violet lithography (EUV) and multi-patterning solutions based on 193nm immersionlithography are the two most common options to achieve the size requirement. In such small features of line and space pattern, line width roughness (LWR) and line edge roughness (LER) contribute significant amount of process variation that impacts both physical and electrical performances. In this paper, we focus on optimizing the line roughness performance by using wafer stress engineering on 30nm pitch line and space pattern. This pattern is generated by a self-aligned quadruple patterning (SAQP) technique for the potential application of fin formation. Our investigation starts by comparing film materials and stress levels in various processing steps and material selection on SAQP integration scheme. From the cross-matrix comparison, we are able to determine the best stack of film selection and stress combination in order to achieve the lowest line roughness performance while obtaining pattern validity after fin etch. This stack is also used to study the step-by-step line roughness performance from SAQP to fin etch. Finally, we will show a successful patterning of 30nm pitch line and space pattern SAQP scheme with 1nm line roughness performance.

Integrated Printed Circuit Board (PCB) Active Cooling With Piezoelectric Actuator

DTIC Science & Technology

2012-09-01

The cooler substrate is a laminated multilayer FR-4 substrate. Individual layers are patterned to support the active element, form a resonant...prepreg epoxy. Individual FR-4 lamina were mechanically machined to pattern each layer. The layers were aligned, stacked, and laminated to form the... laminated with 70/30 copper-nickel alloy or 80/20 nickel-chrome alloy and patterned by means of photolithographic techniques and wet etching in a ferric

Vortex with fourfold defect lines in a simple model of self-propelled particles

NASA Astrophysics Data System (ADS)

Seyed-Allaei, Hamid; Ejtehadi, Mohammad Reza

2016-03-01

We study the formation of a vortex with fourfold symmetry in a minimal model of self-propelled particles, confined inside a squared box, using computer simulations and also theoretical analysis. In addition to the vortex pattern, we observe five other regimes in the system: a homogeneous gaseous phase, band structures, moving clumps, moving clusters, and vibrating rings. All six regimes emerge from controlling the strength of noise and from the contribution of repulsion and alignment interactions. We study the shape of the vortex and its symmetry in detail. The pattern shows exponential defect lines where incoming and outgoing flows of particles collide. We show that alignment and repulsion interactions between particles are necessary to form such patterns. We derive hydrodynamical equations with an introduction of the "small deviation" technique to describe the vortex phase. The method is applicable to other systems as well. Finally, we compare the theory with the results of both computer simulations and an experiment using Quincke rotors. A good agreement between the three is observed.

Patterned Well-Aligned ZnO Nanorods Assisted with Polystyrene Monolayer by Oxygen Plasma Treatment.

PubMed

Choi, Hyun Ji; Lee, Yong-Min; Yu, Jung-Hoon; Hwang, Ki-Hwan; Boo, Jin-Hyo

2016-08-05

Zinc oxide is known as a promising material for sensing devices due to its piezoelectric properties. In particular, the alignment of ZnO nanostructures into ordered nanoarrays is expected to improve the device sensitivity due to the large surface area which can be utilized to capture significant quantities of gas particles. However, ZnO nanorods are difficult to grow on the quartz substrate with well-ordered shape. So, we investigated nanostructures by adjusting the interval distance of the arranged ZnO nanorods using polystyrene (PS) spheres of various sizes (800 nm, 1300 nm and 1600 nm). In addition, oxygen plasma treatment was used to specify the nucleation site of round, patterned ZnO nanorod growth. Therefore, ZnO nanorods were grown on a quartz substrate with a patterned polystyrene monolayer by the hydrothermal method after oxygen plasma treatment. The obtained ZnO nanostructures were characterized by X-ray diffraction (XRD) and field-emission scanning electron microscope (FE-SEM).

Ink-jet printing technology enables self-aligned mould patterning for electroplating in a single step

NASA Astrophysics Data System (ADS)

Meissner, M. V.; Spengler, N.; Mager, D.; Wang, N.; Kiss, S. Z.; Höfflin, J.; While, P. T.; Korvink, J. G.

2015-06-01

We present a new self-aligned, mask-free micro-fabrication method with which to form thick-layered conductive metal micro-structures inside electroplating moulds. Seed layer patterning for electroplating was performed by ink-jet printing using a silver nano-particle ink deposited on SU-8 or Ordyl SY permanent resist. The silver ink contact angle on SU-8 was adjusted by oxygen plasma followed by a hard bake. Besides functioning as a seed layer, the printed structures further served as a shadow mask during patterning of electroplating moulds into negative photoresist. The printed silver tracks remained in strong adhesion to the substrate when exposed to the acidic chemistry of the electroplating bath. To demonstrate the process, we manufactured rectangular, low-resistivity planar micro-coils for use in magnetic resonance microscopy. MRI images of a spring onion with an in-plane resolution down to 10 µm × 10 µm were acquired using a micro-coil on an 11.7 T MRI scanner.

Practice Patterns of School-Based Occupational Therapists Targeting Handwriting: A Knowledge-to-Practice Gap

ERIC Educational Resources Information Center

Cramm, Heidi; Egan, Mary

2015-01-01

Poor handwriting is a common reason for referral to school-based occupational therapy. A survey was used to explore the extent to which current practice patterns in Ontario, Canada, align with evidence on effective intervention for handwriting. Knowledge-to-practice gaps were identified related to focus on performance components versus…

Breath Figures under Electrowetting: Electrically Controlled Evolution of Drop Condensation Patterns

NASA Astrophysics Data System (ADS)

Baratian, Davood; Dey, Ranabir; Hoek, Harmen; van den Ende, Dirk; Mugele, Frieder

2018-05-01

We show that electrowetting (EW) with structured electrodes significantly modifies the distribution of drops condensing onto flat hydrophobic surfaces by aligning the drops and by enhancing coalescence. Numerical calculations demonstrate that drop alignment and coalescence are governed by the drop-size-dependent electrostatic energy landscape that is imposed by the electrode pattern and the applied voltage. Such EW-controlled migration and coalescence of condensate drops significantly alter the statistical characteristics of the ensemble of droplets. The evolution of the drop size distribution displays self-similar characteristics that significantly deviate from classical breath figures on homogeneous surfaces once the electrically induced coalescence cascades set in beyond a certain critical drop size. The resulting reduced surface coverage, coupled with earlier drop shedding under EW, enhances the net heat transfer.

Microbial rRNA: rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils

USDA-ARS?s Scientific Manuscript database

We tested a method of estimating the activity of detectable individual bacterial and archaeal OTUs within a community by calculating ratios of absolute 16S rRNA to rDNA copy numbers. We investigated phylogenetically coherent patterns of activity among soil prokaryotes in non-growing soil communitie...

AN UNEXPECTED TEMPORAL PATTERN OF COLIPHAGE ISOLATION IN GROUNDWATERS SAMPLED FROM WELLS AT VARIED DISTANCES FROM RECLAIMED WATER RECHARGE SITES

EPA Science Inventory

Potable and monitoring wells located in close proximity to a large groundwater recharge project which utilizes a blend of surface water and reclaimed wastewater for recharge were tested for coliphage over a period of 6 months to assess the potential for virus migration. During th...

Tales of the Unexpected: Coping among Female Collegiate Volleyball Players

ERIC Educational Resources Information Center

Holt, Nicholas L.; Berg, Kylie-Joy; Tamminen, Katherine A.

2007-01-01

The purpose of this study was to examine patterns of appraisal, coping, and coping effectiveness in sport. Ten players from a collegiate female volleyball team were interviewed on two occasions, first in the week before a provincial final playoff tournament and in the week following the tournament. Data were transcribed verbatim and subjected to…

False Belief Understanding: The Influence of Person, Grammatical Mood, Counterfactual Reasoning and Working Memory

ERIC Educational Resources Information Center

Muller, Ulrich; Miller, Michael R.; Michalczyk, Kurt; Karapinka, Aaron

2007-01-01

The present study had two major goals. The first goal was to assess the relative difficulty among different versions of the unexpected contents task by systematically varying the dimensions of grammatical mood (indicative vs. subjunctive) and person (self vs. other), and to examine the correlational pattern between these different versions of the…

Children's Developing Knowledge of "Wh"-/Quantifier Question-Answer Relations

ERIC Educational Resources Information Center

Achimova, Asya; Syrett, Kristen; Musolino, Julien; Déprez, Viviane

2017-01-01

In response to questions in which a "wh"-term interacts with a universal quantifier in object position, such as "Who picked every toy?," children as old as 5 years of age often provide a list, pairing toys with the people who picked each of them. This response pattern is unexpected, it has been claimed, because children appear…

Structural Pattern Recognition Techniques for Data Retrieval in Massive Fusion Databases

NASA Astrophysics Data System (ADS)

Vega, J.; Murari, A.; Rattá, G. A.; Castro, P.; Pereira, A.; Portas, A.

2008-03-01

Diagnostics of present day reactor class fusion experiments, like the Joint European Torus (JET), generate thousands of signals (time series and video images) in each discharge. There is a direct correspondence between the physical phenomena taking place in the plasma and the set of structural shapes (patterns) that they form in the signals: bumps, unexpected amplitude changes, abrupt peaks, periodic components, high intensity zones or specific edge contours. A major difficulty related to data analysis is the identification, in a rapid and automated way, of a set of discharges with comparable behavior, i.e. discharges with "similar" patterns. Pattern recognition techniques are efficient tools to search for similar structural forms within the database in a fast an intelligent way. To this end, classification systems must be developed to be used as indexation methods to directly fetch the more similar patterns.

Competition can lead to unexpected patterns in tropical ant communities

NASA Astrophysics Data System (ADS)

Ellwood, M. D. Farnon; Blüthgen, Nico; Fayle, Tom M.; Foster, William A.; Menzel, Florian

2016-08-01

Ecological communities are structured by competitive, predatory, mutualistic and parasitic interactions combined with chance events. Separating deterministic from stochastic processes is possible, but finding statistical evidence for specific biological interactions is challenging. We attempt to solve this problem for ant communities nesting in epiphytic bird's nest ferns (Asplenium nidus) in Borneo's lowland rainforest. By recording the frequencies with which each and every single ant species occurred together, we were able to test statistically for patterns associated with interspecific competition. We found evidence for competition, but the resulting co-occurrence pattern was the opposite of what we expected. Rather than detecting species segregation-the classical hallmark of competition-we found species aggregation. Moreover, our approach of testing individual pairwise interactions mostly revealed spatially positive rather than negative associations. Significant negative interactions were only detected among large ants, and among species of the subfamily Ponerinae. Remarkably, the results from this study, and from a corroborating analysis of ant communities known to be structured by competition, suggest that competition within the ants leads to species aggregation rather than segregation. We believe this unexpected result is linked with the displacement of species following asymmetric competition. We conclude that analysing co-occurrence frequencies across complete species assemblages, separately for each species, and for each unique pairwise combination of species, represents a subtle yet powerful way of detecting structure and compartmentalisation in ecological communities.

Characteristics of ionospheric convection and field-aligned current in the dayside cusp region

NASA Technical Reports Server (NTRS)

Lu, G.; Lyons, L. R.; Reiff, P. H.; Denig, W. F.; Beaujardiere, O. De LA; Kroehl, H. W.; Newell, P. T.; Rich, F. J.; Opgenoorth, H.; Persson, M. A. L.

1995-01-01

The assimilative mapping of ionospheric electrodynamics (AMIE) technique has been used to estimate global distributions of high-latitude ionospheric convection and field-aligned current by combining data obtained nearly simultaneously both from ground and from space. Therefore, unlike the statistical patterns, the 'snapshot' distributions derived by AMIE allow us to examine in more detail the distinctions between field-aligned current systems associated with separate magnetospheric processes, especially in the dayside cusp region. By comparing the field-aligned current and ionospheric convection patterns with the corresponding spectrograms of precipitating particles, the following signatures have been identified: (1) For the three cases studied, which all had an IMF with negative y and z components, the cusp precipitation was encountered by the DMSP satellites in the postnoon sector in the northern hemisphere and in the prenoon sector in the southern hemisphere. The equatorward part of the cusp in both hemispheres is in the sunward flow region and marks the beginning of the flow rotation from sunward to antisunward. (2) The pair of field-aligned currents near local noon, i.e., the cusp/mantle currents, are coincident with the cusp or mantle particle precipitation. In distinction, the field-aligned currents on the dawnside and duskside, i.e., the normal region 1 currents, are usually associated with the plasma sheet particle precipitation. Thus the cusp/mantle currents are generated on open field lines and the region 1 currents mainly on closed field lines. (3) Topologically, the cusp/mantle currents appear as an expansion of the region 1 currents from the dawnside and duskside and they overlap near local noon. When B(sub y) is negative, in the northern hemisphere the downward field-aligned current is located poleward of the upward current; whereas in the southern hemisphere the upward current is located poleward of the downward current. (4) Under the assumption of quasi-steady state reconnection, the location of the separatrix in the ionosphere is estimated and the reconnection velocity is calculated to be between 400 and 550 m/s. The dayside separatrix lies equatorward of the dayside convection throat in the two cases examined.

Optimization of self-aligned double patterning (SADP)-compliant layout designs using pattern matching for sub-20nm metal routing

NASA Astrophysics Data System (ADS)

Wang, Lynn T.-N.; Schroeder, Uwe Paul; Madhavan, Sriram

2017-03-01

A pattern-based methodology for optimizing SADP-compliant layout designs is developed based on identifying cut mask patterns and replacing them with pre-characterized fixing solutions. A pattern-based library of difficult-tomanufacture cut patterns with pre-characterized fixing solutions is built. A pattern-based engine searches for matching patterns in the decomposed layouts. When a match is found, the engine opportunistically replaces the detected pattern with a pre-characterized fixing solution. The methodology was demonstrated on a 7nm routed metal2 block. A small library of 30 cut patterns increased the number of more manufacturable cuts by 38% and metal-via enclosure by 13% with a small parasitic capacitance impact of 0.3%.

Strain Pattern in Supercooled Liquids

NASA Astrophysics Data System (ADS)

Illing, Bernd; Fritschi, Sebastian; Hajnal, David; Klix, Christian; Keim, Peter; Fuchs, Matthias

2016-11-01

Investigations of strain correlations at the glass transition reveal unexpected phenomena. The shear strain fluctuations show an Eshelby-strain pattern [˜cos (4 θ ) /r2 ], characteristic of elastic response, even in liquids, at long times. We address this using a mode-coupling theory for the strain fluctuations in supercooled liquids and data from both video microscopy of a two-dimensional colloidal glass former and simulations of Brownian hard disks. We show that the long-ranged and long-lived strain signatures follow a scaling law valid close to the glass transition. For large enough viscosities, the Eshelby-strain pattern is visible even on time scales longer than the structural relaxation time τ and after the shear modulus has relaxed to zero.

Hierarchically ordered carbon tubes

NASA Astrophysics Data System (ADS)

Pan, Zheng-Wei; Zhu, Hao-Guo; Zhang, Zong-Tao; Im, Hee-Jung; Dai, Sheng; Beach, David B.; Lowndes, Douglas H.

2003-04-01

Micropatterns of hierarchically ordered carbon tubes (i.e., ordered carbon microtubes composed of aligned carbon nanotubes) were grown on a film-like iron/silica substrate consisting of ring-like catalyst patterns. The substrates were prepared by a combined technique, in which the sol-gel method was used to prepare catalyst film and transmission electron microscope grids were used as a shadow mask. In comparison with other techniques that involve sophisticated lithography, this approach represents a simple and low-cost way to the micropatterning of aligned carbon nanotubes.

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

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

Zemla, A; Lang, D; Kostova, T

2010-11-29

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

Unexpected effects of different genetic backgrounds on identification of genomic rearrangements via whole-genome next generation sequencing.

PubMed

Chen, Zhangguo; Gowan, Katherine; Leach, Sonia M; Viboolsittiseri, Sawanee S; Mishra, Ameet K; Kadoishi, Tanya; Diener, Katrina; Gao, Bifeng; Jones, Kenneth; Wang, Jing H

2016-10-21

Whole genome next generation sequencing (NGS) is increasingly employed to detect genomic rearrangements in cancer genomes, especially in lymphoid malignancies. We recently established a unique mouse model by specifically deleting a key non-homologous end-joining DNA repair gene, Xrcc4, and a cell cycle checkpoint gene, Trp53, in germinal center B cells. This mouse model spontaneously develops mature B cell lymphomas (termed G1XP lymphomas). Here, we attempt to employ whole genome NGS to identify novel structural rearrangements, in particular inter-chromosomal translocations (CTXs), in these G1XP lymphomas. We sequenced six lymphoma samples, aligned our NGS data with mouse reference genome (in C57BL/6J (B6) background) and identified CTXs using CREST algorithm. Surprisingly, we detected widespread CTXs in both lymphomas and wildtype control samples, majority of which were false positive and attributable to different genetic backgrounds. In addition, we validated our NGS pipeline by sequencing multiple control samples from distinct tissues of different genetic backgrounds of mouse (B6 vs non-B6). Lastly, our studies showed that widespread false positive CTXs can be generated by simply aligning sequences from different genetic backgrounds of mouse. We conclude that mapping and alignment with reference genome might not be a preferred method for analyzing whole-genome NGS data obtained from a genetic background different from reference genome. Given the complex genetic background of different mouse strains or the heterogeneity of cancer genomes in human patients, in order to minimize such systematic artifacts and uncover novel CTXs, a preferred method might be de novo assembly of personalized normal control genome and cancer cell genome, instead of mapping and aligning NGS data to mouse or human reference genome. Thus, our studies have critical impact on the manner of data analysis for cancer genomics.

The effects of learning on event-related potential correlates of musical expectancy.

PubMed

Carrión, Ricardo E; Bly, Benjamin Martin

2008-09-01

Musical processing studies have shown that unexpected endings in familiar musical sequences produce extended latencies of the P300 component. The present study sought to identify event-related potential (ERP) correlates of musical expectancy by entraining participants with rule-governed chord sequences and testing whether unexpected endings created similar responses. Two experiments were conducted in which participants performed grammaticality classifications without training (Experiment 1) and with training (Experiment 2). In both experiments, deviant chords differing in instrumental timbre elicited a MMN/P3a waveform complex. Violations related to learned patterns elicited an early right anterior negativity and P3b. Latency and amplitude of peak components were modulated by the physical characteristics of the chords, expectations due to prior knowledge of musical harmony, and contextually defined expectations developed through entrainment.

Design pattern mining using distributed learning automata and DNA sequence alignment.

PubMed

Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

2014-01-01

Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA) and deoxyribonucleic acid (DNA) sequences alignment. The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns.

Neuropathological aspects of conservative treatment of scoliosis. A theoretical view point.

PubMed

Czupryna, Krzysztof; Nowotny-Czupryna, Olga; Nowotny, Janusz

2012-01-01

An upright body posture cannot be maintained passively for reasons including a high location of the centre of gravity (COG) and a small support area. Proper alignment of body parts is maintained automatically, tending towards a pattern encoded in the CNS. A particularly important role in posture regulation is played by the short muscles of the back, which respond to being stretched with a contraction. During the early phase of scoliosis, the CNS automatically corrects abnormalities, but over time habituation occurs and the CNS treats them as something normal. Any attempt to restore proper body alignment is treated as an error and CNS automatically restores this abnormal pattern. With a prolonged deviation in body part alignment, CNS treats it as a defect and runs compensatory mechanisms to restore the balance of the body as a whole. Balance is ensured by postural compensation, but this does not restore proper body part alignment. In the treatment of scoliosis, it is important both to slow down progression and to prevent the development of abnormal postural habits, which are part of a vicious circle even without progression. Secondary prevention is therefore needed in all patients. Passive observation limits the possibilities for prevention and contradicts the principle of early implementation of rehabilitation. Depending on the size of the angle of curvature, recommended treatments of scoliosis comprise observation, corset bracing, and surgery. Physiotherapy is often treated as an unconventional and ineffective treatment. Often, the biggest problem is transferring the resulting correction to automatic maintenance of a correct posture in the vertical position. The aim of this paper was to discuss the conservative treatment of scoliosis with regard to difficulties maintaining the correct alignment of the body parts in the vertical position that accompany scoliosis.

Strong IMF By-Related Plasma Convection in the Ionosphere and Cusp Field-Aligned Currents Under Northward IMF Conditions

NASA Technical Reports Server (NTRS)

Le, G.; Lu, G.; Strangeway, R. J.; Pfaff, R. F., Jr.; Vondrak, Richard R. (Technical Monitor)

2001-01-01

We present in this paper an investigation of IMF-By related plasma convection and cusp field-aligned currents using FAST data and AMIE model during a prolonged interval with large positive IMF By and northward Bz conditions (By/Bz much greater than 1). Using the FAST single trajectory observations to validate the global convection patterns at key times and key locations, we have demonstrated that the AMIE procedure provides a reasonably good description of plasma circulations in the ionosphere during this interval. Our results show that the plasma convection in the ionosphere is consistent with the anti-parallel merging model. When the IMF has a strongly positive By component under northward conditions, we find that the global plasma convection forms two cells oriented nearly along the Sun-earth line in the ionosphere. In the northern hemisphere, the dayside cell has clockwise convection mainly circulating within the polar cap on open field lines. A second cell with counterclockwise convection is located in the nightside circulating across the polar cap boundary, The observed two-cell convection pattern appears to be driven by the reconnection along the anti-parallel merging lines poleward of the cusp extending toward the dusk side when IMF By/Bz much greater than 1. The magnetic tension force on the newly reconnected field lines drives the plasma to move from dusk to dawn in the polar cusp region near the polar cap boundary. The field-aligned currents in the cusp region flow downward into the ionosphere. The return field-aligned currents extend into the polar cap in the center of the dayside convection cell. The field-aligned currents are closed through the Peterson currents in the ionosphere, which flow poleward from the polar cap boundary along the electric field direction.

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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

A Pilot Study of Deaf Trauma Survivors’ Experiences: Early Traumas Unique to Being Deaf in a Hearing World

PubMed Central

Wolf Craig, Kelly S.; Hall, Wyatte C.; Ziedonis, Douglas M.

2016-01-01

Conducting semi-structured American Sign Language interviews with 17 Deaf trauma survivors, this pilot study explored Deaf individuals’ trauma experiences and whether these experiences generally align with trauma in the hearing population. Most commonly reported traumas were physical assault, sudden unexpected deaths, and “other” very stressful events. Although some “other” events overlap with traumas in the general population, many are unique to Deaf people (e.g., corporal punishment at oral/aural school if caught using sign language, utter lack of communication with hearing parents). These findings suggest that Deaf individuals may experience developmental traumas distinct to being raised in a hearing world. Such traumas are not captured by available trauma assessments, nor are they considered in evidence-based trauma treatments. PMID:28138351

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

Tripathi, Anjali; Winn, Joshua N.; De Kleer, Katherine R.

We present new spectroscopic and photometric observations of the transiting exoplanetary system WASP-3. Spectra obtained during two separate transits exhibit the Rossiter-McLaughlin (RM) effect and allow us to estimate the sky-projected angle between the planetary orbital axis and the stellar rotation axis, {lambda} = 3.3{sup +2.5}{sub -4.4} deg. This alignment between the axes suggests that WASP-3b has a low orbital inclination relative to the equatorial plane of its parent star. During our first night of spectroscopic measurements, we observed an unexpected redshift briefly exceeding the expected sum of the orbital and RM velocities by 140 m s{sup -1}. This anomalymore » could represent the occultation of material erupting from the stellar photosphere, although it is more likely to be an artifact caused by moonlight scattered into the spectrograph.« less

Self-assembly of skyrmion-dressed chiral nematic colloids with tangential anchoring.

