Asymptotically stable phase synchronization revealed by autoregressive circle maps

NASA Astrophysics Data System (ADS)

Drepper, F. R.

2000-11-01

A specially designed of nonlinear time series analysis is introduced based on phases, which are defined as polar angles in spaces spanned by a finite number of delayed coordinates. A canonical choice of the polar axis and a related implicit estimation scheme for the potentially underlying autoregressive circle map (next phase map) guarantee the invertibility of reconstructed phase space trajectories to the original coordinates. The resulting Fourier approximated, invertibility enforcing phase space map allows us to detect conditional asymptotic stability of coupled phases. This comparatively general synchronization criterion unites two existing generalizations of the old concept and can successfully be applied, e.g., to phases obtained from electrocardiogram and airflow recordings characterizing cardiorespiratory interaction.

Mapped grid methods for long-range molecules and cold collisions

NASA Astrophysics Data System (ADS)

Willner, K.; Dulieu, O.; Masnou-Seeuws, F.

2004-01-01

The paper discusses ways of improving the accuracy of numerical calculations for vibrational levels of diatomic molecules close to the dissociation limit or for ultracold collisions, in the framework of a grid representation. In order to avoid the implementation of very large grids, Kokoouline et al. [J. Chem. Phys. 110, 9865 (1999)] have proposed a mapping procedure through introduction of an adaptive coordinate x subjected to the variation of the local de Broglie wavelength as a function of the internuclear distance R. Some unphysical levels ("ghosts") then appear in the vibrational series computed via a mapped Fourier grid representation. In the present work the choice of the basis set is reexamined, and two alternative expansions are discussed: Sine functions and Hardy functions. It is shown that use of a basis set with fixed nodes at both grid ends is efficient to eliminate "ghost" solutions. It is further shown that the Hamiltonian matrix in the sine basis can be calculated very accurately by using an auxiliary basis of cosine functions, overcoming the problems arising from numerical calculation of the Jacobian J(x) of the R→x coordinate transformation.

A new hyperchaotic map and its application for image encryption

NASA Astrophysics Data System (ADS)

Natiq, Hayder; Al-Saidi, N. M. G.; Said, M. R. M.; Kilicman, Adem

2018-01-01

Based on the one-dimensional Sine map and the two-dimensional Hénon map, a new two-dimensional Sine-Hénon alteration model (2D-SHAM) is hereby proposed. Basic dynamic characteristics of 2D-SHAM are studied through the following aspects: equilibria, Jacobin eigenvalues, trajectory, bifurcation diagram, Lyapunov exponents and sensitivity dependence test. The complexity of 2D-SHAM is investigated using Sample Entropy algorithm. Simulation results show that 2D-SHAM is overall hyperchaotic with the high complexity, and high sensitivity to its initial values and control parameters. To investigate its performance in terms of security, a new 2D-SHAM-based image encryption algorithm (SHAM-IEA) is also proposed. In this algorithm, the essential requirements of confusion and diffusion are accomplished, and the stochastic 2D-SHAM is used to enhance the security of encrypted image. The stochastic 2D-SHAM generates random values, hence SHAM-IEA can produce different encrypted images even with the same secret key. Experimental results and security analysis show that SHAM-IEA has strong capability to withstand statistical analysis, differential attack, chosen-plaintext and chosen-ciphertext attacks.

The Relationship between Self-Assembly and Conformal Mappings

NASA Astrophysics Data System (ADS)

Duque, Carlos; Santangelo, Christian

The isotropic growth of a thin sheet has been used as a way to generate programmed shapes through controlled buckling. We discuss how conformal mappings, which are transformations that locally preserve angles, provide a way to quantify the area growth needed to produce a particular shape. A discrete version of the conformal map can be constructed from circle packings, which are maps between packings of circles whose contact network is preserved. This provides a link to the self-assembly of particles on curved surfaces. We performed simulations of attractive particles on a curved surface using molecular dynamics. The resulting particle configurations were used to generate the corresponding discrete conformal map, allowing us to quantify the degree of area distortion required to produce a particular shape by finding particle configurations that minimize the area distortion.

Tame majorant analyticity for the Birkhoff map of the defocusing nonlinear Schrödinger equation on the circle

NASA Astrophysics Data System (ADS)

Maspero, A.

2018-05-01

For the defocusing nonlinear Schrödinger equation on the circle, we construct a Birkhoff map Φ which is tame majorant analytic in a neighborhood of the origin. Roughly speaking, majorant analytic means that replacing the coefficients of the Taylor expansion of Φ by their absolute values gives rise to a series (the majorant map) which is uniformly and absolutely convergent, at least in a small neighborhood. Tame majorant analytic means that the majorant map of Φ fulfills tame estimates. The proof is based on a new tame version of the Kuksin–Perelman theorem (2010 Discrete Contin. Dyn. Syst. 1 1–24), which is an infinite dimensional Vey type theorem.

Bifurcation structure of successive torus doubling

NASA Astrophysics Data System (ADS)

Sekikawa, Munehisa; Inaba, Naohiko; Yoshinaga, Tetsuya; Tsubouchi, Takashi

2006-01-01

The authors discuss the “embryology” of successive torus doubling via the bifurcation theory, and assert that the coupled map of a logistic map and a circle map has a structure capable of generating infinite number of torus doublings.

MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals

PubMed Central

Nishihara, Hidenori; Plazzi, Federico; Passamonti, Marco; Okada, Norihiro

2016-01-01

SINEs (short interspersed elements) are transposable elements that typically originate independently in each taxonomic clade (order/family). However, some SINE families share a highly similar central sequence and are thus categorized as a SINE superfamily. Although only four SINE superfamilies (CORE-SINEs, V-SINEs, DeuSINEs, and Ceph-SINEs) have been reported so far, it is expected that new SINE superfamilies would be discovered by deep exploration of new SINEs in metazoan genomes. Here we describe 15 SINEs, among which 13 are novel, that have a similar 66-bp central region and therefore constitute a new SINE superfamily, MetaSINEs. MetaSINEs are distributed from fish to cnidarians, suggesting their common evolutionary origin at least 640 Ma. Because the 3′ tails of MetaSINEs are variable, these SINEs most likely survived by changing their partner long interspersed elements for retrotransposition during evolution. Furthermore, we examined the presence of members of other SINE superfamilies in bivalve genomes and characterized eight new SINEs belonging to the CORE-SINEs, V-SINEs, and DeuSINEs, in addition to the MetaSINEs. The broad distribution of bivalve SINEs suggests that at least three SINEs originated in the common ancestor of Bivalvia. Our comparative analysis of the central domains of the SINEs revealed that, in each superfamily, only a restricted region is shared among all of its members. Because the functions of the central domains of the SINE superfamilies remain unknown, such structural information of SINE superfamilies will be useful for future experimental and comparative analyses to reveal why they have been retained in metazoan genomes during evolution. PMID:26872770

Alternate forms of the associated Legendre functions for use in geomagnetic modeling.

USGS Publications Warehouse

Alldredge, L.R.; Benton, E.R.

1986-01-01

An inconvenience attending traditional use of associated Legendre functions in global modeling is that the functions are not separable with respect to the 2 indices (order and degree). In 1973 Merilees suggested a way to avoid the problem by showing that associated Legendre functions of order m and degree m+k can be expressed in terms of elementary functions. This note calls attention to some possible gains in time savings and accuracy in geomagnetic modeling based upon this form. For this purpose, expansions of associated Legendre polynomials in terms of sines and cosines of multiple angles are displayed up to degree and order 10. Examples are also given explaining how some surface spherical harmonics can be transformed into true Fourier series for selected polar great circle paths. -from Authors

MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals.

PubMed

Nishihara, Hidenori; Plazzi, Federico; Passamonti, Marco; Okada, Norihiro

2016-02-12

SINEs (short interspersed elements) are transposable elements that typically originate independently in each taxonomic clade (order/family). However, some SINE families share a highly similar central sequence and are thus categorized as a SINE superfamily. Although only four SINE superfamilies (CORE-SINEs, V-SINEs, DeuSINEs, and Ceph-SINEs) have been reported so far, it is expected that new SINE superfamilies would be discovered by deep exploration of new SINEs in metazoan genomes. Here we describe 15 SINEs, among which 13 are novel, that have a similar 66-bp central region and therefore constitute a new SINE superfamily, MetaSINEs. MetaSINEs are distributed from fish to cnidarians, suggesting their common evolutionary origin at least 640 Ma. Because the 3' tails of MetaSINEs are variable, these SINEs most likely survived by changing their partner long interspersed elements for retrotransposition during evolution. Furthermore, we examined the presence of members of other SINE superfamilies in bivalve genomes and characterized eight new SINEs belonging to the CORE-SINEs, V-SINEs, and DeuSINEs, in addition to the MetaSINEs. The broad distribution of bivalve SINEs suggests that at least three SINEs originated in the common ancestor of Bivalvia. Our comparative analysis of the central domains of the SINEs revealed that, in each superfamily, only a restricted region is shared among all of its members. Because the functions of the central domains of the SINE superfamilies remain unknown, such structural information of SINE superfamilies will be useful for future experimental and comparative analyses to reveal why they have been retained in metazoan genomes during evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Late Cretaceous sub-volcanic structure in the continental shelf off Portugal and its implications on tectonics and seismicity

NASA Astrophysics Data System (ADS)

Neres, Marta; Terrinha, Pedro; Custódio, Susana; Noiva, João; Brito, Pedro; Santos, Joana; Carrilho, Fernando

2017-04-01

Long-lasting and widespread alkaline magmatism is recognized in the west Portuguese margin. Offshore, several volcanic seamounts punctuate the Tore-Madeira Rise and the Estremadura Spur, with known ages between 80 and 100 Ma. Onshore, the major events are the Monchique (69-73 Ma), Sines (75-77 Ma) and Sintra (75-82 Ma) plutons - whose location (aligned along 200 km) and age discrepancy inspired some geodynamic models for Iberia during the Cretaceous - and the Lisbon Volcanic Complex (90-100 Ma). Structural links between them have been proposed but no direct evidence was yet found for it. In this work we present new magnetic data from recent marine magnetic surveys (ROCHEL and MINEPLAT project) conducted off the west Portuguese coast on the continental shelf and slope. A total area of about 3000 km2 between Sintra and Sines was surveyed with line spacing of 1 mile. Very high-resolution multi-channel seismic profiles were simultaneously acquired with the magnetics covering an area of 400 km2 off Sines. Two main primary outcomes arise from these data. On one hand, higher-resolution mapping in regions where magnetic anomalies were already known allows a better understanding of the buried sub-volcanic system. On the other hand, previously unknown NNW-SSE aligned magnetic anomalies were identified along the coast off Sines, possibly corresponding to buried Late Cretaceous alkaline magmatic intrusives. The presence of magmatic bodies was up to now unknown in this region, and these findings reignite the discussion about a structural link connecting the three main on land intrusive complexes, Sintra, Sines and Monchique. In addition to the structural control of the magmatic complexes, seismicity is also an issue as a cluster of seismicity coincident with the Monchique complex has long been known. Smaller clusters coincide with the magnetic anomalies mapped during the ROCHEL and MINEPLAT surveys, as well. We interpret these results in the light of the tectono-magmatism of West Iberia during the Late Cretaceous and at Present, specifically: What was the tectonic control for the emplacement of these magmatic bodies emplaced on the rifted margin? Is the rheological contrast between magmatic bodies and host-rocks controlling the seismicity localization? Publication supported by FCT- project UID/GEO/50019/2013 - Instituto Dom Luiz.

Neurotoxic Doses of Chronic Methamphetamine Trigger Retrotransposition of the Identifier Element in Rat Dorsal Dentate Gyrus

PubMed Central

Moszczynska, Anna; Burghardt, Kyle J.; Yu, Dongyue

2017-01-01

Short interspersed elements (SINEs) are typically silenced by DNA hypermethylation in somatic cells, but can retrotranspose in proliferating cells during adult neurogenesis. Hypomethylation caused by disease pathology or genotoxic stress leads to genomic instability of SINEs. The goal of the present investigation was to determine whether neurotoxic doses of binge or chronic methamphetamine (METH) trigger retrotransposition of the identifier (ID) element, a member of the rat SINE family, in the dentate gyrus genomic DNA. Adult male Sprague-Dawley rats were treated with saline or high doses of binge or chronic METH and sacrificed at three different time points thereafter. DNA methylation analysis, immunohistochemistry and next-generation sequencing (NGS) were performed on the dorsal dentate gyrus samples. Binge METH triggered hypomethylation, while chronic METH triggered hypermethylation of the CpG-2 site. Both METH regimens were associated with increased intensities in poly(A)-binding protein 1 (PABP1, a SINE regulatory protein)-like immunohistochemical staining in the dentate gyrus. The amplification of several ID element sequences was significantly higher in the chronic METH group than in the control group a week after METH, and they mapped to genes coding for proteins regulating cell growth and proliferation, transcription, protein function as well as for a variety of transporters. The results suggest that chronic METH induces ID element retrotransposition in the dorsal dentate gyrus and may affect hippocampal neurogenesis. PMID:28272323

Quasiperiodicity and Frequency Locking in Electronic Conduction in Germanium.

NASA Astrophysics Data System (ADS)

Gwinn, Elisabeth Gray

1987-09-01

This thesis presents an experimental study of a driven spatio-temporal instability in high-field transport in cooled, p-type Ge. The instability is produced at liquid He temperatures by d.c. voltage bias above the threshold for breakdown by impurity impact ionization, and is associated experimentally with voltage-controlled negative differential conductivity. The instability is coupled to an external oscillator by applying a sinusoidal voltage bias across the Ge sample. The driven instability exhibits frequency locking, quasiperiodicity, and chaos as the frequency and amplitude of the sinusoidal bias are varied. An iterative map of the circle provides a simple model for such a coupled, dissipative nonlinear oscillator system. The transition from quasiperiodicity to chaos in this model system occurs in a universal way; for example, the circle map has a universal, self-similar power spectrum at the onset of chaos with the golden mean winding number. When normalized appropriately, the power spectrum at the onset of chaos in the driven instability in Ge displays the same structure, with good agreement between the amplitudes of the experimental and theoretical spectral peaks. The relevance of universal theory to experiment can also be tested with a spectrum of scaling indices f( alpha), which is used to compare the probability distribution for the circle map at the onset of chaos with the golden mean winding number to the distribution of probability on a Poincare section of the experimental attractor. The procedure used to find f(alpha ) for the driven transport instability overcomes the sensitivity of f(alpha) to noise and to deviation from the critical amplitude. The f( alpha) curve for the driven instability in Ge is found to be in good agreement with the universal circle map result.

Rouleaux red blood cells splitting in microscopic thin blood smear images via local maxima, circles drawing, and mapping with original RBCs.

PubMed

Rehman, Amjad; Abbas, Naveed; Saba, Tanzila; Mahmood, Toqeer; Kolivand, Hoshang

2018-04-10

Splitting the rouleaux RBCs from single RBCs and its further subdivision is a challenging area in computer-assisted diagnosis of blood. This phenomenon is applied in complete blood count, anemia, leukemia, and malaria tests. Several automated techniques are reported in the state of art for this task but face either under or over splitting problems. The current research presents a novel approach to split Rouleaux red blood cells (chains of RBCs) precisely, which are frequently observed in the thin blood smear images. Accordingly, this research address the rouleaux splitting problem in a realistic, efficient and automated way by considering the distance transform and local maxima of the rouleaux RBCs. Rouleaux RBCs are splitted by taking their local maxima as the centres to draw circles by mid-point circle algorithm. The resulting circles are further mapped with single RBC in Rouleaux to preserve its original shape. The results of the proposed approach on standard data set are presented and analyzed statistically by achieving an average recall of 0.059, an average precision of 0.067 and F-measure 0.063 are achieved through ground truth with visual inspection. © 2018 Wiley Periodicals, Inc.

A High-Precision Instrument for Mapping of Rotational Errors in Rotary Stages

DOE PAGES

Xu, W.; Lauer, K.; Chu, Y.; ...

2014-11-02

A rotational stage is a key component of every X-ray instrument capable of providing tomographic or diffraction measurements. To perform accurate three-dimensional reconstructions, runout errors due to imperfect rotation (e.g. circle of confusion) must be quantified and corrected. A dedicated instrument capable of full characterization and circle of confusion mapping in rotary stages down to the sub-10 nm level has been developed. A high-stability design, with an array of five capacitive sensors, allows simultaneous measurements of wobble, radial and axial displacements. The developed instrument has been used for characterization of two mechanical stages which are part of an X-ray microscope.

Change in First Leaf Date Between 1951-1960 and 2006-2015

EPA Pesticide Factsheets

This figure shows modeled trends in lilac and honeysuckle first leaf dates at weather stations across the contiguous 48 states. This map compares the average first leaf date during two 10-year periods, developed using data from the USA National Phenology Network. Blue circles represent later leaf dates, and red circles represent earlier. For more information: www.epa.gov/climatechange/science/indicators

Fine tuning breath-hold-based cerebrovascular reactivity analysis models.

PubMed

van Niftrik, Christiaan Hendrik Bas; Piccirelli, Marco; Bozinov, Oliver; Pangalu, Athina; Valavanis, Antonios; Regli, Luca; Fierstra, Jorn

2016-02-01

We elaborate on existing analysis methods for breath-hold (BH)-derived cerebrovascular reactivity (CVR) measurements and describe novel insights and models toward more exact CVR interpretation. Five blood-oxygen-level-dependent (BOLD) fMRI datasets of neurovascular patients with unilateral hemispheric hemodynamic impairment were used to test various BH CVR analysis methods. Temporal lag (phase), percent BOLD signal change (CVR), and explained variance (coherence) maps were calculated using three different sine models and two novel "Optimal Signal" model-free methods based on the unaffected hemisphere and the sagittal sinus fMRI signal time series, respectively. All models showed significant differences in CVR and coherence between the affected-hemodynamic impaired-and unaffected hemisphere. Voxel-wise phase determination significantly increases CVR (0.60 ± 0.18 vs. 0.82 ± 0.27; P < 0.05). Incorporating different durations of breath hold and resting period in one sine model (two-task) did increase coherence in the unaffected hemisphere, as well as eliminating negative phase commonly obtained by one-task frequency models. The novel model-free "optimal signal" methods both explained the BOLD MR data similar to the two task sine model. Our CVR analysis demonstrates an improved CVR and coherence after implementation of voxel-wise phase and frequency adjustment. The novel "optimal signal" methods provide a robust and feasible alternative to the sine models, as both are model-free and independent of compliance. Here, the sagittal sinus model may be advantageous, as it is independent of hemispheric CVR impairment.

A tale of two fractals: The Hofstadter butterfly and the integral Apollonian gaskets

NASA Astrophysics Data System (ADS)

Satija, Indubala I.

2016-11-01

This paper unveils a mapping between a quantum fractal that describes a physical phenomena, and an abstract geometrical fractal. The quantum fractal is the Hofstadter butterfly discovered in 1976 in an iconic condensed matter problem of electrons moving in a two-dimensional lattice in a transverse magnetic field. The geometric fractal is the integer Apollonian gasket characterized in terms of a 300 BC problem of mutually tangent circles. Both of these fractals are made up of integers. In the Hofstadter butterfly, these integers encode the topological quantum numbers of quantum Hall conductivity. In the Apollonian gaskets an infinite number of mutually tangent circles are nested inside each other, where each circle has integer curvature. The mapping between these two fractals reveals a hidden D3 symmetry embedded in the kaleidoscopic images that describe the asymptotic scaling properties of the butterfly. This paper also serves as a mini review of these fractals, emphasizing their hierarchical aspects in terms of Farey fractions.

VHF radar measurements over Andoya (Northern Norway)

NASA Technical Reports Server (NTRS)

Czechowsky, P.; Reid, I. M.; Ruester, R.; Schmidt, G.

1989-01-01

The Mobile SOUSY Radar was operated during the MAP/WINE, the MAC/SINE, and MAC/Epsilon campaigns at Andoya in Northern Norway. A comparison between summer and winter results is presented, in particular the generation and development of the scattering regions, the different power spectral densities and the aspect sensitivities which were derived from six different beam directions.

A Simulation Algorithm to Approximate the Area of Mapped Forest Inventory Plots

Treesearch

William A. Bechtold; Naser E. Heravi; Matthew E. Kinkenon

2003-01-01

Calculating the area of polygons associated with mapped forest inventory plots can be mathematically cumbersome, especially when computing change between inventories. We developed a simulation technique that utilizes a computer-generated dot grid and geometry to estimate the area of mapped polygons within any size circle. The technique also yields a matrix of change in...

SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets.

PubMed

Mao, Hongliang; Wang, Hao

2017-03-01

Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes. The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan , implemented in PERL and supported on Linux. wangh8@fudan.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets

PubMed Central

Mao, Hongliang

2017-01-01

Abstract Motivation: Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. Results: Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes. Availability and Implementation: The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan, implemented in PERL and supported on Linux. Contact: wangh8@fudan.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28062442

A difference tracking algorithm based on discrete sine transform

NASA Astrophysics Data System (ADS)

Liu, HaoPeng; Yao, Yong; Lei, HeBing; Wu, HaoKun

2018-04-01

Target tracking is an important field of computer vision. The template matching tracking algorithm based on squared difference matching (SSD) and standard correlation coefficient (NCC) matching is very sensitive to the gray change of image. When the brightness or gray change, the tracking algorithm will be affected by high-frequency information. Tracking accuracy is reduced, resulting in loss of tracking target. In this paper, a differential tracking algorithm based on discrete sine transform is proposed to reduce the influence of image gray or brightness change. The algorithm that combines the discrete sine transform and the difference algorithm maps the target image into a image digital sequence. The Kalman filter predicts the target position. Using the Hamming distance determines the degree of similarity between the target and the template. The window closest to the template is determined the target to be tracked. The target to be tracked updates the template. Based on the above achieve target tracking. The algorithm is tested in this paper. Compared with SSD and NCC template matching algorithms, the algorithm tracks target stably when image gray or brightness change. And the tracking speed can meet the read-time requirement.

The IAT shows no evidence for Kandinsky's color-shape associations.

PubMed

Makin, Alexis D J; Wuerger, Sophie M

2013-01-01

In the early twentieth century, the Bauhaus revolutionized art and design by using simple colors and forms. Wassily Kandinsky was especially interested in the relationship of these two visual attributes and postulated a fundamental correspondence between color and form: yellow triangle, red square and blue circle. Subsequent empirical studies used preference judgments to test Kandinsky's original color-form combinations, usually yielding inconsistent results. We have set out to test the validity of these postulated associations by using the Implicit Association Test. Participants pressed one of two buttons on each trial. On some trials they classified shapes (e.g., circle or triangle). On interleaved trials they classified colors (e.g., blue or yellow). Response times should theoretically be faster when the button mapping follows Kandinsky's associations: For example, when the left key is used to report blue or circle and the right is used for yellow and triangle, than when the response mapping is the opposite of this (blue or triangle, yellow or circle). Our findings suggest that there is no implicit association between the original color-form combinations. Of the three combinations we tested, there was only a marginal effect in one case. It can be concluded that the IAT does not support Kandinsky's postulated color-form associations, and that these are probably not a universal property of the visual system.

Great circle solution to polarization-based quantum communication (QC) in optical fiber

DOEpatents

Nordholt, Jane Elizabeth; Peterson, Charles Glen; Newell, Raymond Thorson; Hughes, Richard John

2016-03-15

Birefringence in optical fibers is compensated by applying polarization modulation at a receiver. Polarization modulation is applied so that a transmitted optical signal has states of polarization (SOPs) that are equally spaced on the Poincare sphere. Fiber birefringence encountered in propagation between a transmitter and a receiver rotates the great circle on the Poincare sphere that represents the polarization bases used for modulation. By adjusting received polarizations, polarization components of the received optical signal can be directed to corresponding detectors for decoding, regardless of the magnitude and orientation of the fiber birefringence. A transmitter can be configured to transmit in conjugate polarization bases whose SOPs can be represented as equidistant points on a great circle so that the received SOPs are mapped to equidistant points on a great circle and routed to corresponding detectors.

Coming Full Circle in Standard Setting: A Commentary on Wyse

ERIC Educational Resources Information Center

Skaggs, Gary

2013-01-01

The construct map is a particularly good way to approach instrument development, and this author states that he was delighted to read Adam Wyse's thoughts about how to use construct maps for standard setting. For a number of popular standard-setting methods, Wyse shows how typical feedback to panelists fits within a construct map framework.…

Middle Atmosphere Cooperation/Summer in Northern Europe (MAC/SINE) and MAC/Epsilon

NASA Technical Reports Server (NTRS)

Thrane, E. V.

1989-01-01

Two major international campaigns dedicated to the study of middle atmosphere dynamics in high latitudes were successfully completed in 1987. MAC/SINE (Middle Atmosphere Cooperation/Summer in Northern Europe) was carried out during the period 7 June to 19 July, whereas MAC/Epsilon took place in the period 12 October to 15 November. In both campaigns a large number of ground based and rocket techniques were used in a concerted effort to map the dynamical structure of the middle atmosphere over Northern Europe. Although the analysis of the observations has only just started, it is clear that a large and unique data set was obtained, which is believed will provide new insight into the dynamical processes in this interesting region of the atmosphere. A brief overview of the campaigns, their scientific aims, organization and structure is presented.

Functional noncoding sequences derived from SINEs in the mammalian genome.

PubMed

Nishihara, Hidenori; Smit, Arian F A; Okada, Norihiro

2006-07-01

Recent comparative analyses of mammalian sequences have revealed that a large number of nonprotein-coding genomic regions are under strong selective constraint. Here, we report that some of these loci have been derived from a newly defined family of ancient SINEs (short interspersed repetitive elements). This is a surprising result, as SINEs and other transposable elements are commonly thought to be genomic parasites. We named the ancient SINE family AmnSINE1, for Amniota SINE1, because we found it to be present in mammals as well as in birds, and some copies predate the mammalian-bird split 310 million years ago (Mya). AmnSINE1 has a chimeric structure of a 5S rRNA and a tRNA-derived SINE, and is related to five tRNA-derived SINE families that we characterized here in the coelacanth, dogfish shark, hagfish, and amphioxus genomes. All of the newly described SINE families have a common central domain that is also shared by zebrafish SINE3, and we collectively name them the DeuSINE (Deuterostomia SINE) superfamily. Notably, of the approximately 1000 still identifiable copies of AmnSINE1 in the human genome, 105 correspond to loci phylogenetically highly conserved among mammalian orthologs. The conservation is strongest over the central domain. Thus, AmnSINE1 appears to be the best example of a transposable element of which a significant fraction of the copies have acquired genomic functionality.

PCR-based approach to SINE isolation: simple and complex SINEs.

PubMed

Borodulina, Olga R; Kramerov, Dmitri A

2005-04-11

Highly repeated copies of short interspersed elements (SINEs) occur in eukaryotic genomes. The distribution of each SINE family is usually restricted to some genera, families, or orders. SINEs have an RNA polymerase III internal promoter, which is composed of boxes A and B. Here we propose a method for isolation of novel SINE families based on genomic DNA PCR with oligonucleotide identical to box A as a primer. Cloning of the size-heterogeneous PCR-products and sequencing of their terminal regions allow determination of SINE structure. Using this approach, two novel SINE families, Rhin-1 and Das-1, from the genomes of great horseshoe bat (Rhinolophus ferrumequinum) and nine-banded armadillo (Dasypus novemcinctus), respectively, were isolated and studied. The distribution of Rhin-1 is restricted to two of six bat families tested. Copies of this SINE are characterized by frequent internal insertions and significant length (200-270 bp). Das-1 being only 90 bp in length is one of the shortest SINEs known. Most of Das-1 nucleotide sequences demonstrate significant similarity to alanine tRNA which appears to be an evolutionary progenitor of this SINE. Together with three other known SINEs (ID, Vic-1, and CYN), Das-1 constitutes a group of simple SINEs. Interestingly, three SINE families of this group are alanine tRNA-derived. Most probably, this tRNA gave rise to short and simple but successful SINEs several times during mammalian evolution.

SINEBase: a database and tool for SINE analysis.

PubMed

Vassetzky, Nikita S; Kramerov, Dmitri A

2013-01-01

SINEBase (http://sines.eimb.ru) integrates the revisited body of knowledge about short interspersed elements (SINEs). A set of formal definitions concerning SINEs was introduced. All available sequence data were screened through these definitions and the genetic elements misidentified as SINEs were discarded. As a result, 175 SINE families have been recognized in animals, flowering plants and green algae. These families were classified by the modular structure of their nucleotide sequences and the frequencies of different patterns were evaluated. These data formed the basis for the database of SINEs. The SINEBase website can be used in two ways: first, to explore the database of SINE families, and second, to analyse candidate SINE sequences using specifically developed tools. This article presents an overview of the database and the process of SINE identification and analysis.

SINEBase: a database and tool for SINE analysis

PubMed Central

Vassetzky, Nikita S.; Kramerov, Dmitri A.

2013-01-01

SINEBase (http://sines.eimb.ru) integrates the revisited body of knowledge about short interspersed elements (SINEs). A set of formal definitions concerning SINEs was introduced. All available sequence data were screened through these definitions and the genetic elements misidentified as SINEs were discarded. As a result, 175 SINE families have been recognized in animals, flowering plants and green algae. These families were classified by the modular structure of their nucleotide sequences and the frequencies of different patterns were evaluated. These data formed the basis for the database of SINEs. The SINEBase website can be used in two ways: first, to explore the database of SINE families, and second, to analyse candidate SINE sequences using specifically developed tools. This article presents an overview of the database and the process of SINE identification and analysis. PMID:23203982

Changes in Stream Water Temperatures in the Chesapeake Bay Region, 1960-2014

EPA Pesticide Factsheets

This map shows the changes in stream water temperatures in the Chesapeake Bay region from 1960 to 2014. Blue circles represent cooling trends in stream water temperatures, and red circles represent warming trends in stream water temperatures. Data were analyzed by Mike Kolian of EPA in partnership with John Jastram and Karen Rice of the U.S. Geological Survey. For more information: www.epa.gov/climatechange/science/indicators

Wilderness quality mapping - the Australian experiences

Treesearch

Nick Sawyer

2015-01-01

By 1995 wilderness quality maps developed under the Australian Government's National Wilderness Inventory (NWI) program had been published for most of Australia, but few traces of the NWI now remain and the word "wilderness" has become almost unmentionable in government and professional land management circles. Yet its popular appeal is demonstrated by...

A RAB3GAP1 SINE Insertion in Alaskan Huskies with Polyneuropathy, Ocular Abnormalities, and Neuronal Vacuolation (POANV) Resembling Human Warburg Micro Syndrome 1 (WARBM1)

PubMed Central

Wiedmer, Michaela; Oevermann, Anna; Borer-Germann, Stephanie E.; Gorgas, Daniela; Shelton, G. Diane; Drögemüller, Michaela; Jagannathan, Vidhya; Henke, Diana; Leeb, Tosso

2015-01-01

We observed a hereditary phenotype in Alaskan Huskies that was characterized by polyneuropathy with ocular abnormalities and neuronal vacuolation (POANV). The affected dogs developed a progressive severe ataxia, which led to euthanasia between 8 and 16 months of age. The pedigrees were consistent with a monogenic autosomal recessive inheritance. We localized the causative genetic defect to a 4 Mb interval on chromosome 19 by a combined linkage and homozygosity mapping approach. Whole genome sequencing of one affected dog, an obligate carrier, and an unrelated control revealed a 218-bp SINE insertion into exon 7 of the RAB3GAP1 gene. The SINE insertion was perfectly associated with the disease phenotype in a cohort of 43 Alaskan Huskies, and it was absent from 541 control dogs of diverse other breeds. The SINE insertion induced aberrant splicing and led to a transcript with a greatly altered exon 7. RAB3GAP1 loss-of-function variants in humans cause Warburg Micro Syndrome 1 (WARBM1), which is characterized by additional developmental defects compared to canine POANV, whereas Rab3gap1-deficient mice have a much milder phenotype than either humans or dogs. Thus, the RAB3GAP1 mutant Alaskan Huskies provide an interesting intermediate phenotype that may help to better understand the function of RAB3GAP1 in development. Furthermore, the identification of the presumed causative genetic variant will enable genetic testing to avoid the nonintentional breeding of affected dogs. PMID:26596647

Functional noncoding sequences derived from SINEs in the mammalian genome

PubMed Central

Nishihara, Hidenori; Smit, Arian F.A.; Okada, Norihiro

2006-01-01

Recent comparative analyses of mammalian sequences have revealed that a large number of nonprotein-coding genomic regions are under strong selective constraint. Here, we report that some of these loci have been derived from a newly defined family of ancient SINEs (short interspersed repetitive elements). This is a surprising result, as SINEs and other transposable elements are commonly thought to be genomic parasites. We named the ancient SINE family AmnSINE1, for Amniota SINE1, because we found it to be present in mammals as well as in birds, and some copies predate the mammalian-bird split 310 million years ago (Mya). AmnSINE1 has a chimeric structure of a 5S rRNA and a tRNA-derived SINE, and is related to five tRNA-derived SINE families that we characterized here in the coelacanth, dogfish shark, hagfish, and amphioxus genomes. All of the newly described SINE families have a common central domain that is also shared by zebrafish SINE3, and we collectively name them the DeuSINE (Deuterostomia SINE) superfamily. Notably, of the ∼1000 still identifiable copies of AmnSINE1 in the human genome, 105 correspond to loci phylogenetically highly conserved among mammalian orthologs. The conservation is strongest over the central domain. Thus, AmnSINE1 appears to be the best example of a transposable element of which a significant fraction of the copies have acquired genomic functionality. PMID:16717141

Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers.

PubMed

Deragon, Jean-Marc; Zhang, Xiaoyu

2006-12-01

Short interspersed elements (SINEs) are a class of dispersed mobile sequences that use RNA as an intermediate in an amplification process called retroposition. The presence-absence of a SINE at a given locus has been used as a meaningful classification criterion to evaluate phylogenetic relations among species. We review here recent developments in the characterisation of plant SINEs and their use as molecular makers to retrace phylogenetic relations among wild and cultivated Oryza and Brassica species. In Brassicaceae, further use of SINE markers is limited by our partial knowledge of endogenous SINE families (their origin and evolution histories) and by the absence of a clear classification. To solve this problem, phylogenetic relations among all known Brassicaceae SINEs were analyzed and a new classification, grouping SINEs in 15 different families, is proposed. The relative age and size of each Brassicaceae SINE family was evaluated and new phylogenetically supported subfamilies were described. We also present evidence suggesting that new potentially active SINEs recently emerged in Brassica oleracea from the shuffling of preexisting SINE portions. Finally, the comparative evolution history of SINE families present in Arabidopsis thaliana and Brassica oleracea revealed that SINEs were in general more active in the Brassica lineage. The importance of these new data for the use of Brassicaceae SINEs as molecular markers in future applications is discussed.

Newly discovered young CORE-SINEs in marsupial genomes.

PubMed

Munemasa, Maruo; Nikaido, Masato; Nishihara, Hidenori; Donnellan, Stephen; Austin, Christopher C; Okada, Norihiro

2008-01-15

Although recent mammalian genome projects have uncovered a large part of genomic component of various groups, several repetitive sequences still remain to be characterized and classified for particular groups. The short interspersed repetitive elements (SINEs) distributed among marsupial genomes are one example. We have identified and characterized two new SINEs from marsupial genomes that belong to the CORE-SINE family, characterized by a highly conserved "CORE" domain. PCR and genomic dot blot analyses revealed that the distribution of each SINE shows distinct patterns among the marsupial genomes, implying different timing of their retroposition during the evolution of marsupials. The members of Mar3 (Marsupialia 3) SINE are distributed throughout the genomes of all marsupials, whereas the Mac1 (Macropodoidea 1) SINE is distributed specifically in the genomes of kangaroos. Sequence alignment of the Mar3 SINEs revealed that they can be further divided into four subgroups, each of which has diagnostic nucleotides. The insertion patterns of each SINE at particular genomic loci, together with the distribution patterns of each SINE, suggest that the Mar3 SINEs have intensively amplified after the radiation of diprotodontians, whereas the Mac1 SINE has amplified only slightly after the divergence of hypsiprimnodons from other macropods. By compiling the information of CORE-SINEs characterized to date, we propose a comprehensive picture of how SINE evolution occurred in the genomes of marsupials.

Evaluating point count efficiency relative to territory mapping in cropland birds

Treesearch

Andre Cyr; Denis Lepage; Kathryn Freemark

1995-01-01

Species richness, composition, and abundance of farmland birds were compared between point counts (50-m, 100-m, and 150-m radius half circles) and territory mapping on three 40-ha plots in Québec, Canada. Point counts of smaller radii tended to have larger density estimates than counts of larger radii. Territory mapping detected 10 species more than 150-m...

Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo.

PubMed

Yadav, Vijay Pal; Mandal, Prabhat Kumar; Bhattacharya, Alok; Bhattacharya, Sudha

2012-05-22

Non-long terminal repeat Retrotransposons are referred to as long interspersed nuclear elements (LINEs) and their non-autonomous partners are short interspersed nuclear elements (SINEs). It is believed that an active SINE copy, upon retrotransposition, generates near identical copies of itself, which subsequently accumulate mutations resulting in sequence polymorphism. Here we show that when a retrotransposition-competent cell line of the parasitic protist Entamoeba histolytica, transfected with a marked SINE copy, is induced to retrotranspose, >20% of the newly retrotransposed copies are neither identical to the marked SINE nor to the mobilized resident SINEs. Rather they are recombinants of resident SINEs and the marked SINE. They are a consequence of retrotransposition and not DNA recombination, as they are absent in cells not expressing the retrotransposition functions. This high-frequency recombination provides a new explanation for the existence of mosaic SINEs, which may impact on genetic analysis of SINE lineages, and measurement of phylogenetic distances.

The IAT shows no evidence for Kandinsky's color-shape associations

PubMed Central

Makin, Alexis D. J.; Wuerger, Sophie M.

2013-01-01

In the early twentieth century, the Bauhaus revolutionized art and design by using simple colors and forms. Wassily Kandinsky was especially interested in the relationship of these two visual attributes and postulated a fundamental correspondence between color and form: yellow triangle, red square and blue circle. Subsequent empirical studies used preference judgments to test Kandinsky's original color-form combinations, usually yielding inconsistent results. We have set out to test the validity of these postulated associations by using the Implicit Association Test. Participants pressed one of two buttons on each trial. On some trials they classified shapes (e.g., circle or triangle). On interleaved trials they classified colors (e.g., blue or yellow). Response times should theoretically be faster when the button mapping follows Kandinsky's associations: For example, when the left key is used to report blue or circle and the right is used for yellow and triangle, than when the response mapping is the opposite of this (blue or triangle, yellow or circle). Our findings suggest that there is no implicit association between the original color-form combinations. Of the three combinations we tested, there was only a marginal effect in one case. It can be concluded that the IAT does not support Kandinsky's postulated color-form associations, and that these are probably not a universal property of the visual system. PMID:24062709

A comparison of results obtained from foil chaff clouds at 69 deg northern latitude during winter, summer and autumn

NASA Technical Reports Server (NTRS)

Widdel, H. U.; Vonzahn, U.

1989-01-01

Results from high resolution foil chaff experiments flown during the campaigns MAP/WINE (December 83 to February 84), MAC/SINE (June to July 1987) and Epsilon (October to November 1987) at Andenes (Northern Norway) are compared to each other and the differences in wind direction and wave activity during the different seasons are worked out.

The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms

PubMed Central

2014-01-01

Background Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique to the order Carnivora (CanSINEs) yield novel insights on genome evolution in domestic dogs and cats, but less is known about their role in related carnivores. In particular, genome-wide assessment of CanSINE evolution has yet to be completed across the Feliformia (cat-like) suborder of Carnivora. Within Feliformia, the cat family Felidae is composed of 37 species and numerous subspecies organized into eight monophyletic lineages that likely arose 10 million years ago. Using the Felidae family as a reference phylogeny, along with representative taxa from other families of Feliformia, the origin, proliferation and evolution of CanSINEs within the suborder were assessed. Results We identified 93 novel intergenic CanSINE loci in Feliformia. Sequence analyses separated Feliform CanSINEs into two subfamilies, each characterized by distinct RNA polymerase binding motifs and phylogenetic associations. Subfamily I CanSINEs arose early within Feliformia but are no longer under active proliferation. Subfamily II loci are more recent, exclusive to Felidae and show evidence for adaptation to extant RNA polymerase activity. Further, presence/absence distributions of CanSINE loci are largely congruent with taxonomic expectations within Feliformia and the less resolved nodes in the Felidae reference phylogeny present equally ambiguous CanSINE data. SINEs are thought to be nearly impervious to excision from the genome. However, we observed a nearly complete excision of a CanSINEs locus in puma (Puma concolor). In addition, we found that CanSINE proliferation in Felidae frequently targeted existing CanSINE loci for insertion sites, resulting in tandem arrays. Conclusions We demonstrate the existence of at least two SINE families within the Feliformia suborder, one of which is actively involved in insertional mutagenesis. We find SINEs are powerful markers of speciation and conclude that the few inconsistencies with expected patterns of speciation likely represent incomplete lineage sorting, species hybridization and SINE-mediated genome rearrangement. PMID:24947429

Short interspersed elements (SINEs) of the Geomyoidea superfamily rodents.

PubMed

Gogolevsky, Konstantin P; Kramerov, Dmitri A

2006-05-24

A new short interspersed element (SINE) was isolated from the genome of desert kangaroo rat (Dipodomys deserti) using single-primer PCR. This SINE consists of two monomers: the left monomer (IDL) resembles rodent ID element and other tRNAAla(CGC)-derived SINEs, whereas the right one (Geo) shows no similarity with known SINE sequences. PCR and hybridization analyses demonstrated that IDL-Geo SINE is restricted to the rodent superfamily Geomyoidea (families Geomyidea and Heteromyidea). Isolation and analysis of IDL-Geo from California pocket mouse (Chaetodipus californicus) and Botta's pocket gopher (Thomomys bottae) revealed some species-specific features of this SINE family. The structure and evolution of known dimeric SINEs are discussed.

Bov-B-mobilized SINEs in vertebrate genomes.

PubMed

Gogolevsky, Konstantin P; Vassetzky, Nikita S; Kramerov, Dmitri A

2008-01-15

Two new short retroposon families (SINEs) have been found in the genome of springhare Pedetes capensis (Rodentia). One of them, Ped-1, originated from 5S rRNA, while the other one, Ped-2, originated from tRNA-derived SINE ID. In contrast to most currently active mammalian SINEs mobilized by L1 long retrotransposon (LINE), Ped-1 and Ped-2 are mobilized by Bov-B, a LINE family of the widely distributed RTE clade. The 3' part of these SINEs originates from two sequences in the 5' and 3' regions of Bov-B. Such bipartite structure of the LINE-derived part has been revealed in all Bov-B-mobilized SINEs known to date (AfroSINE, Bov-tA, Mar-1, and Ped-1/2), which distinguishes them from other SINEs with only a 3' LINE-derived part. Structural analysis and the distribution of Bov-B LINEs and partner SINEs supports the horizontal transfer of Bov-B, while the SINEs emerged independently in lineages with this LINE.

Seismic Observations and Interpretation in NE China, Infrasound Observations and Interpretation in Utah

DTIC Science & Technology

2010-07-30

from Xu et al., 2005). (b) Map of SMU-IGPCEA Huailai Seismic Network and seismicity ( open circles) for the time period of January 01, 2002 through...the Beijing-Huailai-Fengzhen (H20) refraction/ wide angle reflection profile (Zhu et al., 1997). Open circles are locations of two historical...historycatalog_query.jsp) and the China Seismograph Network ( CSN ) Catalog (http://210.72.96.165/wdcd/csn_catalog_p001.jsp) list a total of 323 earthquakes with magnitude

Sines and Cosines. Part 1 of 3

NASA Technical Reports Server (NTRS)

Apostol, Tom M. (Editor)

1992-01-01

Applying the concept of similarities, the mathematical principles of circular motion and sine and cosine waves are presented utilizing both film footage and computer animation in this 'Project Mathematics' series video. Concepts presented include: the symmetry of sine waves; the cosine (complementary sine) and cosine waves; the use of sines and cosines on coordinate systems; the relationship they have to each other; the definitions and uses of periodic waves, square waves, sawtooth waves; the Gibbs phenomena; the use of sines and cosines as ratios; and the terminology related to sines and cosines (frequency, overtone, octave, intensity, and amplitude).

5S rRNA-derived and tRNA-derived SINEs in fruit bats.