PubMed

Pandey, M B; Porenta, T; Brewer, J; Burkart, A; Copar, S; Zumer, S; Smalyukh, Ivan I

2014-06-01

We describe dipolar nematic colloids comprising mutually bound solid microspheres, three-dimensional skyrmions, and point defects in a molecular alignment field of chiral nematic liquid crystals. Nonlinear optical imaging and numerical modeling based on minimization of Landau-de Gennes free energy reveal that the particle-induced skyrmions resemble torons and hopfions, while matching surface boundary conditions at the interfaces of liquid crystal and colloidal spheres. Laser tweezers and videomicroscopy reveal that the skyrmion-colloidal hybrids exhibit purely repulsive elastic pair interactions in the case of parallel dipoles and an unexpected reversal of interaction forces from repulsive to attractive as the center-to-center distance decreases for antiparallel dipoles. The ensuing elastic self-assembly gives rise to colloidal chains of antiparallel dipoles with particles entangled by skyrmions.

A Pilot Study of Deaf Trauma Survivors' Experiences: Early Traumas Unique to Being Deaf in a Hearing World.

PubMed

Anderson, Melissa L; Wolf Craig, Kelly S; Hall, Wyatte C; Ziedonis, Douglas M

2016-12-01

Conducting semi-structured American Sign Language interviews with 17 Deaf trauma survivors, this pilot study explored Deaf individuals' trauma experiences and whether these experiences generally align with trauma in the hearing population. Most commonly reported traumas were physical assault, sudden unexpected deaths, and "other" very stressful events. Although some "other" events overlap with traumas in the general population, many are unique to Deaf people (e.g., corporal punishment at oral/aural school if caught using sign language, utter lack of communication with hearing parents). These findings suggest that Deaf individuals may experience developmental traumas distinct to being raised in a hearing world. Such traumas are not captured by available trauma assessments, nor are they considered in evidence-based trauma treatments.

Radio frequency measurements and tuning of the China Material Irradiation Facility RFQ

NASA Astrophysics Data System (ADS)

Li, Chenxing; He, Yuan; Wang, Fengfeng; Yu, Peiyan; Yang, Lei; Li, Chunlong; Wang, Wenbin; Xu, Xianbo; Shi, Longbo; Ma, Wei; Sun, Liepeng; Lu, Liang; Wang, Zhijun; Shi, Aimin; Wang, Tieshan

2018-05-01

The full assembly and alignment of the China Material Irradiation Facility RFQ have been completed. Before the completion, the assembly and braze of single segments had been done. Radio frequency measurements of each module with dummy extension undercuts were performed before and after braze. The results reveal that there is no unexpected deformation after braze. After the full assembly, RF measurements and tuning have been performed in order to compensate the errors originated from the fabrication, braze and assembly. The impact of these errors on the field distribution is depressed to a level that is restricted by beam dynamics simulation. In this paper, the procedure of radio frequency measurement and tuning will be expatiated and the ultimate RF parameters of the cavity after tuning will be presented.

Structure of High Latitude Currents in Magnetosphere-Ionosphere Models

NASA Astrophysics Data System (ADS)

Wiltberger, M.; Rigler, E. J.; Merkin, V.; Lyon, J. G.

2017-03-01

Using three resolutions of the Lyon-Fedder-Mobarry global magnetosphere-ionosphere model (LFM) and the Weimer 2005 empirical model we examine the structure of the high latitude field-aligned current patterns. Each resolution was run for the entire Whole Heliosphere Interval which contained two high speed solar wind streams and modest interplanetary magnetic field strengths. Average states of the field-aligned current (FAC) patterns for 8 interplanetary magnetic field clock angle directions are computed using data from these runs. Generally speaking the patterns obtained agree well with results obtained from the Weimer 2005 computing using the solar wind and IMF conditions that correspond to each bin. As the simulation resolution increases the currents become more intense and narrow. A machine learning analysis of the FAC patterns shows that the ratio of Region 1 (R1) to Region 2 (R2) currents decreases as the simulation resolution increases. This brings the simulation results into better agreement with observational predictions and the Weimer 2005 model results. The increase in R2 current strengths also results in the cross polar cap potential (CPCP) pattern being concentrated in higher latitudes. Current-voltage relationships between the R1 and CPCP are quite similar at the higher resolution indicating the simulation is converging on a common solution. We conclude that LFM simulations are capable of reproducing the statistical features of FAC patterns.

Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato

PubMed Central

Ruiz, Mayté; Salazar, Patricio; Counterman, Brian; Medina, Jose Alejandro; Ortiz-Zuazaga, Humberto; Morrison, Anna; Papa, Riccardo

2014-01-01

Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on color pattern. The comimetic species, H. erato and H. melpomene, have parallel hybrid zones in which both species undergo a change from one color pattern form to another. We use restriction-associated DNA sequencing to obtain several thousand genome-wide sequence markers and use these to analyze patterns of population divergence across two pairs of parallel hybrid zones in Peru and Ecuador. We compare two approaches for analysis of this type of data—alignment to a reference genome and de novo assembly—and find that alignment gives the best results for species both closely (H. melpomene) and distantly (H. erato, ∼15% divergent) related to the reference sequence. Our results confirm that the color pattern controlling loci account for the majority of divergent regions across the genome, but we also detect other divergent regions apparently unlinked to color pattern differences. We also use association mapping to identify previously unmapped color pattern loci, in particular the Ro locus. Finally, we identify a new cryptic population of H. timareta in Ecuador, which occurs at relatively low altitude and is mimetic with H. melpomene malleti. PMID:24823669

Structure of high latitude currents in global magnetospheric-ionospheric models

USGS Publications Warehouse

Wiltberger, M; Rigler, E. J.; Merkin, V; Lyon, J. G

2016-01-01

Using three resolutions of the Lyon-Fedder-Mobarry global magnetosphere-ionosphere model (LFM) and the Weimer 2005 empirical model we examine the structure of the high latitude field-aligned current patterns. Each resolution was run for the entire Whole Heliosphere Interval which contained two high speed solar wind streams and modest interplanetary magnetic field strengths. Average states of the field-aligned current (FAC) patterns for 8 interplanetary magnetic field clock angle directions are computed using data from these runs. Generally speaking the patterns obtained agree well with results obtained from the Weimer 2005 computing using the solar wind and IMF conditions that correspond to each bin. As the simulation resolution increases the currents become more intense and narrow. A machine learning analysis of the FAC patterns shows that the ratio of Region 1 (R1) to Region 2 (R2) currents decreases as the simulation resolution increases. This brings the simulation results into better agreement with observational predictions and the Weimer 2005 model results. The increase in R2 current strengths also results in the cross polar cap potential (CPCP) pattern being concentrated in higher latitudes. Current-voltage relationships between the R1 and CPCP are quite similar at the higher resolution indicating the simulation is converging on a common solution. We conclude that LFM simulations are capable of reproducing the statistical features of FAC patterns.

Light-induced quantitative microprinting of biomolecules

NASA Astrophysics Data System (ADS)

Strale, Pierre-Olivier; Azioune, Ammar; Bugnicourt, Ghislain; Lecomte, Yohan; Chahid, Makhlad; Studer, Vincent

2017-02-01

Printing of biomolecules on substrates has developed tremendously in the past few years. The existing methods either rely on slow serial writing processes or on parallelized photolithographic techniques where cumbersome mask alignment procedures usually impair the ability to generate multi-protein patterns. We recently developed a new technology allowing for high resolution multi protein micro-patterning. This technology named "Light-Induced Molecular Adsorption of Proteins (LIMAP)" is based on a water-soluble photo-initiator able to reverse the antifouling property of polymer brushes when exposed to UV light. We developed a wide-field pattern projection system based on a DMD coupled to a conventional microscope which permits to generate arbitrary grayscale patterns of UV light at the micron scale. Interestingly, the density of adsorbed molecules scales with the dose of UV light thus allowing the quantitative patterning of biomolecules. The very low non specific background of biomolecules outside of the UV-exposed areas allows for the sequential printing of multiple proteins without alignment procedures. Protein patterns ranging from 500 nm up to 1 mm can be performed within seconds, as well as gradients of arbitrary shapes. The range of applications of the LIMAP approach extends from the single molecule up to the multicellular scale with an exquisite control over local protein density. We show that it can be used to generate complex protein landscapes useful to study protein-protein, cell-cell and cell-matrix interactions.

Reliability of lower limb alignment measures using an established landmark-based method with a customized computer software program

PubMed Central

Sled, Elizabeth A.; Sheehy, Lisa M.; Felson, David T.; Costigan, Patrick A.; Lam, Miu; Cooke, T. Derek V.

2010-01-01

The objective of the study was to evaluate the reliability of frontal plane lower limb alignment measures using a landmark-based method by (1) comparing inter- and intra-reader reliability between measurements of alignment obtained manually with those using a computer program, and (2) determining inter- and intra-reader reliability of computer-assisted alignment measures from full-limb radiographs. An established method for measuring alignment was used, involving selection of 10 femoral and tibial bone landmarks. 1) To compare manual and computer methods, we used digital images and matching paper copies of five alignment patterns simulating healthy and malaligned limbs drawn using AutoCAD. Seven readers were trained in each system. Paper copies were measured manually and repeat measurements were performed daily for 3 days, followed by a similar routine with the digital images using the computer. 2) To examine the reliability of computer-assisted measures from full-limb radiographs, 100 images (200 limbs) were selected as a random sample from 1,500 full-limb digital radiographs which were part of the Multicenter Osteoarthritis (MOST) Study. Three trained readers used the software program to measure alignment twice from the batch of 100 images, with two or more weeks between batch handling. Manual and computer measures of alignment showed excellent agreement (intraclass correlations [ICCs] 0.977 – 0.999 for computer analysis; 0.820 – 0.995 for manual measures). The computer program applied to full-limb radiographs produced alignment measurements with high inter- and intra-reader reliability (ICCs 0.839 – 0.998). In conclusion, alignment measures using a bone landmark-based approach and a computer program were highly reliable between multiple readers. PMID:19882339

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

PubMed

Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi

2007-02-15

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

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

PubMed

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

2013-09-01

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

Optimal time following fluorescein instillation to evaluate rigid gas permeable contact lens fit.

PubMed

Wolffsohn, James S; Tharoo, Ali; Lakhlani, Nikita

2015-04-01

To examine the optimum time at which fluorescein patterns of gas permeable lenses (GPs) should be evaluated. Aligned, 0.2mm steep and 0.2mm flat GPs were fitted to 17 patients (aged 20.6 ± 1.1 years, 10 male). Fluorescein was applied to their upper temporal bulbar conjunctiva with a moistened fluorescein strip. Digital slit lamp images (CSO, Italy) at 10× magnification of the fluorescein pattern viewed with blue light through a yellow filter were captured every 15s. Fluorescein intensity in central, mid peripheral and edge regions of the superior, inferior, temporal and nasal quadrants of the lens were graded subjectively using a +2 to -2 scale and using ImageJ software on the simultaneously captured images. Subjectively graded and objectively image analysed fluorescein intensity changed with time (p < 0.001), lens region (centre, mid-periphery and edge: p < 0.05) and there was interaction between lens region with lens fit (p < 0.001). For edge band width, there was a significant effect of time (F = 118.503, p < 0.001) and lens fit (F = 5.1249, p = 0.012). The expected alignment, flat and steep fitting patterns could be seen from approximately after 30 to 180 s subjectively and 15 to 105 s in captured images. Although the stability of fluorescein intensity can start to decline in as little as 45 s post fluorescein instillation, the diagnostic pattern of alignment, steep or flat fit is seen in each meridian by subjective observation from about 30s to 3 min indicating this is the most appropriate time window to evaluate GP lenses in clinical practice. Copyright © 2014 British Contact Lens Association. Published by Elsevier Ltd. All rights reserved.

Fabric Development in a Late-Hercynian Magmatic Strike-Slip Shear Zone in Southern Corsica: Indications of Melt-Supported Large-Scale Deformation Localization

NASA Astrophysics Data System (ADS)

Kruhl, J. H.; Vernon, R. H.

2009-05-01

The calc-alcaline granitoids of the Hercynian Corsica Batholith show a large-scale magmatic flow pattern, outlined by the alignment of large (mm-cm) euhedral feldspar crystals. The trend of the steep magmatic foliation is generally N-S in the northern part of the island, swings to approximately E-W orientation in the central part of the Batholith and back again to approximately N-S orientation in the southern part. This pattern is intensified by large-scale magmatic layering, mainly kilometer long lenses and layers of mafic and intermediate intrusions into the granitoids. On the macro- to micro-scale, magma mingling and mixing are present, reflecting the complex intrusion history and the compositional variability of the Corsica Batholith on different scales. Around the Golf of Valinco, a steep, sinistral magmatic shear zone is represented by E-W trending magmatic layering in mingled dioritic, tonalitic, and granitic magmas - previously misleadingly interpreted as migmatites - and by a magmatic flow foliation formed by the alignment of platy feldspar crystals, as well as amphibole and biotite. Characteristic magmatic structures include multiple thin layering, boudinage, monoclinic folding, melt-injected micro shear zones, and fragmenting and back- veining of dioritic enclaves. The intensity of grain alignment roughly correlates with the thickness of layers. It is low in thick and short boudins and high in cm-thin and cm-m long layers. The monoclinic folds refold the magmatic layering. Flat faces of amphibole and biotite grains are aligned in the axial planes of the folds. The feldspar crystals are locally recrystallized to a few large polygonal grains (up to 1 mm across), and quartz commonly shows chessboard subgrain patterns. No further indications of solid-state deformation are present. Field observations, as well as pattern quantification on variably oriented rock surfaces, indicate variations of crystal alignment and fabric anisotropy in cm- to more than 100m-wide bands parallel to the E-W oriented layering, and various stages of melt-present fragmentation. These variations are interpreted as variations of flow intensity and possibly strain-rate variation. The observations on the macro- as well as the micro-scale point to repeated injection of mafic to felsic magma and crystallization in the presence of a regional stress field. The resulting km-scale sinistral, sub-horizontal synmagmatic shear zone reflects large-scale movements during late-Hercynian crustal reorganization and represents an excellent example of localization of deformation into magma-enriched parts of the continental crust.

Spatial Organization In Europe of Decadal and Interdecadal Fluctuations In Annual Rainfall

NASA Astrophysics Data System (ADS)

Lucero, O. A.; Rodriguez, N. C.

In this research the spatial patterns of decadal and bidecadal fluctuations in annual rainfall in Europe are identified. Filtering of time series of anomaly of annual rainfall is carried out using the Morlet wavelet technique. Reconstruction is achieved by sum- ming the contributions from bands of wavelet timescales; the decadal band and the bidecadal band are composed of contributions from the band of (10- to 17-year] and (17- to 27- year] timescales respectively. Results indicate that 1) the spatial organi- zation of decadal and bidecadal components of annual rainfall are standing wave-like organized patterns. Three standing decadal fluctuations zonally aligned formed the spatial pattern from 1900 until 1931; thereafter the pattern changed into a NW-SE orientation. The decadal band shows an average 12-year period. 2) The spatial orga- nization of bidecadal component was composed of three standing fluctuations since 1903 to 1986. After 1987 two standing bidecadal fluctuations were located on Europe. The orientation of bidecadal fluctuations changed during the period under study. Until 1913 the spatial pattern of the bidecadal component was zonally aligned. Since 1913 until 1986 the three bidecadal fluctuations composing the spatial pattern were aligned SW U NE; starting 1987 the spatial pattern is composed of two standing fluctuations zonally aligned. The bidecadal spatial pattern shows an average period of 20- to 22- year length. 3) At decadal and bidecadal timescales, the first principal component of the spatial field of anomaly of annual rainfall and the NAO index are connected. The upper positive third (lower negative third) of values of first principal component are indicative of extensive area with positive (negative) anomaly of annual rainfall. 4) At decadal timescale the relative phase between the first PC and the NAO index changes through the period under study; these changes define three regimes: 1) Dur- ing the regime covering the period 1900 (start of period under study) to about 1945, at the time of peak values of decadal NAO-index it takes place a transition between extremes (a neutral state) of the decadal rainfall spatial pattern (first PC takes small absolute values). Besides, for positive (negative) peak value of NAO index the spatial pattern of annual rainfall is evolving toward an area of predominantly positive (nega- tive) anomaly. 2) The second regime starts about 1946 and reaches up to early 1980s. At the time of negative (positive) peak of decadal NAO there is a prevailing spatial pattern of positive (negative) anomaly of decadal rainfall. 3) The third regime starts 1 about late 1970s and reaches to the end of the period under study (in 1996). There is a change of relative phase within this period in late 1980s. In this regime a spatial pattern of prevailing positive or negative anomaly of decadal rainfall takes place dur- ing values of decadal NAO close to zero. 5) At bidecadal timescale the relative phase between the first PC and the NAO index remains almost constant through the period under study. The first PC of the transformed bidecadal component of annual rainfall anomaly attains its positive (negative) peak about three years before the bidecadal component of NAO reaches its negative (positive) peak. 2

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.

Anxiety and the Processing of Emotionally Threatening Stimuli: Distinctive Patterns of Selective Attention among High- and Low-Test-Anxious Children.

ERIC Educational Resources Information Center

Vasey, Michael W.; And Others

1996-01-01

Tested for bias toward shifting attention toward threatening stimuli among high-anxious children and away from such stimuli among low-anxious children, ages 11-14. Results supported the predicted attentional bias toward threat cues among high-test-anxious children. Unexpectedly, the predicted attentional bias away from threat cues among…

Trade in Higher Education Services in Malaysia: Key Policy Challenges

ERIC Educational Resources Information Center

Tham, Siew Yean

2010-01-01

In recent years, Malaysia has emerged as an unexpected contender in the world market for international students in higher education. Recognizing this sector as a potential new source of growth and export revenue, Malaysia aims to become a regional hub for higher education. In view of this, the objectives of this paper are to profile the pattern of…

Widespread inbreeding and unexpected geographic patterns of genetic variation in eastern hemlock (Tsuga canadensis), an imperiled North American conifer

Treesearch

Kevin M. Potter; Robert M. Jetton; William S. Dvorak; Valerie D. Hipkins; Rusty Rhea; W. Andrew Whittier

2012-01-01

Eastern hemlock (Tsuga canadensis [L.] Carr.) is an ecologically important tree species experiencing severe mortality across much of its eastern North American distribution, caused by infestation of the exotic hemlock woolly adelgid (Adelges tsugae Annand). To guide gene conservation strategies for this imperiled conifer, we conducted a range-wide genetic variation...

Detecting leaf phenology of seasonally moist tropical forests in South America with multi-temporal MODIS images.

Treesearch

Xiangming Xiao; Stephen Hagen; Qingyuan Zhang; Michael Keller; Berrien Moore III

2006-01-01

Leaf phenology of tropical evergreen forests affects carbon and water fluxes. In an earlier study of a seasonally moist evergreen tropical forest site in the Amazon basin, time series data of Enhanced Vegetation Index (EVI) from the VEGETATION and Moderate Resolution Imaging Spectroradiometer (MODIS) sensors showed an unexpected seasonal pattern, with higher EVI in the...

Micropatterned photoalignment for wavefront controlled switchable optical devices

NASA Astrophysics Data System (ADS)

Glazar, Nikolaus

Photoalignment is a well-established technique for surface alignment of the liquid crystal director. Previously, chrome masks were necessary for patterned photoalignment but were difficult to use, costly, and inflexible. To extend the capabilities of photoalignment we built an automated maskless multi-domain photoalignment device based on a DMD (digital multimirror device) projection system. The device is capable of creating arbitrary photoalignment patterns with micron-sized features. Pancharatnam-Berry phase (PB-phase) is a geometric phase that arises from cyclic change of polarization state. By varying the azimuthal anchoring angle in a hybrid-aligned liquid crystal cell we can control the spatial variation of the PB-phase shift. Using our automated photoalignment device to align the liquid crystal arbitrary wave front manipulations are possible. The PB-phase shift effect is maximized when the cell is tuned to have a half-wave retardation and disappears at full-wave retardation, so the cell can be switched on and off by applying a voltage. Two wavefront controlled devices developed using this technique will be discussed: A switchable liquid crystal phase shift mask for creating sub-diffraction sized photolithographic features, and a transparent diffractive display that utilizes a switchable liquid crystal diffraction grating.

Retention-error patterns in complex alphanumeric serial-recall tasks.

PubMed

Mathy, Fabien; Varré, Jean-Stéphane

2013-01-01

We propose a new method based on an algorithm usually dedicated to DNA sequence alignment in order to both reliably score short-term memory performance on immediate serial-recall tasks and analyse retention-error patterns. There can be considerable confusion on how performance on immediate serial list recall tasks is scored, especially when the to-be-remembered items are sampled with replacement. We discuss the utility of sequence-alignment algorithms to compare the stimuli to the participants' responses. The idea is that deletion, substitution, translocation, and insertion errors, which are typical in DNA, are also typical putative errors in short-term memory (respectively omission, confusion, permutation, and intrusion errors). We analyse four data sets in which alphanumeric lists included a few (or many) repetitions. After examining the method on two simple data sets, we show that sequence alignment offers 1) a compelling method for measuring capacity in terms of chunks when many regularities are introduced in the material (third data set) and 2) a reliable estimator of individual differences in short-term memory capacity. This study illustrates the difficulty of arriving at a good measure of short-term memory performance, and also attempts to characterise the primary factors underpinning remembering and forgetting.

Cellular and Nuclear Alignment Analysis for Determining Epithelial Cell Chirality

PubMed Central

Raymond, Michael J.; Ray, Poulomi; Kaur, Gurleen; Singh, Ajay V.; Wan, Leo Q.

2015-01-01

Left-right (LR) asymmetry is a biologically conserved property in living organisms that can be observed in the asymmetrical arrangement of organs and tissues and in tissue morphogenesis, such as the directional looping of the gastrointestinal tract and heart. The expression of LR asymmetry in embryonic tissues can be appreciated in biased cell alignment. Previously an in vitro chirality assay was reported by patterning multiple cells on microscale defined geometries and quantified the cell phenotype–dependent LR asymmetry, or cell chirality. However, morphology and chirality of individual cells on micropatterned surfaces has not been well characterized. Here, a Python-based algorithm was developed to identify and quantify immunofluorescence stained individual epithelial cells on multicellular patterns. This approach not only produces results similar to the image intensity gradient-based method reported previously, but also can capture properties of single cells such as area and aspect ratio. We also found that cell nuclei exhibited biased alignment. Around 35% cells were misaligned and were typically smaller and less elongated. This new imaging analysis approach is an effective tool for measuring single cell chirality inside multicellular structures and can potentially help unveil biophysical mechanisms underlying cellular chiral bias both in vitro and in vivo. PMID:26294010

4 channel × 10 Gb/s bidirectional optical subassembly using silicon optical bench with precise passive optical alignment.

PubMed

Kang, Eun Kyu; Lee, Yong Woo; Ravindran, Sooraj; Lee, Jun Ki; Choi, Hee Ju; Ju, Gun Wu; Min, Jung Wook; Song, Young Min; Sohn, Ik-Bu; Lee, Yong Tak

2016-05-16

We demonstrate an advanced structure for optical interconnect consisting of 4 channel × 10 Gb/s bidirectional optical subassembly (BOSA) formed using silicon optical bench (SiOB) with tapered fiber guiding holes (TFGHs) for precise and passive optical alignment of vertical-cavity surface-emitting laser (VCSEL)-to-multi mode fiber (MMF) and MMF-to-photodiode (PD). The co-planar waveguide (CPW) transmission line (Tline) was formed on the backside of silicon substrate to reduce the insertion loss of electrical data signal. The 4 channel VCSEL and PD array are attached at the end of CPW Tline using a flip-chip bonder and solder pad. The 12-channel ribbon fiber is simply inserted into the TFGHs of SiOB and is passively aligned to the VCSEL and PD in which no additional coupling optics are required. The fabricated BOSA shows high coupling efficiency and good performance with the clearly open eye patterns and a very low bit error rate of less than 10^-12 order at a data rate of 10 Gb/s with a PRBS pattern of 2³¹-1.