PubMed

Gogolevsky, Konstantin P; Vassetzky, Nikita S; Kramerov, Dmitri A

2009-05-01

Most short retroposons (SINEs) descend from cellular tRNA of 7SL RNA. Here, four new SINEs were found in megabats (Megachiroptera) but neither in microbats nor in other mammals. Two of them, MEG-RS and MEG-RL, descend from another cellular RNA, 5S rRNA; one (MEG-T2) is a tRNA-derived SINE; and MEG-TR is a hybrid tRNA/5S rRNA SINE. Insertion locus analysis suggests that these SINEs were active in the recent fruit bat evolution. Analysis of MEG-RS and MEG-RL in comparison with other few 5S rRNA-derived SINEs demonstrates that the internal RNA polymerase III promoter is their most invariant region, while the secondary structure is more variable. The mechanisms underlying the modular structure of these and other SINEs as well as their variation are discussed. The scenario of evolution of MEG SINEs is proposed.

Isolation and characterization of active LINE and SINEs from the eel.

PubMed

Kajikawa, Masaki; Ichiyanagi, Kenji; Tanaka, Nozomu; Okada, Norihiro

2005-03-01

Long interspersed elements (LINEs) and short interspersed elements (SINEs) are retrotransposons. These elements can mobilize by the "copy-and-paste" mechanism, in which their own RNA is reverse-transcribed into complementary DNA (cDNA). LINEs and SINEs not only are components of eukaryotic genomes but also drivers of genomic evolution. Thus, studies of the amplification mechanism of LINEs and SINEs are important for understanding eukaryotic genome evolution. Here we report the characterization of one LINE family (UnaL2) and two SINE families (UnaSINE1 and UnaSINE2) from the eel (Anguilla japonica) genome. UnaL2 is approximately 3.6 kilobases (kb) and encodes only one open reading frame (ORF). UnaL2 belongs to the stringent type--thought to be a major group of LINEs--and can mobilize in HeLa cells. We also show that UnaL2 and the two UnaSINEs have similar 3' tails, and that both UnaSINE1 and UnaSINE2 can be mobilized by UnaL2 in HeLa cells. These elements are thus useful for delineating the amplification mechanism of stringent type LINEs as well as that of SINEs.

Diversification, evolution and methylation of short interspersed nuclear element families in sugar beet and related Amaranthaceae species.

PubMed

Schwichtenberg, Katrin; Wenke, Torsten; Zakrzewski, Falk; Seibt, Kathrin M; Minoche, André; Dohm, Juliane C; Weisshaar, Bernd; Himmelbauer, Heinz; Schmidt, Thomas

2016-01-01

Short interspersed nuclear elements (SINEs) are non-autonomous non-long terminal repeat retrotransposons which are widely distributed in eukaryotic organisms. While SINEs have been intensively studied in animals, only limited information is available about plant SINEs. We analysed 22 SINE families from seven genomes of the Amaranthaceae family and identified 34 806 SINEs, including 19 549 full-length copies. With the focus on sugar beet (Beta vulgaris), we performed a comparative analysis of the diversity, genomic and chromosomal organization and the methylation of SINEs to provide a detailed insight into the evolution and age of Amaranthaceae SINEs. The lengths of consensus sequences of SINEs range from 113 nucleotides (nt) up to 224 nt. The SINEs show dispersed distribution on all chromosomes but were found with higher incidence in subterminal euchromatic chromosome regions. The methylation of SINEs is increased compared with their flanking regions, and the strongest effect is visible for cytosines in the CHH context, indicating an involvement of asymmetric methylation in the silencing of SINEs. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Bad Colourmaps Can Hide Big Structures

NASA Astrophysics Data System (ADS)

Kovesi, Peter

2014-05-01

Colourmaps are often selected with little awareness of the perceptual distortions they might introduce. A colourmap can be thought of as a line or curve drawn through a three dimensional colour space. Individual data values are mapped to positions along this line which, in turn, allows them to be mapped to a colour. For a colourmap to be effective it is important that the perceptual contrast that occurs as one moves along the line in the colour space is close to uniform. Many colourmaps are designed as piecewise linear paths through RGB space. This is a poor colour space to use because it is not perceptually uniform. Accordingly many colourmaps supplied by vendors have uneven perceptual contrast over their range. They may include points of locally high colour contrast leading you to think there might be some anomaly in your data when there is none. Conversely, colourmaps may also have flat spots of low perceptual contrast that prevent you from seeing features in your data. In some cases it is possible for structures having a magnitude of 10% of the full data range to be completely hidden by a flat spot in the colourmap. The deficiencies of many colourmaps can be revealed using a simple test image consisting of a high frequency sine wave superimposed on a ramp function. The amplitude of the sine wave is modulated from a maximum value at the top of the image to zero at the bottom. Ideally the sine wave should be uniformly visible across the image at all points on the ramp. For many colourmaps this will not be the case. At the very bottom of the image, where the sine wave amplitude has been modulated to 0, we just have a linear ramp which simply reproduces the colourmap. Given that the underlying data is a featureless ramp the colourmap should not induce the perception of any features across the bottom of the test image. Good colourmaps are difficult to design. A greyscale colourmap is generally a safe choice but is not always what is desired. For non-greyscale colourmaps the perceptual colour contrast between adjacent entries of the map should be constant across the whole colourmap. In addition, and more importantly, the colour lightness change between successive entries in the colourmap should also be constant. These conditions, if observed, constrain the design of colourmaps considerably, and they exclude the construction of rainbow style colourmaps. It is shown that good colourmaps can be formed from smooth curves constructed in a perceptually uniform colour space such as CIELAB. Colour lightness values should be monotonically increasing at a constant rate while at the same time the colourmap curve should stay close to the boundary of the colour space gamut to ensure that the colours are vivid.

Understanding map projections: Chapter 15

USGS Publications Warehouse

Usery, E. Lynn; Kent, Alexander J.; Vujakovic, Peter

2018-01-01

It has probably never been more important in the history of cartography than now that people understand how maps work. With increasing globalization, for example, world maps provide a key format for the transmission of information, but are often poorly used. Examples of poor understanding and use of projections and the resultant maps are many; for instance, the use of rectangular world maps in the United Kingdom press to show Chinese and Korean missile ranges as circles, something which can only be achieved on equidistant projections and then only from one launch point (Vujakovic, 2014).

The Evolution of SINEs and LINEs in the genus Chironomus (Diptera).

PubMed

Papusheva, Ekaterina; Gruhl, Mary C; Berezikov, Eugene; Groudieva, Tatiana; Scherbik, Svetlana V; Martin, Jon; Blinov, Alexander; Bergtrom, Gerald

2004-03-01

Genomic DNA amplification from 51 species of the family Chironomidae shows that most contain relatives of NLRCth1 LINE and CTRT1 SINE retrotransposons first found in Chironomus thummi. More than 300 cloned PCR products were sequenced. The amplified region of the reverse transcriptase gene in the LINEs is intact and highly conserved, suggesting active elements. The SINEs are less conserved, consistent with minimal/no selection after transposition. A mitochondrial gene phylogeny resolves the Chironomus genus into six lineages (Guryev et al. 2001). LINE and SINE phylogenies resolve five of these lineages, indicating their monophyletic origin and vertical inheritance. However, both the LINE and the SINE tree topologies differ from the species phylogeny, resolving the elements into "clusters I-IV" and "cluster V" families. The data suggest a descent of all LINE and SINE subfamilies from two major families. Based on the species phylogeny, a few LINEs and a larger number of SINEs are cladisitically misplaced. Most misbranch with LINEs or SINEs from species with the same families of elements. From sequence comparisons, cladistically misplaced LINEs and several misplaced SINEs arose by convergent base substitutions. More diverged SINEs result from early transposition and some are derived from multiple source SINEs in the same species. SINEs from two species (C. dorsalis, C. pallidivittatus), expected to belong to the clusters I-IV family, branch instead with cluster V family SINEs; apparently both families predate separation of cluster V from clusters I-IV species. Correlation of the distribution of active SINEs and LINEs, as well as similar 3' sequence motifs in CTRT1 and NLRCth1, suggests coevolving retrotransposon pairs in which CTRT1 transposition depends on enzymes active during NLRCth1 LINE mobility.

Electron microscopic studies of bacteriophage M13 DNA replication. [Escherichia coli

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

Allison, D.P.; Ganesan, A.T.; Olson, A.C.

Intracellular forms of M13 phage DNA isolated after infection of Escherichia coli with wild-type phage have been studied by electron microscopy and ultracentrifugation. The data indicate the involvement of rolling-circle intermediates in single-stranded DNA synthesis. In addition to single-stranded, circular DNA, we observed covalently closed and nicked replicative-form (RF) DNAs, dimer RF DNAs, concatenated RF DNAs, RF DNAs with single-stranded tails (sigma, rolling circles), and, occasionally, RF DNAs with theta structures. The tails in sigma molecules are always single stranded and are never longer than the DNA from mature phage; the proportion of sigma to other RF molecules does notmore » change significantly with time after infection. The origin of single-stranded DNA synthesis has been mapped by electron microscopy at a unique location on RF DNA by use of partial denaturation mapping and restriction endonuclease digestion. This location is between gene IV and gene II, and synthesis proceeds in a counterclockwise direction on the conventional genetic map.« less

Probing the statistics of transport in the Hénon Map

NASA Astrophysics Data System (ADS)

Alus, O.; Fishman, S.; Meiss, J. D.

2016-09-01

The phase space of an area-preserving map typically contains infinitely many elliptic islands embedded in a chaotic sea. Orbits near the boundary of a chaotic region have been observed to stick for long times, strongly influencing their transport properties. The boundary is composed of invariant "boundary circles." We briefly report recent results of the distribution of rotation numbers of boundary circles for the Hénon quadratic map and show that the probability of occurrence of small integer entries of their continued fraction expansions is larger than would be expected for a number chosen at random. However, large integer entries occur with probabilities distributed proportionally to the random case. The probability distributions of ratios of fluxes through island chains is reported as well. These island chains are neighbours in the sense of the Meiss-Ott Markov-tree model. Two distinct universality families are found. The distributions of the ratio between the flux and orbital period are also presented. All of these results have implications for models of transport in mixed phase space.

The Perception of "Sine-Wave Speech" by Adults with Developmental Dyslexia.

ERIC Educational Resources Information Center

Rosner, Burton S.; Talcott, Joel B.; Witton, Caroline; Hogg, James D.; Richardson, Alexandra J.; Hansen, Peter C.; Stein, John F.

2003-01-01

"Sine-wave speech" sentences contain only four frequency-modulated sine waves, lacking many acoustic cues present in natural speech. Adults with (n=19) and without (n=14) dyslexia were asked to reproduce orally sine-wave utterances in successive trials. Results suggest comprehension of sine-wave sentences is impaired in some adults with…

SINEs.

PubMed

Kramerov, Dmitri A; Vassetzky, Nikita S

2011-01-01

Short interspersed elements (SINEs) are mobile genetic elements that invade the genomes of many eukaryotes. Since their discovery about 30 years ago, many gaps in our understanding of the biology and function of SINEs have been filled. This review summarizes the past and recent advances in the studies of SINEs. The structure and origin of SINEs as well as the processes involved in their amplification, transcription, RNA processing, reverse transcription, and integration of a SINE copy into the genome are considered. Then we focus on the significance of SINEs for the host genomes. While these genomic parasites can be deleterious to the cell, the long-term being in the genome has made SINEs a valuable source of genetic variation providing regulatory elements for gene expression, alternative splice sites, polyadenylation signals, and even functional RNA genes. Copyright © 2011 John Wiley & Sons, Ltd.

Carnivore-specific SINEs (Can-SINEs): distribution, evolution, and genomic impact.

PubMed

Walters-Conte, Kathryn B; Johnson, Diana L E; Allard, Marc W; Pecon-Slattery, Jill

2011-01-01

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics.

Carnivore-Specific SINEs (Can-SINEs): Distribution, Evolution, and Genomic Impact

PubMed Central

Johnson, Diana L.E.; Allard, Marc W.; Pecon-Slattery, Jill

2011-01-01

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics. PMID:21846743

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

PubMed Central

Tong, Chaobo; Guo, Baocheng; He, Shunping

2009-01-01

Background Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 × 105 and 1.7 × 105 per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family. PMID:19224649

Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives.

PubMed

Schröder, Christiane; Bleidorn, Christoph; Hartmann, Stefanie; Tiedemann, Ralph

2009-12-15

Investigating the dog genome we found 178965 introns with a moderate length of 200-1000 bp. A screening of these sequences against 23 different repeat libraries to find insertions of short interspersed elements (SINEs) detected 45276 SINEs. Virtually all of these SINEs (98%) belong to the tRNA-derived Can-SINE family. Can-SINEs arose about 55 million years ago before Carnivora split into two basal groups, the Caniformia (dog-like carnivores) and the Feliformia (cat-like carnivores). Genome comparisons of dog and cat recovered 506 putatively informative SINE loci for caniformian phylogeny. In this study we show how to use such genome information of model organisms to research the phylogeny of related non-model species of interest. Investigating a dataset including representatives of all major caniformian lineages, we analysed 24 randomly chosen loci for 22 taxa. All loci were amplifiable and revealed 17 parsimony-informative SINE insertions. The screening for informative SINE insertions yields a large amount of sequence information, in particular of introns, which contain reliable phylogenetic information as well. A phylogenetic analysis of intron- and SINE sequence data provided a statistically robust phylogeny which is congruent with the absence/presence pattern of our SINE markers. This phylogeny strongly supports a sistergroup relationship of Musteloidea and Pinnipedia. Within Pinnipedia, we see strong support from bootstrapping and the presence of a SINE insertion for a sistergroup relationship of the walrus with the Otariidae.

Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes[W

PubMed Central

Wenke, Torsten; Döbel, Thomas; Sörensen, Thomas Rosleff; Junghans, Holger; Weisshaar, Bernd; Schmidt, Thomas

2011-01-01

Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. We developed a tool designated SINE-Finder for the targeted discovery of tRNA-derived SINEs. We analyzed sequence data of 16 plant genomes, including 13 angiosperms and three gymnosperms and identified 17,829 full-length and truncated SINEs falling into 31 families showing the widespread occurrence of SINEs in higher plants. The investigation focused on potato (Solanum tuberosum), resulting in the detection of seven different SolS SINE families consisting of 1489 full-length and 870 5′ truncated copies. Consensus sequences of full-length members range in size from 106 to 244 bp depending on the SINE family. SolS SINEs populated related species and evolved separately, which led to some distinct subfamilies. Solanaceae SINEs are dispersed along chromosomes and distributed without clustering but with preferred integration into short A-rich motifs. They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3′ end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families. PMID:21908723

Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes.

PubMed

Wenke, Torsten; Döbel, Thomas; Sörensen, Thomas Rosleff; Junghans, Holger; Weisshaar, Bernd; Schmidt, Thomas

2011-09-01

Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. We developed a tool designated SINE-Finder for the targeted discovery of tRNA-derived SINEs. We analyzed sequence data of 16 plant genomes, including 13 angiosperms and three gymnosperms and identified 17,829 full-length and truncated SINEs falling into 31 families showing the widespread occurrence of SINEs in higher plants. The investigation focused on potato (Solanum tuberosum), resulting in the detection of seven different SolS SINE families consisting of 1489 full-length and 870 5' truncated copies. Consensus sequences of full-length members range in size from 106 to 244 bp depending on the SINE family. SolS SINEs populated related species and evolved separately, which led to some distinct subfamilies. Solanaceae SINEs are dispersed along chromosomes and distributed without clustering but with preferred integration into short A-rich motifs. They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3' end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families.

Sauria SINEs: Novel short interspersed retroposable elements that are widespread in reptile genomes.

PubMed

Piskurek, Oliver; Austin, Christopher C; Okada, Norihiro

2006-05-01

SINEs are short interspersed retrotransposable elements that invade new genomic sites. Their retrotransposition depends on reverse transcriptase and endonuclease activities encoded by partner LINEs (long interspersed elements). Recent genomic research has demonstrated that retroposons account for at least 40% of the human genome. Hitherto, more than 30 families of SINEs have been characterized in mammalian genomes, comprising approximately 4600 extant species; the distribution and extent of SINEs in reptilian genomes, however, are poorly documented. With more than 7400 species of lizards and snakes, Squamata constitutes the largest and most diverse group of living reptiles. We have discovered and characterized a novel SINE family, Sauria SINEs, whose members are widely distributed among genomes of lizards, snakes, and tuataras. Sauria SINEs comprise a 5' tRNA-related region, a tRNA-unrelated region, and a 3' tail region (containing short tandem repeats) derived from LINEs. We distinguished eight Sauria SINE subfamilies in genomes of four major squamate lineages and investigated their evolutionary relationships. Our data illustrate the overall efficacy of Sauria SINEs as novel retrotransposable markers for elucidation of squamate evolutionary history. We show that all Sauria SINEs share an identical 3' sequence with Bov-B LINEs and propose that they utilize the enzymatic machinery of Bov-B LINEs for their own retrotransposition. This finding, along with the ubiquity of Bov-B LINEs previously demonstrated in squamate genomes, suggests that these LINEs have been an active partner of Sauria SINEs since this SINE family was generated more than 200 million years ago.

Development and application of SINE multilocus and quantitative genetic markers to study oilseed rape (Brassica napus L.) crops.

PubMed

Allnutt, T R; Roper, K; Henry, C

2008-01-23

A genetic marker system based on the S1 Short Interspersed Elements (SINEs) in the important commercial crop, oilseed rape ( Brassica napus L.) has been developed. SINEs provided a successful multilocus, dominant marker system that was capable of clearly delineating winter- and spring-type crop varieties. Sixteen of 20 varieties tested showed unique profiles from the 17 polymorphic SINE markers generated. The 3' or 5' flank region of nine SINE markers were cloned, and DNA was sequenced. In addition, one putative pre-transposition SINE allele was cloned and sequenced. Two SINE flanking sequences were used to design real-time PCR assays. These quantitative SINE assays were applied to study the genetic structure of eight fields of oilseed rape crops. Studied fields were more genetically diverse than expected for the chosen loci (mean H T = 0.23). The spatial distribution of SINE marker frequencies was highly structured in some fields, suggesting locations of volunteer impurities within the crop. In one case, the assay identified a mislabeling of the crop variety. SINE markers were a useful tool for crop genetics, phylogenetics, variety identification, and purity analysis. The use and further application of quantitative, real-time PCR markers are discussed.

Non-Commutative Rational Yang-Baxter Maps

NASA Astrophysics Data System (ADS)

Doliwa, Adam

2014-03-01

Starting from multidimensional consistency of non-commutative lattice-modified Gel'fand-Dikii systems, we present the corresponding solutions of the functional (set-theoretic) Yang-Baxter equation, which are non-commutative versions of the maps arising from geometric crystals. Our approach works under additional condition of centrality of certain products of non-commuting variables. Then we apply such a restriction on the level of the Gel'fand-Dikii systems what allows to obtain non-autonomous (but with central non-autonomous factors) versions of the equations. In particular, we recover known non-commutative version of Hirota's lattice sine-Gordon equation, and we present an integrable non-commutative and non-autonomous lattice modified Boussinesq equation.

Clustering Multiple Sclerosis Subgroups with Multifractal Methods and Self-Organizing Map Algorithm

NASA Astrophysics Data System (ADS)

Karaca, Yeliz; Cattani, Carlo

Magnetic resonance imaging (MRI) is the most sensitive method to detect chronic nervous system diseases such as multiple sclerosis (MS). In this paper, Brownian motion Hölder regularity functions (polynomial, periodic (sine), exponential) for 2D image, such as multifractal methods were applied to MR brain images, aiming to easily identify distressed regions, in MS patients. With these regions, we have proposed an MS classification based on the multifractal method by using the Self-Organizing Map (SOM) algorithm. Thus, we obtained a cluster analysis by identifying pixels from distressed regions in MR images through multifractal methods and by diagnosing subgroups of MS patients through artificial neural networks.

Short Interspersed Nuclear Element (SINE) Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293

PubMed Central

Kanhayuwa, Lakkhana; Coutts, Robert H. A.

2016-01-01

Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4–14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140–493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3’-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50–65% and 60–75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259–343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity. PMID:27736869

Short Interspersed Nuclear Element (SINE) Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293.

PubMed

Kanhayuwa, Lakkhana; Coutts, Robert H A

2016-01-01

Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4-14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140-493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3'-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50-65% and 60-75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259-343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity.

Distribution of Vesta Dark Materials, Southern View

NASA Image and Video Library

2013-01-03

This map shows the distribution of dark materials throughout the southern hemisphere of the giant asteroid Vesta. The circles, diamonds, and stars show where the dark material appears in craters, spots and topographic highs.

On the Circulation Manifold for Two Adjacent Lifting Sections

NASA Technical Reports Server (NTRS)

Zannetti, Luca; Iollo, Angelo

1998-01-01

The circulation functional relative to two adjacent lifting sections is studied for two cases. In the first case we consider two adjacent circles. The circulation is computed as a function of the displacement of the secondary circle along the axis joining the two centers and of the angle of attack of the secondary circle, The gradient of such functional is computed by deriving a set of elliptic functions with respect both to their argument and to their Period. In the second case studied, we considered a wing-flap configuration. The circulation is computed by some implicit mappings, whose differentials with respect to the variation of the geometrical configuration in the physical space are found by divided differences. Configurations giving rise to local maxima and minima in the circulation manifold are presented.

Polyadenylation of RNA transcribed from mammalian SINEs by RNA polymerase III: Complex requirements for nucleotide sequences.

PubMed

Borodulina, Olga R; Golubchikova, Julia S; Ustyantsev, Ilia G; Kramerov, Dmitri A

2016-02-01

It is generally accepted that only transcripts synthesized by RNA polymerase II (e.g., mRNA) were subject to AAUAAA-dependent polyadenylation. However, we previously showed that RNA transcribed by RNA polymerase III (pol III) from mouse B2 SINE could be polyadenylated in an AAUAAA-dependent manner. Many species of mammalian SINEs end with the pol III transcriptional terminator (TTTTT) and contain hexamers AATAAA in their A-rich tail. Such SINEs were united into Class T(+), whereas SINEs lacking the terminator and AATAAA sequences were classified as T(-). Here we studied the structural features of SINE pol III transcripts that are necessary for their polyadenylation. Eight and six SINE families from classes T(+) and T(-), respectively, were analyzed. The replacement of AATAAA with AACAAA in T(+) SINEs abolished the RNA polyadenylation. Interestingly, insertion of the polyadenylation signal (AATAAA) and pol III transcription terminator in T(-) SINEs did not result in polyadenylation. The detailed analysis of three T(+) SINEs (B2, DIP, and VES) revealed areas important for the polyadenylation of their pol III transcripts: the polyadenylation signal and terminator in A-rich tail, β region positioned immediately downstream of the box B of pol III promoter, and τ region located upstream of the tail. In DIP and VES (but not in B2), the τ region is a polypyrimidine motif which is also characteristic of many other T(+) SINEs. Most likely, SINEs of different mammals acquired these structural features independently as a result of parallel evolution. Copyright © 2015 Elsevier B.V. All rights reserved.