Alignment of human cardiomyocytes on laser patterned biphasic core/shell nanowire assemblies

NASA Astrophysics Data System (ADS)

Kiefer, Karin; Lee, Juseok; Haidar, Ayman; Martinez Miró, Marina; Akkan, Cagri Kaan; Veith, Michael; Cenk Aktas, Oral; Abdul-Khaliq, Hashim

2014-12-01

The management of end stage heart failure patients is only possible by heart transplantation or by the implantation of artificial hearts as a bridge for later transplantation. However, these therapeutic strategies are limited by a lack of donor hearts and by the associated complications, such as coagulation and infection, due to the used artificial mechanical circulatory assist devices. Therefore, new strategies for myocardial regenerative approaches are under extensive research to produce contractile myocardial tissue in the future to replace non-contractile myocardial ischemic and scarred tissue. Different approaches, such as cell transplantation, have been studied intensively. Although successful approaches have been observed, there are still limitations to the application. It is envisaged that myocardial tissue engineering can be used to help replace infarcted non-contractile tissue. The developed tissue should later mimic the aligned fibrillar structure of the extracellular matrix and provide important guidance cues for the survival, function and the needed orientation of cardiomyocytes. Nanostructured surfaces have been tested to provide a guided direction that cells can follow. In the present study, the cellular adhesion/alignment of human cardiomyocytes and the biocompatibility have been investigated after cultivation on different laser-patterned nanowires compared with unmodified nanowires. As a result, the nanostructured surfaces possessed good biocompatibility before and after laser modification. The laser-induced scalability of the pattern enabled the growth and orientation of the adhered myocardial tissue. Such approaches may be used to modify the surface of potential scaffolds to develop myocardial contractile tissue in the future.

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

PubMed

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

2012-11-27

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

Manipulating mammalian cell morphologies using chemical-mechanical polished integrated circuit chips

NASA Astrophysics Data System (ADS)

Moussa, Hassan I.; Logan, Megan; Siow, Geoffrey C.; Phann, Darron L.; Rao, Zheng; Aucoin, Marc G.; Tsui, Ting Y.

2017-12-01

Tungsten chemical-mechanical polished integrated circuits were used to study the alignment and immobilization of mammalian (Vero) cells. These devices consist of blanket silicon oxide thin films embedded with micro- and nano-meter scale tungsten metal line structures on the surface. The final surfaces are extremely flat and smooth across the entire substrate, with a roughness in the order of nanometers. Vero cells were deposited on the surface and allowed to adhere. Microscopy examinations revealed that cells have a strong preference to adhere to tungsten over silicon oxide surfaces with up to 99% of cells adhering to the tungsten portion of the surface. Cells self-aligned and elongated into long threads to maximize contact with isolated tungsten lines as thin as 180 nm. The orientation of the Vero cells showed sensitivity to the tungsten line geometric parameters, such as line width and spacing. Up to 93% of cells on 10 μm wide comb structures were aligned within ± 20° of the metal line axis. In contrast, only 22% of cells incubated on 0.18 μm comb patterned tungsten lines were oriented within the same angular interval. This phenomenon is explained using a simple model describing cellular geometry as a function of pattern width and spacing, which showed that cells will rearrange their morphology to maximize their contact to the embedded tungsten. Finally, it was discovered that the materials could be reused after cleaning the surfaces, while maintaining cell alignment capability.

Manipulating mammalian cell morphologies using chemical-mechanical polished integrated circuit chips.

PubMed

Moussa, Hassan I; Logan, Megan; Siow, Geoffrey C; Phann, Darron L; Rao, Zheng; Aucoin, Marc G; Tsui, Ting Y

2017-01-01

Tungsten chemical-mechanical polished integrated circuits were used to study the alignment and immobilization of mammalian (Vero) cells. These devices consist of blanket silicon oxide thin films embedded with micro- and nano-meter scale tungsten metal line structures on the surface. The final surfaces are extremely flat and smooth across the entire substrate, with a roughness in the order of nanometers. Vero cells were deposited on the surface and allowed to adhere. Microscopy examinations revealed that cells have a strong preference to adhere to tungsten over silicon oxide surfaces with up to 99% of cells adhering to the tungsten portion of the surface. Cells self-aligned and elongated into long threads to maximize contact with isolated tungsten lines as thin as 180 nm. The orientation of the Vero cells showed sensitivity to the tungsten line geometric parameters, such as line width and spacing. Up to 93% of cells on 10 μm wide comb structures were aligned within ± 20° of the metal line axis. In contrast, only ~22% of cells incubated on 0.18 μm comb patterned tungsten lines were oriented within the same angular interval. This phenomenon is explained using a simple model describing cellular geometry as a function of pattern width and spacing, which showed that cells will rearrange their morphology to maximize their contact to the embedded tungsten. Finally, it was discovered that the materials could be reused after cleaning the surfaces, while maintaining cell alignment capability.

Manipulating mammalian cell morphologies using chemical-mechanical polished integrated circuit chips

PubMed Central

Moussa, Hassan I.; Logan, Megan; Siow, Geoffrey C.; Phann, Darron L.; Rao, Zheng; Aucoin, Marc G.; Tsui, Ting Y.

2017-01-01

Abstract Tungsten chemical-mechanical polished integrated circuits were used to study the alignment and immobilization of mammalian (Vero) cells. These devices consist of blanket silicon oxide thin films embedded with micro- and nano-meter scale tungsten metal line structures on the surface. The final surfaces are extremely flat and smooth across the entire substrate, with a roughness in the order of nanometers. Vero cells were deposited on the surface and allowed to adhere. Microscopy examinations revealed that cells have a strong preference to adhere to tungsten over silicon oxide surfaces with up to 99% of cells adhering to the tungsten portion of the surface. Cells self-aligned and elongated into long threads to maximize contact with isolated tungsten lines as thin as 180 nm. The orientation of the Vero cells showed sensitivity to the tungsten line geometric parameters, such as line width and spacing. Up to 93% of cells on 10 μm wide comb structures were aligned within ± 20° of the metal line axis. In contrast, only ~22% of cells incubated on 0.18 μm comb patterned tungsten lines were oriented within the same angular interval. This phenomenon is explained using a simple model describing cellular geometry as a function of pattern width and spacing, which showed that cells will rearrange their morphology to maximize their contact to the embedded tungsten. Finally, it was discovered that the materials could be reused after cleaning the surfaces, while maintaining cell alignment capability. PMID:29152017

Efficient color-tunable multiexcitonic dual wavelength emission from Type II semiconductor tetrapods.

PubMed

Wu, Wen-Ya; Li, Mingjie; Lian, Jie; Wu, Xiangyang; Yeow, Edwin K L; Jhon, Mark H; Chan, Yinthai

2014-09-23

We synthesized colloidal InP/ZnS seeded CdS tetrapods by harnessing the structural stability of the InP/ZnS seed nanocrystals at the high reaction temperatures needed to grow the CdS arms. Because of an unexpected Type II band alignment at the interface of the InP/ZnS core and CdS arms that enhanced the occurrence of radiative excitonic recombination in CdS, these tetrapods were found to be capable of exhibiting highly efficient multiexcitonic dual wavelength emission of equal intensity at spectrally distinct wavelengths of ∼485 and ∼675 nm. Additionally, the Type II InP/ZnS seeded CdS tetrapods displayed a wider range of pump-dependent emission color-tunability (from red to white to blue) within the context of a CIE 1931 chromaticity diagram and possessed higher photostability due to suppressed multiexcitonic Auger recombination when compared to conventional Type I CdSe seeded CdS tetrapods. By employing time-resolved spectroscopy measurements, we were able to attribute the wide emission color-tunability to the large valence band offset between InP and CdS. This work highlights the importance of band alignment in the synthetic design of semiconductor nanoheterostructures, which can exhibit color-tunable multiwavelength emission with high efficiency and photostability.

Effect of Ground Layer Patterns with Slits on Conducted Noise Currents from Printed Circuit Board

NASA Astrophysics Data System (ADS)

Maeno, Tsuyoshi; Unou, Takanori; Ichikawa, Kouji; Fujiwara, Osamu

Electromagnetic disturbances for vehicle-mounted radios can be caused by conducted noise currents that flows out from electronic equipment for vehicles to wire-harnesses. In this paper, for reducing the conducted noise currents from electronic equipment for vehicles, we made a simulation and experiment on how ground patterns affect the noise currents from three-layer printed circuit boards (PCBs) with slit-types and plane-type ground patterns. As a result, we could confirm that slits on a ground pattern allow conducted noise currents to flow out from PCBs to wire-harnesses. For the PCBs with plane-type ground and one of three slit-type patterns, on the other hand, both the simulation and examination showed that resonance phenomena occur at unexpected low-frequencies. A circuit analysis revealed that the above phenomena can be caused by the imbalance of a bridge circuit consisting of the trace circuits on the PCB.

MCAW-DB: A glycan profile database capturing the ambiguity of glycan recognition patterns.

PubMed

Hosoda, Masae; Takahashi, Yushi; Shiota, Masaaki; Shinmachi, Daisuke; Inomoto, Renji; Higashimoto, Shinichi; Aoki-Kinoshita, Kiyoko F

2018-05-11

Glycan-binding protein (GBP) interaction experiments, such as glycan microarrays, are often used to understand glycan recognition patterns. However, oftentimes the interpretation of glycan array experimental data makes it difficult to identify discrete GBP binding patterns due to their ambiguity. It is known that lectins, for example, are non-specific in their binding affinities; the same lectin can bind to different monosaccharides or even different glycan structures. In bioinformatics, several tools to mine the data generated from these sorts of experiments have been developed. These tools take a library of predefined motifs, which are commonly-found glycan patterns such as sialyl-Lewis X, and attempt to identify the motif(s) that are specific to the GBP being analyzed. In our previous work, as opposed to using predefined motifs, we developed the Multiple Carbohydrate Alignment with Weights (MCAW) tool to visualize the state of the glycans being recognized by the GBP under analysis. We previously reported on the effectiveness of our tool and algorithm by analyzing several glycan array datasets from the Consortium of Functional Glycomics (CFG). In this work, we report on our analysis of 1081 data sets which we collected from the CFG, the results of which we have made publicly and freely available as a database called MCAW-DB. We introduce this database, its usage and describe several analysis results. We show how MCAW-DB can be used to analyze glycan-binding patterns of GBPs amidst their ambiguity. For example, the visualization of glycan-binding patterns in MCAW-DB show how they correlate with the concentrations of the samples used in the array experiments. Using MCAW-DB, the patterns of glycans found to bind to various GBP-glycan binding proteins are visualized, indicating the binding "environment" of the glycans. Thus, the ambiguity of glycan recognition is numerically represented, along with the patterns of monosaccharides surrounding the binding region. The profiles in MCAW-DB could potentially be used as predictors of affinity of unknown or novel glycans to particular GBPs by comparing how well they match the existing profiles for those GBPs. Moreover, as the glycan profiles of diseased tissues become available, glycan alignments could also be used to identify glycan biomarkers unique to that tissue. Databases of these alignments may be of great use for drug discovery. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

PubMed Central

2013-01-01

Background It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enough for searching large sequence databases because of the high computational costs of the underlying sequence-structure alignment problem. Results We present new fast index-based and online algorithms for approximate matching of RNA sequence-structure patterns supporting a full set of edit operations on single bases and base pairs. Our methods efficiently compute semi-global alignments of structural RNA patterns and substrings of the target sequence whose costs satisfy a user-defined sequence-structure edit distance threshold. For this purpose, we introduce a new computing scheme to optimally reuse the entries of the required dynamic programming matrices for all substrings and combine it with a technique for avoiding the alignment computation of non-matching substrings. Our new index-based methods exploit suffix arrays preprocessed from the target database and achieve running times that are sublinear in the size of the searched sequences. To support the description of RNA molecules that fold into complex secondary structures with multiple ordered sequence-structure patterns, we use fast algorithms for the local or global chaining of approximate sequence-structure pattern matches. The chaining step removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our improved online algorithm is faster than the best previous method by up to factor 45. Our best new index-based algorithm achieves a speedup of factor 560. Conclusions The presented methods achieve considerable speedups compared to the best previous method. This, together with the expected sublinear running time of the presented index-based algorithms, allows for the first time approximate matching of RNA sequence-structure patterns in large sequence databases. Beyond the algorithmic contributions, we provide with RaligNAtor a robust and well documented open-source software package implementing the algorithms presented in this manuscript. The RaligNAtor software is available at http://www.zbh.uni-hamburg.de/ralignator. PMID:23865810

Identification of Abnormal System Noise Temperature Patterns in Deep Space Network Antennas Using Neural Network Trained Fuzzy Logic

NASA Technical Reports Server (NTRS)

Lu, Thomas; Pham, Timothy; Liao, Jason

2011-01-01

This paper presents the development of a fuzzy logic function trained by an artificial neural network to classify the system noise temperature (SNT) of antennas in the NASA Deep Space Network (DSN). The SNT data were classified into normal, marginal, and abnormal classes. The irregular SNT pattern was further correlated with link margin and weather data. A reasonably good correlation is detected among high SNT, low link margin and the effect of bad weather; however we also saw some unexpected non-correlations which merit further study in the future.

An intriguing high performance liquid chromatogram of a double heterozygosity for Hb Q-India/Hb D-Punjab.

PubMed

Badyal, Rama Kumari; Chhabra, Sanjeev; Sharma, Prashant; Das, Reena

2014-01-01

Cation exchange high performance liquid chromatography (HPLC) is commonly utilized as the first method of screening for thalassemias and hemoglobinopathies worldwide. This method of diagnosis requires knowledge of the clinical background and complete blood counts as well as skill and experience in interpreting the sometimes complex results produced. An asymptomatic 27-year-old pregnant North Indian woman was found to have a highly unusual chromatographic pattern with multiple unexpected peaks during routine antenatal screening. Most concerning was a C-window peak as Hb C (HBB: c.19G>A) is rare in ethnic Asian Indian populations. Cellulose acetate electrophoresis at alkaline pH (8.6) and parental screening were performed. These revealed the correct diagnosis to be a double heterozygosity for Hb Q-India (HBA1: c.193G>C) (an uncommon asymptomatic α-globin chain variant) plus Hb D-Punjab (HBB: c.364G>C) (a β-globin chain variant that is common in this region and is asymptomatic in the heterozygous state). The unexpected C-window peak was the hybrid of the abnormal α-Q-India and β-D-Punjab globin chains. Another small peak was explained as a variant Hb A2 formed by the combination of α-Q-India and δ-globin chains. Hematopathologists should be cognizant of the complex pattern resulting from coinheritance of both α- and β-globin structural variants. Second-line testing and parental testing are invaluable in resolving unknown peaks, especially if rare or unexpected variants are being considered. Although both Hb Q-India and Hb D-Punjab are relatively common in northwestern India, to the best of our knowledge, only two recent reports describe a total of three cases of such diagnostically puzzling coinheritance.

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

PubMed

Tondon, Abhishek; Kaunas, Roland

2014-01-01

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

Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria

PubMed Central

Balagam, Rajesh; Igoshin, Oleg A.

2015-01-01

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

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

Controlling orientational order in block copolymers using low-intensity magnetic fields

PubMed Central

Choo, Youngwoo; Kawabata, Kohsuke; Kaufman, Gilad; Feng, Xunda; Di, Xiaojun; Rokhlenko, Yekaterina; Mahajan, Lalit H.; Ndaya, Dennis; Kasi, Rajeswari M.

2017-01-01

The interaction of fields with condensed matter during phase transitions produces a rich variety of physical phenomena. Self-assembly of liquid crystalline block copolymers (LC BCPs) in the presence of a magnetic field, for example, can result in highly oriented microstructures due to the LC BCP’s anisotropic magnetic susceptibility. We show that such oriented mesophases can be produced using low-intensity fields (<0.5 T) that are accessible using permanent magnets, in contrast to the high fields (>4 T) and superconducting magnets required to date. Low-intensity field alignment is enabled by the addition of labile mesogens that coassemble with the system’s nematic and smectic A mesophases. The alignment saturation field strength and alignment kinetics have pronounced dependences on the free mesogen concentration. Highly aligned states with orientation distribution coefficients close to unity were obtained at fields as small as 0.2 T. This remarkable field response originates in an enhancement of alignment kinetics due to a reduction in viscosity, and increased magnetostatic energy due to increases in grain size, in the presence of labile mesogens. These developments provide routes for controlling structural order in BCPs, including the possibility of producing nontrivial textures and patterns of alignment by locally screening fields using magnetic nanoparticles. PMID:29078379

ERP correlates of unexpected word forms in a picture–word study of infants and adults

PubMed Central

Duta, M.D.; Styles, S.J.; Plunkett, K.

2012-01-01

We tested 14-month-olds and adults in an event-related potentials (ERPs) study in which pictures of familiar objects generated expectations about upcoming word forms. Expected word forms labelled the picture (word condition), while unexpected word forms mismatched by either a small deviation in word medial vowel height (mispronunciation condition) or a large deviation from the onset of the first speech segment (pseudoword condition). Both infants and adults showed sensitivity to both types of unexpected word form. Adults showed a chain of discrete effects: positivity over the N1 wave, negativity over the P2 wave (PMN effect) and negativity over the N2 wave (N400 effect). Infants showed a similar pattern, including a robust effect similar to the adult P2 effect. These observations were underpinned by a novel visualisation method which shows the dynamics of the ERP within bands of the scalp over time. The results demonstrate shared processing mechanisms across development, as even subtle deviations from expected word forms were indexed in both age groups by a reduction in the amplitude of characteristic waves in the early auditory evoked potential. PMID:22483072

Some See It, Some Don’t: Exploring the Relation between Inattentional Blindness and Personality Factors

PubMed Central

Kreitz, Carina; Schnuerch, Robert; Gibbons, Henning; Memmert, Daniel

2015-01-01

Human awareness is highly limited, which is vividly demonstrated by the phenomenon that unexpected objects go unnoticed when attention is focused elsewhere (inattentional blindness). Typically, some people fail to notice unexpected objects while others detect them instantaneously. Whether this pattern reflects stable individual differences is unclear to date. In particular, hardly anything is known about the influence of personality on the likelihood of inattentional blindness. To fill this empirical gap, we examined the role of multiple personality factors, namely the Big Five, BIS/BAS, absorption, achievement motivation, and schizotypy, in these failures of awareness. In a large-scale sample (N = 554), susceptibility to inattentional blindness was associated with a low level of openness to experience and marginally with a low level of achievement motivation. However, in a multiple regression analysis, only openness emerged as an independent, negative predictor. This suggests that the general tendency to be open to experience extends to the domain of perception. Our results complement earlier work on the possible link between inattentional blindness and personality by demonstrating, for the first time, that failures to consciously perceive unexpected objects reflect individual differences on a fundamental dimension of personality. PMID:26011567

Minimally invasive corticotomy in orthodontics using a three-dimensional printed CAD/CAM surgical guide.

PubMed

Cassetta, M; Giansanti, M; Di Mambro, A; Calasso, S; Barbato, E

2016-09-01

The aim of this prospective study was to evaluate the effectiveness of an innovative, minimally invasive, flapless corticotomy procedure in orthodontics. The STROBE guidelines were followed. Ten patients with severe dental crowding and a class I molar relationship were selected to receive orthodontic treatment with clear aligners and corticotomy-facilitated orthodontics. The mean age of these patients was 21 years (range 17-28, standard deviation 6.08 years); the male to female ratio was 2:1. The main outcome was a reduction in the total treatment time to correct dental crowding. The secondary outcomes were periodontal index changes, the degree of root resorption, and patient perceptions of the method used, assessed using the short-form Oral Health Impact Profile (OHIP-14). The occurrence of early surgical complications or unexpected events was also recorded. All patients completed the treatment to correct dental crowding. The average treatment time was reduced by two-thirds. The procedure did not significantly modify the periodontal indices or oral health-related quality of life. No early surgical complications or unexpected events were observed. In short, the results indicate that this new procedure is safe and accelerates tooth movement without periodontal complications or discomfort. However, the efficacy of this procedure must be confirmed in controlled clinical trials. Copyright © 2016 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Ordered to isotropic morphology transition in pattern-directed dewetting of polymer thin films on substrates with different feature heights.

PubMed

Roy, Sudeshna; Mukherjee, Rabibrata

2012-10-24

Controlled dewetting of a thin polymer film on a topographically patterned substrate is an interesting approach for aligning isotropic dewetted structures. In this article, we investigate the influence of substrate feature height (H(S)) on the dewetting pathway and final pattern morphology by studying the dewetting of polystyrene (PS) thin films on grating substrates with identical periodicity (λ(P) = 1.5 μm), but H(S) varying between 10 nm and 120 nm. We identify four distinct categories of final dewetted morphology, with different extent of ordering: (1) array of aligned droplets (H(S) ≈ 120 nm); (2) aligned undulating ribbons (H(S) ≈ 70-100 nm); (3) multilength scale structures with coexisting large droplets uncorrelated to the substrate and smaller droplets/ribbons aligned along the stripes (H(S) ≈ 40-60 nm); and (4) large droplets completely uncorrelated to the substrate (H(S) < 25 nm). The distinct morphologies across the categories are attributed to two major factors: (a) whether the as-cast film is continuous (H(S)≤ 80 nm) or discontinuous (H(S)≥ 100 nm) and (b) in case of a continuous film, whether the film ruptures along each substrate stripe (H(S)≥ 70 nm) or with nucleation of random holes that are not correlated to the substrate features (H(S)≤ 60 nm). While the ranges of H(S) values indicated in the parentheses are valid for PS films with an equivalent thickness (h(E)) ≈ 50.3 nm on a flat substrate, a change in h(E) merely alters the cut-off values of H(S), as the final dewetted morphologies and transition across categories remain generically unaltered. We finally show that the structures obtained by dewetting on different H(S) substrates exhibits different levels of hydrophobicity because of combined spatial variation of chemical and topographic contrast along the surface. Thus, the work reported in this article can find potential application in fabricating surfaces with controlled wettability.

Technological innovations for a sustainable business model in the semiconductor industry

NASA Astrophysics Data System (ADS)

Levinson, Harry J.

2014-09-01

Increasing costs of wafer processing, particularly for lithographic processes, have made it increasingly difficult to achieve simultaneous reductions in cost-per-function and area per device. Multiple patterning techniques have made possible the fabrication of circuit layouts below the resolution limit of single optical exposures but have led to significant increases in the costs of patterning. Innovative techniques, such as self-aligned double patterning (SADP) have enabled good device performance when using less expensive patterning equipment. Other innovations have directly reduced the cost of manufacturing. A number of technical challenges must be overcome to enable a return to single-exposure patterning using short wavelength optical techniques, such as EUV patterning.

Increased endothelial cell adhesion and elongation on micron-patterned nano-rough poly(dimethylsiloxane) films.

PubMed

Ranjan, Ashwini; Webster, Thomas J

2009-07-29

The success of synthetic vascular grafts is largely determined by their ability to promote vital endothelial cell functions such as adhesion, alignment, proliferation, and extracellular matrix (ECM) deposition. Developing such biomaterials requires the design and fabrication of materials that mimic select properties of native extracellular matrices. Furthermore, cells of the native endothelium have elongated and aligned morphology in the direction of blood flow, yet few materials promote this type of morphology initially, but rather rely on blood flow to orient endothelial cells. Therefore, the objective of this in vitro study was to design a biomaterial that mimics the conditions of the micro- and nano-environment of vascular intima tissue suitable for endothelial cell adhesion and elongation to improve the efficacy of small synthetic vascular grafts. Towards this end, patterned poly(dimethylsiloxane) (PDMS) films consisting of periodic arrays of nano-grooves (500 nm), with spacings ranging from 22 to 80 microm, and alternating nano- and micron roughness were fabricated using a novel electron beam physical vapor deposition method followed by polymer casting. By varying pattern spacing, the area of micron- and nano-rough surface was controlled. In vitro rat aortic endothelial cell adhesion and elongation studies indicated that endothelial cell function was enhanced on patterned PDMS surfaces with the widest spacing and greatest surface area of nano-roughness, as compared to more narrow pattern spacings and non-patterned PDMS surfaces. Specifically, endothelial cells adherent on PDMS patterned films of the widest spacing (greatest nano-rough area) displayed almost twice as much elongation as cells on non-patterned surfaces. For these reasons, the present study highlighted design criteria (the use of micron patterns of nano-features on PDMS) that may contribute to the intelligent design of new-generation vascular grafts.