Selective repression of SINE transcription by RNA polymerase III.

PubMed

Varshney, Dhaval; Vavrova-Anderson, Jana; Oler, Andrew J; Cairns, Bradley R; White, Robert J

2015-01-01

A million copies of the Alu short interspersed nuclear element (SINE) are scattered throughout the human genome, providing ∼11% of our total DNA. SINEs spread by retrotransposition, using a transcript generated by RNA polymerase (pol) III from an internal promoter. Levels of these pol III-dependent Alu transcripts are far lower than might be expected from the abundance of the template. This was believed to reflect transcriptional suppression through DNA methylation, denying pol III access to most SINEs through chromatin-mediated effects. Contrary to expectations, our recent study found no evidence that methylation of SINE DNA reduces its occupancy or expression by pol III. However, histone H3 associated with SINEs is prominently methylated on lysine 9, a mark that correlates with transcriptional silencing. The SUV39 methyltransferases that deposit this mark can be found at many SINEs. Furthermore, a selective inhibitor of SUV39 stimulates pol III recruitment to these loci, as well as SINE expression. These data suggest that methylation of histone H3 rather than DNA may mediate repression of SINE transcription by pol III, at least under the conditions we studied.

Inverse PCR-based method for isolating novel SINEs from genome.

PubMed

Han, Yawei; Chen, Liping; Guan, Lihong; He, Shunping

2014-04-01

Short interspersed elements (SINEs) are moderately repetitive DNA sequences in eukaryotic genomes. Although eukaryotic genomes contain numerous SINEs copy, it is very difficult and laborious to isolate and identify them by the reported methods. In this study, the inverse PCR was successfully applied to isolate SINEs from Opsariichthys bidens genome in Eastern Asian Cyprinid. A group of SINEs derived from tRNA(Ala) molecular had been identified, which were named Opsar according to Opsariichthys. SINEs characteristics were exhibited in Opsar, which contained a tRNA(Ala)-derived region at the 5' end, a tRNA-unrelated region, and AT-rich region at the 3' end. The tRNA-derived region of Opsar shared 76 % sequence similarity with tRNA(Ala) gene. This result indicated that Opsar could derive from the inactive or pseudogene of tRNA(Ala). The reliability of method was tested by obtaining C-SINE, Ct-SINE, and M-SINEs from Ctenopharyngodon idellus, Megalobrama amblycephala, and Cyprinus carpio genomes. This method is simpler than the previously reported, which successfully omitted many steps, such as preparation of probes, construction of genomic libraries, and hybridization.

Novel SINEs families in Medicago truncatula and Lotus japonicus: bioinformatic analysis.

PubMed

Gadzalski, Marek; Sakowicz, Tomasz

2011-07-01

Although short interspersed elements (SINEs) were discovered nearly 30 years ago, the studies of these genomic repeats were mostly limited to animal genomes. Very little is known about SINEs in legumes--one of the most important plant families. Here we report identification, genomic distribution and molecular features of six novel SINE elements in Lotus japonicus (named LJ_SINE-1, -2, -3) and Medicago truncatula (MT_SINE-1, -2, -3), model species of legume. They possess all the structural features commonly found in short interspersed elements including RNA polymerase III promoter, polyA tail and flanking repeats. SINEs described here are present in low to moderate copy numbers from 150 to 3000. Bioinformatic analyses were used to searched public databases, we have shown that three of new SINE elements from M. truncatula seem to be characteristic of Medicago and Trifolium genera. Two SINE families have been found in L. japonicus and one is present in both M. truncatula and L. japonicus. In addition, we are discussing potential activities of the described elements. Copyright © 2011 Elsevier B.V. All rights reserved.

PCR and magnetic bead-mediated target capture for the isolation of short interspersed nucleotide elements in fishes.

PubMed

Liu, Dong; Zhu, Guoli; Tang, Wenqiao; Yang, Jinquan; Guo, Hongyi

2012-01-01

Short interspersed nucleotide elements (SINEs), a type of retrotransposon, are widely distributed in various genomes with multiple copies arranged in different orientations, and cause changes to genes and genomes during evolutionary history. This can provide the basis for determining genome diversity, genetic variation and molecular phylogeny, etc. SINE DNA is transcribed into RNA by polymerase III from an internal promoter, which is composed of two conserved boxes, box A and box B. Here we present an approach to isolate novel SINEs based on these promoter elements. Box A of a SINE is obtained via PCR with only one primer identical to box B (B-PCR). Box B and its downstream sequence are acquired by PCR with one primer corresponding to box A (A-PCR). The SINE clone produced by A-PCR is selected as a template to label a probe with biotin. The full-length SINEs are isolated from the genomic pool through complex capture using the biotinylated probe bound to magnetic particles. Using this approach, a novel SINE family, Cn-SINE, from the genomes of Coilia nasus, was isolated. The members are 180-360 bp long. Sequence homology suggests that Cn-SINEs evolved from a leucine tRNA gene. This is the first report of a tRNA(Leu)-related SINE obtained without the use of a genomic library or inverse PCR. These results provide new insights into the origin of SINEs.

PCR and Magnetic Bead-Mediated Target Capture for the Isolation of Short Interspersed Nucleotide Elements in Fishes

PubMed Central

Liu, Dong; Zhu, Guoli; Tang, Wenqiao; Yang, Jinquan; Guo, Hongyi

2012-01-01

Short interspersed nucleotide elements (SINEs), a type of retrotransposon, are widely distributed in various genomes with multiple copies arranged in different orientations, and cause changes to genes and genomes during evolutionary history. This can provide the basis for determining genome diversity, genetic variation and molecular phylogeny, etc. SINE DNA is transcribed into RNA by polymerase III from an internal promoter, which is composed of two conserved boxes, box A and box B. Here we present an approach to isolate novel SINEs based on these promoter elements. Box A of a SINE is obtained via PCR with only one primer identical to box B (B-PCR). Box B and its downstream sequence are acquired by PCR with one primer corresponding to box A (A-PCR). The SINE clone produced by A-PCR is selected as a template to label a probe with biotin. The full-length SINEs are isolated from the genomic pool through complex capture using the biotinylated probe bound to magnetic particles. Using this approach, a novel SINE family, Cn-SINE, from the genomes of Coilia nasus, was isolated. The members are 180–360 bp long. Sequence homology suggests that Cn-SINEs evolved from a leucine tRNA gene. This is the first report of a tRNALeu-related SINE obtained without the use of a genomic library or inverse PCR. These results provide new insights into the origin of SINEs. PMID:22408437

Genome-wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat

PubMed Central

Ben-David, Smadar; Yaakov, Beery; Kashkush, Khalil

2013-01-01

Short interspersed nuclear elements (SINEs) are non-autonomous non-LTR retroelements that are present in most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, they are poorly studied in plants, especially in wheat (Triticum aestivum). We used quantitative PCR of various wheat species to determine the copy number of a wheat SINE family, termed Au SINE, combined with computer-assisted analyses of the publicly available 454 pyrosequencing database of T. aestivum. In addition, we utilized site-specific PCR on 57 Au SINE insertions, transposon methylation display and transposon display on newly formed wheat polyploids to assess retrotranspositional activity, epigenetic status and genetic rearrangements in Au SINE, respectively. We retrieved 3706 different insertions of Au SINE from the 454 pyrosequencing database of T. aestivum, and found that most of the elements are inserted in A/T-rich regions, while approximately 38% of the insertions are associated with transcribed regions, including known wheat genes. We observed typical retrotransposition of Au SINE in the second generation of a newly formed wheat allohexaploid, and massive hypermethylation in CCGG sites surrounding Au SINE in the third generation. Finally, we observed huge differences in the copy numbers in diploid Triticum and Aegilops species, and a significant increase in the copy numbers in natural wheat polyploids, but no significant increase in the copy number of Au SINE in the first four generations for two of three newly formed allopolyploid species used in this study. Our data indicate that SINEs may play a prominent role in the genomic evolution of wheat through stress-induced activation. PMID:23855320

Genome-wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat.

PubMed

Ben-David, Smadar; Yaakov, Beery; Kashkush, Khalil

2013-10-01

Short interspersed nuclear elements (SINEs) are non-autonomous non-LTR retroelements that are present in most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, they are poorly studied in plants, especially in wheat (Triticum aestivum). We used quantitative PCR of various wheat species to determine the copy number of a wheat SINE family, termed Au SINE, combined with computer-assisted analyses of the publicly available 454 pyrosequencing database of T. aestivum. In addition, we utilized site-specific PCR on 57 Au SINE insertions, transposon methylation display and transposon display on newly formed wheat polyploids to assess retrotranspositional activity, epigenetic status and genetic rearrangements in Au SINE, respectively. We retrieved 3706 different insertions of Au SINE from the 454 pyrosequencing database of T. aestivum, and found that most of the elements are inserted in A/T-rich regions, while approximately 38% of the insertions are associated with transcribed regions, including known wheat genes. We observed typical retrotransposition of Au SINE in the second generation of a newly formed wheat allohexaploid, and massive hypermethylation in CCGG sites surrounding Au SINE in the third generation. Finally, we observed huge differences in the copy numbers in diploid Triticum and Aegilops species, and a significant increase in the copy numbers in natural wheat polyploids, but no significant increase in the copy number of Au SINE in the first four generations for two of three newly formed allopolyploid species used in this study. Our data indicate that SINEs may play a prominent role in the genomic evolution of wheat through stress-induced activation. © 2013 Ben-Gurion University The Plant Journal © 2013 John Wiley & Sons Ltd.

Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome.

PubMed

Barghini, Elena; Mascagni, Flavia; Natali, Lucia; Giordani, Tommaso; Cavallini, Andrea

2017-02-01

Short Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE identification has been carried out only in a limited number of plant species. This lack of information is apparent especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying SINEs. We have identified, for the first time, 227 putative SINEs of the olive tree (Olea europaea), that constitute one of the few sets of such sequences in dicotyledonous species. The identified SINEs ranged from 140 to 362 bp in length and were characterised with regard to the occurrence of the tRNA domain in their sequence. The majority of identified elements resulted in single copy or very lowly repeated, often in association with genic sequences. Analysis of sequence similarity allowed us to identify two major groups of SINEs showing different abundances in the olive tree genome, the former with sequence similarity to SINEs of Scrophulariaceae and Solanaceae and the latter to SINEs of Salicaceae. A comparison of sequence conservation between olive SINEs and LTR retrotransposon families suggested that SINE expansion in the genome occurred especially in very ancient times, before LTR retrotransposon expansion, and presumably before the separation of the rosids (to which Oleaceae belong) from the Asterids. Besides providing data on olive SINEs, our results demonstrate the suitability of the pipeline employed for SINE identification. Applying this pipeline will favour further structural and functional analyses on these relatively unknown elements to be performed also in other plant species, even in the absence of a reference genome, and will allow establishing general evolutionary patterns for this kind of repeats in plants.

SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

PubMed Central

Varshney, Dhaval; Vavrova-Anderson, Jana; Oler, Andrew J.; Cowling, Victoria H.; Cairns, Bradley R.; White, Robert J.

2015-01-01

Short interspersed nuclear elements (SINEs), such as Alu, spread by retrotransposition, which requires their transcripts to be copied into DNA and then inserted into new chromosomal sites. This can lead to genetic damage through insertional mutagenesis and chromosomal rearrangements between non-allelic SINEs at distinct loci. SINE DNA is heavily methylated and this was thought to suppress its accessibility and transcription, thereby protecting against retrotransposition. Here we provide several lines of evidence that methylated SINE DNA is occupied by RNA polymerase III, including the use of high-throughput bisulphite sequencing of ChIP DNA. We find that loss of DNA methylation has little effect on accessibility of SINEs to transcription machinery or their expression in vivo. In contrast, a histone methyltransferase inhibitor selectively promotes SINE expression and occupancy by RNA polymerase III. The data suggest that methylation of histones rather than DNA plays a dominant role in suppressing SINE transcription. PMID:25798578

Effects of ocular aberrations on contrast detection in noise.

PubMed

Liang, Bo; Liu, Rong; Dai, Yun; Zhou, Jiawei; Zhou, Yifeng; Zhang, Yudong

2012-08-06

We use adaptive optics (AO) techniques to manipulate the ocular aberrations and elucidate the effects of these ocular aberrations on contrast detection in a noisy background. The detectability of sine wave gratings at frequencies of 4, 8, and 16 circles per degree (cpd) was measured in a standard two-interval force-choice staircase procedure against backgrounds of various levels of white noise. The observer's ocular aberrations were either corrected with AO or left uncorrected. In low levels of external noise, contrast detection thresholds are always lowered by AO correction, whereas in high levels of external noise, they are generally elevated by AO correction. Higher levels of external noise are required to make this threshold elevation observable when signal spatial frequencies increase from 4 to 16 cpd. The linear-amplifier-model fit shows that mostly sampling efficiency and equivalent noise both decrease with AO correction. Our findings indicate that ocular aberrations could be beneficial for contrast detection in high-level noises. The implications of these findings are discussed.

Novel SINE families from salmons validate Parahucho (Salmonidae) as a distinct genus and give evidence that SINEs can incorporate LINE-related 3'-tails of other SINEs.

PubMed

Matveev, Vitaliy; Nishihara, Hidenori; Okada, Norihiro

2007-08-01

Short interspersed elements (SINEs) constitute a group of retroposons propagating in the genome via a mechanism of reverse transcription, in which they depend on the enzymatic machinery of long retroposons (LINEs). Over 70 SINE families have been described to date from the genomes of various eukaryotes. Here, we characterize two novel SINEs from salmons (Actinopterygii: Salmonoidei). The first family, termed SlmI, was shown to be widespread among all genera of the suborder. These SINEs have a tRNA(Leu)-related promoter region at their 5'-end, a unique central conserved domain with a subfamily-specific region, and an end with RSg-1-LINE-derived 3'-terminus preceding the A/T-rich tail. The same LINE-related segment is also shared by two other salmonid SINEs: HpaI and OS-SINE1. The structural peculiarities and overall sequence identity of the SlmI 3'-terminus suggest that it has been acquired from HpaI SINEs but not directly from the partner LINE. This region plays a crucial role in the process of retrotransposition of short interspersed elements, and the case of its SINE-to-SINE transmission is the first recorded to date. Possible scenarios and potential evolutionary implications of the observed interaction between short retroposons are discussed. Apart from the above, we found a copy of the SlmI SINE in the GenBank entry for the blood fluke, Schistosoma japonicum (Trematoda: Strigeiformes) -- a trematode causing one of the most important human helminth infections, with its genome known to host other groups of salmonoid retroposons. In the present article, we suggest our views with regard to possible ways in which such an intensive horizontal transfer of salmonoid retroposons to the schistosomal genome occurs. The second novel SINE family, termed SlmII, originates from one of the SlmI subfamilies, with which it shares the same tRNA-related region, central domain, and a part of RSg-1-derived segment, but has a different 3'-tail of unidentified origin. Its distribution among salmonids validates Parahucho (Japanese huchen) as a distinct monotypic genus.

SINE Retrotransposition: Evaluation of Alu Activity and Recovery of De Novo Inserts.

PubMed

Ade, Catherine; Roy-Engel, Astrid M

2016-01-01

Mobile element activity is of great interest due to its impact on genomes. However, the types of mobile elements that inhabit any given genome are remarkably varied. Among the different varieties of mobile elements, the Short Interspersed Elements (SINEs) populate many genomes, including many mammalian species. Although SINEs are parasites of Long Interspersed Elements (LINEs), SINEs have been highly successful in both the primate and rodent genomes. When comparing copy numbers in mammals, SINEs have been vastly more successful than other nonautonomous elements, such as the retropseudogenes and SVA. Interestingly, in the human genome the copy number of Alu (a primate SINE) outnumbers LINE-1 (L1) copies 2 to 1. Estimates suggest that the retrotransposition rate for Alu is tenfold higher than LINE-1 with about 1 insert in every twenty births. Furthermore, Alu-induced mutagenesis is responsible for the majority of the documented instances of human retroelement insertion-induced disease. However, little is known on what contributes to these observed differences between SINEs and LINEs. The development of an assay to monitor SINE retrotransposition in culture has become an important tool for the elucidation of some of these differences. In this chapter, we present details of the SINE retrotransposition assay and the recovery of de novo inserts. We also focus on the nuances that are unique to the SINE assay.

Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay.

PubMed

Lucas, Bronwyn A; Lavi, Eitan; Shiue, Lily; Cho, Hana; Katzman, Sol; Miyoshi, Keita; Siomi, Mikiko C; Carmel, Liran; Ares, Manuel; Maquat, Lynne E

2018-01-30

Primate-specific Alu short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3'-untranslated regions (3'-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs. To explore this possibility, we searched for orthologous gene pairs, each carrying a species-specific 3'-UTR SINE and each regulated by SMD, by measuring changes in mRNA abundance after individual depletion of two SMD factors, Staufen1 (STAU1) and UPF1, in both human and mouse myoblasts. We identified and confirmed orthologous gene pairs with 3'-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20-25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.

Evolutionary modes of emergence of short interspersed nuclear element (SINE) families in grasses.

PubMed

Kögler, Anja; Schmidt, Thomas; Wenke, Torsten

2017-11-01

Short interspersed nuclear elements (SINEs) are non-autonomous transposable elements which are propagated by retrotransposition and constitute an inherent part of the genome of most eukaryotic species. Knowledge of heterogeneous and highly abundant SINEs is crucial for de novo (or improvement of) annotation of whole genome sequences. We scanned Poaceae genome sequences of six important cereals (Oryza sativa, Triticum aestivum, Hordeum vulgare, Panicum virgatum, Sorghum bicolor, Zea mays) and Brachypodium distachyon to examine the diversity and evolution of SINE populations. We comparatively analyzed the structural features, distribution, evolutionary relation and abundance of 32 SINE families and subfamilies within grasses, comprising 11 052 individual copies. The investigation of activity profiles within the Poaceae provides insights into their species-specific diversification and amplification. We found that Poaceae SINEs (PoaS) fall into two length categories: simple SINEs of up to 180 bp and dimeric SINEs larger than 240 bp. Detailed analysis at the nucleotide level revealed that multimerization of related and unrelated SINE copies is an important evolutionary mechanism of SINE formation. We conclude that PoaS families diversify by massive reshuffling between SINE families, likely caused by insertion of truncated copies, and provide a model for this evolutionary scenario. Twenty-eight of 32 PoaS families and subfamilies show significant conservation, in particular either in the 5' or 3' regions, across Poaceae species and share large sequence stretches with one or more other PoaS families. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Ring-type structures in the Planck map of the CMB

NASA Astrophysics Data System (ADS)

An, Daniel; Meissner, Krzysztof A.; Nurowski, Paweł

2018-01-01

We present the results of the quest for ring-type structures on the maps observed by the Planck satellite. The results show that the vicinity of one radius (γ = 0.14 rad) of the rings is distinguished. Twisting the circles into deformed ellipses gives a pronounced drop of significance with the increase of twisting; however, this behaviour is also present in some statistically isotropic simulations.

Analysis and machine mapping of the distribution of band recoveries

USGS Publications Warehouse

Cowardin, L.M.

1977-01-01

A method of calculating distance and bearing from banding site to recovery location based on the solution of a spherical triangle is presented. X and Y distances on an ordinate grid were applied to computer plotting of recoveries on a map. The advantages and disadvantages of tables of recoveries by State or degree block, axial lines, and distance of recovery from banding site for presentation and comparison of the spatial distribution of band recoveries are discussed. A special web-shaped partition formed by concentric circles about the point of banding and great circles at 30-degree intervals through the point of banding has certain advantages over other methods. Comparison of distributions by means of a X? contingency test is illustrated. The statistic V = X?/N can be used as a measure of difference between two distributions of band recoveries and its possible use is illustrated as a measure of the degree of migrational homing.

A comparison of two conformal mapping techniques applied to an aerobrake body

NASA Technical Reports Server (NTRS)

Hommel, Mark J.

1987-01-01

Conformal mapping is a classical technique which has been utilized for solving problems in aerodynamics and hydrodynamics. Conformal mapping has been successfully applied in the construction of grids around airfoils, engine inlets and other aircraft configurations. Conformal mapping techniques were applied to an aerobrake body having an axis of symmetry. Two different approaches were utilized: (1) Karman-Trefftz transformation; and (2) Point Wise Schwarz Christoffel transformation. In both cases, the aerobrake body was mapped onto a near circle, and a grid was generated in the mapped plane. The mapped body and grid were then mapped back into physical space and the properties of the associated grids were examined. Advantages and disadvantages of both approaches are discussed.

Gyrator transform of generalized sine-Gaussian beams and conversion an edge-dislocation into a vortex

NASA Astrophysics Data System (ADS)

Zhu, Kaicheng; Tang, Huiqin; Tang, Ying; Xia, Hui

2014-12-01

We proposed a scheme that converts a sine-Gaussian beam with an edge dislocation into a dark hollow beam with a vortex. Based on the gyrator transform (GT) relation, the closed-form field distribution of generalized sine-Gaussian beams passing through a GT system is derived; the intensity distribution and the corresponding phase distribution associated with the transforming generalized sine-Gaussian beams are analyzed. According to the numerical method, the distributions are graphically demonstrated and found that, for appropriate beam parameters and the GT angle, dark hollow vortex beams with topological charge 1 can be achieved using sine-Gaussian beams carrying an edge dislocation. Moreover, the orbital angular momentum content of a GT sine-Gaussian beam is analyzed. It is proved that the GT retains the odd- or even-order spiral harmonics structures of generalized sine-Gaussian beams in the transform process. In particular, it is wholly possible to convert an edge dislocation embedded in sine-Gaussian beams into a vortex with GT. The study also reveals that to obtain a dark hollow beam making use of GT of cos-Gaussian beams is impossible.

RUDI, a short interspersed element of the V-SINE superfamily widespread in molluscan genomes.

PubMed

Luchetti, Andrea; Šatović, Eva; Mantovani, Barbara; Plohl, Miroslav

2016-06-01

Short interspersed elements (SINEs) are non-autonomous retrotransposons that are widespread in eukaryotic genomes. They exhibit a chimeric sequence structure consisting of a small RNA-related head, an anonymous body and an AT-rich tail. Although their turnover and de novo emergence is rapid, some SINE elements found in distantly related species retain similarity in certain core segments (or highly conserved domains, HCD). We have characterized a new SINE element named RUDI in the bivalve molluscs Ruditapes decussatus and R. philippinarum and found this element to be widely distributed in the genomes of a number of mollusc species. An unexpected structural feature of RUDI is the HCD domain type V, which was first found in non-amniote vertebrate SINEs and in the SINE from one cnidarian species. In addition to the V domain, the overall sequence conservation pattern of RUDI elements resembles that found in ancient AmnSINE (~310 Myr old) and Au SINE (~320 Myr old) families, suggesting that RUDI might be among the most ancient SINE families. Sequence conservation suggests a monophyletic origin of RUDI. Nucleotide variability and phylogenetic analyses suggest long-term vertical inheritance combined with at least one horizontal transfer event as the most parsimonious explanation for the observed taxonomic distribution.

Mobile Element Evolution Playing Jigsaw—SINEs in Gastropod and Bivalve Mollusks

PubMed Central

Matetovici, Irina; Sajgo, Szilard; Ianc, Bianca; Ochis, Cornelia; Bulzu, Paul; Popescu, Octavian; Damert, Annette

2016-01-01

SINEs (Short INterspersed Elements) are widely distributed among eukaryotes. Some SINE families are organized in superfamilies characterized by a shared central domain. These central domains are conserved across species, classes, and even phyla. Here we report the identification of two novel such superfamilies in the genomes of gastropod and bivalve mollusks. The central conserved domain of the first superfamily is present in SINEs in Caenogastropoda and Vetigastropoda as well as in all four subclasses of Bivalvia. We designated the domain MESC (Romanian for MElc—snail and SCoica—mussel) because it appears to be restricted to snails and mussels. The second superfamily is restricted to Caenogastropoda. Its central conserved domain—Snail—is related to the Nin-DC domain. Furthermore, we provide evidence that a 40-bp subdomain of the SINE V-domain is conserved in SINEs in mollusks and arthropods. It is predicted to form a stable stem-loop structure that is preserved in the context of the overall SINE RNA secondary structure in invertebrates. Our analysis also recovered short retrotransposons with a Long INterspersed Element (LINE)-derived 5′ end. These share the body and/or the tail with transfer RNA (tRNA)-derived SINEs within and across species. Finally, we identified CORE SINEs in gastropods and bivalves—extending the distribution range of this superfamily. PMID:26739168

Brady's Geothermal Field - Map of DAS, Nodal, Vibroseis and Reftek Station Deployment

DOE Data Explorer

Kurt Feigl

2016-10-15

Map of DAS, nodal, vibroseis and Reftek stations during March 2016 deployment. The plot on the left has nodal stations labeled; the plot on the right has vibroseis observations labeled. Stations are shown in map-view using Brady's rotated X-Y coordinates with side plots denoting elevation with respect to the WGS84 ellipsoid. Blue circles denote vibroseis data, x symbols denote DAS (cyan for horizontal and magenta for vertical), black asterisks denote Reftek data, and red plus signs denote nodal data. This map can be found on UW-Madison's askja server at /PoroTomo/DATA/MAPS/Deployment_Stations.pdf

Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family-specific impact on gene structure and genome organization.

PubMed

Seibt, Kathrin M; Wenke, Torsten; Muders, Katja; Truberg, Bernd; Schmidt, Thomas

2016-05-01

Short interspersed nuclear elements (SINEs) are highly abundant non-autonomous retrotransposons that are widespread in plants. They are short in size, non-coding, show high sequence diversity, and are therefore mostly not or not correctly annotated in plant genome sequences. Hence, comparative studies on genomic SINE populations are rare. To explore the structural organization and impact of SINEs, we comparatively investigated the genome sequences of the Solanaceae species potato (Solanum tuberosum), tomato (Solanum lycopersicum), wild tomato (Solanum pennellii), and two pepper cultivars (Capsicum annuum). Based on 8.5 Gbp sequence data, we annotated 82 983 SINE copies belonging to 10 families and subfamilies on a base pair level. Solanaceae SINEs are dispersed over all chromosomes with enrichments in distal regions. Depending on the genome assemblies and gene predictions, 30% of all SINE copies are associated with genes, particularly frequent in introns and untranslated regions (UTRs). The close association with genes is family specific. More than 10% of all genes annotated in the Solanaceae species investigated contain at least one SINE insertion, and we found genes harbouring up to 16 SINE copies. We demonstrate the involvement of SINEs in gene and genome evolution including the donation of splice sites, start and stop codons and exons to genes, enlargement of introns and UTRs, generation of tandem-like duplications and transduction of adjacent sequence regions. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.

PubMed

Tajaddod, Mansoureh; Tanzer, Andrea; Licht, Konstantin; Wolfinger, Michael T; Badelt, Stefan; Huber, Florian; Pusch, Oliver; Schopoff, Sandy; Janisiw, Michael; Hofacker, Ivo; Jantsch, Michael F

2016-10-25

Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution. Moreover, Alu elements within mRNAs have also been reported to control gene expression at different levels. Here, we undertake a genome-wide analysis of insertion patterns of human Alus within transcribed portions of the genome. Multiple, nearby insertions of SINEs within one transcript are more abundant in tandem orientation than in inverted orientation. Indeed, analysis of transcriptome-wide expression levels of 15 ENCODE cell lines suggests a cis-repressive effect of inverted Alu elements on gene expression. Using reporter assays, we show that the negative effect of inverted SINEs on gene expression is independent of known sensors of double-stranded RNAs. Instead, transcriptional elongation seems impaired, leading to reduced mRNA levels. Our study suggests that there is a bias against multiple SINE insertions that can promote intramolecular base pairing within a transcript. Moreover, at a genome-wide level, mRNAs harboring inverted SINEs are less expressed than mRNAs harboring single or tandemly arranged SINEs. Finally, we demonstrate a novel mechanism by which inverted SINEs can impact on gene expression by interfering with RNA polymerase II.

A star recognition method based on the Adaptive Ant Colony algorithm for star sensors.

PubMed

Quan, Wei; Fang, Jiancheng

2010-01-01

A new star recognition method based on the Adaptive Ant Colony (AAC) algorithm has been developed to increase the star recognition speed and success rate for star sensors. This method draws circles, with the center of each one being a bright star point and the radius being a special angular distance, and uses the parallel processing ability of the AAC algorithm to calculate the angular distance of any pair of star points in the circle. The angular distance of two star points in the circle is solved as the path of the AAC algorithm, and the path optimization feature of the AAC is employed to search for the optimal (shortest) path in the circle. This optimal path is used to recognize the stellar map and enhance the recognition success rate and speed. The experimental results show that when the position error is about 50″, the identification success rate of this method is 98% while the Delaunay identification method is only 94%. The identification time of this method is up to 50 ms.

Comparative evolution history of SINEs in Arabidopsis thaliana and Brassica oleracea: evidence for a high rate of SINE loss.

PubMed

Lenoir, A; Pélissier, T; Bousquet-Antonelli, C; Deragon, J M

2005-01-01

Brassica oleracea and Arabidopsis thaliana belong to the Brassicaceae(Cruciferae) family and diverged 16 to 19 million years ago. Although the genome size of B. oleracea (approximately 600 million base pairs) is more than four times that of A. thaliana (approximately 130 million base pairs), their gene content is believed to be very similar with more than 85% sequence identity in the coding region. Therefore, this important difference in genome size is likely to reflect a different rate of non-coding DNA accumulation. Transposable elements (TEs) constitute a major fraction of non-coding DNA in plant species. A different rate in TE accumulation between two closely related species can result in significant genome size variations in a short evolutionary period. Short interspersed elements (SINEs) are non-autonomous retroposons that have invaded the genome of most eukaryote species. Several SINE families are present in B. oleracea and A. thaliana and we found that two of them (called RathE1 and RathE2) are present in both species. In this study, the tempo of evolution of RathE1 and RathE2 SINE families in both species was compared. We observed that most B. oleracea RathE2 SINEs are "young" (close to the consensus sequence) and abundant while elements from this family are more degenerated and much less abundant in A. thaliana. However, the situation is different for the RathE1 SINE family for which the youngest elements are found in A. thaliana. Surprisingly, no SINE was found to occupy the same (orthologous) genomic locus in both species suggesting that either these SINE families were not amplified at a significant rate in the common ancestor of the two species or that older elements were lost and only the recent (lineage-specific) insertions remain. To test this latter hypothesis, loci containing a recently inserted SINE in the A. thaliana col-0 ecotype were selected and characterized in several other A. thaliana ecotypes. In addition to the expected SINE containing allele and the pre-integrative allele (i.e. the "empty" allele), we observed in the different ecotypes, alleles with truncated portions of the SINE (up to the complete loss of the element) and of the immediate genomic flanking sequences. The absence of SINEs in orthologous positions between B. oleracea and A. thaliana and the presence in recently diverged A. thaliana ecotypes of alleles containing severely truncated SINEs suggest a very high rate of SINE loss in these species.

Erlang circular model motivated by inverse stereographic projection

NASA Astrophysics Data System (ADS)

Pramesti, G.

2018-05-01

The Erlang distribution is a special case of the Gamma distribution with the shape parameter is an integer. This paper proposed a new circular model used inverse stereographic projection. The inverse stereographic projection which is a mapping that projects a random variable from a real line onto a circle can be used in circular statistics to construct a distribution on the circle from real domain. From the circular model, then can be derived the characteristics of the Erlang circular model such as the mean resultant length, mean direction, circular variance and trigonometric moments of the distribution.

Speed skills: measuring the visual speed analyzing properties of primate MT neurons.

PubMed

Perrone, J A; Thiele, A

2001-05-01

Knowing the direction and speed of moving objects is often critical for survival. However, it is poorly understood how cortical neurons process the speed of image movement. Here we tested MT neurons using moving sine-wave gratings of different spatial and temporal frequencies, and mapped out the neurons' spatiotemporal frequency response profiles. The maps typically had oriented ridges of peak sensitivity as expected for speed-tuned neurons. The preferred speed estimate, derived from the orientation of the maps, corresponded well to the preferred speed when moving bars were presented. Thus, our data demonstrate that MT neurons are truly sensitive to the object speed. These findings indicate that MT is not only a key structure in the analysis of direction of motion and depth perception, but also in the analysis of object speed.

Origin and evolution of SINEs in eukaryotic genomes.

PubMed

Kramerov, D A; Vassetzky, N S

2011-12-01

Short interspersed elements (SINEs) are one of the two most prolific mobile genomic elements in most of the higher eukaryotes. Although their biology is still not thoroughly understood, unusual life cycle of these simple elements amplified as genomic parasites makes their evolution unique in many ways. In contrast to most genetic elements including other transposons, SINEs emerged de novo many times in evolution from available molecules (for example, tRNA). The involvement of reverse transcription in their amplification cycle, huge number of genomic copies and modular structure allow variation mechanisms in SINEs uncommon or rare in other genetic elements (module exchange between SINE families, dimerization, and so on.). Overall, SINE evolution includes their emergence, progressive optimization and counteraction to the cell's defense against mobile genetic elements.

SINE sequences detect DNA fingerprints in salmonid fishes.

PubMed

Spruell, P; Thorgaard, G H

1996-04-01

DNA probes homologous to two previously described salmonid short interspersed nuclear elements (SINEs) detected DNA fingerprint patterns in 14 species of salmonid fishes. The probes showed more homology to some species than to others and little homology to three nonsalmonid fishes. The DNA fingerprint patterns derived from the SINE probes are individual-specific and inherited in a Mendelian manner. Probes derived from different regions of the same SINE detect only partially overlapping banding patterns, reflecting a more complex SINE structure than has been previously reported. Like the human Alu sequence, the SINEs found in salmonids could provide useful genetic markers and primer sites for PCR-based techniques. These elements may be more desirable for some applications than traditional DNA fingerprinting probes that detect tandemly repeated arrays.

Topographic control of sorted circle morphology on Svalbard

NASA Astrophysics Data System (ADS)

Voigt, Joana; Hauber, Ernst; Reiss, Dennis; Hiesinger, Harald; Johnsson, Andreas; van Gasselt, Stephan; Balme, Matt; Head, Jim; de Verra, Jean-Pierre; Steinbrügge, Gregor; Jaumann, Ralf

2015-04-01

Patterned ground is a typical phenomenon in polar, subpolar and alpine regions [1]. As it is commonly (but not necessarily!) related to freeze-thaw cycles, its presence on Mars could possibly point to locations and periods where and when liquid water existed in the recent past [2]. Sorted circles are a class of patterned ground that was tentatively identified in Elysium Planitia (Mars) [3], but this interpretation has been challenged on the basis of physical considerations [4]. Without direct access to potential patterned ground on Mars, the analysis of terrestrial analogues can inform the interpretation of Martian landforms. Svalbard (Norway) offers a wide variety of permafrost features that are morphologically analogous to Martian cold-climate landforms [5]. It hosts some of the best examples of sorted circles on Earth, which are located on the westernmost tip of Brøgger peninsula, on a broad strand flat that is characterized by a series of postglacial beach ridges [6]. Here we report on our analysis of sorted circle morphology (especially their plan-view shape, i.e. their "roundness" or ellipticity) and its correlation with local topography (slopes, curvature). Sorted circle morphology was determined from HRSC-AX images (for details on the flight campaign and image properties see ref [5]) and through field work. Topographic information comes from a 50 cm gridded DEM derived from HRSC-AX stereo images. We measured sorted circle morphology (ellipticity, azimuth of major axis) along a WNW-ESE traverse that runs from the inland towards the sea and is oriented perpendicular to the local beach ridge trend. Selected areas with homogeneous sorted circle appearance were visually mapped, and compared to the average slope, aspect, and the calculated topographic wetness index (TWI). Furthermore the whole traverse was classified into four different morphologies of the sorted patterned ground (sorted circles, sorted "ellipses", sorted nets and areas without patterned ground). For these morphologies, we also measured the slope, aspect and TWI to correlate the topographical parameters with the geomorphological characteristics of the patterned ground, and with predictions from modeling [7]. Our results confirm that the dependence of morphology on topography of sorted circles can be measured using a combination of plan-view and topographic remote sensing data. Thus, as the same quality of data is available on Mars, these same measurements could be made there in order to test whether the circle morphology depends on the local relief patterns in the same ways as in our terrestrial study. A positive result would argue that the Martian features may have formed in the same way (freeze-thaw) as the terrestrial ones. [1] Washburn, A.L. (1956) Geol. Soc. Amer. Bull. 67, 823-866. [2] Balme et al. (2013) Prog. Phys. Geog. 37, 289-324. [3] Balme et al. (2009) Icarus 200, 30-38. [4] Kreslavsky, M.A., Head, J.W. (2014) LPSC 45, abstract 2715. [5] Hauber et al. (2011) GSA Spec. Paper 483, 177-201. [6] Tolgensbakk, J., Sollid, J.L. (1987) Kvadehuksletta, Geomorfologi og Kvartærgeologi (geomorphological map; scale 1:10,000), Universitet i Oslo. [7] Kessler, M.A., Werner, B.T. (2003) Science 299, 380-383.

Distribution, Diversity, and Long-Term Retention of Grass Short Interspersed Nuclear Elements (SINEs).

PubMed

Mao, Hongliang; Wang, Hao

2017-08-01

Instances of highly conserved plant short interspersed nuclear element (SINE) families and their enrichment near genes have been well documented, but little is known about the general patterns of such conservation and enrichment and underlying mechanisms. Here, we perform a comprehensive investigation of the structure, distribution, and evolution of SINEs in the grass family by analyzing 14 grass and 5 other flowering plant genomes using comparative genomics methods. We identify 61 SINE families composed of 29,572 copies, in which 46 families are first described. We find that comparing with other grass TEs, grass SINEs show much higher level of conservation in terms of genomic retention: The origin of at least 26% families can be traced to early grass diversification and these families are among most abundant SINE families in 86% species. We find that these families show much higher level of enrichment near protein coding genes than families of relatively recent origin (51%:28%), and that 40% of all grass SINEs are near gene and the percentage is higher than other types of grass TEs. The pattern of enrichment suggests that differential removal of SINE copies in gene-poor regions plays an important role in shaping the genomic distribution of these elements. We also identify a sequence motif located at 3' SINE end which is shared in 17 families. In short, this study provides insights into structure and evolution of SINEs in the grass family. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

V-SINEs: A New Superfamily of Vertebrate SINEs That Are Widespread in Vertebrate Genomes and Retain a Strongly Conserved Segment within Each Repetitive Unit

PubMed Central

Ogiwara, Ikuo; Miya, Masaki; Ohshima, Kazuhiko; Okada, Norihiro

2002-01-01

We have identified a new superfamily of vertebrate short interspersed repetitive elements (SINEs), designated V-SINEs, that are widespread in fishes and frogs. Each V-SINE includes a central conserved domain preceded by a 5′-end tRNA-related region and followed by a potentially recombinogenic (TG)n tract, with a 3′ tail derived from the 3′ untranslated region (UTR) of the corresponding partner long interspersed repetitive element (LINE) that encodes a functional reverse transcriptase. The central domain is strongly conserved and is even found in SINEs in the lamprey genome, suggesting that V-SINEs might be ∼550 Myr old or older in view of the timing of divergence of the lamprey lineage from the bony fish lineage. The central conserved domain might have been subject to some form of positive selection. Although the contemporary 3′ tails of V-SINEs differ from one another, it is possible that the original 3′ tail might have been replaced, via recombination, by the 3′ tails of more active partner LINEs, thereby retaining retropositional activity and the ability to survive for long periods on the evolutionary time scale. It seems plausible that V-SINEs may have some function(s) that have been maintained by the coevolution of SINEs and LINEs during the evolution of vertebrates. [The sequences reported in this paper have been deposited in the DDBJ/GenBank database under accession nos. AB072981–AB073004. Supplemental figures are available online at http://www.genome.org.] PMID:11827951

Families of short interspersed elements in the genome of the oomycete plant pathogen, Phytophthora infestans.

PubMed

Whisson, Stephen C; Avrova, Anna O; Lavrova, Olga; Pritchard, Leighton

2005-04-01

The first known families of tRNA-related short interspersed elements (SINEs) in the oomycetes were identified by exploiting the genomic DNA sequence resources for the potato late blight pathogen, Phytophthora infestans. Fifteen families of tRNA-related SINEs, as well as predicted tRNAs, and other possible RNA polymerase III-transcribed sequences were identified. The size of individual elements ranges from 101 to 392 bp, representing sequences present from low (1) to highly abundant (over 2000) copy number in the P. infestans genome, based on quantitative PCR analysis. Putative short direct repeat sequences (6-14 bp) flanking the elements were also identified for eight of the SINEs. Predicted SINEs were named in a series prefixed infSINE (for infestans-SINE). Two SINEs were apparently present as multimers of tRNA-related units; four copies of a related unit for infSINEr, and two unrelated units for infSINEz. Two SINEs, infSINEh and infSINEi, were typically located within 400 bp of each other. These were also the only two elements identified as being actively transcribed in the mycelial stage of P. infestans by RT-PCR. It is possible that infSINEh and infSINEi represent active retrotransposons in P. infestans. Based on the quantitative PCR estimates of copy number for all of the elements identified, tRNA-related SINEs were estimated to comprise 0.3% of the 250 Mb P. infestans genome. InfSINE-related sequences were found to occur in species throughout the genus Phytophthora. However, seven elements were shown to be exclusive to P. infestans.

Evolution of Two Short Interspersed Elements in Callorhinchus milii (Chondrichthyes, Holocephali) and Related Elements in Sharks and the Coelacanth

PubMed Central

Plazzi, Federico; Mantovani, Barbara

2017-01-01

Abstract Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two HCD-SINE families in the elephant shark Callorhinchus milii, one specific to the holocephalan lineage (CmiSINEs) and another one (SacSINE1-CM) with homologous elements in sharks and the coelacanth (SacSINE1s, LmeSINE1s). The analyses of their relationships indicated that these elements share the same 3′-tail, which would have allowed both elements to rise to high copy number by exploiting the C. milii L2-2_CM long interspersed element (LINE) enzymes. Molecular clock analysis on SINE activity in C. milii genome evidenced two replication bursts occurring right after two major events in the holocephalan evolution: the end-Permian mass extinction and the radiation of modern Holocephali. Accordingly, the same analysis on the coelacanth homologous elements, LmeSINE1, identified a replication wave close to the split age of the two extant Latimeria species. The genomic distribution of the studied SINEs pointed out contrasting results: some elements were preferentially sorted out from gene regions, but accumulated in flanking regions, while others appear more conserved within genes. Moreover, data from the C. milii transcriptome suggest that these SINEs could be involved in miRNA biogenesis and may be targets for miRNA-based regulation. PMID:28505260

Mobile Element Evolution Playing Jigsaw - SINEs in Gastropod and Bivalve Mollusks.

PubMed

Matetovici, Irina; Sajgo, Szilard; Ianc, Bianca; Ochis, Cornelia; Bulzu, Paul; Popescu, Octavian; Damert, Annette

2016-01-06

SINEs (Short INterspersed Elements) are widely distributed among eukaryotes. Some SINE families are organized in superfamilies characterized by a shared central domain. These central domains are conserved across species, classes, and even phyla. Here we report the identification of two novel such superfamilies in the genomes of gastropod and bivalve mollusks. The central conserved domain of the first superfamily is present in SINEs in Caenogastropoda and Vetigastropoda as well as in all four subclasses of Bivalvia. We designated the domain MESC (Romanian for MElc-snail and SCoica-mussel) because it appears to be restricted to snails and mussels. The second superfamily is restricted to Caenogastropoda. Its central conserved domain-Snail-is related to the Nin-DC domain. Furthermore, we provide evidence that a 40-bp subdomain of the SINE V-domain is conserved in SINEs in mollusks and arthropods. It is predicted to form a stable stem-loop structure that is preserved in the context of the overall SINE RNA secondary structure in invertebrates. Our analysis also recovered short retrotransposons with a Long INterspersed Element (LINE)-derived 5' end. These share the body and/or the tail with transfer RNA (tRNA)-derived SINEs within and across species. Finally, we identified CORE SINEs in gastropods and bivalves-extending the distribution range of this superfamily. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Analysis of the 227 bp short interspersed nuclear element (SINE) insertion of the promoter of the myostatin (MSTN) gene in different horse breeds.