Enhancement of Water Evaporation on Solid Surfaces with Nanoscale Hydrophobic-Hydrophilic Patterns.

PubMed

Wan, Rongzheng; Wang, Chunlei; Lei, Xiaoling; Zhou, Guoquan; Fang, Haiping

2015-11-06

Using molecular dynamics simulations, we show that the evaporation of nanoscale water on hydrophobic-hydrophilic patterned surfaces is unexpectedly faster than that on any surfaces with uniform wettability. The key to this phenomenon is that, on the patterned surface, the evaporation rate from the hydrophilic region only slightly decreases due to the correspondingly increased water thickness; meanwhile, a considerable number of water molecules evaporate from the hydrophobic region despite the lack of water film. Most of the evaporated water from the hydrophobic region originates from the hydrophilic region by diffusing across the contact lines. Further analysis shows that the evaporation rate from the hydrophobic region is approximately proportional to the total length of the contact lines.

Fast and accurate phylogeny reconstruction using filtered spaced-word matches

PubMed Central

Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-01-01

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

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

PubMed

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

2017-04-01

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

Making a Back-Illuminated Imager with Back-Side Contact and Alignment Markers

NASA Technical Reports Server (NTRS)

Pain, Bedabrata

2008-01-01

A design modification and a fabrication process that implements the modification have been conceived to solve two problems encountered in the development of back-illuminated, back-sidethinned complementary metal oxide/ semiconductor (CMOS) image-detector integrated circuits. The two problems are (1) how to form metal electrical-contact pads on the back side that are electrically connected through the thickness in proper alignment with electrical contact points on the front side and (2) how to provide alignment keys on the back side to ensure proper registration of backside optical components (e.g., microlenses and/or color filters) with the front-side pixel pattern. The essence of the design modification is to add metal plugs that extend from the desired front-side locations through the thickness and protrude from the back side of the substrate. The plugs afford the required front-to-back electrical conduction, and the protrusions of the plugs serve as both the alignment keys and the bases upon which the back-side electrical-contact pads can be formed.

DNATagger, colors for codons.

PubMed

Scherer, N M; Basso, D M

2008-09-16

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

Scalable quantum computer architecture with coupled donor-quantum dot qubits

DOEpatents

Schenkel, Thomas; Lo, Cheuk Chi; Weis, Christoph; Lyon, Stephen; Tyryshkin, Alexei; Bokor, Jeffrey

2014-08-26

A quantum bit computing architecture includes a plurality of single spin memory donor atoms embedded in a semiconductor layer, a plurality of quantum dots arranged with the semiconductor layer and aligned with the donor atoms, wherein a first voltage applied across at least one pair of the aligned quantum dot and donor atom controls a donor-quantum dot coupling. A method of performing quantum computing in a scalable architecture quantum computing apparatus includes arranging a pattern of single spin memory donor atoms in a semiconductor layer, forming a plurality of quantum dots arranged with the semiconductor layer and aligned with the donor atoms, applying a first voltage across at least one aligned pair of a quantum dot and donor atom to control a donor-quantum dot coupling, and applying a second voltage between one or more quantum dots to control a Heisenberg exchange J coupling between quantum dots and to cause transport of a single spin polarized electron between quantum dots.

Hydrodynamic Equations for Flocking Models without Velocity Alignment

NASA Astrophysics Data System (ADS)

Peruani, Fernando

2017-10-01

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

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures.

PubMed

Goldenberg, Ofir; Erez, Elana; Nimrod, Guy; Ben-Tal, Nir

2009-01-01

ConSurf-DB is a repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using standard methods. The evolutionary conservation of each amino acid position in the alignment was calculated using the Rate4Site algorithm, implemented in the ConSurf web server. The algorithm takes into account the phylogenetic relations between the aligned proteins and the stochastic nature of the evolutionary process explicitly. Rate4Site assigns a conservation level for each position in the multiple sequence alignment using an empirical Bayesian inference. Visual inspection of the conservation patterns on the 3D structure often enables the identification of key residues that comprise the functionally important regions of the protein. The repository is updated with the latest PDB entries on a monthly basis and will be rebuilt annually. ConSurf-DB is available online at http://consurfdb.tau.ac.il/

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures

PubMed Central

Goldenberg, Ofir; Erez, Elana; Nimrod, Guy; Ben-Tal, Nir

2009-01-01

ConSurf-DB is a repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using standard methods. The evolutionary conservation of each amino acid position in the alignment was calculated using the Rate4Site algorithm, implemented in the ConSurf web server. The algorithm takes into account the phylogenetic relations between the aligned proteins and the stochastic nature of the evolutionary process explicitly. Rate4Site assigns a conservation level for each position in the multiple sequence alignment using an empirical Bayesian inference. Visual inspection of the conservation patterns on the 3D structure often enables the identification of key residues that comprise the functionally important regions of the protein. The repository is updated with the latest PDB entries on a monthly basis and will be rebuilt annually. ConSurf-DB is available online at http://consurfdb.tau.ac.il/ PMID:18971256

All diamond self-aligned thin film transistor

DOEpatents

Gerbi, Jennifer [Champaign, IL

2008-07-01

A substantially all diamond transistor with an electrically insulating substrate, an electrically conductive diamond layer on the substrate, and a source and a drain contact on the electrically conductive diamond layer. An electrically insulating diamond layer is in contact with the electrically conductive diamond layer, and a gate contact is on the electrically insulating diamond layer. The diamond layers may be homoepitaxial, polycrystalline, nanocrystalline or ultrananocrystalline in various combinations.A method of making a substantially all diamond self-aligned gate transistor is disclosed in which seeding and patterning can be avoided or minimized, if desired.

Toward the growth of an aligned single-layer MoS2 film.

PubMed

Kim, Daeho; Sun, Dezheng; Lu, Wenhao; Cheng, Zhihai; Zhu, Yeming; Le, Duy; Rahman, Talat S; Bartels, Ludwig

2011-09-20

Molybdenum disulfide (molybdenite) monolayer islands and flakes have been grown on a copper surface at comparatively low temperature and mild conditions through sulfur loading of the substrate using thiophenol (benzenethiol) followed by the evaporation of Mo atoms and annealing. The MoS(2) islands show a regular Moiré pattern in scanning tunneling microscopy, attesting to their atomic ordering and high quality. They are all aligned with the substrate high-symmetry directions providing for rotational-domain-free monolayer growth. © 2011 American Chemical Society

The Astronomical Orientation of Ancient Greek Temples

PubMed Central

Salt, Alun M.

2009-01-01

Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity. PMID:19936239

The astronomical orientation of ancient Greek temples.

PubMed

Salt, Alun M

2009-11-19

Despite its appearing to be a simple question to answer, there has been no consensus as to whether or not the alignments of ancient Greek temples reflect astronomical intentions. Here I present the results of a survey of archaic and classical Greek temples in Sicily and compare them with temples in Greece. Using a binomial test I show strong evidence that there is a preference for solar orientations. I then speculate that differences in alignment patterns between Sicily and Greece reflect differing pressures in the expression of ethnic identity.

Characteristic Exponent of Normal and Oblique Rolls in Homeotropically Aligned Nematic Liquid Crystal

NASA Astrophysics Data System (ADS)

Saraswati, V.; Nugroho, F.

2018-04-01

Soft-mode turbulence (SMT) is one of an experimental example of spatiotemporal chaos, observed in electroconvection system of homeotropically aligned nematic liquid crystal (NLC), due to a non-linear interaction between Nambu-Goldstone mode denoted by the C(r)- director and the convective mode q(r). There are two types of stripe patterns in the SMT, namely normal rolls (NR) and oblique rolls (OR) which separated by a point of applied frequency, called the Lifshitz frequency (f L ). We report a study of the phase transition from normal to oblique rolls by observing the patterns with an applied frequency below and beyond of fL . The temporal fluctuations of the pattern images had been analyzed using autocorrelation function. It fits with Kohlrausch Williams Watts (KWW) function, showing there is a dynamical glass-forming liquid in the transition of NR-OR regime. Also, we found a new type of defect in the NR regime which never been reported before, a dynamic defect which takes the shape of a ring first to a spot in the end.

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

PubMed Central

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

2012-01-01

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

Patterned growth of individual and multiple vertically aligned carbon nanofibers

NASA Astrophysics Data System (ADS)

Merkulov, V. I.; Lowndes, D. H.; Wei, Y. Y.; Eres, G.; Voelkl, E.

2000-06-01

The results of studies of patterned growth of vertically aligned carbon nanofibers (VACNFs) prepared by plasma-enhanced chemical vapor deposition are reported. Nickel (Ni) dots of various diameters and Ni lines with variable widths and shapes were fabricated using electron beam lithography and evaporation, and served for catalytic growth of VACNFs whose structure was determined by high resolution transmission electron microscopy. It is found that upon plasma pre-etching and heating up to 600-700 °C, thin films of Ni break into droplets which initiate the growth of VACNFs. Above a critical dot size multiple droplets are formed, and consequently multiple VACNFs grow from a single evaporated dot. For dot sizes smaller than the critical size only one droplet is formed, resulting in a single VACNF. In the case of a patterned line, the growth mechanism is similar to that from a dot. VACNFs grow along the line, and above a critical linewidth multiple VACNFs are produced across the line. The mechanism of the formation of single and multiple catalyst droplets and subsequently of VACNFs is discussed.

Spontaneous emergence of milling (vortex state) in a Vicsek-like model

NASA Astrophysics Data System (ADS)

Costanzo, A.; Hemelrijk, C. K.

2018-04-01

Collective motion is of interest to laymen and scientists in different fields. In groups of animals, many patterns of collective motion arise such as polarized schools and mills (i.e. circular motion). Collective motion can be generated in computational models of different degrees of complexity. In these models, moving individuals coordinate with others nearby. In the more complex models, individuals attract each other, aligning their headings, and avoiding collisions. Simpler models may include only one or two of these types of interactions. The collective pattern that interests us here is milling, which is observed in many animal species. It has been reproduced in the more complex models, but not in simpler models that are based only on alignment, such as the well-known Vicsek model. Our aim is to provide insight in the minimal conditions required for milling by making minimal modifications to the Vicsek model. Our results show that milling occurs when both the field of view and the maximal angular velocity are decreased. Remarkably, apart from milling, our minimal model also exhibits many of the other patterns of collective motion observed in animal groups.

Periodic Grating-like Patterns Induced by Self-Assembly of Gelator Fibres in Nematic Gels.

PubMed

Topnani, Neha B; Prutha, N; Pratibha, R

2018-03-15

Periodic orientation patterns occurring in nematic gels, revealed by optical and scanning electron microscopy, are found to be formed by spontaneous self-assembly of fibrous aggregates of a low-molecular-weight organogelator in an aligned thermotropic liquid crystal (LC). Self-organization into periodic structures is also reflected in a calorimetric study, which shows the occurrence of three thermoreversible states, namely, isotropic liquid, nematic and nematic gel. The segregation and self-assembly of the fibrous aggregates leading to pattern formation are attributed to the highly polar LC and to hydrogen bonding between gelator molecules, as shown by X-ray diffraction and vibrational spectroscopy. This study aims to investigate in detail the effect of the chemical nature and alignment of an anisotropic solvent on the morphology of the gelator fibres and the resulting gelation process. The periodic organization of LC-rich and fibre-rich regions can also provide a way to obtain templates for positioning nanoparticle arrays in an LC matrix, which can lead to novel devices. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Package for integrated optic circuit and method

DOEpatents

Kravitz, Stanley H.; Hadley, G. Ronald; Warren, Mial E.; Carson, Richard F.; Armendariz, Marcelino G.

1998-01-01

A structure and method for packaging an integrated optic circuit. The package comprises a first wall having a plurality of microlenses formed therein to establish channels of optical communication with an integrated optic circuit within the package. A first registration pattern is provided on an inside surface of one of the walls of the package for alignment and attachment of the integrated optic circuit. The package in one embodiment may further comprise a fiber holder for aligning and attaching a plurality of optical fibers to the package and extending the channels of optical communication to the fibers outside the package. In another embodiment, a fiber holder may be used to hold the fibers and align the fibers to the package. The fiber holder may be detachably connected to the package.

Multi-slice ultrasound image calibration of an intelligent skin-marker for soft tissue artefact compensation.

PubMed

Masum, M A; Pickering, M R; Lambert, A J; Scarvell, J M; Smith, P N

2017-09-06

In this paper, a novel multi-slice ultrasound (US) image calibration of an intelligent skin-marker used for soft tissue artefact compensation is proposed to align and orient image slices in an exact H-shaped pattern. Multi-slice calibration is complex, however, in the proposed method, a phantom based visual alignment followed by transform parameters estimation greatly reduces the complexity and provides sufficient accuracy. In this approach, the Hough Transform (HT) is used to further enhance the image features which originate from the image feature enhancing elements integrated into the physical phantom model, thus reducing feature detection uncertainty. In this framework, slice by slice image alignment and calibration are carried out and this provides manual ease and convenience. Copyright © 2016 Elsevier Ltd. All rights reserved.

Extracellular Recordings of Patterned Human Pluripotent Stem Cell-Derived Cardiomyocytes on Aligned Fibers.

PubMed

Li, Junjun; Minami, Itsunari; Yu, Leqian; Tsuji, Kiyotaka; Nakajima, Minako; Qiao, Jing; Suzuki, Masato; Shimono, Ken; Nakatsuji, Norio; Kotera, Hitetoshi; Liu, Li; Chen, Yong

2016-01-01

Human induced pluripotent stem cell (hiPSC) derived cardiomyocytes (CMs) hold high potential for use in drug assessment and myocardial regeneration. To create tissue-like constructs of CMs for extracellular monitoring, we placed aligned fibers (AFs) on the surface of a microelectrode array and then seeded hiPSC-CMs for subsequent monitoring for 14 days. As expected, the CMs organized into anisotropic and matured tissue and the extracellular recordings showed reduced premature beating higher signal amplitude and a higher probability of T-wave detection as compared to the culture without fibers. The CMs on the aligned fibers samples also exhibited anisotropic propagation of the field potential. These results therefore suggest that the hiPSC-CMs cultured on AFs can be used more reliably for cell based assays.

Extracellular Recordings of Patterned Human Pluripotent Stem Cell-Derived Cardiomyocytes on Aligned Fibers

PubMed Central

Minami, Itsunari; Yu, Leqian; Nakajima, Minako; Qiao, Jing; Shimono, Ken; Nakatsuji, Norio; Kotera, Hitetoshi; Chen, Yong

2016-01-01

Human induced pluripotent stem cell (hiPSC) derived cardiomyocytes (CMs) hold high potential for use in drug assessment and myocardial regeneration. To create tissue-like constructs of CMs for extracellular monitoring, we placed aligned fibers (AFs) on the surface of a microelectrode array and then seeded hiPSC-CMs for subsequent monitoring for 14 days. As expected, the CMs organized into anisotropic and matured tissue and the extracellular recordings showed reduced premature beating higher signal amplitude and a higher probability of T-wave detection as compared to the culture without fibers. The CMs on the aligned fibers samples also exhibited anisotropic propagation of the field potential. These results therefore suggest that the hiPSC-CMs cultured on AFs can be used more reliably for cell based assays. PMID:27446217

Three-dimensionally modulated anisotropic structure for diffractive optical elements created by one-step three-beam polarization holographic photoalignment

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

Kawai, Kotaro, E-mail: s135016@stn.nagaokaut.ac.jp; Sakamoto, Moritsugu; Noda, Kohei

2016-03-28

A diffractive optical element with a three-dimensional liquid crystal (LC) alignment structure for advanced control of polarized beams was fabricated by a highly efficient one-step photoalignment method. This study is of great significance because different two-dimensional continuous and complex alignment patterns can be produced on two alignment films by simultaneously irradiating an empty glass cell composed of two unaligned photocrosslinkable polymer LC films with three-beam polarized interference beam. The polarization azimuth, ellipticity, and rotation direction of the diffracted beams from the resultant LC grating widely varied depending on the two-dimensional diffracted position and the polarization states of the incident beams.more » These polarization diffraction properties are well explained by theoretical analysis based on Jones calculus.« less

Package for integrated optic circuit and method

DOEpatents

Kravitz, S.H.; Hadley, G.R.; Warren, M.E.; Carson, R.F.; Armendariz, M.G.

1998-08-04

A structure and method are disclosed for packaging an integrated optic circuit. The package comprises a first wall having a plurality of microlenses formed therein to establish channels of optical communication with an integrated optic circuit within the package. A first registration pattern is provided on an inside surface of one of the walls of the package for alignment and attachment of the integrated optic circuit. The package in one embodiment may further comprise a fiber holder for aligning and attaching a plurality of optical fibers to the package and extending the channels of optical communication to the fibers outside the package. In another embodiment, a fiber holder may be used to hold the fibers and align the fibers to the package. The fiber holder may be detachably connected to the package. 6 figs.

Effect of alignment changes on socket reaction moments during gait in transfemoral and knee-disarticulation prostheses: case series.

PubMed

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

2013-09-27

The alignment of a lower-limb prosthesis is critical to the successful prosthetic fitting and utilization by the wearer. Loads generated by the socket applied to the residual limb while walking are thought to be different in transfemoral and knee-disarticulation prostheses. The aim of this case series was to compare the socket reaction moments between transfemoral and knee-disarticulation prostheses and to investigate the effect of alignment changes on them. Two amputees, one with a transfemoral prosthesis and another with a knee-disarticulation prosthesis, participated in this study. A Smart Pyramid™ was used to measure socket reaction moments while walking under 9 selected alignment conditions; including nominally aligned, angle malalignments of 6° (flexion, extension, abduction and adduction) and translation malalignments of 15 mm (anterior, posterior, medial and lateral) of the socket relative to the foot. This study found that the pattern of the socket reaction moments was similar between transfemoral and knee-disarticulation prostheses. An extension moment in the sagittal plane and a varus moment in the coronal plane were dominant during stance under the nominally aligned condition. This study also demonstrated that alignment changes might have consistent effects on the socket reaction moments in transfemoral and knee-disarticulation prostheses. Extension and posterior translation of the socket resulted in increases in an extension moment, while abduction and lateral translation of the socket resulted in increases in a varus moment. The socket reaction moments may potentially serve as useful biomechanical parameters to evaluate alignment in transfemoral and knee-disarticulation prostheses. Copyright © 2013 Elsevier Ltd. All rights reserved.

Synthesis of (±)-amathaspiramide F and discovery of an unusual stereocontrolling element for the [2,3]-Stevens rearrangement.

PubMed

Soheili, Arash; Tambar, Uttam K

2013-10-04

A formal total synthesis of (±)-amathaspiramide F through a tandem palladium-catalyzed allylic amination/[2,3]-Stevens rearrangement is reported. The unexpected diastereoselectivity of the [2,3]-Stevens rearrangement was controlled by the substitution patterns of an aromatic ring. This discovery represents a new stereocontrolling element for [2,3]-sigmatropic rearrangements in complex molecular settings.

Rethinking the longitudinal stream temperature paradigm: region-wide comparison of thermal infrared imagery reveals unexpected complexity of river temperatures

Treesearch

Aimee H. Fullerton; Christian E. Torgersen; Joshua J. Lawler; Russell N. Faux; Ashley Steel; Timothy J. Beechie; Joseph L. Ebersole; Scott G. Leibowitz

2015-01-01

Prevailing theory suggests that stream temperature warms asymptotically in a downstream direction, beginning at the temperature of the source in the headwaters and levelling off downstream as it converges to matchmeteorological conditions.However, there have been few empirical examples of longitudinal patterns of temperature in large rivers due to a paucity of data. We...

Meta-Profiles of Gene Expression during Aging: Limited Similarities between Mouse and Human and an Unexpectedly Decreased Inflammatory Signature

PubMed Central

Swindell, William R.; Johnston, Andrew; Sun, Liou; Xing, Xianying; Fisher, Gary J.; Bulyk, Martha L.; Elder, James T.; Gudjonsson, Johann E.

2012-01-01

Background Skin aging is associated with intrinsic processes that compromise the structure of the extracellular matrix while promoting loss of functional and regenerative capacity. These processes are accompanied by a large-scale shift in gene expression, but underlying mechanisms are not understood and conservation of these mechanisms between humans and mice is uncertain. Results We used genome-wide expression profiling to investigate the aging skin transcriptome. In humans, age-related shifts in gene expression were sex-specific. In females, aging increased expression of transcripts associated with T-cells, B-cells and dendritic cells, and decreased expression of genes in regions with elevated Zeb1, AP-2 and YY1 motif density. In males, however, these effects were contrasting or absent. When age-associated gene expression patterns in human skin were compared to those in tail skin from CB6F1 mice, overall human-mouse correspondence was weak. Moreover, inflammatory gene expression patterns were not induced with aging of mouse tail skin, and well-known aging biomarkers were in fact decreased (e.g., Clec7a, Lyz1 and Lyz2). These unexpected patterns and weak human-mouse correspondence may be due to decreased abundance of antigen presenting cells in mouse tail skin with age. Conclusions Aging is generally associated with a pro-inflammatory state, but we have identified an exception to this pattern with aging of CB6F1 mouse tail skin. Aging therefore does not uniformly heighten inflammatory status across all mouse tissues. Furthermore, we identified both intercellular and intracellular mechanisms of transcriptome aging, including those that are sex- and species-specific. PMID:22413003

Abundance patterns of evolved stars with Hipparcos parallaxes and ages based on the APOGEE data base

NASA Astrophysics Data System (ADS)

Jia, Y. P.; Chen, Y. Q.; Zhao, G.; Bari, M. A.; Zhao, J. K.; Tan, K. F.

2018-01-01

We investigate the abundance patterns for four groups of stars at evolutionary phases from sub-giant to red clump (RC) and trace the chemical evolution of the disc by taking 21 individual elemental abundances from APOGEE and ages from evolutionary models with the aid of Hipparcos distances. We find that the abundances of six elements (Si, S, K, Ca, Mn and Ni) are similar from the sub-giant phase to the RC phase. In particular, we find that a group of stars with low [C/N] ratios, mainly from the second sequence of RC stars, show that there is a difference in the transfer efficiency of the C-N-O cycle between the main and the secondary RC sequences. We also compare the abundance patterns of C-N, Mg-Al and Na-O with giant stars in globular clusters from APOGEE and find that field stars follow similar patterns as M107, a metal-rich globular cluster with [M/H] ∼- 1.0, which shows that the self-enrichment mechanism represented by strong C-N, Mg-Al and Na-O anti-correlations may not be important as the metallicity reaches [M/H] > -1.0 dex. Based on the abundances of above-mentioned six elements and [Fe/H], we investigate age versus abundance relations and find some old super-metal-rich stars in our sample. Their properties of old age and being rich in metal are evidence for stellar migration. The age versus metallicity relations in low-[α/M] bins show unexpectedly positive slopes. We propose that the fresh metal-poor gas infalling on to the Galactic disc may be the precursor for this unexpected finding.

Domain alignment within ferroelectric/dielectric PbTiO 3 /SrTiO 3 superlattice nanostructures

DOE PAGES

Park, Joonkyu; Mangeri, John; Zhang, Qingteng; ...

2018-01-01

The ferroelectric domain pattern within lithographically defined PbTiO 3/SrTiO 3ferroelectric/dielectric heteroepitaxial superlattice nanostructures is strongly influenced by the edges of the structures.

Dynamical patterns in nematic active matter on a sphere

NASA Astrophysics Data System (ADS)

Henkes, Silke; Marchetti, M. Cristina; Sknepnek, Rastko

2018-04-01

Using simulations of self-propelled agents with short-range repulsion and nematic alignment, we explore the dynamical phases of a dense active nematic confined to the surface of a sphere. We map the nonequilibrium phase diagram as a function of curvature, alignment strength, and activity. Our model reproduces several phases seen in recent experiments on active microtubule bundles confined the surfaces of vesicles. At low driving, we recover the equilibrium nematic ground state with four +1 /2 defects. As the driving is increased, geodesic forces drive the transition to a polar band wrapping around an equator, with large empty spherical caps corresponding to two +1 defects at the poles. Upon further increasing activity, the bands fold onto themselves, and the system eventually transitions to a turbulent state marked by the proliferation of pairs of topological defects. We highlight the key role of the nematic persistence length in controlling pattern formation in these confined systems with positive Gaussian curvature.

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

Laser-fiber coupling by means of a silicon micro-optical bench and a self-aligned soldering process

NASA Astrophysics Data System (ADS)

Schmidt, Jan P.; Cordes, A.; Mueller, Joerg; Burkhardt, Hans

1995-02-01

The alignment of laser diodes to monomode fibers has to meet extremely close tolerances for a low coupling loss. Typically < 0.5 micrometers in lateral and vertical direction and less than two degrees in angle deviation are allowed for a coupling loss below 2 dB. Presently such close tolerances can only be met by gluing or soldering both components on separate base plates and combining them via piezoactivated alignment monitoring the output of the circuit and then gluing them using UV-hardening epoxies. Such a procedure is not very economical and not useful for mass applications. This paper presents the principle and realization of a silicon micro-optical bench for laser-fiber-coupling, which avoids the above mentioned disadvantages. The micro-optical bench is realized using well controlled plasma etching processes to transfer the guiding patterns for the laser and the fiber into the silicon substrate, keeping geometry tolerances below +/- 0.5 micrometers in lateral and vertical direction. Mounting the laser diode by means of a self-aligned soldering process, an additional contribution to the precise alignment of the laser is further improved.

Surface-Constrained Volumetric Brain Registration Using Harmonic Mappings

PubMed Central

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

2015-01-01

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

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.

A study of substrate-liquid crystal interaction

NASA Astrophysics Data System (ADS)

Zhang, Baoshe

This thesis concerns the study of substrate-liquid crystal interaction from two different angles. In one approach, we used the IPS (in-plane switching) technique to investigate the liquid crystal alignment by rubbed polyimide films. The IPS mode of liquid crystal cell operation is facilitated through comb electrodes capable of producing planar electric field. We have fabricated comb electrodes with a periodicity of 2 mum in order to confine the planar electric field close to the liquid crystal-substrate interface. Through optical transmittance measurements and comparison with theoretical predictions based on the Ladau-de Gennes formalism, we found the experimental data to be consistent with the physical picture of soft anchoring, in which the liquid crystal director at the substrate interface is rotated azimuthally under the planar electric field. As a result, we were able to obtain the azimuthal anchoring strength as a fitting parameter of the theory. This part of the thesis thus presents evidence(s) for director switching at the liquid crystal-substrate interface, as well as a method for measuring the azimuthal anchoring strength through optical means. In the second approach, we used nano-lithographic technique to fabricate textured two dimensional periodic patterns on silicon wafers, and examined the resulting liquid crystal alignment effect of such textured substrates. It was found that with decreasing periodicity, there exists an orientational transition from a state in which the liquid crystal alignment copies the substrate pattern at larger periodicity, to a state of uniform alignment at smaller periodicity. In our system, this transition occurs at a periodicity between 0.4 mum and 0.8 mum. Through theoretical simulations based on the model of competition between the elastic distortion energy and the interfacial anchoring potential, it was found that there is indeed a first-order abrupt transition when the periodicity is decreased. This is due to the fact that the elastic distortion energy scales as the inverse of the periodicity squared. Hence when the periodicity is decreased, the elastic distortion energy increases rapidly. At the critical periodicity the elastic distortion energy crosses the interfacial anchoring potential, below which the uniform alignment becomes the lower energy state. The uniform-aligned state was confirmed by the excellent theory-experiment agreement on spectral measurements, in conjunction with the optical microscope observations. In the uniform-aligned state, a large pretilt angle (35°) was obtained.

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

PubMed Central

2011-01-01

Background Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome. Methods We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays. Results Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%. We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the SLC45A3-ELK4 e4-e2 TIC to ERG-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines. Conclusions Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as MSMB-NCOA4, may play functional roles in cancer. PMID:21261984

The Association Between Visual Assessment of Quality of Movement and Three-Dimensional Analysis of Pelvis, Hip, and Knee Kinematics During a Lateral Step Down Test.

PubMed

Rabin, Alon; Portnoy, Sigal; Kozol, Zvi

2016-11-01

Rabin, A, Portnoy, S, and Kozol, Z. The association between visual assessment of quality of movement and three-dimensional analysis of pelvis, hip, and knee kinematics during a lateral step down test. J Strength Cond Res 30(11): 3204-3211, 2016-Altered movement patterns including contralateral pelvic drop, increased hip adduction, knee abduction, and external rotation have been previously implicated in several lower extremity pathologies. Although various methods exist for assessing movement patterns, real-time visual observation is the most readily available method. The purpose of this study was to determine whether differing visual ratings of trunk, pelvis, and knee alignment, as well as overall quality of movement, are associated with differences in 3-dimensional trunk, pelvis, hip, or knee kinematics during a lateral step down test. Trunk, pelvis, and knee alignment of 30 healthy participants performing the lateral step down were visually rated as "good" or "faulty" based on previously established criteria. An additional categorization of overall quality of movement as either good or moderate was performed based on the aggregate score of each individual rating criterion. Three-dimensional motion analysis of trunk, pelvis, hip, and knee kinematics was simultaneously performed. A faulty pelvis alignment displayed a greater peak contralateral pelvic drop (effect size [ES], 1.65; p < 0.01) and a greater peak hip adduction (ES: 1.04, p = 0.01) compared with participants with a good pelvis alignment. Participants with a faulty knee alignment displayed greater peak knee external rotation compared with participants with a good knee alignment (ES, 0.78; p = 0.02). Participants with an overall moderate quality of movement displayed increased peak contralateral pelvic drop (ES, 1.07; p = 0.01) and peak knee external rotation (ES, 0.72; p = 0.04) compared with those with an overall good quality of movement. Visual rating of quality of movement during a lateral step down test, as performed by an experienced physical therapist, is associated with differences in several kinematics previously implicated in various pathologies.

Impaired cellulose synthase guidance leads to stem torsion and twists phyllotactic patterns in Arabidopsis.

PubMed

Landrein, Benoît; Lathe, Rahul; Bringmann, Martin; Vouillot, Cyril; Ivakov, Alexander; Boudaoud, Arezki; Persson, Staffan; Hamant, Olivier

2013-05-20

The parallel alignment of stiff cellulose microfibrils in plant-cell walls mediates anisotropic growth. This is largely controlled by cortical microtubules, which drive the insertion and trajectory of the cellulose synthase (CESA) complex at the plasma membrane. The CESA interactive protein 1 (CSI1) acts as a physical linker between CESA and cortical microtubules. Here we show that the inflorescence stems of csi1 mutants exhibit subtle right-handed torsion. Because cellulose deposition is largely uncoupled from cortical microtubules in csi1, we hypothesize that strictly transverse deposition of microfibrils in the wild-type is replaced by a helical orientation of uniform handedness in the mutant and that the helical microfibril alignment generates torsion. Interestingly, both elastic and viscous models for an expanding cell predict that a net helical orientation of microfibrils gives rise to a torque. We indeed observed tilted microfibrils in csi1 cells, and the torsion was almost absent in a csi1 prc1 background with impaired cellulose synthesis. In addition, the stem torsion led to a novel bimodal and robust phyllotactic pattern in the csi1 mutant, illustrating how growth perturbations can replace one robust mathematical pattern with a different, equally robust pattern. Copyright © 2013 Elsevier Ltd. All rights reserved.

Stripe-like Clay Nanotubes Patterns in Glass Capillary Tubes for Capture of Tumor Cells.

PubMed

Liu, Mingxian; He, Rui; Yang, Jing; Zhao, Wei; Zhou, Changren

2016-03-01

Here, we used capillary tubes to evaporate an aqueous dispersion of halloysite nanotubes (HNTs) in a controlled manner to prepare a patterned surface with ordered alignment of the nanotubes . Sodium polystyrenesulfonate (PSS) was added to improve the surface charges of the tubes. An increased negative charge of HNTs is realized by PSS coating (from -26.1 mV to -52.2 mV). When the HNTs aqueous dispersion concentration is higher than 10%, liquid crystal phenomenon of the dispersion is found. A typical shear flow behavior and decreased viscosity upon shear is found when HNTs dispersions with concentrations higher than 10%. Upon drying the HNTs aqueous dispersion in capillary tubes, a regular pattern is formed in the wall of the tube. The width and spacing of the bands increase with HNTs dispersion concentration and decrease with the drying temperature for a given initial concentration. Morphology results show that an ordered alignment of HNTs is found especially for the sample of 10%. The patterned surface can be used as a model for preparing PDMS molding with regular micro-/nanostructure. Also, the HNTs rough surfaces can provide much higher tumor cell capture efficiency compared to blank glass surfaces. The HNTs ordered surfaces provide promising application for biomedical areas such as biosensors.

Predictive Feedback Can Account for Biphasic Responses in the Lateral Geniculate Nucleus

PubMed Central

Jehee, Janneke F. M.; Ballard, Dana H.

2009-01-01

Biphasic neural response properties, where the optimal stimulus for driving a neural response changes from one stimulus pattern to the opposite stimulus pattern over short periods of time, have been described in several visual areas, including lateral geniculate nucleus (LGN), primary visual cortex (V1), and middle temporal area (MT). We describe a hierarchical model of predictive coding and simulations that capture these temporal variations in neuronal response properties. We focus on the LGN-V1 circuit and find that after training on natural images the model exhibits the brain's LGN-V1 connectivity structure, in which the structure of V1 receptive fields is linked to the spatial alignment and properties of center-surround cells in the LGN. In addition, the spatio-temporal response profile of LGN model neurons is biphasic in structure, resembling the biphasic response structure of neurons in cat LGN. Moreover, the model displays a specific pattern of influence of feedback, where LGN receptive fields that are aligned over a simple cell receptive field zone of the same polarity decrease their responses while neurons of opposite polarity increase their responses with feedback. This phase-reversed pattern of influence was recently observed in neurophysiology. These results corroborate the idea that predictive feedback is a general coding strategy in the brain. PMID:19412529

Quantifying frontal plane knee motion during single limb squats: reliability and validity of 2-dimensional measures.

PubMed

Gwynne, Craig R; Curran, Sarah A

2014-12-01

Clinical assessment of lower limb kinematics during dynamic tasks may identify individuals who demonstrate abnormal movement patterns that may lead to etiology of exacerbation of knee conditions such as patellofemoral joint (PFJt) pain. The purpose of this study was to determine the reliability, validity and associated measurement error of a clinically appropriate two-dimensional (2-D) procedure of quantifying frontal plane knee alignment during single limb squats. Nine female and nine male recreationally active subjects with no history of PFJt pain had frontal plane limb alignment assessed using three-dimensional (3-D) motion analysis and digital video cameras (2-D analysis) while performing single limb squats. The association between 2-D and 3-D measures was quantified using Pearson's product correlation coefficients. Intraclass correlation coefficients (ICCs) were determined for within- and between-session reliability of 2-D data and standard error of measurement (SEM) was used to establish measurement error. Frontal plane limb alignment assessed with 2-D analysis demonstrated good correlation compared with 3-D methods (r = 0.64 to 0.78, p < 0.001). Within-session (0.86) and between-session ICCs (0.74) demonstrated good reliability for 2-D measures and SEM scores ranged from 2° to 4°. 2-D measures have good consistency and may provide a valid measure of lower limb alignment when compared to existing 3-D methods. Assessment of lower limb kinematics using 2-D methods may be an accurate and clinically useful alternative to 3-D motion analysis when identifying individuals who demonstrate abnormal movement patterns associated with PFJt pain. 2b.

Recombinant transfer in the basic genome of E. coli

DOE PAGES

Dixit, Purushottam; Studier, F. William; Pang, Tin Yau; ...

2015-07-07

An approximation to the ~4-Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ~90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single bp mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly betweenmore » genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome-pairs have one or two recombinant transfers of length ~40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kbp. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. As a result, most recombinant transfers seem likely to be due to generalized transduction by co-evolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.« less

Recombinant transfer in the basic genome of E. coli

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

Dixit, Purushottam; Studier, F. William; Pang, Tin Yau

An approximation to the ~4-Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ~90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single bp mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly betweenmore » genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome-pairs have one or two recombinant transfers of length ~40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kbp. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. As a result, most recombinant transfers seem likely to be due to generalized transduction by co-evolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.« less

Laser beam alignment and profilometry using diagnostic fluorescent safety mirrors

NASA Astrophysics Data System (ADS)

Lizotte, Todd E.

2011-03-01

There are a wide range of laser beam delivery systems in use for various purposes; including industrial and medical applications. Virtually all such beam delivery systems for practical purposes employ optical systems comprised of mirrors and lenses to shape, focus and guide the laser beam down to the material being processed. The goal of the laser beam delivery is to set the optimum parameters and to "fold" the beam path to reduce the mechanical length of the optical system, thereby allowing a physically compact system. In many cases, even a compact system can incorporate upwards of six mirrors and a comparable number of lenses all needing alignment so they are collinear. One of the major requirements for use of such systems in industry is a method of safe alignment. The alignment process requires that the aligner determine where the beam strikes each element. The aligner should also preferably be able to determine the shape or pattern of the laser beam at that point and its relative power. These alignments are further compounded in that the laser beams generated are not visible to the unaided human eye. Such beams are also often of relatively high power levels, and are thereby a significant hazard to the eyes of the aligner. Obvious an invisible beam makes it nearly impossible to align laser system without some form of optical assistance. The predominant method of visually aligning the laser beam delivery is the use of thermal paper, paper cards or fluorescing card material. The use of paper products which have limited power handling capability or coated plastics can produce significant debris and contaminants within the beam line that ultimately damage the optics. The use of the cards can also create significant laser light scatter jeopardizing the safety of the person aligning the system. This paper covers a new safety mirror design for use with at various UV and Near IR wavelengths (193 nm to 1064 nm) within laser beam delivery systems and how its use can provide benefits covering eye safety, precise alignment and beam diagnostics.

High-density patterned media fabrication using jet and flash imprint lithography

NASA Astrophysics Data System (ADS)

Ye, Zhengmao; Ramos, Rick; Brooks, Cynthia; Simpson, Logan; Fretwell, John; Carden, Scott; Hellebrekers, Paul; LaBrake, Dwayne; Resnick, Douglas J.; Sreenivasan, S. V.

2011-04-01

The Jet and Flash Imprint Lithography (J-FIL®) process uses drop dispensing of UV curable resists for high resolution patterning. Several applications, including patterned media, are better, and more economically served by a full substrate patterning process since the alignment requirements are minimal. Patterned media is particularly challenging because of the aggressive feature sizes necessary to achieve storage densities required for manufacturing beyond the current technology of perpendicular recording. In this paper, the key process steps for the application of J-FIL to pattern media fabrication are reviewed with special attention to substrate cleaning, vapor adhesion of the adhesion layer and imprint performance at >300 disk per hour. Also discussed are recent results for imprinting discrete track patterns at half pitches of 24nm and bit patterned media patterns at densities of 1 Tb/in2.

Design Pattern Mining Using Distributed Learning Automata and DNA Sequence Alignment

PubMed Central

Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

2014-01-01

Context Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. Objective This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA) and deoxyribonucleic acid (DNA) sequences alignment. Method The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. Results The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. Conclusion The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns. PMID:25243670

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

PubMed

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

2017-01-01

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

Mineral crystal alignment in mineralized fracture callus determined by 3D small-angle X-ray scattering

NASA Astrophysics Data System (ADS)

Liu, Yifei; Manjubala, Inderchand; Roschger, Paul; Schell, Hanna; Duda, Georg N.; Fratzl, Peter

2010-10-01

Callus tissue formed during bone fracture healing is a mixture of different tissue types as revealed by histological analysis. But the structural characteristics of mineral crystals within the healing callus are not well known. Since two-dimensional (2D) scanning small-angle X-ray scattering (sSAXS) patterns showed that the size and orientation of callus crystals vary both spatially and temporally [1] and 2D electron microscopic analysis implies an anisotropic property of the callus morphology, the mineral crystals within the callus are also expected to vary in size and orientation in 3D. Three-dimensional small-angle X-ray scattering (3D SAXS), which combines 2D SAXS patterns collected at different angles of sample tilting, has been previously applied to investigate bone minerals in horse radius [2] and oim/oim mouse femur/tibia [3]. We implement a similar 3D SAXS method but with a different way of data analysis to gather information on the mineral alignment in fracture callus. With the proposed accurate yet fast assessment of 3D SAXS information, it was shown that the plate shaped mineral particles in the healing callus were aligned in groups with their predominant orientations occurring as a fiber texture.

A new way of measuring wiggling pattern in SADP for 3D NAND technology

NASA Astrophysics Data System (ADS)

Mi, Jian; Chen, Ziqi; Tu, Li Ming; Mao, Xiaoming; Liu, Gong Cai; Kawada, Hiroki

2018-03-01

A new metrology method of quantitatively measuring wiggling patterns in a Self-Aligned Double Patterning (SADP) process for 2D NAND technology has been developed with a CD-SEM metrology program on images from a Review-SEM system. The metrology program provided accurate modeling of various wiggling patterns. The Review-SEM system provided a-few-micrometer-wide Field of View (FOV), which exceeds precision-guaranteed FOV of a conventional CD-SEM. The result has been effectively verified by visual inspection on vertically compressed images compared with Wiggling Index from this new method. A best-known method (BKM) system has been developed with connected HW and SW to automatically measure wiggling patterns.

The effect of concentration in the patterning of silica particles by the soft lithographic technique

NASA Astrophysics Data System (ADS)

Singh, Akanksha; Malek, Chantal Khan; Kulkarni, Sulabha K.

2008-12-01

Soft lithography provides remarkable surface patterning techniques to organize colloidal particles for a wide variety of applications. In particular, micromolding in capillaries (MIMIC) has emerged as a patterning method in the nanometer to micrometer scale in a single step by using templating and directing nanoparticles via capillary forces in the channel. The present work reports the results of the micropatterning of monodispersed silica particles of ~338 ± 2 nm size in ethanol medium, using MIMIC on silicon substrates. The effect of the concentration of silica particles on the patterning has been investigated. The patterns are well aligned and completely filled at 2 wt% concentration of silica particles.

Unexpected recovery after robotic locomotor training at physiologic stepping speed: a single-case design.

PubMed

Spiess, Martina R; Jaramillo, Jeffrey P; Behrman, Andrea L; Teraoka, Jeffrey K; Patten, Carolynn

2012-08-01

To investigate the effect of walking speed on the emergence of locomotor electromyogram (EMG) patterns in an individual with chronic incomplete spinal cord injury (SCI), and to determine whether central pattern generator activity during robotic locomotor training (RLT) transfers to volitional EMG activity during overground walking. Single-case (B-A-B; experimental treatment-withdrawal-experimental treatment) design. Freestanding rehabilitation research center. A 50-year-old man who was nonambulatory for 16 months after incomplete SCI (sub-T11). The participant completed two 6-week blocks of RLT, training 4 times per week for 30 minutes per session at walking speeds up to 5km/h (1.4m/s) over continuous bouts lasting up to 17 minutes. Surface EMG was recorded weekly during RLT and overground walking. The Walking Index for Spinal Cord Injury (WISCI-II) was assessed daily during training blocks. During week 4, reciprocal, patterned EMG emerged during RLT. EMG amplitude modulation revealed a curvilinear relationship over the range of walking speeds from 1.5 to 5km/h (1.4m/s). Functionally, the participant improved from being nonambulatory (WISCI-II 1/20), to walking overground with reciprocal stepping using knee-ankle-foot orthoses and a walker (WISCI-II 9/20). EMG was also observed during overground walking. These functional gains were maintained greater than 4 years after locomotor training (LT). Here we report an unexpected course of locomotor recovery in an individual with chronic incomplete SCI. Through RLT at physiologic walking speeds, it was possible to activate the central pattern generator even 16 months postinjury. Further, to a certain degree, improvements from RLT transferred to overground walking. Our results suggest that LT-induced changes affect the central pattern generator and allow supraspinal inputs to engage residual spinal pathways. Copyright © 2012 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

A rib-specific multimodal registration algorithm for fused unfolded rib visualization using PET/CT

NASA Astrophysics Data System (ADS)

Kaftan, Jens N.; Kopaczka, Marcin; Wimmer, Andreas; Platsch, Günther; Declerck, Jérôme

2014-03-01

Respiratory motion affects the alignment of PET and CT volumes from PET/CT examinations in a non-rigid manner. This becomes particularly apparent if reviewing fine anatomical structures such as ribs when assessing bone metastases, which frequently occur in many advanced cancers. To make this routine diagnostic task more efficient, a fused unfolded rib visualization for 18F-NaF PET/CT is presented. It allows to review the whole rib cage in a single image. This advanced visualization is enabled by a novel rib-specific registration algorithm that rigidly optimizes the local alignment of each individual rib in both modalities based on a matched filter response function. More specifically, rib centerlines are automatically extracted from CT and subsequently individually aligned to the corresponding bone-specific PET rib uptake pattern. The proposed method has been validated on 20 PET/CT scans acquired at different clinical sites. It has been demonstrated that the presented rib- specific registration method significantly improves the rib alignment without having to run complex deformable registration algorithms. At the same time, it guarantees that rib lesions are not further deformed, which may otherwise affect quantitative measurements such as SUVs. Considering clinically relevant distance thresholds, the centerline portion with good alignment compared to the ground truth improved from 60:6% to 86:7% after registration while approximately 98% can be still considered as acceptably aligned.

Effect of Sterilization Methods on Electrospun Poly(lactic acid) (PLA) Fiber Alignment for Biomedical Applications.

PubMed

Valente, T A M; Silva, D M; Gomes, P S; Fernandes, M H; Santos, J D; Sencadas, V

2016-02-10

Medically approved sterility methods should be a major concern when developing a polymeric scaffold, mainly when commercialization is envisaged. In the present work, poly(lactic acid) (PLA) fiber membranes were processed by electrospinning with random and aligned fiber alignment and sterilized under UV, ethylene oxide (EO), and γ-radiation, the most common ones for clinical applications. It was observed that UV light and γ-radiation do not influence fiber morphology or alignment, while electrospun samples treated with EO lead to fiber orientation loss and morphology changing from cylindrical fibers to ribbon-like structures, accompanied to an increase of polymer crystallinity up to 28%. UV light and γ-radiation sterilization methods showed to be less harmful to polymer morphology, without significant changes in polymer thermal and mechanical properties, but a slight increase of polymer wettability was detected, especially for the samples treated with UV radiation. In vitro results indicate that both UV and γ-radiation treatments of PLA membranes allow the adhesion and proliferation of MG 63 osteoblastic cells in a close interaction with the fiber meshes and with a growth pattern highly sensitive to the underlying random or aligned fiber orientation. These results are suggestive of the potential of both γ-radiation sterilized PLA membranes for clinical applications in regenerative medicine, especially those where customized membrane morphology and fiber alignment is an important issue.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

The cognitive nuances of surprising events: exposure to unexpected stimuli elicits firing variations in neurons of the dorsal CA1 hippocampus.