PubMed

Dall'Olio, Stefania; Scotti, Emilio; Fontanesi, Luca; Tassinari, Marco

2014-01-01

The myostatin (MSTN) gene encodes a protein known to be a negative regulator of muscle mass in mammalian species. Different polymorphisms of the horse (Equus caballus) MSTN gene have been identified, including single nucleotide polymorphisms and a short interspersed nuclear element (SINE) insertion of 227 bp within the promoter of the gene. The SINE insertion has been associated with performance traits in Thoroughbred racehorses and it was proposed as a predictor of optimum racing distance. The aims of this study were to perform in silico analysis to identify putative gains or abrogation of transcription-factor binding sites (TFBSs) generated by the SINE allele of the promoter and to analyse the frequency of the SINE insertion in horses used for racing (gallop and trot) and other purposes. The SINE insertion was genotyped in 227 horses from 10 breeds belonging to different morphological types (brachimorphic, mesomorphic, meso-dolichomorphic and dolichomorphic). The presence of the insertion was confirmed in the Quarter Horse (SINE allele frequency of 0.81) and in the Thoroughbred (0.51), whereas the SINE allele did not segregate in any of the other analysed breeds. As the SINE MSTN gene polymorphism may be population or breed specific, it is not a useful marker for association studies in all breeds.

Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure.

PubMed

Borodulina, O R; Kramerov, D A

2001-10-01

Four tRNA-related SINE families were isolated from the genome of the shrew Sorex araneus (SOR element), mole Mogera robusta (TAL element), and hedgehog Mesechinus dauuricus (ERI-1 and ERI-2 elements). Each of these SINEs families is specific for a single Insectivora family: SOR, for Soricidae (shrews); TAL, for Talpidae (moles and desmans); ERI-1 and ERI-2, for Erinaceidae (hedgehogs). There is a long polypyrimidine region (TC-motif) in TAL, ERI-1, and ERI-2 elements located immediately upstream of an A-rich tail with polyadenylation signals (AATAAA) and an RNA polymerase III terminator (T(4-6)) or TCT(3-4)). Ten out of 14 analyzed mammalian tRNA-related SINE families have an A-rich tail similar to that of TAL, ERI-1, and ERI-2 elements. These elements were assigned to class T+. The other four SINEs including SOR element have no polyadenylation signal and transcription terminator in their A-rich tail and were assigned to class T-. Class T+ SINEs occur only in mammals, and most of them have a long polypyrimidine region. Possible models of retroposition of class T+ and T- SINEs are discussed.

Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs.

PubMed

Ichiyanagi, Kenji

2013-01-01

Short interspersed elements (SINEs) are a class of retrotransposons, which amplify their copy numbers in their host genomes by retrotransposition. More than a million copies of SINEs are present in a mammalian genome, constituting over 10% of the total genomic sequence. In contrast to the other two classes of retrotransposons, long interspersed elements (LINEs) and long terminal repeat (LTR) elements, SINEs are transcribed by RNA polymerase III. However, like LINEs and LTR elements, the SINE transcription is likely regulated by epigenetic mechanisms such as DNA methylation, at least for human Alu and mouse B1. Whereas SINEs and other transposable elements have long been thought as selfish or junk DNA, recent studies have revealed that they play functional roles at their genomic locations, for example, as distal enhancers, chromatin boundaries and binding sites of many transcription factors. These activities imply that SINE retrotransposition has shaped the regulatory network and chromatin landscape of their hosts. Whereas it is thought that the epigenetic mechanisms were originated as a host defense system against proliferation of parasitic elements, this review discusses a possibility that the same mechanisms are also used to regulate the SINE-derived functions.

Conserved domains and SINE diversity during animal evolution.

PubMed

Luchetti, Andrea; Mantovani, Barbara

2013-10-01

Eukaryotic genomes harbour a number of mobile genetic elements (MGEs); moving from one genomic location to another, they are known to impact on the host genome. Short interspersed elements (SINEs) are well-represented, non-autonomous retroelements and they are likely the most diversified MGEs. In some instances, sequence domains conserved across unrelated SINEs have been identified; remarkably, one of these, called Nin, has been conserved since the Radiata-Bilateria splitting. Here we report on two new domains: Inv, derived from Nin, identified in insects and in deuterostomes, and Pln, restricted to polyneopteran insects. The identification of Inv and Pln sequences allowed us to retrieve new SINEs, two in insects and one in a hemichordate. The diverse structural combination of the different domains in different SINE families, during metazoan evolution, offers a clearer view of SINE diversity and their frequent de novo emergence through module exchange, possibly underlying the high evolutionary success of SINEs. © 2013 Elsevier Inc. All rights reserved.

Zernike expansion of derivatives and Laplacians of the Zernike circle polynomials.

PubMed

Janssen, A J E M

2014-07-01

The partial derivatives and Laplacians of the Zernike circle polynomials occur in various places in the literature on computational optics. In a number of cases, the expansion of these derivatives and Laplacians in the circle polynomials are required. For the first-order partial derivatives, analytic results are scattered in the literature. Results start as early as 1942 in Nijboer's thesis and continue until present day, with some emphasis on recursive computation schemes. A brief historic account of these results is given in the present paper. By choosing the unnormalized version of the circle polynomials, with exponential rather than trigonometric azimuthal dependence, and by a proper combination of the two partial derivatives, a concise form of the expressions emerges. This form is appropriate for the formulation and solution of a model wavefront sensing problem of reconstructing a wavefront on the level of its expansion coefficients from (measurements of the expansion coefficients of) the partial derivatives. It turns out that the least-squares estimation problem arising here decouples per azimuthal order m, and per m the generalized inverse solution assumes a concise analytic form so that singular value decompositions are avoided. The preferred version of the circle polynomials, with proper combination of the partial derivatives, also leads to a concise analytic result for the Zernike expansion of the Laplacian of the circle polynomials. From these expansions, the properties of the Laplacian as a mapping from the space of circle polynomials of maximal degree N, as required in the study of the Neumann problem associated with the transport-of-intensity equation, can be read off within a single glance. Furthermore, the inverse of the Laplacian on this space is shown to have a concise analytic form.

Origin and evolution of SINEs in eukaryotic genomes

PubMed Central

Kramerov, D A; Vassetzky, N S

2011-01-01

Short interspersed elements (SINEs) are one of the two most prolific mobile genomic elements in most of the higher eukaryotes. Although their biology is still not thoroughly understood, unusual life cycle of these simple elements amplified as genomic parasites makes their evolution unique in many ways. In contrast to most genetic elements including other transposons, SINEs emerged de novo many times in evolution from available molecules (for example, tRNA). The involvement of reverse transcription in their amplification cycle, huge number of genomic copies and modular structure allow variation mechanisms in SINEs uncommon or rare in other genetic elements (module exchange between SINE families, dimerization, and so on.). Overall, SINE evolution includes their emergence, progressive optimization and counteraction to the cell's defense against mobile genetic elements. PMID:21673742

Physical map of the Brucella melitensis 16 M chromosome.

PubMed Central

Allardet-Servent, A; Carles-Nurit, M J; Bourg, G; Michaux, S; Ramuz, M

1991-01-01

We present the first restriction map of the Brucella melitensis 16 M chromosome obtained by Southern blot hybridization of SpeI, XhoI, and XbaI fragments separated by pulsed-field gel electrophoresis. All restriction fragments (a total of 113) were mapped into an open circle. The main difficulty in mapping involved the exceedingly high number of restriction fragments, as was expected considering the 59% G + C content of the Brucella genome. Several cloned genes were placed on this map, especially rRNA operons which are repeated three times. The size of the B. melitensis chromosome, estimated as 2,600 kb long in a previous study, appeared longer (3,130 kb) by restriction mapping. This restriction map is an initial approach to achieve a genetic map of the Brucella chromosome. Images PMID:2007548

SINEs, evolution and genome structure in the opossum.

PubMed

Gu, Wanjun; Ray, David A; Walker, Jerilyn A; Barnes, Erin W; Gentles, Andrew J; Samollow, Paul B; Jurka, Jerzy; Batzer, Mark A; Pollock, David D

2007-07-01

Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.

Evolution of Two Short Interspersed Elements in Callorhinchus milii (Chondrichthyes, Holocephali) and Related Elements in Sharks and the Coelacanth.

PubMed

Luchetti, Andrea; Plazzi, Federico; Mantovani, Barbara

2017-06-01

Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two HCD-SINE families in the elephant shark Callorhinchus milii, one specific to the holocephalan lineage (CmiSINEs) and another one (SacSINE1-CM) with homologous elements in sharks and the coelacanth (SacSINE1s, LmeSINE1s). The analyses of their relationships indicated that these elements share the same 3'-tail, which would have allowed both elements to rise to high copy number by exploiting the C. milii L2-2_CM long interspersed element (LINE) enzymes. Molecular clock analysis on SINE activity in C. milii genome evidenced two replication bursts occurring right after two major events in the holocephalan evolution: the end-Permian mass extinction and the radiation of modern Holocephali. Accordingly, the same analysis on the coelacanth homologous elements, LmeSINE1, identified a replication wave close to the split age of the two extant Latimeria species. The genomic distribution of the studied SINEs pointed out contrasting results: some elements were preferentially sorted out from gene regions, but accumulated in flanking regions, while others appear more conserved within genes. Moreover, data from the C. milii transcriptome suggest that these SINEs could be involved in miRNA biogenesis and may be targets for miRNA-based regulation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Developing a medication communication framework across continuums of care using the Circle of Care Modeling approach.

PubMed

Kitson, Nicole A; Price, Morgan; Lau, Francis Y; Showler, Grey

2013-10-17

Medication errors are a common type of preventable errors in health care causing unnecessary patient harm, hospitalization, and even fatality. Improving communication between providers and between providers and patients is a key aspect of decreasing medication errors and improving patient safety. Medication management requires extensive collaboration and communication across roles and care settings, which can reduce (or contribute to) medication-related errors. Medication management involves key recurrent activities (determine need, prescribe, dispense, administer, and monitor/evaluate) with information communicated within and between each. Despite its importance, there is a lack of conceptual models that explore medication communication specifically across roles and settings. This research seeks to address that gap. The Circle of Care Modeling (CCM) approach was used to build a model of medication communication activities across the circle of care. CCM positions the patient in the centre of his or her own healthcare system; providers and other roles are then modeled around the patient as a web of relationships. Recurrent medication communication activities were mapped to the medication management framework. The research occurred in three iterations, to test and revise the model: Iteration 1 consisted of a literature review and internal team discussion, Iteration 2 consisted of interviews, observation, and a discussion group at a Community Health Centre, and Iteration 3 consisted of interviews and a discussion group in the larger community. Each iteration provided further detail to the Circle of Care medication communication model. Specific medication communication activities were mapped along each communication pathway between roles and to the medication management framework. We could not map all medication communication activities to the medication management framework; we added Coordinate as a separate and distinct recurrent activity. We saw many examples of coordination activities, for instance, Medical Office Assistants acting as a liaison between pharmacists and family physicians to clarify prescription details. Through the use of CCM we were able to unearth tacitly held knowledge to expand our understanding of medication communication. Drawing out the coordination activities could be a missing piece for us to better understand how to streamline and improve multi-step communication processes with a goal of improving patient safety.

Developing a medication communication framework across continuums of care using the Circle of Care Modeling approach

PubMed Central

2013-01-01

Background Medication errors are a common type of preventable errors in health care causing unnecessary patient harm, hospitalization, and even fatality. Improving communication between providers and between providers and patients is a key aspect of decreasing medication errors and improving patient safety. Medication management requires extensive collaboration and communication across roles and care settings, which can reduce (or contribute to) medication-related errors. Medication management involves key recurrent activities (determine need, prescribe, dispense, administer, and monitor/evaluate) with information communicated within and between each. Despite its importance, there is a lack of conceptual models that explore medication communication specifically across roles and settings. This research seeks to address that gap. Methods The Circle of Care Modeling (CCM) approach was used to build a model of medication communication activities across the circle of care. CCM positions the patient in the centre of his or her own healthcare system; providers and other roles are then modeled around the patient as a web of relationships. Recurrent medication communication activities were mapped to the medication management framework. The research occurred in three iterations, to test and revise the model: Iteration 1 consisted of a literature review and internal team discussion, Iteration 2 consisted of interviews, observation, and a discussion group at a Community Health Centre, and Iteration 3 consisted of interviews and a discussion group in the larger community. Results Each iteration provided further detail to the Circle of Care medication communication model. Specific medication communication activities were mapped along each communication pathway between roles and to the medication management framework. We could not map all medication communication activities to the medication management framework; we added Coordinate as a separate and distinct recurrent activity. We saw many examples of coordination activities, for instance, Medical Office Assistants acting as a liaison between pharmacists and family physicians to clarify prescription details. Conclusions Through the use of CCM we were able to unearth tacitly held knowledge to expand our understanding of medication communication. Drawing out the coordination activities could be a missing piece for us to better understand how to streamline and improve multi-step communication processes with a goal of improving patient safety. PMID:24134454

Soliton evolution and radiation loss for the sine-Gordon equation.

PubMed

Smyth, N F; Worthy, A L

1999-08-01

An approximate method for describing the evolution of solitonlike initial conditions to solitons for the sine-Gordon equation is developed. This method is based on using a solitonlike pulse with variable parameters in an averaged Lagrangian for the sine-Gordon equation. This averaged Lagrangian is then used to determine ordinary differential equations governing the evolution of the pulse parameters. The pulse evolves to a steady soliton by shedding dispersive radiation. The effect of this radiation is determined by examining the linearized sine-Gordon equation and loss terms are added to the variational equations derived from the averaged Lagrangian by using the momentum and energy conservation equations for the sine-Gordon equation. Solutions of the resulting approximate equations, which include loss, are found to be in good agreement with full numerical solutions of the sine-Gordon equation.

LINEs Contribute to the Origins of Middle Bodies of SINEs besides 3′ Tails

PubMed Central

2018-01-01

Abstract Short interspersed elements (SINEs), which are nonautonomous transposable elements, require the transposition machinery of long interspersed elements (LINEs) to mobilize. SINEs are composed of two or more independently originating parts. The 5′ region is called the “head” and is derived mainly from small RNAs, and the 3′ region (“tail”) originates from the 3′ region of LINEs and is responsible for being recognized by counterpart LINE proteins. The origin of the middle “body” of SINEs is enigmatic, although significant sequence similarities among SINEs from very diverse species have been observed. Here, a systematic analysis of the similarities among SINEs and LINEs deposited on Repbase, a comprehensive database of eukaryotic repeat sequences was performed. Three primary findings are described: 1) The 5′ regions of only two clades of LINEs, RTE and Vingi, were revealed to have contributed to the middle parts of SINEs; 2) The linkage of the 5′ and 3′ parts of LINEs can be lost due to occasional tail exchange of SINEs; and 3) The previously proposed Ceph-domain was revealed to be a fusion of a CORE-domain and a 5′ part of RTE clade of LINE. Based on these findings, a hypothesis that the 5′ parts of bipartite nonautonomous LINEs, which possess only the 5′ and 3′ regions of the original LINEs, can contribute to the undefined middle part of SINEs is proposed. PMID:29325122

Increased levels of B1 and B2 SINE transcripts in mouse fibroblast cells due to minute virus of mice infection.

PubMed

Williams, Warren P; Tamburic, Lillian; Astell, Caroline R

2004-10-01

Minute virus of mice (MVM), an autonomous parvovirus, has served as a model for understanding parvovirus infection including host cell response to infection. In this paper, we report the effect of MVM infection on host cell gene expression in mouse fibroblast cells (LA9 cells), analyzed by differential display. Somewhat surprisingly, our data reveal that few cellular protein-coding genes appear to be up- or downregulated and identify the murine B1 and B2 short interspersed element (SINE) transcripts as being increased upon MVM infection. Primer extension assays confirm the effect of MVM infection on SINE expression and demonstrate that both SINEs are upregulated in a roughly linear fashion throughout MVM infection. They also demonstrate that the SINE response was due to RNA polymerase III transcription and not contaminating DNA or RNA polymerase II transcription. Furthermore, expression of MVM NS1, the major nonstructural protein, by transient transfection also leads to an increase in both murine SINEs. We believe this is the first time that the B1 and B2 SINEs have been shown to be altered by viral infection and the first time parvovirus infection has been shown to increase SINE expression. The increase in SINE transcripts caused by MVM infection does not appear to be due to an increase in either of the basal transcription factors TFIIIC110 or 220, in contrast to that which has been shown for other viruses.

Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions.

PubMed

Muramoto, Hiroki; Yagi, Shintaro; Hirabayashi, Keiji; Sato, Shinya; Ohgane, Jun; Tanaka, Satoshi; Shiota, Kunio

2010-08-01

Embryonic stem cells (ESCs) have a distinctive epigenome, which includes their genome-wide DNA methylation modification status, as represented by the ESC-specific hypomethylation of tissue-dependent and differentially methylated regions (T-DMRs) of Pou5f1 and Nanog. Here, we conducted a genome-wide investigation of sequence characteristics associated with T-DMRs that were differentially methylated between ESCs and somatic cells, by focusing on transposable elements including short interspersed elements (SINEs), long interspersed elements (LINEs) and long terminal repeats (LTRs). We found that hypomethylated T-DMRs were predominantly present in SINE-rich/LINE-poor genomic loci. The enrichment for SINEs spread over 300 kb in cis and there existed SINE-rich genomic domains spreading continuously over 1 Mb, which contained multiple hypomethylated T-DMRs. The characterization of sequence information showed that the enriched SINEs were relatively CpG rich and belonged to specific subfamilies. A subset of the enriched SINEs were hypomethylated T-DMRs in ESCs at Dppa3 gene locus, although SINEs are overall methylated in both ESCs and the liver. In conclusion, we propose that SINE enrichment is the genomic property of regions harboring hypomethylated T-DMRs in ESCs, which is a novel aspect of the ESC-specific epigenomic information.

Analysis and Compensation for Lateral Chromatic Aberration in a Color Coding Structured Light 3D Measurement System.

PubMed

Huang, Junhui; Xue, Qi; Wang, Zhao; Gao, Jianmin

2016-09-03

While color-coding methods have improved the measuring efficiency of a structured light three-dimensional (3D) measurement system, they decreased the measuring accuracy significantly due to lateral chromatic aberration (LCA). In this study, the LCA in a structured light measurement system is analyzed, and a method is proposed to compensate the error caused by the LCA. Firstly, based on the projective transformation, a 3D error map of LCA is constructed in the projector images by using a flat board and comparing the image coordinates of red, green and blue circles with the coordinates of white circles at preselected sample points within the measurement volume. The 3D map consists of the errors, which are the equivalent errors caused by LCA of the camera and projector. Then in measurements, error values of LCA are calculated and compensated to correct the projector image coordinates through the 3D error map and a tri-linear interpolation method. Eventually, 3D coordinates with higher accuracy are re-calculated according to the compensated image coordinates. The effectiveness of the proposed method is verified in the following experiments.

Analysis and Compensation for Lateral Chromatic Aberration in a Color Coding Structured Light 3D Measurement System

PubMed Central

Huang, Junhui; Xue, Qi; Wang, Zhao; Gao, Jianmin

2016-01-01

While color-coding methods have improved the measuring efficiency of a structured light three-dimensional (3D) measurement system, they decreased the measuring accuracy significantly due to lateral chromatic aberration (LCA). In this study, the LCA in a structured light measurement system is analyzed, and a method is proposed to compensate the error caused by the LCA. Firstly, based on the projective transformation, a 3D error map of LCA is constructed in the projector images by using a flat board and comparing the image coordinates of red, green and blue circles with the coordinates of white circles at preselected sample points within the measurement volume. The 3D map consists of the errors, which are the equivalent errors caused by LCA of the camera and projector. Then in measurements, error values of LCA are calculated and compensated to correct the projector image coordinates through the 3D error map and a tri-linear interpolation method. Eventually, 3D coordinates with higher accuracy are re-calculated according to the compensated image coordinates. The effectiveness of the proposed method is verified in the following experiments. PMID:27598174

Mapping of electrical muscle stimulation using MRI

NASA Technical Reports Server (NTRS)

Adams, Gregory R.; Harris, Robert T.; Woodard, Daniel; Dudley, Gary A.

1993-01-01

The pattern of muscle contractile activity elicited by electromyostimulation (EMS) was mapped and compared to the contractile-activity pattern produced by voluntary effort. This was done by examining the patterns and the extent of contrast shift, as indicated by T2 values, im magnetic resonance (MR) images after isometric activity of the left m. quadriceps of human subjects was elicited by EMS (1-sec train of 500-microsec sine wave pulses at 50 Hz) or voluntary effort. The results suggest that, whereas EMS stimulates the same fibers repeatedly, thereby increasing the metabolic demand and T2 values, the voluntary efforts are performed by more diffuse asynchronous activation of skeletal muscle even at forces up to 75 percent of maximal to maintain performance.

Insect seasonality: circle map analysis of temperature-driven life cycles.

PubMed

Powell, James A; Logan, Jesse A

2005-05-01

Maintaining an adaptive seasonality, with life cycle events occurring at appropriate times of year and in synchrony with cohorts and ephemeral resources, is a basic ecological requisite for many cold-blooded organisms. There are many mechanisms for synchronizing developmental milestones, such as egg laying (oviposition), egg hatching, cocoon opening, and the emergence of adults. These are often irreversible, specific to particular life stages, and include diapause, an altered physiological state which can be reversed by some synchronizing environmental cue (e.g. photoperiod). However, many successful organisms display none of these mechanisms for maintaining adaptive seasonality. In this paper, we briefly review the mathematical relationship between environmental temperatures and developmental timing and discuss the consequences of viewing these models as circle maps from the cycle of yearly oviposition dates and temperatures to oviposition dates for subsequent generations. Of particular interest biologically are life cycles which are timed to complete in exactly 1 year, or univoltine cycles. Univoltinism, associated with reproductive success for many temperate species, is related to stable fixed points of the developmental circle map. Univoltine fixed points are stable and robust in broad temperature bands, but lose stability suddenly to maladaptive cycles at the edges of these bands. Adaptive seasonality may therefore break down with little warning with constantly increasing or decreasing temperature change, as in scenarios for global warming. These ideas are illustrated and explored in the context of Mountain Pine Beetle (Dendroctonus ponderosae Hopkins) occurring in the marginal thermal habitat of central Idaho's Rocky Mountains. Applications of these techniques have not been widely explored by the applied math community, but are likely to provide great insight into the response of biological systems to climate change.

Transcriptional activation of short interspersed elements by DNA-damaging agents.