PubMed

Valenti, Ornella; Mikus, Nace; Klausberger, Thomas

2018-05-22

The ability to recognize novel situations is among the most fascinating and vital of the brain functions. A hypothesis posits that encoding of novelty is prompted by failures in expectancy, according to computation matching incoming information with stored events. Thus, unexpected changes in context are detected within the hippocampus and transferred to downstream structures, eliciting the arousal of the dopamine system. Nevertheless, the precise locus of detection is a matter of debate. The dorsal CA1 hippocampus (dCA1) appears as an ideal candidate for operating a mismatch computation and discriminating the occurrence of diverse stimuli within the same environment. In this study, we sought to determine dCA1 neuronal firing during the experience of novel stimuli embedded in familiar contexts. We performed population recordings while head-fixed mice navigated virtual environments. Three stimuli were employed, namely a novel pattern of visual cues, an odor, and a reward with enhanced valence. The encounter of unexpected events elicited profound variations in dCA1 that were assessed both as opposite rate directions and altered network connectivity. When experienced in sequence, novel stimuli elicited specific responses that often exhibited cross-sensitization. Short-latency, event-triggered responses were in accordance with the detection of novelty being computed within dCA1. We postulate that firing variations trigger neuronal disinhibition, and constitute a fundamental mechanism in the processing of unexpected events and in learning. Elucidating the mechanisms underlying detection and computation of novelty might help in understanding hippocampal-dependent cognitive dysfunctions associated with neuropathologies and psychiatric conditions.

[Individual identification of cadaver parts after a bomb explosion using oligonucleotide fingerprinting by (GTG)5].

PubMed

Kondo, T; Ohshima, T

1998-01-01

A blind shell suddenly and unexpectedly exploded, and 20 dismembered human remains were discovered. DNA fingerprint was performed to determine whether the 20 human remains were derived from one person or not. DNA was isolated from each of the remains and digested by the restriction enzyme Hinf I and Hae III and hybridized with the oligonucleotide probe (GTG)5. DNA fingerprint using Hinf I demonstrated the same band pattern in 17 out of the 20 remains. However, in the remaining 3 samples, two novel strange bands were observed. DNA fingerprint using Hae III showed completely identical pattern in all of the remains.

Patterns of Occurrence and Marine Mammal Acoustic Behavior in Relation to Navy Sonar Activity Off Jacksonville, Florida.

PubMed

Oswald, Julie N; Norris, Thomas F; Yack, Tina M; Ferguson, Elizabeth L; Kumar, Anurag; Nissen, Jene; Bell, Joel

2016-01-01

Passive acoustic data collected from marine autonomous recording units deployed off Jacksonville, FL (from 13 September to 8 October 2009 and 3 December 2009 to 8 January 2010), were analyzed for detection of cetaceans and Navy sonar. Cetaceans detected included Balaenoptera acutorostrata, Eubalaena glacialis, B. borealis, Physeter macrocephalus, blackfish, and delphinids. E. glacialis were detected at shallow and, somewhat unexpectedly, deep sites. P. macrocephalus were characterized by a strong diel pattern. B. acutorostrata showed the strongest relationship between sonar activity and vocal behavior. These results provide a preliminary assessment of cetacean occurrence off Jacksonville and new insights on vocal responses to sonar.

The heart-break of social rejection versus the brain wave of social acceptance

PubMed Central

van der Molen, Maurits W.; Sahibdin, Priya P.; Franken, Ingmar H. A.

2014-01-01

The effect of social rejection on cardiac and brain responses was examined in a study in which participants had to decide on the basis of pictures of virtual peers whether these peers would like them or not. Physiological and behavioral responses to expected and unexpected acceptance and rejection were compared. It was found that participants expected that about 50% of the virtual judges gave them a positive judgment. Cardiac deceleration was strongest for unexpected social rejection. In contrast, the brain response was strongest to expected acceptance and was characterized by a positive deflection peaking around 325 ms following stimulus onset and the observed difference was maximal at fronto-central positions. The cardiac and electro-cortical responses were not related. It is hypothesized that these differential response patterns might be related to earlier described differential involvement of the dorsal and ventral portion of the anterior cingulate cortex. PMID:23887821

Electrically switchable photonic liquid crystal devices for routing of a polarized light wave

NASA Astrophysics Data System (ADS)

Rushnova, Irina I.; Melnikova, Elena A.; Tolstik, Alexei L.; Muravsky, Alexander A.

2018-04-01

The new mode of LC alignment based on photoalignment AtA-2 azo dye where the refractive interface between orthogonal orientations of the LC director exists without voltage and disappeared or changed with critical voltage has been proposed. The technology to fabricate electrically controlled liquid crystal elements for spatial separation and switching of linearly polarized light beams on the basis of the total internal reflection effect has been significantly improved. Its distinctive feature is the application of a composite alignment material comprising two sublayers of Nylon-6 and AtA-2 photoalignment azo dye offering patterned liquid crystal director orientation with high alignment quality value q = 0 . 998. The fabricated electrically controlled spatially structured liquid crystal devices enable implementation of propagation directions separation for orthogonally polarized light beams and their switching with minimal crosstalk.

AWARE: Adaptive Software Monitoring and Dynamic Reconfiguration for Critical Infrastructure Protection

DTIC Science & Technology

2015-04-29

in which we applied these adaptation patterns to an adaptive news web server intended to tolerate extremely heavy, unexpected loads. To address...collection of existing models used as benchmarks for OO-based refactoring and an existing web -based repository called REMODD to provide users with model...invariant properties. Specifically, we developed Avida- MDE (based on the Avida digital evolution platform) to support the automatic generation of software

Oculomotor Capture by New and Unannounced Color Singletons during Visual Search.

PubMed

Retell, James D; Venini, Dustin; Becker, Stefanie I

2015-07-01

The surprise capture hypothesis states that a stimulus will capture attention to the extent that it is preattentively available and deviates from task-expectancies. Interestingly, it has been noted by Horstmann (Psychological Science 13: 499-505. doi: 10.1111/1467-9280.00488, 2002, Human Perception and Performance 31: 1039-1060. doi: 10.1037/00961523.31.5.1039, 2005, Psychological Research, 70, 13-25, 2006) that the time course of capture by such classes of stimuli appears distinct from that of capture by expected stimuli. Specifically, attention shifts to an unexpected stimulus are delayed relative to an expected stimulus (delayed onset account). Across two experiments, we investigated this claim under conditions of unguided (Exp. 1) and guided (Exp. 2) search using eye-movements as the primary index of attentional selection. In both experiments, we found strong evidence of surprise capture for the first presentation of an unannounced color singleton. However, in both experiments the pattern of eye-movements was not consistent with a delayed onset account of attention capture. Rather, we observed costs associated with the unexpected stimulus only once the target had been selected. We propose an interference account of surprise capture to explain our data and argue that this account also can explain existing patterns of data in the literature.

The unexpected but understandable dynamics of mating, paternity and paternal care in the ocellated wrasse

PubMed Central

Alonzo, Suzanne H.; Heckman, Kellie L.

2010-01-01

Although theory generally predicts that males should reduce paternal care in response to cues that predict increased sperm competition and decreased paternity, empirical patterns are equivocal. Some studies have found the predicted decrease in male care with increased sperm competition, while even more studies report no effect of paternity or sperm competition on male care. Here, we report the first example, to our knowledge, of paternal care increasing with the risk and intensity of sperm competition, in the ocellated wrasse (Symphodus ocellatus). Theory also predicts that if paternal care varies and is important to female fitness, female choice among males and male indicators traits of expected paternal care should evolve. Despite a non-random distribution of mating success among nests, we found no evidence for female choice among parental males. Finally, we document the highest published levels of extra-pair paternity for a species with exclusive and obligate male care: genetic paternity analyses revealed cuckoldry at 100 per cent of nests and 28 per cent of all offspring were not sired by the male caring for them. While not predicted by any existing theory, these unexpected reproductive patterns become understandable if we consider how male and female mating and parental care interact simultaneously in this and probably many other species. PMID:19812085

Development of a Self Aligned CMOS Process for Flash Lamp Annealed Polycrystalline Silicon TFTs

NASA Astrophysics Data System (ADS)

Bischoff, Paul

The emerging active matrix liquid crystal (AMLCD) display market requires a high performing semiconductor material to meet rising standards of operation. Currently amorphous silicon (a-Si) dominates the market but it does not have the required mobility for it to be used in AMLCD manufacturing. Other materials have been developed including crystallizing a-Si into poly-silicon. A new approach to crystallization through the use of flash lamp annealing (FLA) decreases manufacturing time and greatly improves carrier mobility. Previous work on FLA silicon for the use in CMOS transistors revealed significant lateral dopant diffusion into the channel greatly increasing the minimum channel length required for a working device. This was further confounded by the gate overlap due to misalignment during lithography patterning steps. Through the use of furnace dopant activation instead of FLA dopant activation and a self aligned gate the minimum size transistor can be greatly reduced. A new lithography mask and process flow were developed for the furnace annealing and self aligned gate. Fabrication of the self aligned devices resulted in oxidation of the Molybdenum self aligned gate. Further development is needed to successfully manufacture these devices. Non-self aligned transistors were made simultaneously with self aligned devices and used the furnace activation. These devices showed an increase in sheet resistance from 250 O to 800 O and lower mobility from 380 to 40.2 V/cm2s. The lower mobility can be contributed to an increase in implanted trap density indicating furnace annealing is an inferior activation method over FLA. The minimum transistor size however was reduced from 20 to 5 mum. With improvements in the self aligned process high performing small devices can be manufactured.

L-GRAAL: Lagrangian graphlet-based network aligner.

PubMed

Malod-Dognin, Noël; Pržulj, Nataša

2015-07-01

Discovering and understanding patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions. L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/. n.malod-dognin@imperial.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Direct patterning of highly-conductive graphene@copper composites using copper naphthenate as a resist for graphene device applications.

PubMed

Bi, Kaixi; Xiang, Quan; Chen, Yiqin; Shi, Huimin; Li, Zhiqin; Lin, Jun; Zhang, Yongzhe; Wan, Qiang; Zhang, Guanhua; Qin, Shiqiao; Zhang, Xueao; Duan, Huigao

2017-11-09

We report an electron-beam lithography process to directly fabricate graphene@copper composite patterns without involving metal deposition, lift-off and etching processes using copper naphthenate as a high-resolution negative-tone resist. As a commonly used industrial painting product, copper naphthenate is extremely cheap with a long shelf time but demonstrates an unexpected patterning resolution better than 10 nm. With appropriate annealing under a hydrogen atmosphere, the produced graphene@copper composite patterns show high conductivity of ∼400 S cm -1 . X-ray diffraction, conformal Raman spectroscopy and X-ray photoelectron spectroscopy were used to analyze the chemical composition of the final patterns. With the properties of high resolution and high conductivity, the patterned graphene@copper composites could be used as conductive pads and interconnects for graphene electronic devices with ohmic contacts. Compared to common fabrication processes involving metal evaporation and lift-off steps, this pattern-transfer-free fabrication process using copper naphthenate resist is direct and simple but allows comparable device performance in practical device applications.

Shape dependence of slip length on patterned hydrophobic surfaces

NASA Astrophysics Data System (ADS)

Gu, Xiaokun; Chen, Min

2011-08-01

The effects of solid-liquid interfacial shape on the boundary velocity slip of patterned hydrophobic surfaces are investigated. The scaling law in literature is extended to demonstrate the role of such shape, indicating a decrease of the effective slip length with increasing interfacial roughness. A patterned surface with horizontally aligned carbon nanotube arrays reaches an effective slip length of 83 nm, by utilizing large intrinsic slippage of carbon nanotube while keeping away from the negative effects of interfacial curvature through the flow direction. The results emphasize the importance of avoiding the solid-liquid interfacial roughness in low-friction patterned surface design and manufacture.

"Liquid-liquid-solid"-type superoleophobic surfaces to pattern polymeric semiconductors towards high-quality organic field-effect transistors.

PubMed

Wu, Yuchen; Su, Bin; Jiang, Lei; Heeger, Alan J

2013-12-03

Precisely aligned organic-liquid-soluble semiconductor microwire arrays have been fabricated by "liquid-liquid-solid" type superoleophobic surfaces directed fluid drying. Aligned organic 1D micro-architectures can be built as high-quality organic field-effect transistors with high mobilities of >10 cm(2) ·V(-1) ·s(-1) and current on/off ratio of more than 10(6) . All these studies will boost the development of 1D microstructures of organic semiconductor materials for potential application in organic electronics. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Studying internal and external magnetic fields in Japan using MAGSAT data

NASA Technical Reports Server (NTRS)

Fukushima, N. (Principal Investigator); Maeda, H.; Yukutake, T.; Tanaka, M.; Oshima, S.; Ogawa, K.; Kawamura, M.; Miyazaki, Y.; Uyeda, S.; Kobayashi, K.

1980-01-01

Examination of the total intensity data of CHRONIT on a few paths over Japan and its neighboring sea shows MAGSAT is extremely useful for studying the local magnetic anomaly. In high latitudes, the signatures of field aligned currents are clearly recognized. These include (1) the persistent basic pattern of current flow; (2) the more intense currents in the summer hemisphere than in the winter hemisphere; (3) more fluctuations in current intensities in summer dawn hours; and (4) apparent dawn-dusk asymmetry in the field-aligned current intensity between the north and south polar regions.

Simple measurement of lenticular lens quality for autostereoscopic displays

NASA Astrophysics Data System (ADS)

Gray, Stuart; Boudreau, Robert A.

2013-03-01

Lenticular lens based autostereoscopic 3D displays are finding many applications in digital signage and consumer electronics devices. A high quality 3D viewing experience requires the lenticular lens be properly aligned with the pixels on the display device so that each eye views the correct image. This work presents a simple and novel method for rapidly assessing the quality of a lenticular lens to be used in autostereoscopic displays. Errors in lenticular alignment across the entire display are easily observed with a simple test pattern where adjacent views are programmed to display different colors.

Improved Orifice Plate for Spray Gun

NASA Technical Reports Server (NTRS)

Cunningham, W.

1986-01-01

Erratic spray pattern of commercial spray gun changed to repeatable one by simple redesign of two parts. In modified spray gun orifice plate and polytetrafluoroethylene bushing redesigned to assure centering and alignment with nozzle. Such improvement useful in many industrial applications requiring repeatable spray patterns. Might include spraying of foam insulation, paint, other protective coatings, detergents, abrasives, adhesives, process chemicals, or fuels. Unmodified spray gun produces erratic spray because lateral misalignment between orifice plate and nozzle.

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

PubMed

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

2015-03-17

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

Pattern centric design based sensitive patterns and process monitor in manufacturing

NASA Astrophysics Data System (ADS)

Hsiang, Chingyun; Cheng, Guojie; Wu, Kechih

2017-03-01

When design rule is mitigating to smaller dimension, process variation requirement is tighter than ever and challenges the limits of device yield. Masks, lithography, etching and other processes have to meet very tight specifications in order to keep defect and CD within the margins of the process window. Conventionally, Inspection and metrology equipments are utilized to monitor and control wafer quality in-line. In high throughput optical inspection, nuisance and review-classification become a tedious labor intensive job in manufacturing. Certain high-resolution SEM images are taken to validate defects after optical inspection. These high resolution SEM images catch not only optical inspection highlighted point, also its surrounding patterns. However, this pattern information is not well utilized in conventional quality control method. Using this complementary design based pattern monitor not only monitors and analyzes the variation of patterns sensitivity but also reduce nuisance and highlight defective patterns or killer defects. After grouping in either single or multiple layers, systematic defects can be identified quickly in this flow. In this paper, we applied design based pattern monitor in different layers to monitor process variation impacts on all kinds of patterns. First, the contour of high resolutions SEM image is extracted and aligned to design with offset adjustment and fine alignment [1]. Second, specified pattern rules can be applied on design clip area, the same size as SEM image, and form POI (pattern of interest) areas. Third, the discrepancy of contour and design measurement at different pattern types in measurement blocks. Fourth, defective patterns are reported by discrepancy detection criteria and pattern grouping [4]. Meanwhile, reported pattern defects are ranked by number and severity by discrepancy. In this step, process sensitive high repeatable systematic defects can be identified quickly Through this design based process pattern monitor method, most of optical inspection nuisances can be filtered out at contour to design discrepancy measurement. Daily analysis results are stored at database as reference to compare with incoming data. Defective pattern library contains existing and known systematic defect patterns which help to catch and identify new pattern defects or process impacts. On the other hand, this defect pattern library provides extra valuable information for mask, pattern and defects verification, inspection care area generation, further OPC fix and process enhancement and investigation.

Adhesive micro-line periodicity determines guidance of axonal outgrowth†

PubMed Central

Huang, Yu; Fothergill, Thomas; Lumbard, Derek C.; Dent, Erik W.; Williams, Justin C.

2014-01-01

Adhesive micro-lines of various sub-cellular geometries were created using a non-traditional micro stamping technique. This technique employed the use of commercially available diffraction gratings as the molds for the micro stamps, a method which is quick and inexpensive, and which could easily be adopted as a patterning tool in a variety of research efforts. The atypical saw-tooth profile of the micro stamps enabled a unique degree of control and flexibility over patterned line and gap widths. Cortical neurons cultured on patterned poly-lysine micro-lines on PDMS exhibit a startling transition in axonal guidance: From the expected parallel guidance to an unexpected perpendicular guidance that becomes dominant as patterned lines and gaps become sufficiently narrow. This transition is most obvious when the lines are narrow relative to gaps, while the periodicity of the pattern is reduced. Axons growing perpendicular to micro-lines exhibited ‘vinculated’ growth, a unique morphological phenotype consisting of periodic orthogonal extensions along the axon. PMID:23250489

An equilibrium-point model of electromyographic patterns during single-joint movements based on experimentally reconstructed control signals.

PubMed

Latash, M L; Goodman, S R

1994-01-01

The purpose of this work has been to develop a model of electromyographic (EMG) patterns during single-joint movements based on a version of the equilibrium-point hypothesis, a method for experimental reconstruction of the joint compliant characteristics, the dual-strategy hypothesis, and a kinematic model of movement trajectory. EMG patterns are considered emergent properties of hypothetical control patterns that are equally affected by the control signals and peripheral feedback reflecting actual movement trajectory. A computer model generated the EMG patterns based on simulated movement kinematics and hypothetical control signals derived from the reconstructed joint compliant characteristics. The model predictions have been compared to published recordings of movement kinematics and EMG patterns in a variety of movement conditions, including movements over different distances, at different speeds, against different-known inertial loads, and in conditions of possible unexpected decrease in the inertial load. Changes in task parameters within the model led to simulated EMG patterns qualitatively similar to the experimentally recorded EMG patterns. The model's predictive power compares it favourably to the existing models of the EMG patterns. Copyright © 1994. Published by Elsevier Ltd.

The frictional response of patterned soft polymer surfaces

NASA Astrophysics Data System (ADS)

Rand, Charles J.

2008-10-01

Friction plays an intricate role in our everyday lives, it is therefore critical to understand the underlying features of friction to better help control and manipulate the response anywhere two surfaces in contact move past each other by a sliding motion. Here we present results targeting a thorough understanding of soft material friction and how it can be manipulated with patterns. We found that the naturally occurring length scale or periodicity (lambda) of frictionally induced patterns, Schallamach waves, could be described using two materials properties (critical energy release rate Gc and complex modulus (E*), i.e. lambdainfinity Gc /E*). Following this, we evaluated the effect of a single defect at a sliding interface. Sliding over a defect can be used to model the sliding from one feature to another in a patterned surface. Defects decreased the sliding frictional force by as much as 80% sliding and this decrease was attributed to changes in tangential stiffness of the sliding interface. The frictional response of surface wrinkles, where multiple edges or defects are acting in concert, was also evaluated. Wrinkles were shown to decrease friction (F) and changes in contact area (A) could not describe this decrease. A tangential stiffness correction factor (fx) and changes in the critical energy release rate were used to describe this deviation (F infinity Gc *A*fx/ℓ, where ℓ is a materials defined length scale of dissipation). This scaling can be used to describe the friction of any topographically patterned surface including the Gecko's foot, where the feature size is smaller than ℓ and thus replaces ℓ, increasing the friction compared to a flat surface. Also, mechanically-induced surface defects were used to align osmotically driven surface wrinkles by creating stress discontinuities that convert the global biaxial stress state to local uniaxial stresses. Defect spacing was used to control the alignment process at the surface of the wrinkled rigid film/soft elastomer interface. These aligned wrinkled surfaces can be used to tune the adhesion and friction of an interface. The work presented here gives insight into tuning the friction of a soft polymeric surface as well as understanding the friction of complex hierarchical structures.

Development of a reinforced electrochemically aligned collagen bioscaffold for tendon tissue engineering applications

NASA Astrophysics Data System (ADS)

Uquillas Paredes, Jorge Alfredo

Type-I collagen is a promising biomaterial that can be used to synthesize bioscaffolds as a strategy to regenerate and repair damaged tendons. The existing in vitro prepared collagen bioscaffolds are in the form of gels, foams, or extruded fibers. These bioscaffolds readily present sites for attachment of biological factors and cells; however, they have extremely poor biomechanical properties in comparison to the properties of native tendons. The biomechanical function of type-I collagen bioscaffolds needs to be elevated to the level of natural tissues for this biomaterial to replace mechanically challenged tendons in a functionally meaningful way. The overall goal of this dissertation is to develop a reinforced electrochemically aligned collagenous bioscaffold for applications in tendon tissue engineering. The bioscaffold is synthesized by a unique electrochemical process via isoelectric focusing (IEF) to attain a very high degree of molecular alignment and packing density. This dissertation presents progress made on four aims: A) development of simple and descriptive electrochemical theory via the mathematical model of IEF and the forces acting on collagen alignment under an electric field; B) optimization of the post-alignment PBS treatment step to achieve d- banding pattern in uncrosslinked electrochemically aligned collagen (ELAC) bioscaffolds; C) optimization of the best crosslinking protocol to produce the strongest possible ELAC biomaterial with excellent cellular compatibility; and D) in vivo evaluation of the biocompatibility and biodegradability properties of electronically aligned collagen bioscaffolds. The results of this dissertation provide strong evidence showing that reinforced ELAC bioscaffolds could be used clinically in the future to repair damaged tendons.

Directed ordering of phase separated domains and dewetting of thin polymer blend films on a topographically patterned substrate.

PubMed

Bhandaru, Nandini; Karim, Alamgir; Mukherjee, Rabibrata

2017-07-21

Substrate pattern guided self-organization of ultrathin and confined polymeric films on a topographically patterned substrate is a useful approach for obtaining ordered meso and nano structures over large areas, particularly if the ordering is achieved during film preparation itself, eliminating any post-processing such as thermal or solvent vapor annealing. By casting a dilute solution of two immiscible polymers, polystyrene (PS) and polymethylmethacrylate (PMMA), from a common solvent (toluene) on a topographically patterned substrate with a grating geometry, we show the formation of self-organized meso patterns with various degrees of ordering. The morphology depends on both the concentration of the dispensed solution (C n ) and the blend composition (R B ). Depending on the extent of dewetting during spin coating, the final morphologies can be classified into three distinct categories. At a very low C n the solution dewets fully, resulting in isolated polymer droplets aligned along substrate grooves (Type 1). Type 2 structures comprising isolated threads with aligned phase separated domains along each substrate groove are observed at intermediate C n . A continuous film (Type 3) is obtained above a critical concentration (C n *) that depends on R B . While the extent of ordering of the domains gradually diminishes with an increase in film thickness for Type 3 patterns, the size of the domains remains much smaller than that on a flat substrate, resulting in significant downsizing of the features due to the lateral confinement imposed on the phase separation process by the topographic patterns. Finally, we show that some of these structures exhibit excellent broadband anti-reflection (AR) properties.

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.

Regulation of cell arrangement using a novel composite micropattern.

PubMed

Liu, Xiaoyi; Liu, Yaoping; Zhao, Feng; Hun, Tingting; Li, Shan; Wang, Yuguang; Sun, Weijie; Wang, Wei; Sun, Yan; Fan, Yubo

2017-11-01

Micropatterning technique has been used to control single cell geometry in many researches, however, this is no report that it is used to control multicelluar geometry, which not only control single cell geometry but also organize those cells by a certain pattern. In this work, a composite protein micropattern is developed to control both cell shape and cell location simultaneously. The composite micropattern consists of a central circle 15 μm in diameter for single-cell capture, surrounded by small, square arrays (3 μm × 3 μm) for cell spreading. This is surrounded by a border 2 μm wide for restricting cell edges. The composite pattern results in two-cell and three-cell capture efficiencies of 32.1% ± 1.94% and 24.2% ± 2.89%, respectively, representing an 8.52% and 9.58% increase, respectively, over rates of original patterns. Fluorescent imaging of cytoskeleton alignment demonstrates that actin is gradually aligned parallel to the direction of the entire pattern arrangement, rather than to that of a single pattern. This indicates that cell arrangement is also an important factor in determining cell physiology. This composite micropattern could be a potential method to precisely control multi-cells for cell junctions, cell interactions, cell signal transduction, and eventually for tissue rebuilding study. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 3093-3101, 2017. © 2017 Wiley Periodicals, Inc.

Structure of high latitude currents in magnetosphere-ionosphere models

NASA Astrophysics Data System (ADS)

Wiltberger, M. J.; Lyon, J.; Merkin, V. G.; Rigler, E. J.

2016-12-01

Using three resolutions of the Lyon-Fedder-Mobarry global magnetosphere-ionosphere model (LFM) and the Weimer 2005 empirical model the structure of the high latitude field-aligned current patterns is examined. Each LFM resolution was run for the entire Whole Heliosphere Interval (WHI), which contained two high-speed solar wind streams and modest interplanetary magnetic field strengths. Average states of the field-aligned current (FAC) patterns for 8 interplanetary magnetic field clock angle directions are computed using data from these runs. Generally speaking the patterns obtained agree well with results from the Weimer 2005 computed using the solar wind and IMF conditions that correspond to each bin. As the simulation resolution increases the currents become more intense and confined. A machine learning analysis of the FAC patterns shows that the ratio of Region 1 (R1) to Region 2 (R2) currents decreases as the simulation resolution increases. This brings the simulation results into better agreement with observational predictions and the Weimer 2005 model results. The increase in R2 current strengths in the model also results in a better shielding of mid- and low-latitude ionosphere from the polar cap convection, also in agreement with observations. Current-voltage relationships between the R1 strength and the cross-polar cap potential (CPCP) are quite similar at the higher resolutions indicating the simulation is converging on a common solution. We conclude that LFM simulations are capable of reproducing the statistical features of FAC patterns.

Biomechanical Characterization of Cardiomyocyte Using PDMS Pillar with Microgrooves

PubMed Central

Oyunbaatar, Nomin-Erdene; Lee, Deok-Hyu; Patil, Swati J.; Kim, Eung-Sam; Lee, Dong-Weon

2016-01-01

This paper describes the surface-patterned polydimethylsiloxane (PDMS) pillar arrays for enhancing cell alignment and contraction force in cardiomyocytes. The PDMS micropillar (μpillar) arrays with microgrooves (μgrooves) were fabricated using a unique micro-mold made using SU-8 double layer processes. The spring constant of the μpillar arrays was experimentally confirmed using atomic force microscopy (AFM). After culturing cardiac cells on the two different types of μpillar arrays, with and without grooves on the top of μpillar, the characteristics of the cardiomyocytes were analyzed using a custom-made image analysis system. The alignment of the cardiomyocytes on the μgrooves of the μpillars was clearly observed using a DAPI staining process. The mechanical force generated by the contraction force of the cardiomyocytes was derived from the displacement of the μpillar arrays. The contraction force of the cardiomyocytes aligned on the μgrooves was 20% higher than that of the μpillar arrays without μgrooves. The experimental results prove that applied geometrical stimulus is an effective method for aligning and improving the contraction force of cardiomyocytes. PMID:27517924

Observations of ionospheric convection vortices - Signatures of momentum transfer

NASA Technical Reports Server (NTRS)

Mchenry, M. A.; Clauer, C. R.; Friis-Christensen, E.; Kelly, J. D.

1988-01-01

Several classes of traveling vortices in the dayside ionospheric flow have been detected and tracked using the Greenland magnetometer chain. One class observed during quiet times consists of a continuous series of vortices moving generally antisunward for several hours at a time. Assuming each vortex to be the convection pattern produced by a small field aligned current moving across the ionosphere, the amount of field aligned current was found by fitting a modeled ground magnetic signature to measurements from the chain of magnetometers. The calculated field aligned current is seen to be steady for each vortex and neighboring vortices have currents of opposite sign. Low altitude DMSP observations indicate the vortices are on field lines which map to the inner edge of the low latitude boundary layer. Because the vortices are conjugate to the boundary layer, repeat in a regular fashion and travel antisunward, it is argued that this class of vortices is caused by surface waves at the magnetopause. No strong correlations between field aligned current strength and solar wind density, velocity, or Bz is found.

Log-odds sequence logos

PubMed Central

Yu, Yi-Kuo; Capra, John A.; Stojmirović, Aleksandar; Landsman, David; Altschul, Stephen F.

2015-01-01

Motivation: DNA and protein patterns are usefully represented by sequence logos. However, the methods for logo generation in common use lack a proper statistical basis, and are non-optimal for recognizing functionally relevant alignment columns. Results: We redefine the information at a logo position as a per-observation multiple alignment log-odds score. Such scores are positive or negative, depending on whether a column’s observations are better explained as arising from relatedness or chance. Within this framework, we propose distinct normalized maximum likelihood and Bayesian measures of column information. We illustrate these measures on High Mobility Group B (HMGB) box proteins and a dataset of enzyme alignments. Particularly in the context of protein alignments, our measures improve the discrimination of biologically relevant positions. Availability and implementation: Our new measures are implemented in an open-source Web-based logo generation program, which is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/index.html. A stand-alone version of the program is also available from this site. Contact: altschul@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25294922

Optimize of shrink process with X-Y CD bias on hole pattern

NASA Astrophysics Data System (ADS)

Koike, Kyohei; Hara, Arisa; Natori, Sakurako; Yamauchi, Shohei; Yamato, Masatoshi; Oyama, Kenichi; Yaegashi, Hidetami

2017-03-01

Gridded design rules[1] is major process in configuring logic circuit used 193-immersion lithography. In the scaling of grid patterning, we can make 10nm order line and space pattern by using multiple patterning techniques such as self-aligned multiple patterning (SAMP) and litho-etch- litho-etch (LELE)[2][3][4] . On the other hand, Line cut process has some error parameters such as pattern defect, placement error, roughness and X-Y CD bias with the decreasing scale. We tried to cure hole pattern roughness to use additional process such as Line smoothing[5] . Each smoothing process showed different effect. As the result, CDx shrink amount is smaller than CDy without one additional process. In this paper, we will report the pattern controllability comparison of EUV and 193-immersion. And we will discuss optimum method about CD bias on hole pattern.

Phenotypic Covariation and Morphological Diversification in the Ruminant Skull.

PubMed

Haber, Annat

2016-05-01

Differences among clades in their diversification patterns result from a combination of extrinsic and intrinsic factors. In this study, I examined the role of intrinsic factors in the morphological diversification of ruminants, in general, and in the differences between bovids and cervids, in particular. Using skull morphology, which embodies many of the adaptations that distinguish bovids and cervids, I examined 132 of the 200 extant ruminant species. As a proxy for intrinsic constraints, I quantified different aspects of the phenotypic covariation structure within species and compared them with the among-species divergence patterns, using phylogenetic comparative methods. My results show that for most species, divergence is well aligned with their phenotypic covariance matrix and that those that are better aligned have diverged further away from their ancestor. Bovids have dispersed into a wider range of directions in morphospace than cervids, and their overall disparity is higher. This difference is best explained by the lower eccentricity of bovids' within-species covariance matrices. These results are consistent with the role of intrinsic constraints in determining amount, range, and direction of dispersion and demonstrate that intrinsic constraints can influence macroevolutionary patterns even as the covariance structure evolves.

Optical bandgap modelling from the structural arrangement of carbon nanotubes.

PubMed

Butler, Timothy P; Rashid, Ijaz; Montelongo, Yunuen; Amaratunga, Gehan A J; Butt, Haider

2018-06-14

The optical bandgap properties of vertically-aligned carbon nanotube (VACNT) arrays were probed through their interaction with white light, with the light reflected from the rotating arrays measured with a spectrometer. The precise deterministic control over the structure of vertically-aligned carbon nanotube arrays through electron beam lithography and well-controlled growth conditions brings with it the ability to produce exotic photonic crystals over a relatively large area. The characterisation of the behaviour of these materials in the presence of light is a necessary first step toward application. Relatively large area array structures of high-quality VACNTs were fabricated in square, hexagonal, circular and pseudorandom patterned arrays with length scales on the order of those of visible light for the purpose of investigating how they may be used to manipulate an impinging light beam. In order to investigate the optical properties of these arrays a set of measurement apparatus was designed which allowed the accurate measurement of their optical bandgap characteristics. The patterned samples were rotated under the illuminating white light beam, revealing interesting optical bandgap results caused by the changing patterns and relative positions of the scattering elements (VACNTs).

Delayed response and biosonar perception explain movement coordination in trawling bats.

PubMed

Giuggioli, Luca; McKetterick, Thomas J; Holderied, Marc

2015-03-01

Animal coordinated movement interactions are commonly explained by assuming unspecified social forces of attraction, repulsion and alignment with parameters drawn from observed movement data. Here we propose and test a biologically realistic and quantifiable biosonar movement interaction mechanism for echolocating bats based on spatial perceptual bias, i.e. actual sound field, a reaction delay, and observed motor constraints in speed and acceleration. We found that foraging pairs of bats flying over a water surface swapped leader-follower roles and performed chases or coordinated manoeuvres by copying the heading a nearby individual has had up to 500 ms earlier. Our proposed mechanism based on the interplay between sensory-motor constraints and delayed alignment was able to recreate the observed spatial actor-reactor patterns. Remarkably, when we varied model parameters (response delay, hearing threshold and echolocation directionality) beyond those observed in nature, the spatio-temporal interaction patterns created by the model only recreated the observed interactions, i.e. chases, and best matched the observed spatial patterns for just those response delays, hearing thresholds and echolocation directionalities found to be used by bats. This supports the validity of our sensory ecology approach of movement coordination, where interacting bats localise each other by active echolocation rather than eavesdropping.

New techniques enable comparative analysis of microtubule orientation, wall texture, and growth rate in intact roots of Arabidopsis.

PubMed

Sugimoto, K; Williamson, R E; Wasteneys, G O

2000-12-01

This article explores root epidermal cell elongation and its dependence on two structural elements of cells, cortical microtubules and cellulose microfibrils. The recent identification of Arabidopsis morphology mutants with putative cell wall or cytoskeletal defects demands a procedure for examining and comparing wall architecture and microtubule organization patterns in this species. We developed methods to examine cellulose microfibrils by field emission scanning electron microscopy and microtubules by immunofluorescence in essentially intact roots. We were able to compare cellulose microfibril and microtubule alignment patterns at equivalent stages of cell expansion. Field emission scanning electron microscopy revealed that Arabidopsis root epidermal cells have typical dicot primary cell wall structure with prominent transverse cellulose microfibrils embedded in pectic substances. Our analysis showed that microtubules and microfibrils have similar orientation only during the initial phase of elongation growth. Microtubule patterns deviate from a predominantly transverse orientation while cells are still expanding, whereas cellulose microfibrils remain transverse until well after expansion finishes. We also observed microtubule-microfibril alignment discord before cells enter their elongation phase. This study and the new technology it presents provide a starting point for further investigations on the physical properties of cell walls and their mechanisms of assembly.

Coherent Pattern Prediction in Swarms of Delay-Coupled Agents

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

Multilayer Microfluidic Devices Created From A Single Photomask

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

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

2013-08-28

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

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

PubMed

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

2018-05-09

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

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

NASA Astrophysics Data System (ADS)

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

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

enoLOGOS: a versatile web tool for energy normalized sequence logos

PubMed Central

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

2005-01-01

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

Campaign 1.7 Pu Aging. Development of Time of Flight Secondary Ion Mass Spectroscopy

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

Venhaus, Thomas J.

2015-09-09

The first application of Time-of-Flight Secondary Ion Mass Spectroscopy (ToF-SIMS) to an aged plutonium surface has resulted in a rich set of surface chemistry data, as well as some unexpected results. FY15 was highlighted by not only the first mapping of hydrogen-containing features within the metal, but also a prove-in series of experiments using the system’s Sieverts Reaction Cell. These experiments involved successfully heating the sample to ~450 oC for nearly 24 hours while the sample was dosed several times with hydrogen, followed by an in situ ToF-SIMS analysis. During this year, the data allowed for better and more consistentmore » identification of the myriad peaks that result from the SIMS sputter process. In collaboration with the AWE (U.K), the system was also fully aligned for sputter depth profiling for future experiments.« less

Solid friction between soft filaments.

PubMed

Ward, Andrew; Hilitski, Feodor; Schwenger, Walter; Welch, David; Lau, A W C; Vitelli, Vincenzo; Mahadevan, L; Dogic, Zvonimir

2015-06-01

Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments' overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes's drag, can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. Our findings demonstrate how altering a filament's elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials.

Solid friction between soft filaments

NASA Astrophysics Data System (ADS)

Ward, Andrew; Hilitski, Feodor; Schwenger, Walter; Welch, David; Lau, A. W. C.; Vitelli, Vincenzo; Mahadevan, L.; Dogic, Zvonimir

2015-06-01

Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments’ overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes’s drag, can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. Our findings demonstrate how altering a filament’s elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials.

Stacking faults density driven collapse of magnetic energy in hcp-cobalt nano-magnets

NASA Astrophysics Data System (ADS)

Nong, H. T. T.; Mrad, K.; Schoenstein, F.; Piquemal, J.-Y.; Jouini, N.; Leridon, B.; Mercone, S.

2017-06-01

Cobalt nanowires with different shape parameters were synthesized via the polyol process. By calculating the magnetic energy product (BH max) both for dried nano-powder and for nanowires in their synthesis solution, we observed unexpected independent BH max values from the nanowires shape. A good alignment of the nanowires leads to a higher BH max value. Our results show that the key parameter driving the magnetic energy product of the cobalt nanowires is the stacking fault density. An exponential collapse of the magnetic energy is observed at very low percentage of structural faults. Cobalt nanowires with almost perfect hcp crystalline structures should present high magnetic energy, which is promising for application in rare earth-free permanent magnets. Oral talk at 8th International Workshop on Advanced Materials Science and Nanotechnology (IWAMSN2016), 8-12 November 2016, Ha Long City, Vietnam.

Phase separation of DMDBS from iPP, and controlled crystalline orientation

NASA Astrophysics Data System (ADS)

Sreenivas, K.; Kumaraswamy, Guruswamy; Basargekar, R. S.

2012-02-01

We report an unexpected dependence of DMDBS phase separation temperature on the molecular weight of the matrix isotactic polypropylene (iPP). DMDBS crystallizes out at lower temperatures for iPP with decreasing molecular weight (and correspondingly lower tacticity). This molecular weight dependence is unique to iPP, and is not observed for either syndiotactic PP or for random ethylene-PP copolymers. We show that thermodynamic Flory-type arguments are unable to rationalize the observed results. We also results on extrusion film casting of iPP containing DMDBS and show that flow-alignment of DMDBS networks template the orientation of PP crystals. The modulus and yield strength increase on addition of DMDBS, relative to the neat iPP. Tensile modulus and yield stress of drawn films increase with the degree of orientation, and we are able to achieve a substantial increase even at relatively low draw ratios.

The CAMEO barium release - E/parallel/ fields over the polar cap

NASA Technical Reports Server (NTRS)

Heppner, J. P.; Miller, M. L.; Pongratz, M. B.; Smith, G. M.; Smith, L. L.; Mende, S. B.; Nath, N. R.

1981-01-01

Four successive thermite barium releases at an altitude of 965 km over polar cap invariant latitudes 84 to 76 deg near magnetic midnight were conducted from the orbiting second stage of the vehicle that launched Nimbus 7; the releases were made as part of the CAMEO (Chemically Active Material Ejected in Orbit) program. This was the first opportunity to observe the behavior of conventional barium release when conducted at orbital velocity in the near-earth magnetic field. The principal unexpected characteristic in the release dynamics was the high, 1.4 to 2.6 km/s, initial Ba(+) expansion velocity relative to an expected velocity of 0.9 km/s. Attention is also given to neutral cloud expansion, initial ion cloud expansion, convective motion, and the characteristics of field-aligned motion. The possibility of measuring parallel electric fields over the polar cap by observing perturbations in the motion of the visible ions is assessed.

Solid friction between soft filaments

DOE PAGES

Ward, Andrew; Hilitski, Feodor; Schwenger, Walter; ...

2015-03-02

Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments’ overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes’s drag,more » can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. In conclusion, our findings demonstrate how altering a filament’s elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials.« less

Digital Plasmonic Patterning for Localized Tuning of Hydrogel Stiffness.

PubMed

Hribar, Kolin C; Choi, Yu Suk; Ondeck, Matthew; Engler, Adam J; Chen, Shaochen

2014-08-20

The mechanical properties of the extracellular matrix (ECM) can dictate cell fate in biological systems. In tissue engineering, varying the stiffness of hydrogels-water-swollen polymeric networks that act as ECM substrates-has previously been demonstrated to control cell migration, proliferation, and differentiation. Here, "digital plasmonic patterning" (DPP) is developed to mechanically alter a hydrogel encapsulated with gold nanorods using a near-infrared laser, according to a digital (computer-generated) pattern. DPP can provide orders of magnitude changes in stiffness, and can be tuned by laser intensity and speed of writing. In vitro cellular experiments using A7R5 smooth muscle cells confirm cell migration and alignment according to these patterns, making DPP a useful technique for mechanically patterning hydrogels for various biomedical applications.

Spiral and never-settling patterns in active systems

NASA Astrophysics Data System (ADS)

Yang, X.; Marenduzzo, D.; Marchetti, M. C.

2014-01-01

We present a combined numerical and analytical study of pattern formation in an active system where particles align, possess a density-dependent motility, and are subject to a logistic reaction. The model can describe suspensions of reproducing bacteria, as well as polymerizing actomyosin gels in vitro or in vivo. In the disordered phase, we find that motility suppression and growth compete to yield stable or blinking patterns, which, when dense enough, acquire internal orientational ordering to give asters or spirals. We predict these may be observed within chemotactic aggregates in bacterial fluids. In the ordered phase, the reaction term leads to previously unobserved never-settling patterns which can provide a simple framework to understand the formation of motile and spiral patterns in intracellular actin systems.

Antenna radiation patterns in the whistler wave regime measured in a large laboratory plasma

NASA Technical Reports Server (NTRS)

Stenzel, R. L.

1976-01-01

Antenna radiation patterns of balanced electric dipoles and shielded magnetic loop antennas are obtained by measuring the relative wave amplitude with a small receiver antenna scanned around the exciter in a large uniform collisionless magnetized laboratory plasma in the whistler wave regime. The boundary effects are assumed to be negligible even for many farfield patterns. Characteristic differences are observed between electrically short and long antennas, the former exhibiting resonance cones and the latter showing dipole-like antenna patterns along the magnetic field. Resonance cones due to small electric dipoles and magnetic loops are observed in both the near zone and the far zone. A self-focusing process is revealed which produces a pencil-shaped field-aligned radiation pattern.

Simple and effective graphene laser processing for neuron patterning application

NASA Astrophysics Data System (ADS)

Lorenzoni, Matteo; Brandi, Fernando; Dante, Silvia; Giugni, Andrea; Torre, Bruno

2013-06-01

A straightforward fabrication technique to obtain patterned substrates promoting ordered neuron growth is presented. Chemical vapor deposition (CVD) single layer graphene (SLG) was machined by means of single pulse UV laser ablation technique at the lowest effective laser fluence in order to minimize laser damage effects. Patterned substrates were then coated with poly-D-lysine by means of a simple immersion in solution. Primary embryonic hippocampal neurons were cultured on our substrate, demonstrating an ordered interconnected neuron pattern mimicking the pattern design. Surprisingly, the functionalization is more effective on the SLG, resulting in notably higher alignment for neuron adhesion and growth. Therefore the proposed technique should be considered a valuable candidate to realize a new generation of highly specialized biosensors.

Simple and effective graphene laser processing for neuron patterning application

PubMed Central

Lorenzoni, Matteo; Brandi, Fernando; Dante, Silvia; Giugni, Andrea; Torre, Bruno

2013-01-01

A straightforward fabrication technique to obtain patterned substrates promoting ordered neuron growth is presented. Chemical vapor deposition (CVD) single layer graphene (SLG) was machined by means of single pulse UV laser ablation technique at the lowest effective laser fluence in order to minimize laser damage effects. Patterned substrates were then coated with poly-D-lysine by means of a simple immersion in solution. Primary embryonic hippocampal neurons were cultured on our substrate, demonstrating an ordered interconnected neuron pattern mimicking the pattern design. Surprisingly, the functionalization is more effective on the SLG, resulting in notably higher alignment for neuron adhesion and growth. Therefore the proposed technique should be considered a valuable candidate to realize a new generation of highly specialized biosensors. PMID:23739674

Endothelial cell motility, coordination and pattern formation during vasculogenesis.

PubMed

Czirok, Andras

2013-01-01

How vascular networks assemble is a fundamental problem of developmental biology that also has medical importance. To explain the organizational principles behind vascular patterning, we must understand how can tissue level structures be controlled through cell behavior patterns like motility and adhesion that, in turn, are determined by biochemical signal transduction processes? We discuss the various ideas that have been proposed as mechanisms for vascular network assembly: cell motility guided by extracellular matrix alignment (contact guidance), chemotaxis guided by paracrine and autocrine morphogens, and multicellular sprouting guided by cell-cell contacts. All of these processes yield emergent patterns, thus endothelial cells can form an interconnected structure autonomously, without guidance from an external pre-pattern. © 2013 Wiley Periodicals, Inc.

Activity Structures and the Unfolding of Problem-Solving Actions in High-School Chemistry Classrooms

NASA Astrophysics Data System (ADS)

Criswell, Brett A.; Rushton, Greg T.

2014-02-01

In this paper, we argue for a more systematic approach for studying the relationship between classroom practices and scientific practices—an approach that will likely better support the systemic reforms being promoted in the Next Generation Science Standards in the USA and similar efforts in other countries. One component of that approach is looking at how the nature of the activity structure may influence the relative alignment between classroom and scientific practices. To that end, we build on previously published research related to the practices utilized by five high-school chemistry teachers as they enacted problem-solving activities in which students were likely to generate proposals that were not aligned with normative scientific understandings. In that prior work, our analysis had emphasized micro-level features of the talk interactions and how they related to the way students' ideas were explored; in the current paper, the analysis zooms out to consider the macro-level nature of the enactments associated with the activity structure of each lesson examined. Our data show that there were two general patterns to the activity structure across the 14 lessons scrutinized, and that each pattern had associated with it a constellation of features that impinged on the way the problem space was navigated. A key finding is that both activity structures (the expansive and the open) had features that aligned with scientific practices espoused in the Next Generation Science Standards—and both had features that were not aligned with those practices. We discuss the nature of these two structures, evidence of the relationship of each structure to key features of how the lessons unfolded, and the implications of these findings for both future research and the training of teachers.

Temporal Integration Windows in Neural Processing and Perception Aligned to Saccadic Eye Movements.

PubMed

Wutz, Andreas; Muschter, Evelyn; van Koningsbruggen, Martijn G; Weisz, Nathan; Melcher, David

2016-07-11

When processing dynamic input, the brain balances the opposing needs of temporal integration and sensitivity to change. We hypothesized that the visual system might resolve this challenge by aligning integration windows to the onset of newly arriving sensory samples. In a series of experiments, human participants observed the same sequence of two displays separated by a brief blank delay when performing either an integration or segregation task. First, using magneto-encephalography (MEG), we found a shift in the stimulus-evoked time courses by a 150-ms time window between task signals. After stimulus onset, multivariate pattern analysis (MVPA) decoding of task in occipital-parietal sources remained above chance for almost 1 s, and the task-decoding pattern interacted with task outcome. In the pre-stimulus period, the oscillatory phase in the theta frequency band was informative about both task processing and behavioral outcome for each task separately, suggesting that the post-stimulus effects were caused by a theta-band phase shift. Second, when aligning stimulus presentation to the onset of eye fixations, there was a similar phase shift in behavioral performance according to task demands. In both MEG and behavioral measures, task processing was optimal first for segregation and then integration, with opposite phase in the theta frequency range (3-5 Hz). The best fit to neurophysiological and behavioral data was given by a dampened 3-Hz oscillation from stimulus or eye fixation onset. The alignment of temporal integration windows to input changes found here may serve to actively organize the temporal processing of continuous sensory input. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

The western submerged sector of the Ischia volcanic island (Tyrrhenian Sea, Italy): new insights into its volcano-tectonic evolution

NASA Astrophysics Data System (ADS)

Passaro, Salvatore; de Alteriis, Giovanni; Milano, Girolamo; Fedi, Maurizio; Florio, Giovanni

2010-05-01

The Island of Ischia is a volcanic complex located in the northern boundary of the Gulf of Naples (south-eastern Tyrrhenian Sea, Italy). The island represents only the 30% of a larger, E-W trending, volcanic ridge and likely controlled by a regional tectonic lineament. Despite the many geo-volcanological and geophysical investigations conducted on the island since long time, still little is the knowledge of its offshore. Several marine surveys have been carried out over the past 10 years from IAMC - CNR research institute (Naples, Italy) mostly in the frame of INGV and GNV projects, funded by Italy Civil Protection Department. Such surveys have largely improved the knowledge of the entire volcanic complex. Multibeam bathymetry surveys has revealed several, previously unexpected, morphological and morphostructural features. Moreover some structural patterns and volcano alignments offshore show similarities with those occurring at a regional scale in the Campania region and, locally, between the island of Procida and Phlegrean Fields. Here we report the joint interpretation of geophysical data focused on the western underwater sector of the island. Interpretation was chiefly based on processing/inversion of magnetic data in turn constrained by bathymetry and seismic reflection profiles. Magnetic data, acquired by the IAMC during two different cruises in 2000 and 2002 onboard of the Urania R/V oceanographic vessel, put in evidence that the western seafloor of Ischia is characterized by the presence of a strong residual magnetic anomaly field of complex behaviour, somewhere correlated to local bathymetry. These two last methods allowed to define and distinguish between undersea and subsurface magnetic (i.e. magmatic) basement. Interpretation was also constrained by seismological data.

CLINICAL APPLICATION OF THE RIGHT SIDELYING RESPIRATORY LEFT ADDUCTOR PULL BACK EXERCISE

PubMed Central

2013-01-01

Problem: Lumbopelvic‐femoral conditions are common and may be associated with asymmetrical musculoskeletal and respiratory impairments and postural mal‐alignment called a Left Anterior Interior Chain (AIC) pattern. An inherent pattern of asymmetry involves the trunk/ribs/spine/pelvis/hip joints and includes the tendency to stand on the right leg and shift the center of gravity to the right which may result for example, in a tight left posterior hip capsule, poorly approximated left hip, long/weak left adductors, internal obliques (IO) and transverse abdominus (TA), short/strong/over active paraspinals and muscles on the right anterior outlet (adductors, levator ani and obturator internus), a left rib flare and a decreased respiratory diaphragm zone of apposition (ZOA). The Solution: A therapeutic exercise technique that can address impairments associated with postural asymmetry may be beneficial in improving function, reducing and/or eliminating pain causation, and improving breathing. The Right Sidelying Left Respiratory Adductor Pull Back is an exercise designed to affect alignment of the lumbopelvic‐femoral region by influencing the left posterior ischiofemoral ligament, ZOA and right anterior outlet and left anterior inlet (rectus femoris, sartorius), activating/shortening the left adductors, left IO/TA's and inhibiting/lengthening the paraspinals, bilaterally. Discussion: The exercise technique is often used by Physical Therapists, Physical Therapist assistants and Athletic Trainers as an initial exercise to positively affect position/alignment of the lumbopelvic‐femoral region, referred to as “repositioning,” by clinicians who use it. Four published case studies have used similar exercises to address the above impairments associated with a Left AIC pattern and in each 100% improvement in function and pain intensity was described. This particular exercise technique is relatively new and warrants future research. PMID:23772350

Book lung development in juveniles and adults of the cobweb spider, Parasteatoda tepidariorum C. L. Koch, 1841 (Araneomorphae, Theridiidae).

PubMed

Farley, Roger D

2018-03-01

Light and transmission electron microscopy were used to study the development of new book lung lamellae in juvenile and adult spiders (Parasteatoda tepidariorum). As hypothesized earlier in a study of embryos, mesenchyme cells dispersed throughout the opisthosoma (EMT) are a likely source of precursor epithelial cells (MET) for the new lamellae. The precursor cells in juveniles and adults continue many of the complex activities observed in embryos, e.g., migration, alignment, lumen formation, thinning, elongation, and secretion of the cuticle of air channel walls and trabeculae. The apicobasal polarity of precursor cells for new channels is apparently induced by the polarity pattern of precursor cells of channels produced earlier. Thus, new air and hemolymph channels extend and continue the alternating pattern of older channels. At sites more distant from the spiracle and atrium, new channels are usually produced by the mode II process (intracellular alignment and merging of vesicles). These air channels have bridging trabeculae and are quite stable in size throughout their length. At sites closer to the spiracle and atrium, new channels may be produced by mode I (coalescence of merocrine vesicle secretion). This raises the hypothesis that structural and functional differences in mode I and II channels and differing oxygen and fluid conditions with distance from the spiracle and atrium determine the mode of formation of new channels. Observations herein support an earlier hypothesis that there is some intercellular apical/apical and basal/basal affinity among the opposed surfaces of aligned precursor cells. This results in the alternating pattern of air channels at the apical and hemolymph channels at the basal cell surfaces. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Clinical application of the right sidelying respiratory left adductor pull back exercise.

PubMed

Boyle, Kyndall L

2013-06-01

Lumbopelvic-femoral conditions are common and may be associated with asymmetrical musculoskeletal and respiratory impairments and postural mal-alignment called a Left Anterior Interior Chain (AIC) pattern. An inherent pattern of asymmetry involves the trunk/ribs/spine/pelvis/hip joints and includes the tendency to stand on the right leg and shift the center of gravity to the right which may result for example, in a tight left posterior hip capsule, poorly approximated left hip, long/weak left adductors, internal obliques (IO) and transverse abdominus (TA), short/strong/over active paraspinals and muscles on the right anterior outlet (adductors, levator ani and obturator internus), a left rib flare and a decreased respiratory diaphragm zone of apposition (ZOA). A therapeutic exercise technique that can address impairments associated with postural asymmetry may be beneficial in improving function, reducing and/or eliminating pain causation, and improving breathing. The Right Sidelying Left Respiratory Adductor Pull Back is an exercise designed to affect alignment of the lumbopelvic-femoral region by influencing the left posterior ischiofemoral ligament, ZOA and right anterior outlet and left anterior inlet (rectus femoris, sartorius), activating/shortening the left adductors, left IO/TA's and inhibiting/lengthening the paraspinals, bilaterally. The exercise technique is often used by Physical Therapists, Physical Therapist assistants and Athletic Trainers as an initial exercise to positively affect position/alignment of the lumbopelvic-femoral region, referred to as "repositioning," by clinicians who use it. Four published case studies have used similar exercises to address the above impairments associated with a Left AIC pattern and in each 100% improvement in function and pain intensity was described. This particular exercise technique is relatively new and warrants future research.

Interspecific variation in mitochondrial serine transfer RNA (UCN) in Euptychiina butterflies (Lepidoptera: Satyrinae): structure and alignment.

PubMed

Marín, Mario Alejandro; López, Andrés; Uribe, Sandra Inés

2012-06-01

The nucleotide variation and structural patterns of mitochondrial RNA molecule have been proposed as useful tools in molecular systematics; however, their usefulness is always subject to a proper assessment of homology in the sequence alignment. The present study describes the secondary structure of mitochondrial tRNA for the amino acid serine (UCN) on 13 Euptychiina species and the evaluation of its potential use for evolutionary studies in this group of butterflies. The secondary structure of tRNAs showed variation among the included species except between Hermeuptychia sp1 and sp2. Variation was concentrated in the ribotimidina-pseudouridine-cystosine (TψC), dihydrouridine (DHU) and variable loops and in the DHU and TψC arms. These results suggest this region as a potential marker useful for taxonomic differentiation of species in this group and also confirm the importance of including information from the secondary structure of tRNA to optimize the alignments.

An Automatic Registration Algorithm for 3D Maxillofacial Model

NASA Astrophysics Data System (ADS)

Qiu, Luwen; Zhou, Zhongwei; Guo, Jixiang; Lv, Jiancheng

2016-09-01

3D image registration aims at aligning two 3D data sets in a common coordinate system, which has been widely used in computer vision, pattern recognition and computer assisted surgery. One challenging problem in 3D registration is that point-wise correspondences between two point sets are often unknown apriori. In this work, we develop an automatic algorithm for 3D maxillofacial models registration including facial surface model and skull model. Our proposed registration algorithm can achieve a good alignment result between partial and whole maxillofacial model in spite of ambiguous matching, which has a potential application in the oral and maxillofacial reparative and reconstructive surgery. The proposed algorithm includes three steps: (1) 3D-SIFT features extraction and FPFH descriptors construction; (2) feature matching using SAC-IA; (3) coarse rigid alignment and refinement by ICP. Experiments on facial surfaces and mandible skull models demonstrate the efficiency and robustness of our algorithm.

Transferring vertically aligned carbon nanotubes onto a polymeric substrate using a hot embossing technique for microfluidic applications.

PubMed

Mathur, A; Roy, S S; McLaughlin, J A

2010-07-06

We explored the hot embossing method for transferring vertically aligned carbon nanotubes (CNTs) into microfluidic channels, fabricated on poly-methyl-methacrylate (PMMA). Patterned and unpatterned CNTs were synthesized by microwave plasma-enhanced chemical vapour deposition on silicon to work as a stamp. For hot embossing, 115 degrees C and 1 kN force for 2 min were found to be the most suitable parameters for the complete transfer of aligned CNTs on the PMMA microchannel. Raman and SEM studies were used to analyse the microstructure of CNTs before and after hot embossing. The PMMA microparticles with dimensions (approx. 10 microm in diameter) similar to red blood cells were successfully filtered using laminar flow through these microfluidic channels. Finally, a microfluidic-based point-of-care device for blood filtration and detection of bio-molecules is drawn schematically.

Transferring vertically aligned carbon nanotubes onto a polymeric substrate using a hot embossing technique for microfluidic applications

PubMed Central

Mathur, A.; Roy, S. S.; McLaughlin, J. A.

2010-01-01

We explored the hot embossing method for transferring vertically aligned carbon nanotubes (CNTs) into microfluidic channels, fabricated on poly-methyl-methacrylate (PMMA). Patterned and unpatterned CNTs were synthesized by microwave plasma-enhanced chemical vapour deposition on silicon to work as a stamp. For hot embossing, 115°C and 1 kN force for 2 min were found to be the most suitable parameters for the complete transfer of aligned CNTs on the PMMA microchannel. Raman and SEM studies were used to analyse the microstructure of CNTs before and after hot embossing. The PMMA microparticles with dimensions (approx. 10 µm in diameter) similar to red blood cells were successfully filtered using laminar flow through these microfluidic channels. Finally, a microfluidic-based point-of-care device for blood filtration and detection of bio-molecules is drawn schematically. PMID:20147316

van der Waals Heterostructures with High Accuracy Rotational Alignment.

PubMed

Kim, Kyounghwan; Yankowitz, Matthew; Fallahazad, Babak; Kang, Sangwoo; Movva, Hema C P; Huang, Shengqiang; Larentis, Stefano; Corbet, Chris M; Taniguchi, Takashi; Watanabe, Kenji; Banerjee, Sanjay K; LeRoy, Brian J; Tutuc, Emanuel

2016-03-09

We describe the realization of van der Waals (vdW) heterostructures with accurate rotational alignment of individual layer crystal axes. We illustrate the approach by demonstrating a Bernal-stacked bilayer graphene formed using successive transfers of monolayer graphene flakes. The Raman spectra of this artificial bilayer graphene possess a wide 2D band, which is best fit by four Lorentzians, consistent with Bernal stacking. Scanning tunneling microscopy reveals no moiré pattern on the artificial bilayer graphene, and tunneling spectroscopy as a function of gate voltage reveals a constant density of states, also in agreement with Bernal stacking. In addition, electron transport probed in dual-gated samples reveals a band gap opening as a function of transverse electric field. To illustrate the applicability of this technique to realize vdW heterostructuctures in which the functionality is critically dependent on rotational alignment, we demonstrate resonant tunneling double bilayer graphene heterostructures separated by hexagonal boron-nitride dielectric.

High power density capacitor and method of fabrication

DOEpatents

Tuncer, Enis

2012-11-20

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

Directionally Aligned Amorphous Polymer Chains via Electrohydrodynamic-Jet Printing: Analysis of Morphology and Polymer Field-Effect Transistor Characteristics.

PubMed

Kim, Yebyeol; Bae, Jaehyun; Song, Hyun Woo; An, Tae Kyu; Kim, Se Hyun; Kim, Yun-Hi; Park, Chan Eon

2017-11-15

Electrohydrodynamic-jet (EHD-jet) printing provides an opportunity to directly assembled amorphous polymer chains in the printed pattern. Herein, an EHD-jet printed amorphous polymer was employed as the active layer for fabrication of organic field-effect transistors (OFETs). Under optimized conditions, the field-effect mobility (μ FET ) of the EHD-jet printed OFETs was 5 times higher than the highest μ FET observed in the spin-coated OFETs, and this improvement was achieved without the use of complex surface templating or additional pre- or post-deposition processing. As the chain alignment can be affected by the surface energy of the dielectric layer in EHD-jet printed OFETs, dielectric layers with varying wettability were examined. Near-edge X-ray absorption fine structure measurements were performed to compare the amorphous chain alignment in OFET active layers prepared by EHD-jet printing and spin coating.

High-frequency self-aligned graphene transistors with transferred gate stacks.

PubMed

Cheng, Rui; Bai, Jingwei; Liao, Lei; Zhou, Hailong; Chen, Yu; Liu, Lixin; Lin, Yung-Chen; Jiang, Shan; Huang, Yu; Duan, Xiangfeng

2012-07-17

Graphene has attracted enormous attention for radio-frequency transistor applications because of its exceptional high carrier mobility, high carrier saturation velocity, and large critical current density. Herein we report a new approach for the scalable fabrication of high-performance graphene transistors with transferred gate stacks. Specifically, arrays of gate stacks are first patterned on a sacrificial substrate, and then transferred onto arbitrary substrates with graphene on top. A self-aligned process, enabled by the unique structure of the transferred gate stacks, is then used to position precisely the source and drain electrodes with minimized access resistance or parasitic capacitance. This process has therefore enabled scalable fabrication of self-aligned graphene transistors with unprecedented performance including a record-high cutoff frequency up to 427 GHz. Our study defines a unique pathway to large-scale fabrication of high-performance graphene transistors, and holds significant potential for future application of graphene-based devices in ultra-high-frequency circuits.

Visible diffraction from quasi-crystalline arrays of carbon nanotubes

NASA Astrophysics Data System (ADS)

Butler, Timothy P.; Butt, Haider; Wilkinson, Timothy D.; Amaratunga, Gehan A. J.

2015-08-01

Large area arrays of vertically-aligned carbon nanotubes (VACNTs) are patterned in a quasi-crystalline Penrose tile arrangement through electron beam lithography definition of Ni catalyst dots and subsequent nanotube growth by plasma-enhanced chemical vapour deposition. When illuminated with a 532 nm laser beam high-quality and remarkable diffraction patterns are seen. The diffraction is well matched to theoretical calculations which assume apertures to be present at the location of the VACNTs for transmitted light. The results show that VACNTs act as diffractive elements in reflection and can be used as spatially phased arrays for producing tailored diffraction patterns.

Computing sparse derivatives and consecutive zeros problem

NASA Astrophysics Data System (ADS)

Chandra, B. V. Ravi; Hossain, Shahadat

2013-02-01

We describe a substitution based sparse Jacobian matrix determination method using algorithmic differentiation. Utilizing the a priori known sparsity pattern, a compression scheme is determined using graph coloring. The "compressed pattern" of the Jacobian matrix is then reordered into a form suitable for computation by substitution. We show that the column reordering of the compressed pattern matrix (so as to align the zero entries into consecutive locations in each row) can be viewed as a variant of traveling salesman problem. Preliminary computational results show that on the test problems the performance of nearest-neighbor type heuristic algorithms is highly encouraging.

Direct Observation of Azimuthal Correlations between DNA in Hydrated Aggregates

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

Kornyshev, Alexei A.; Lee, Dominic J.; Wynveen, Aaron

2005-09-30

This study revisits the classical x-ray diffraction patterns from hydrated, noncrystalline fibers originally used to establish the helical structure of DNA. We argue that changes in these diffraction patterns with DNA packing density reveal strong azimuthally dependent interactions between adjacent molecules up to {approx}40 A interaxial or {approx}20 A surface-to-surface separations. These interactions appear to force significant torsional 'straightening' of DNA and strong azimuthal alignment of nearest neighbor molecules. The results are in good agreement with the predictions of recent theoretical models relating DNA-DNA interactions to the helical symmetry of their surface charge patterns.

Surface Acoustic Waves Grant Superior Spatial Control of Cells Embedded in Hydrogel Fibers.

PubMed

Lata, James P; Guo, Feng; Guo, Jinshan; Huang, Po-Hsun; Yang, Jian; Huang, Tony Jun

2016-10-01

By exploiting surface acoustic waves and a coupling layer technique, cells are patterned within a photosensitive hydrogel fiber to mimic physiological cell arrangement in tissues. The aligned cell-polymer matrix is polymerized with short exposure to UV light and the fiber is extracted. These patterned cell fibers are manipulated into simple and complex architectures, demonstrating feasibility for tissue-engineering applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

3D structural patterns in scalable, elastomeric scaffolds guide engineered tissue architecture.

PubMed

Kolewe, Martin E; Park, Hyoungshin; Gray, Caprice; Ye, Xiaofeng; Langer, Robert; Freed, Lisa E

2013-08-27

Microfabricated elastomeric scaffolds with 3D structural patterns are created by semiautomated layer-by-layer assembly of planar polymer sheets with through-pores. The mesoscale interconnected pore architectures governed by the relative alignment of layers are shown to direct cell and muscle-like fiber orientation in both skeletal and cardiac muscle, enabling scale up of tissue constructs towards clinically relevant dimensions. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of utilization of desert habitats with dynamic simulation

USGS Publications Warehouse

Williams, B.K.

1986-01-01

The effects of climate and herbivores on cool desert shrubs in north-western Utah were investigated with a dynamic simulation model. Cool desert shrublands are extensively managed as grazing lands, and are defoliated annually by domestic livestock. A primary production model was used to simulate harvest yields and shrub responses under a variety of climatic regimes and defoliation patterns. The model consists of six plant components, and it is based on equations of growth analysis. Plant responses were simulated under various combinations of 20 annual weather patterns and 14 defoliation strategies. Results of the simulations exhibit some unexpected linearities in model behavior, and emphasize the importance of both the pattern of climate and the level of plant vigor in determining optimal harvest strategies. Model behaviors are interpreted in terms of shrub morphology, physiology and ecology.

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

Strons, Philip; Bailey, James L.

Anemometer readings alone cannot provide a complete picture of air flow patterns at an open gloveport. Having a means to visualize air flow for field tests in general provides greater insight by indicating direction in addition to the magnitude of the air flow velocities in the region of interest. Furthermore, flow visualization is essential for Computational Fluid Dynamics (CFD) verification, where important modeling assumptions play a significant role in analyzing the chaotic nature of low-velocity air flow. A good example is shown Figure 1, where an unexpected vortex pattern occurred during a field test that could not have been measuredmore » relying only on anemometer readings. Here by, observing and measuring the patterns of the smoke flowing into the gloveport allowed the CFD model to be appropriately updated to match the actual flow velocities in both magnitude and direction.« less

Formation of polarity convergences underlying shoot outgrowths

PubMed Central

Abley, Katie; Sauret-Güeto, Susanna; Marée, Athanasius FM; Coen, Enrico

2016-01-01

The development of outgrowths from plant shoots depends on formation of epidermal sites of cell polarity convergence with high intracellular auxin at their centre. A parsimonious model for generation of convergence sites is that cell polarity for the auxin transporter PIN1 orients up auxin gradients, as this spontaneously generates convergent alignments. Here we test predictions of this and other models for the patterns of auxin biosynthesis and import. Live imaging of outgrowths from kanadi1 kanadi2 Arabidopsis mutant leaves shows that they arise by formation of PIN1 convergence sites within a proximodistal polarity field. PIN1 polarities are oriented away from regions of high auxin biosynthesis enzyme expression, and towards regions of high auxin importer expression. Both expression patterns are required for normal outgrowth emergence, and may form part of a common module underlying shoot outgrowths. These findings are more consistent with models that spontaneously generate tandem rather than convergent alignments. DOI: http://dx.doi.org/10.7554/eLife.18165.001 PMID:27478985

Stacked Fresnel Zone Plates for High Energy X-rays

NASA Astrophysics Data System (ADS)

Snigireva, Irina; Snigirev, Anatoly; Vaughan, Gavin; Di Michiel, Marco; Kohn, Viktor; Yunkin, Vyacheslav; Grigoriev, Maxim

2007-01-01

A stacking technique was developed in order to increase focusing efficiency of Fresnel zone plates (FZP) at high energies. Two identical Si chips each of which containing 9 FZPs were used for stacking. Alignment of the chips was achieved by on-line observation of the moiré pattern. The formation of moiré patterns was studied theoretically and experimentally at different experimental conditions. To provide the desired stability Si-chips were bonded together with slow solidification speed epoxy glue. A technique of angular alignment in order to compensate a linear displacement in the process of gluing was proposed. Two sets of stacked FZPs were experimentally tested to focus 15 and 50 keV x rays. The gain in the efficiency by factor 2.5 was demonstrated at 15 keV. The focal spot of 1.8 μm vertically and 14 μm horizontally with 35% efficiency was measured at 50 keV. Forecast for the stacking of nanofocusing FZPs was discussed.

Hard X-ray focusing by stacked Fresnel zone plates

NASA Astrophysics Data System (ADS)

Snigireva, Irina; Snigirev, Anatoly; Kohn, Viktor; Yunkin, Vyacheslav; Grigoriev, Maxim; Kuznetsov, Serguei; Vaughan, Gavin; Di Michiel, Marco

2007-09-01

Stacking technique was developed in order to increase focusing efficiency of Fresnel zone plates at high energies. Two identical Si chips each of which containing Fresnel zone plates were used for stacking. Alignment of the chips was achieved by on-line observation of the moiré pattern from the two zone plates. The formation of moiré patterns was studied theoretically and experimentally at different experimental conditions. To provide the desired stability Si-chips with zone plates were bonded together with slow solidification speed epoxy glue. Technique of angular alignment in order to compensate a linear displacement in the process of gluing was proposed. Two sets of stacked FZPs were produced and experimentally tested to focus 15 and 50 keV X-rays. Gain in the efficiency by factor 2.5 was demonstrated at 15 keV. Focal spot of 1.8 μm vertically and 14 μm horizontally with 35% efficiency was measured at 50 keV. Forecast for the stacking of nanofocusing Fresnel zone plates was discussed.