PubMed

Rudin, C M; Thompson, C B

2001-01-01

Short interspersed elements (SINEs), typified by the human Alu repeat, are RNA polymerase III (pol III)-transcribed sequences that replicate within the genome through an RNA intermediate. Replication of SINEs has been extensive in mammalian evolution: an estimated 5% of the human genome consists of Alu repeats. The mechanisms regulating transcription, reverse transcription, and reinsertion of SINE elements in genomic DNA are poorly understood. Here we report that expression of murine SINE transcripts of both the B1 and B2 classes is strongly upregulated after prolonged exposure to cisplatin, etoposide, or gamma radiation. A similar induction of Alu transcripts in human cells occurs under these conditions. This induction is not due to a general upregulation of pol III activity in either species. Genotoxic treatment of murine cells containing an exogenous human Alu element induced Alu transcription. Concomitant with the increased expression of SINEs, an increase in cellular reverse transcriptase was observed after exposure to these same DNA-damaging agents. These findings suggest that genomic damage may be an important activator of SINEs, and that SINE mobility may contribute to secondary malignancy after exposure to DNA-damaging chemotherapy.

Unsteady loading on an airfoil of arbitrary thickness

NASA Astrophysics Data System (ADS)

Glegg, Stewart A. L.; Devenport, William

2009-01-01

The unsteady loading on an airfoil of arbitrary thickness is evaluated by using the generalized form of Blasius theorem and a conformal mapping that maps the airfoil surface onto a circle. For a blade vortex interaction the results show that the time history of the unsteady loading is determined by the passage of the vortex relative to the leading edge singularity in the circle plane. The singularity lies inside the circle and moves to a smaller radius as the thickness is increased, causing the unsteady loading pulse to be smoothed. The effect of angle of attack is to move the stagnation point relative to the leading edge singularity and this significantly increases the unsteady lift if the vortex passes on the suction side of the airfoil. These characteristics are different for a step upwash gust, which is considered as a simplified model of a large scale turbulent gust. It is shown that the time history of the magnitude of the unsteady loading is almost completely unaltered by angle of attack for the step gust, but it's direction of action rotates forward by an angle equal to the angle of attack, extending an earlier result by Howe for a flat plate in a turbulent flow to airfoils of arbitrary thickness. However spectral analysis of the gust shows that the high frequency blade response is reduced as the thickness of the airfoil is increased.

White blood cell segmentation by circle detection using electromagnetism-like optimization.

PubMed

Cuevas, Erik; Oliva, Diego; Díaz, Margarita; Zaldivar, Daniel; Pérez-Cisneros, Marco; Pajares, Gonzalo

2013-01-01

Medical imaging is a relevant field of application of image processing algorithms. In particular, the analysis of white blood cell (WBC) images has engaged researchers from fields of medicine and computer vision alike. Since WBCs can be approximated by a quasicircular form, a circular detector algorithm may be successfully applied. This paper presents an algorithm for the automatic detection of white blood cells embedded into complicated and cluttered smear images that considers the complete process as a circle detection problem. The approach is based on a nature-inspired technique called the electromagnetism-like optimization (EMO) algorithm which is a heuristic method that follows electromagnetism principles for solving complex optimization problems. The proposed approach uses an objective function which measures the resemblance of a candidate circle to an actual WBC. Guided by the values of such objective function, the set of encoded candidate circles are evolved by using EMO, so that they can fit into the actual blood cells contained in the edge map of the image. Experimental results from blood cell images with a varying range of complexity are included to validate the efficiency of the proposed technique regarding detection, robustness, and stability.

White Blood Cell Segmentation by Circle Detection Using Electromagnetism-Like Optimization

PubMed Central

Oliva, Diego; Díaz, Margarita; Zaldivar, Daniel; Pérez-Cisneros, Marco; Pajares, Gonzalo

2013-01-01

Medical imaging is a relevant field of application of image processing algorithms. In particular, the analysis of white blood cell (WBC) images has engaged researchers from fields of medicine and computer vision alike. Since WBCs can be approximated by a quasicircular form, a circular detector algorithm may be successfully applied. This paper presents an algorithm for the automatic detection of white blood cells embedded into complicated and cluttered smear images that considers the complete process as a circle detection problem. The approach is based on a nature-inspired technique called the electromagnetism-like optimization (EMO) algorithm which is a heuristic method that follows electromagnetism principles for solving complex optimization problems. The proposed approach uses an objective function which measures the resemblance of a candidate circle to an actual WBC. Guided by the values of such objective function, the set of encoded candidate circles are evolved by using EMO, so that they can fit into the actual blood cells contained in the edge map of the image. Experimental results from blood cell images with a varying range of complexity are included to validate the efficiency of the proposed technique regarding detection, robustness, and stability. PMID:23476713

A Metaphorical Insight into Educational Planning.

ERIC Educational Resources Information Center

Inbar, Dan E.

1991-01-01

Considers educational planning as a communication of shared symbols creating intent geared toward change. Elaborates 11 groups of metaphorical images of planning (as circle, recipe, compass, map, puzzle, tree, maze, Ariadne's thread, prediction, art, and spider's web) bridging impression and expression. Relates this metaphorical analysis to…

The nucleotide sequence of a segment of Trypanosoma brucei mitochondrial maxi-circle DNA that contains the gene for apocytochrome b and some unusual unassigned reading frames.

PubMed Central

Benne, R; De Vries, B F; Van den Burg, J; Klaver, B

1983-01-01

The nucleotide sequence of a 2.5-kb segment of the maxi-circle of Trypanosoma brucei mtDNA has been determined. The segment contains the gene for apocytochrome b, which displays about 25% homology at the amino acid level to the apocytochrome b gene from fungal and mammalian mtDNAs. Northern blot and S1 nuclease analyses have yielded accurate map positions of an RNA species in an area that coincides with the reading frame. The segment also contains two pairs of overlapping unassigned reading frames, which lack homology with any known mitochondrial gene or URF. The DNA sequence in these areas is AG-rich (70%), resulting in URFs with an unusually high level of glycine and charged amino acids (60%). They may not encode proteins, in spite of their size and the fact that abundant transcripts are mapped in these areas. Images PMID:6314266

Modified sine bar device measures small angles with high accuracy

NASA Technical Reports Server (NTRS)

Thekaekara, M.

1968-01-01

Modified sine bar device measures small angles with enough accuracy to calibrate precision optical autocollimators. The sine bar is a massive bar of steel supported by two cylindrical rods at one end and one at the other.

A Free Database of Auto-detected Full-sun Coronal Hole Maps

NASA Astrophysics Data System (ADS)

Caplan, R. M.; Downs, C.; Linker, J.

2016-12-01

We present a 4-yr (06/10/2010 to 08/18/14 at 6-hr cadence) database of full-sun synchronic EUV and coronal hole (CH) maps made available on a dedicated web site (http://www.predsci.com/chd). The maps are generated using STEREO/EUVI A&B 195Å and SDO/AIA 193Å images through an automated pipeline (Caplan et al, (2016) Ap.J. 823, 53).Specifically, the original data is preprocessed with PSF-deconvolution, a nonlinear limb-brightening correction, and a nonlinear inter-instrument intensity normalization. Coronal holes are then detected in the preprocessed images using a GPU-accelerated region growing segmentation algorithm. The final results from all three instruments are then merged and projected to form full-sun sine-latitude maps. All the software used in processing the maps is provided, which can easily be adapted for use with other instruments and channels. We describe the data pipeline and show examples from the database. We also detail recent CH-detection validation experiments using synthetic EUV emission images produced from global thermodynamic MHD simulations.

Volcanic hazards and aviation safety

USGS Publications Warehouse

Casadevall, Thomas J.; Thompson, Theodore B.; Ewert, John W.; ,

1996-01-01

An aeronautical chart was developed to determine the relative proximity of volcanoes or ash clouds to the airports and flight corridors that may be affected by volcanic debris. The map aims to inform and increase awareness about the close spatial relationship between volcanoes and aviation operations. It shows the locations of the active volcanoes together with selected aeronautical navigation aids and great-circle routes. The map mitigates the threat that volcanic hazards pose to aircraft and improves aviation safety.

Design a light pattern of multiple concentric circles for LED fishing lamps using Fourier series and an energy mapping method.

PubMed

Shen, S C; Li, J S; Huang, M C

2014-06-02

Fourier series and an energy mapping method were used in this study to design a lens that produces a light pattern of multiple concentric circles (LPMCC) for a light-emitting diode (LED) fishing lamp. Fourier series were used to represent the light intensity distribution curve (LIDC) of the LPMCC light pattern. Energy mapping involves performing angular energy mapping based on the LIDCs of an LED light source and LPMCC to design a freeform lens. Type I and Type II LPMCC lenses were designed according to the phototaxis behavior of fish to create a LPMCC light pattern of interleaving light-dark zones that attracts fish shoals to stay in an area for a long period. The experimental results indicated that, in comparing the LIDCs of the Type I and II lenses with the respective simulation values, the normalized cross-correlation (NCC) value reached 96%. According to a 24-hour observation of the phototaxis of Poecilia reticulata to evaluate the effectiveness of the proposed light pattern to attract fish, when a fish shoal was habituated to a light source that emitted constant illumination light, it gradually moved away from the intense light zone and hovered around the junction of the light and dark zones. In the future, the design used in this study can be applied to LED fishing lamps to replace traditional fishing lamps.

Characterization of Three Novel SINE Families with Unusual Features in Helicoverpa armigera

PubMed Central

Wang, Jianjun; Wang, Aina; Han, Zhaojun; Zhang, Zan; Li, Fei; Li, Xianchun

2012-01-01

Although more than 120 families of short interspersed nuclear elements (SINEs) have been isolated from the eukaryotic genomes, little is known about SINEs in insects. Here, we characterize three novel SINEs from the cotton bollworm, Helicoverpa armigera. Two of them, HaSE1 and HaSE2, share similar 5′ -structure including a tRNA-related region immediately followed by conserved central domain. The 3′ -tail of HaSE1 is significantly similar to that of one LINE retrotransposon element, HaRTE1.1, in H. armigera genome. The 3′ -region of HaSE2 showed high identity with one mariner-like element in H. armigera. The third family, termed HaSE3, is a 5S rRNA-derived SINE and shares both body part and 3′-tail with HaSE1, thus may represent the first example of a chimera generated by recombination between 5S rRNA and tRNA-derived SINE in insect species. Further database searches revealed the presence of these SINEs in several other related insect species, but not in the silkworm, Bombyx mori, indicating a relatively narrow distribution of these SINEs in Lepidopterans. Apart from above, we found a copy of HaSE2 in the GenBank EST entry for the cotton aphid, Aphis gossypii, suggesting the occurrence of horizontal transfer. PMID:22319625

Simulation of Structures Exhibiting Instability Under Thermal-Mechanical Transient Loading

DTIC Science & Technology

2015-08-25

4 2.1.4 Application to half- sine arches...shallow arches ....................................................... 9 2.2.2 Half- sine arches... sine arches, parabolic arches and cylindrical panels. 2.1 Arches with Geometric Imperfections The nonlinear equilibrium and buckling equations are

Analysis of swept-sine runs during modal identification

NASA Astrophysics Data System (ADS)

Gloth, G.; Sinapius, M.

2004-11-01

Experimental modal analysis of large aerospace structures in Europe combine nowadays the benefits of the very reliable but time-consuming phase resonance method and the application of phase separation techniques evaluating frequency response functions (FRF). FRFs of a test structure can be determined by a variety of means. Applied excitation signal waveforms include harmonic signals like stepped-sine excitation, periodic signals like multi-sine excitation, transient signals like impulse and swept-sine excitation, and stochastic signals like random. The current article focuses on slow swept-sine excitation which is a good trade-off between magnitude of excitation level needed for large aircraft and testing time. However, recent ground vibration tests (GVTs) brought up that reliable modal data from swept-sine test runs depend on a proper data processing. The article elucidates the strategy of modal analysis based on swept-sine excitation. The standards for the application of slowly swept sinusoids defined by the international organisation for standardisation in ISO 7626 part 2 are critically reviewed. The theoretical background of swept-sine testing is expounded with particular emphasis to the transition through structural resonances. The effect of different standard procedures of data processing like tracking filter, fast Fourier transform (FFT), and data reduction via averaging are investigated with respect to their influence on the FRFs and modal parameters. Particular emphasis is given to FRF distortions evoked by unsuitable data processing. All data processing methods are investigated on a numerical example. Their practical usefulness is demonstrated on test data taken from a recent GVT on a large aircraft. The revision of ISO 7626 part 2 is suggested regarding the application of slow swept-sine excitation. Recommendations about the proper FRF estimation from slow swept-sine excitation are given in order to enable the optimisation on these applications for future modal survey tests of large aerospace structures.

Pstl repeat: a family of short interspersed nucleotide element (SINE)-like sequences in the genomes of cattle, goat, and buffalo.

PubMed

Sheikh, Faruk G; Mukhopadhyay, Sudit S; Gupta, Prabhakar

2002-02-01

The PstI family of elements are short, highly repetitive DNA sequences interspersed throughout the genome of the Bovidae. We have cloned and sequenced some members of the PstI family from cattle, goat, and buffalo. These elements are approximately 500 bp, have a copy number of 2 x 10(5) - 4 x 10(5), and comprise about 4% of the haploid genome. Studies of nucleotide sequence homology indicate that the buffalo and goat PstI repeats (type II) are similar types of short interspersed nucleotide element (SINE) sequences, but the cattle PstI repeat (type I) is considerably more divergent. Additionally, the goat PstI sequence showed significant sequence homology with bovine serine tRNA, and is therefore likely derived from serine tRNA. Interestingly, Southern hybridization suggests that both types of SINEs (I and II) are present in all the species of Bovidae. Dendrogram analysis indicates that cattle PstI SINE is similar to bovine Alu-like SINEs. Goat and buffalo SINEs formed a separate cluster, suggesting that these two types of SINEs evolved separately in the genome of the Bovidae.

Mathematics education graduate students' understanding of trigonometric ratios

NASA Astrophysics Data System (ADS)

Yiǧit Koyunkaya, Melike

2016-10-01

This study describes mathematics education graduate students' understanding of relationships between sine and cosine of two base angles in a right triangle. To explore students' understanding of these relationships, an elaboration of Skemp's views of instrumental and relational understanding using Tall and Vinner's concept image and concept definition was developed. Nine students volunteered to complete three paper and pencil tasks designed to elicit evidence of understanding and three students among these nine students volunteered for semi-structured interviews. As a result of fine-grained analysis of the students' responses to the tasks, the evidence of concept image and concept definition as well as instrumental and relational understanding of trigonometric ratios was found. The unit circle and a right triangle were identified as students' concept images, and the mnemonic was determined as their concept definition for trigonometry, specifically for trigonometric ratios. It is also suggested that students had instrumental understanding of trigonometric ratios while they were less flexible to act on trigonometric ratio tasks and had limited relational understanding. Additionally, the results indicate that graduate students' understanding of the concept of angle mediated their understanding of trigonometry, specifically trigonometric ratios.

Evolutionary history of 7SL RNA-derived SINEs in Supraprimates.

PubMed

Kriegs, Jan Ole; Churakov, Gennady; Jurka, Jerzy; Brosius, Jürgen; Schmitz, Jürgen

2007-04-01

The evolutionary relationships of 7SL RNA-derived SINEs such as the primate Alu or the rodent B1 elements have hitherto been obscure. We established an unambiguous phylogenetic tree for Supraprimates, and derived intraordinal relationships of the 7SL RNA-derived SINEs. As well as new elements in Tupaia and primates, we also found that the purported ancestral fossil Alu monomer was restricted to Primates, and provide here the first description of a potential chimeric promoter box region in SINEs.

Retrotransposons as regulators of gene expression

PubMed Central

Elbarbary, Reyad A.; Lucas, Bronwyn A.; Maquat, Lynne E.

2016-01-01

Transposable elements (TEs) are both a boon and a bane to eukaryotic organisms, depending on where they integrate into the genome and how their sequences function once integrated. We focus on two types of TEs: long interspersed elements (LINEs) and short interspersed elements (SINEs). LINEs and SINEs are retrotransposons; that is, they transpose via an RNA intermediate. We discuss how LINEs and SINEs have expanded in eukaryotic genomes and contribute to genome evolution. An emerging body of evidence indicates that LINEs and SINEs function to regulate gene expression by affecting chromatin structure, gene transcription, pre-mRNA processing, or aspects of mRNA metabolism. We also describe how adenosine-to-inosine editing influences SINE function and how ongoing retrotransposition is countered by the body’s defense mechanisms. PMID:26912865

The Nature of Infinity in Quantum Field Calculations

NASA Astrophysics Data System (ADS)

Kriske, Richard

2011-05-01

In many textbooks on Quantum Field Theory it has been noted that an infinity is taken a circle and the flux is calculated from the A field in that manner. There are of course many such examples of this sort of calculation using infinity as a circle. This author would like to point out that if the three dimensions of space are curved and the one dimension of time is not, in say a four space, infinity is the horizon, which is not a circle but rather a sphere; as long as space-time is curved uniformly, smoothly and has positive curvature. This author believes the math may be in error, since maps of the CMBR seem to indicate a ``Swiss-Cheese'' type of topology, wherein the Sphere at infinity (the Horizon of the Universe), has holes in it that can readily be seen. This author believes that these irregularities most certainly have a calculable effect on QED, QCD and Quantum Field Theory.

Possible involvement of SINEs in mammalian-specific brain formation

PubMed Central

Sasaki, Takeshi; Nishihara, Hidenori; Hirakawa, Mika; Fujimura, Koji; Tanaka, Mikiko; Kokubo, Nobuhiro; Kimura-Yoshida, Chiharu; Matsuo, Isao; Sumiyama, Kenta; Saitou, Naruya; Shimogori, Tomomi; Okada, Norihiro

2008-01-01

Retroposons, such as short interspersed elements (SINEs) and long interspersed elements (LINEs), are the major constituents of higher vertebrate genomes. Although there are many examples of retroposons' acquiring function, none has been implicated in the morphological innovations specific to a certain taxonomic group. We previously characterized a SINE family, AmnSINE1, members of which constitute a part of conserved noncoding elements (CNEs) in mammalian genomes. We proposed that this family acquired genomic functionality or was exapted after retropositioning in a mammalian ancestor. Here we identified 53 new AmnSINE1 loci and refined 124 total loci, two of which were further analyzed. Using a mouse enhancer assay, we demonstrate that one SINE locus, AS071, 178 kbp from the gene FGF8 (fibroblast growth factor 8), is an enhancer that recapitulates FGF8 expression in two regions of the developing forebrain, namely the diencephalon and the hypothalamus. Our gain-of-function analysis revealed that FGF8 expression in the diencephalon controls patterning of thalamic nuclei, which act as a relay center of the neocortex, suggesting a role for FGF8 in mammalian-specific forebrain patterning. Furthermore, we demonstrated that the locus, AS021, 392 kbp from the gene SATB2, controls gene expression in the lateral telencephalon, which is thought to be a signaling center during development. These results suggest important roles for SINEs in the development of the mammalian neuronal network, a part of which was initiated with the exaptation of AmnSINE1 in a common mammalian ancestor. PMID:18334644

Possible involvement of SINEs in mammalian-specific brain formation.

PubMed

Sasaki, Takeshi; Nishihara, Hidenori; Hirakawa, Mika; Fujimura, Koji; Tanaka, Mikiko; Kokubo, Nobuhiro; Kimura-Yoshida, Chiharu; Matsuo, Isao; Sumiyama, Kenta; Saitou, Naruya; Shimogori, Tomomi; Okada, Norihiro

2008-03-18

Retroposons, such as short interspersed elements (SINEs) and long interspersed elements (LINEs), are the major constituents of higher vertebrate genomes. Although there are many examples of retroposons' acquiring function, none has been implicated in the morphological innovations specific to a certain taxonomic group. We previously characterized a SINE family, AmnSINE1, members of which constitute a part of conserved noncoding elements (CNEs) in mammalian genomes. We proposed that this family acquired genomic functionality or was exapted after retropositioning in a mammalian ancestor. Here we identified 53 new AmnSINE1 loci and refined 124 total loci, two of which were further analyzed. Using a mouse enhancer assay, we demonstrate that one SINE locus, AS071, 178 kbp from the gene FGF8 (fibroblast growth factor 8), is an enhancer that recapitulates FGF8 expression in two regions of the developing forebrain, namely the diencephalon and the hypothalamus. Our gain-of-function analysis revealed that FGF8 expression in the diencephalon controls patterning of thalamic nuclei, which act as a relay center of the neocortex, suggesting a role for FGF8 in mammalian-specific forebrain patterning. Furthermore, we demonstrated that the locus, AS021, 392 kbp from the gene SATB2, controls gene expression in the lateral telencephalon, which is thought to be a signaling center during development. These results suggest important roles for SINEs in the development of the mammalian neuronal network, a part of which was initiated with the exaptation of AmnSINE1 in a common mammalian ancestor.

Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.

PubMed

Greally, John M

2002-01-08

To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature indicates that the sequence characteristics of currently imprinted regions existed before the mammalian radiation. Transitions from imprinted to nonimprinted genomic regions in cis are characterized by a sharp inflection in SINE content, demonstrating that this genomic characteristic can help predict the presence and extent of regions undergoing imprinting. During primate evolution, SINE accumulation in imprinted regions occurred at a decreased rate compared with control loci. The constraint on SINE accumulation in imprinted regions may be mediated by an active selection process. This selection could be because of SINEs attracting and spreading methylation, as has been found at other loci. Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival.

A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus).

PubMed

Churakov, Gennady; Smit, Arian F A; Brosius, Jürgen; Schmitz, Jürgen

2005-04-01

About half of the mammalian genome is composed of retroposons. Long interspersed elements (LINEs) and short interspersed elements (SINEs) are the most abundant repetitive elements and account for about 21% and 13% of the human genome, respectively. SINEs have been detected in all major mammalian lineages, except for the South American order Xenarthra, also termed Edentata (armadillos, anteaters, and sloths). Investigating this order, we discovered a novel high-copy-number family of tRNA derived SINEs in the nine-banded armadillo Dasypus novemcinctus, a species that successfully crossed the Central American land bridge to North America in the Pliocene. A specific computer algorithm was developed, and we detected and extracted 687 specific SINEs from databases. Termed DAS-SINEs, we further divided them into six distinct subfamilies. We extracted tRNA(Ala)-derived monomers, two types of dimers, and three subfamilies of chimeric fusion products of a tRNA(Ala) domain and an approximately 180-nt sequence of thus far unidentified origin. Comparisons of secondary structures of the DAS-SINEs' tRNA domains suggest selective pressure to maintain a tRNA-like D-arm structure in the respective founder RNAs, as shown by compensatory mutations. By analysis of subfamily-specific genetic variability, comparison of the proportion of direct repeats, and analysis of self-integrations as well as key events of dimerization and deletions or insertions, we were able to delineate the evolutionary history of the DAS-SINE subfamilies.

Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome

PubMed Central

Greally, John M.

2002-01-01

To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature indicates that the sequence characteristics of currently imprinted regions existed before the mammalian radiation. Transitions from imprinted to nonimprinted genomic regions in cis are characterized by a sharp inflection in SINE content, demonstrating that this genomic characteristic can help predict the presence and extent of regions undergoing imprinting. During primate evolution, SINE accumulation in imprinted regions occurred at a decreased rate compared with control loci. The constraint on SINE accumulation in imprinted regions may be mediated by an active selection process. This selection could be because of SINEs attracting and spreading methylation, as has been found at other loci. Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival. PMID:11756672

Think, Jane, Think. See Jane Think. Go, Jane... Metacognition and Learning in the Library

ERIC Educational Resources Information Center

Jaeger, Paige

2007-01-01

Buzzwords are as prolific in educational circles as bunny rabbits are in spring. Over the last 10 years everyone has heard the buzz of multiculturism, multiple intelligences, learning modalities, essential questions, cultural literacy, media literacy, differentiated instruction, learning by design, curriculum alignment, curriculum mapping,…

Landsat's international partners

USGS Publications Warehouse

Byrnes, Raymond A.

2012-01-01

Since the launch of the first Landsat satellite 40 years ago, International Cooperators (ICs) have formed a key strategic alliance with the U.S. Geological Survey (USGS) to not only engage in Landsat data downlink services but also to enable a foundation for scientific and technical collaboration. The map below shows the locations of all ground stations operated by the United States and IC ground station network for the direct downlink and distribution of Landsat 5 (L5) and Landsat 7 (L7) image data. The circles show the approximate area over which each station has the capability for direct reception of Landsat data. The red circles show the components of the L5 ground station network, the green circles show components of the L7 station network, and the dashed circles show stations with dual (L5 and L7) status. The yellow circles show L5 short-term ("campaign") stations that contribute to the USGS Landsat archive. Ground stations in South Dakota and Australia currently serve as the primary data capture facilities for the USGS Landsat Ground Network (LGN). The Landsat Ground Station (LGS) is located at the USGS Earth Resources Observation and Science (EROS) Center in Sioux Falls, South Dakota. The Alice Springs (ASN) ground station is located at the Geoscience Australia facility in Alice Springs, Australia. These sites receive the image data, via X-band Radio Frequency (RF) link, and the spacecraft housekeeping data, via S-band RF link. LGS also provides tracking services and a command link to the spacecrafts.

Ghost circles in lattice Aubry-Mather theory

NASA Astrophysics Data System (ADS)

Mramor, Blaz; Rink, Bob

Monotone lattice recurrence relations such as the Frenkel-Kontorova lattice, arise in Hamiltonian lattice mechanics, as models for ferromagnetism and as discretization of elliptic PDEs. Mathematically, they are a multi-dimensional counterpart of monotone twist maps. Such recurrence relations often admit a variational structure, so that the solutions x:Z→R are the stationary points of a formal action function W(x). Given any rotation vector ω∈R, classical Aubry-Mather theory establishes the existence of a large collection of solutions of ∇W(x)=0 of rotation vector ω. For irrational ω, this is the well-known Aubry-Mather set. It consists of global minimizers and it may have gaps. In this paper, we study the parabolic gradient flow {dx}/{dt}=-∇W(x) and we will prove that every Aubry-Mather set can be interpolated by a continuous gradient-flow invariant family, the so-called 'ghost circle'. The existence of these ghost circles is known in dimension d=1, for rational rotation vectors and Morse action functions. The main technical result of this paper is therefore a compactness theorem for lattice ghost circles, based on a parabolic Harnack inequality for the gradient flow. This implies the existence of lattice ghost circles of arbitrary rotation vectors and for arbitrary actions. As a consequence, we can give a simple proof of the fact that when an Aubry-Mather set has a gap, then this gap must be filled with minimizers, or contain a non-minimizing solution.

Circles-in-the-sky searches and observable cosmic topology in a flat universe

NASA Astrophysics Data System (ADS)

Mota, B.; Rebouças, M. J.; Tavakol, R.

2010-05-01

In a universe with a detectable nontrivial spatial topology, the last scattering surface contains pairs of matching circles with the same distribution of temperature fluctuations—the so-called circles-in-the-sky. Searches for nearly antipodal circles-in-the-sky in maps of cosmic microwave background radiation have so far been unsuccessful. This negative outcome, along with recent theoretical results concerning the detectability of nearly flat compact topologies, is sufficient to exclude a detectable nontrivial topology for most observers in very nearly flat positively and negatively curved universes, whose total matter-energy density satisfies 0<|Ωtot-1|≲10-5. Here, we investigate the consequences of these searches for observable nontrivial topologies if the Universe turns out to be exactly flat (Ωtot=1). We demonstrate that in this case, the conclusions deduced from such searches can be radically different. We show that, although there is no characteristic topological scale in the flat manifolds, for all multiply-connected orientable flat manifolds, it is possible to directly study the action of the holonomies in order to obtain a general upper bound on the angle that characterizes the deviation from antipodicity of pairs of matching circles associated with the shortest closed geodesic. This bound is valid for all observers and all possible values of the compactification length parameters. We also show that in a flat universe, there are observers for whom the circles-in-the-sky searches already undertaken are insufficient to exclude the possibility of a detectable nontrivial spatial topology. It is remarkable how such small variations in the spatial curvature of the Universe, which are effectively indistinguishable geometrically, can have such a drastic effect on the detectability of cosmic topology. Another important outcome of our results is that they offer a framework with which to make statistical inferences from future circles-in-the-sky searches on whether the Universe is exactly flat.

Retrotransposons as regulators of gene expression.

PubMed

Elbarbary, Reyad A; Lucas, Bronwyn A; Maquat, Lynne E

2016-02-12

Transposable elements (TEs) are both a boon and a bane to eukaryotic organisms, depending on where they integrate into the genome and how their sequences function once integrated. We focus on two types of TEs: long interspersed elements (LINEs) and short interspersed elements (SINEs). LINEs and SINEs are retrotransposons; that is, they transpose via an RNA intermediate. We discuss how LINEs and SINEs have expanded in eukaryotic genomes and contribute to genome evolution. An emerging body of evidence indicates that LINEs and SINEs function to regulate gene expression by affecting chromatin structure, gene transcription, pre-mRNA processing, or aspects of mRNA metabolism. We also describe how adenosine-to-inosine editing influences SINE function and how ongoing retrotransposition is countered by the body's defense mechanisms. Copyright © 2016, American Association for the Advancement of Science.

SINEs as driving forces in genome evolution.

PubMed

Schmitz, J

2012-01-01

SINEs are short interspersed elements derived from cellular RNAs that repetitively retropose via RNA intermediates and integrate more or less randomly back into the genome. SINEs propagate almost entirely vertically within their host cells and, once established in the germline, are passed on from generation to generation. As non-autonomous elements, their reverse transcription (from RNA to cDNA) and genomic integration depends on the activity of the enzymatic machinery of autonomous retrotransposons, such as long interspersed elements (LINEs). SINEs are widely distributed in eukaryotes, but are especially effectively propagated in mammalian species. For example, more than a million Alu-SINE copies populate the human genome (approximately 13% of genomic space), and few master copies of them are still active. In the organisms where they occur, SINEs are a challenge to genomic integrity, but in the long term also can serve as beneficial building blocks for evolution, contributing to phenotypic heterogeneity and modifying gene regulatory networks. They substantially expand the genomic space and introduce structural variation to the genome. SINEs have the potential to mutate genes, to alter gene expression, and to generate new parts of genes. A balanced distribution and controlled activity of such properties is crucial to maintaining the organism's dynamic and thriving evolution. Copyright © 2012 S. Karger AG, Basel.

The optimal digital filters of sine and cosine transforms for geophysical transient electromagnetic method

NASA Astrophysics Data System (ADS)

Zhao, Yun-wei; Zhu, Zi-qiang; Lu, Guang-yin; Han, Bo

2018-03-01

The sine and cosine transforms implemented with digital filters have been used in the Transient electromagnetic methods for a few decades. Kong (2007) proposed a method of obtaining filter coefficients, which are computed in the sample domain by Hankel transform pair. However, the curve shape of Hankel transform pair changes with a parameter, which usually is set to be 1 or 3 in the process of obtaining the digital filter coefficients of sine and cosine transforms. First, this study investigates the influence of the parameter on the digital filter algorithm of sine and cosine transforms based on the digital filter algorithm of Hankel transform and the relationship between the sine, cosine function and the ±1/2 order Bessel function of the first kind. The results show that the selection of the parameter highly influences the precision of digital filter algorithm. Second, upon the optimal selection of the parameter, it is found that an optimal sampling interval s also exists to achieve the best precision of digital filter algorithm. Finally, this study proposes four groups of sine and cosine transform digital filter coefficients with different length, which may help to develop the digital filter algorithm of sine and cosine transforms, and promote its application.

Search asymmetry: a diagnostic for preattentive processing of separable features.

PubMed

Treisman, A; Souther, J

1985-09-01

The search rate for a target among distractors may vary dramatically depending on which stimulus plays the role of target and which that of distractors. For example, the time required to find a circle distinguished by an intersecting line is independent of the number of regular circles in the display, whereas the time to find a regular circle among circles with lines increases linearly with the number of distractors. The pattern of performance suggests parallel processing when the target has a unique distinguishing feature and serial self-terminating search when the target is distinguished only by the absence of a feature that is present in all the distractors. The results are consistent with feature-integration theory (Treisman & Gelade, 1980), which predicts that a single feature should be detected by the mere presence of activity in the relevant feature map, whereas tasks that require subjects to locate multiple instances of a feature demand focused attention. Search asymmetries may therefore offer a new diagnostic to identify the primitive features of early vision. Several candidate features are examined in this article: Colors, line ends or terminators, and closure (in the sense of a partly or wholly enclosed area) appear to be functional features; connectedness, intactness (absence of an intersecting line), and acute angles do not.

Guinea Pig ID-Like Families of SINEs

PubMed Central

Kass, David H.; Schaetz, Brian A.; Beitler, Lindsey; Bonney, Kevin M.; Jamison, Nicole; Wiesner, Cathy

2009-01-01

Previous studies have indicated a paucity of SINEs within the genomes of the guinea pig and nutria, representatives of the Hystricognathi suborder of rodents. More recent work has shown that the guinea pig genome contains a large number of B1 elements, expanding to various levels among different rodents. In this work we utilized A–B PCR and screened GenBank with sequences from isolated clones to identify potentially uncharacterized SINEs within the guinea pig genome, and identified numerous sequences with a high degree of similarity (>92%) specific to the guinea pig. The presence of A-tails and flanking direct repeats associated with these sequences supported the identification of a full-length SINE, with a consensus sequence notably distinct from other rodent SINEs. Although most similar to the ID SINE, it clearly was not derived from the known ID master gene (BC1), hence we refer to this element as guinea pig ID-like (GPIDL). Using the consensus to screen the guinea pig genomic database (Assembly CavPor2) with Ensembl BlastView, we estimated at least 100,000 copies, which contrasts markedly to just over 100 copies of ID elements. Additionally we provided evidence of recent integrations of GPIDL as two of seven analyzed conserved GPIDL-containing loci demonstrated presence/absence variants in Cavia porcellus and C. aperea. Using intra-IDL PCR and sequence analyses we also provide evidence that GPIDL is derived from a hystricognath-specific SINE family. These results demonstrate that this SINE family continues to contribute to the dynamics of genomes of hystricognath rodents. PMID:19232383

Guinea pig ID-like families of SINEs.

PubMed

Kass, David H; Schaetz, Brian A; Beitler, Lindsey; Bonney, Kevin M; Jamison, Nicole; Wiesner, Cathy

2009-05-01

Previous studies have indicated a paucity of SINEs within the genomes of the guinea pig and nutria, representatives of the Hystricognathi suborder of rodents. More recent work has shown that the guinea pig genome contains a large number of B1 elements, expanding to various levels among different rodents. In this work we utilized A-B PCR and screened GenBank with sequences from isolated clones to identify potentially uncharacterized SINEs within the guinea pig genome, and identified numerous sequences with a high degree of similarity (>92%) specific to the guinea pig. The presence of A-tails and flanking direct repeats associated with these sequences supported the identification of a full-length SINE, with a consensus sequence notably distinct from other rodent SINEs. Although most similar to the ID SINE, it clearly was not derived from the known ID master gene (BC1), hence we refer to this element as guinea pig ID-like (GPIDL). Using the consensus to screen the guinea pig genomic database (Assembly CavPor2) with Ensembl BlastView, we estimated at least 100,000 copies, which contrasts markedly to just over 100 copies of ID elements. Additionally we provided evidence of recent integrations of GPIDL as two of seven analyzed conserved GPIDL-containing loci demonstrated presence/absence variants in Cavia porcellus and C. aperea. Using intra-IDL PCR and sequence analyses we also provide evidence that GPIDL is derived from a hystricognath-specific SINE family. These results demonstrate that this SINE family continues to contribute to the dynamics of genomes of hystricognath rodents.

Global transport in a nonautonomous periodic standard map

DOE PAGES

Calleja, Renato C.; del-Castillo-Negrete, D.; Martinez-del-Rio, D.; ...

2017-04-14

A non-autonomous version of the standard map with a periodic variation of the perturbation parameter is introduced and studied via an autonomous map obtained from the iteration of the nonautonomous map over a period. Symmetry properties in the variables and parameters of the map are found and used to find relations between rotation numbers of invariant sets. The role of the nonautonomous dynamics on period-one orbits, stability and bifurcation is studied. The critical boundaries for the global transport and for the destruction of invariant circles with fixed rotation number are studied in detail using direct computation and a continuation method.more » In the case of global transport, the critical boundary has a particular symmetrical horn shape. Here, the results are contrasted with similar calculations found in the literature.« less

Global transport in a nonautonomous periodic standard map

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

Calleja, Renato C.; del-Castillo-Negrete, D.; Martinez-del-Rio, D.

A non-autonomous version of the standard map with a periodic variation of the perturbation parameter is introduced and studied via an autonomous map obtained from the iteration of the nonautonomous map over a period. Symmetry properties in the variables and parameters of the map are found and used to find relations between rotation numbers of invariant sets. The role of the nonautonomous dynamics on period-one orbits, stability and bifurcation is studied. The critical boundaries for the global transport and for the destruction of invariant circles with fixed rotation number are studied in detail using direct computation and a continuation method.more » In the case of global transport, the critical boundary has a particular symmetrical horn shape. Here, the results are contrasted with similar calculations found in the literature.« less

Measuring Differential Delays With Sine-Squared Pulses

NASA Technical Reports Server (NTRS)

Hurst, Robert N.

1994-01-01

Technique for measuring differential delays among red, green, and blue components of video signal transmitted on different parallel channels exploits sine-squared pulses that are parts of standard test signals transmitted during vertical blanking interval of frame period. Technique does not entail expense of test-signal generator. Also applicable to nonvideo signals including sine-squared pulses.

CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs.

PubMed

Gilbert, N; Labuda, D

1999-03-16

A 65-bp "core" sequence is dispersed in hundreds of thousands copies in the human genome. This sequence was found to constitute the central segment of a group of short interspersed elements (SINEs), referred to as mammalian-wide interspersed repeats, that proliferated before the radiation of placental mammals. Here, we propose that the core identifies an ancient tRNA-like SINE element, which survived in different lineages such as mammals, reptiles, birds, and fish, as well as mollusks, presumably for >550 million years. This element gave rise to a number of sequence families (CORE-SINEs), including mammalian-wide interspersed repeats, whose distinct 3' ends are shared with different families of long interspersed elements (LINEs). The evolutionary success of the generic CORE-SINE element can be related to the recruitment of the internal promoter from highly transcribed host RNA as well as to its capacity to adapt to changing retropositional opportunities by sequence exchange with actively amplifying LINEs. It reinforces the notion that the very existence of SINEs depends on the cohabitation with both LINEs and the host genome.

CORE-SINEs: Eukaryotic short interspersed retroposing elements with common sequence motifs

PubMed Central

Gilbert, Nicolas; Labuda, Damian

1999-01-01

A 65-bp “core” sequence is dispersed in hundreds of thousands copies in the human genome. This sequence was found to constitute the central segment of a group of short interspersed elements (SINEs), referred to as mammalian-wide interspersed repeats, that proliferated before the radiation of placental mammals. Here, we propose that the core identifies an ancient tRNA-like SINE element, which survived in different lineages such as mammals, reptiles, birds, and fish, as well as mollusks, presumably for >550 million years. This element gave rise to a number of sequence families (CORE-SINEs), including mammalian-wide interspersed repeats, whose distinct 3′ ends are shared with different families of long interspersed elements (LINEs). The evolutionary success of the generic CORE-SINE element can be related to the recruitment of the internal promoter from highly transcribed host RNA as well as to its capacity to adapt to changing retropositional opportunities by sequence exchange with actively amplifying LINEs. It reinforces the notion that the very existence of SINEs depends on the cohabitation with both LINEs and the host genome. PMID:10077603

Earthquakes in and near the northeastern United States, 1638-1998

USGS Publications Warehouse

Wheeler, R.L.; Trevor, N.K.; Tarr, A.C.; Crone, A.J.

2000-01-01

The data are those used to make a large-format, colored map of earthquakes in the northeastern United States and adjacent parts of Canada and the Atlantic Ocean (Wheeler, 2000; Wheeler and others, 2001; references in Data_Quality_Information, Lineage). The map shows the locations of 1,069 known earthquakes of magnitude 3.0 or larger, and is designed for a non-technical audience. Colored circles represent earthquake locations, colored and sized by magnitude. Short descriptions, colonial-era woodcuts, newspaper headlines, and photographs summarize the dates, times of day, damage, and other effects of notable earthquakes. The base map shows color-coded elevation, shaded to emphasize relief.

C*-algebras associated with reversible extensions of logistic maps

NASA Astrophysics Data System (ADS)

Kwaśniewski, Bartosz K.

2012-10-01

The construction of reversible extensions of dynamical systems presented in a previous paper by the author and A.V. Lebedev is enhanced, so that it applies to arbitrary mappings (not necessarily with open range). It is based on calculating the maximal ideal space of C*-algebras that extends endomorphisms to partial automorphisms via partial isometric representations, and involves a new set of 'parameters' (the role of parameters is played by chosen sets or ideals). As model examples, we give a thorough description of reversible extensions of logistic maps and a classification of systems associated with compression of unitaries generating homeomorphisms of the circle. Bibliography: 34 titles.

RNA-Seq Analysis to Measure the Expression of SINE Retroelements.

PubMed

Román, Ángel Carlos; Morales-Hernández, Antonio; Fernández-Salguero, Pedro M

2016-01-01

The intrinsic features of retroelements, like their repetitive nature and disseminated presence in their host genomes, demand the use of advanced methodologies for their bioinformatic and functional study. The short length of SINE (short interspersed elements) retrotransposons makes such analyses even more complex. Next-generation sequencing (NGS) technologies are currently one of the most widely used tools to characterize the whole repertoire of gene expression in a specific tissue. In this chapter, we will review the molecular and computational methods needed to perform NGS analyses on SINE elements. We will also describe new methods of potential interest for researchers studying repetitive elements. We intend to outline the general ideas behind the computational analyses of NGS data obtained from SINE elements, and to stimulate other scientists to expand our current knowledge on SINE biology using RNA-seq and other NGS tools.

Sine Rotation Vector Method for Attitude Estimation of an Underwater Robot

PubMed Central

Ko, Nak Yong; Jeong, Seokki; Bae, Youngchul

2016-01-01

This paper describes a method for estimating the attitude of an underwater robot. The method employs a new concept of sine rotation vector and uses both an attitude heading and reference system (AHRS) and a Doppler velocity log (DVL) for the purpose of measurement. First, the acceleration and magnetic-field measurements are transformed into sine rotation vectors and combined. The combined sine rotation vector is then transformed into the differences between the Euler angles of the measured attitude and the predicted attitude; the differences are used to correct the predicted attitude. The method was evaluated according to field-test data and simulation data and compared to existing methods that calculate angular differences directly without a preceding sine rotation vector transformation. The comparison verifies that the proposed method improves the attitude estimation performance. PMID:27490549

Perish, then publish: Thomas Harriot and the sine law of refraction.

PubMed

Fishman, R S

2000-03-01

A talented young scientist, Thomas Harriot, wrote the first English account of the New World, "A Briefe and True Report of the New Found Land of Virginia," distinguished by its serious effort to describe and understand the American Indian. Harriot went on to make innovations in mathematics and was one of the first astronomers to use the telescope. His largely unappreciated contribution to the history of ophthalmology was the first formulation of the sine law of refraction of light, found in his unpublished papers long after his death in 1621. Willebrord Snell discovered the sine law in Holland in 1621 but also died without formally publishing it. Rene Descartes first published the sine law in 1637. The sine law of refraction became not only the prime law of all lens systems but ushered in a new world of physical laws.

Mössbauer spectra linearity improvement by sine velocity waveform followed by linearization process

NASA Astrophysics Data System (ADS)

Kohout, Pavel; Frank, Tomas; Pechousek, Jiri; Kouril, Lukas

2018-05-01

This note reports the development of a new method for linearizing the Mössbauer spectra recorded with a sine drive velocity signal. Mössbauer spectra linearity is a critical parameter to determine Mössbauer spectrometer accuracy. Measuring spectra with a sine velocity axis and consecutive linearization increases the linearity of spectra in a wider frequency range of a drive signal, as generally harmonic movement is natural for velocity transducers. The obtained data demonstrate that linearized sine spectra have lower nonlinearity and line width parameters in comparison with those measured using a traditional triangle velocity signal.

Effects of Variability Associated with the Antarctic Circumpolar Current on Sound Propagation in the Ocean

DTIC Science & Technology

2008-09-01

showing shot locations (circles) and IMS hydrophone station locations ( triangles ), superimposed on a map of group velocities derived using average fall...E. McDonald (1991). Perth- Bermuda sound propagation (1960): Adiabatic mode interpretation, J. Acoust. Soc. Am. 90: 2586–2594. Jensen, F. B., W. A

Seafarers, Great Circles, and a Tad of Rhumb: Understanding the Mercator Misconception

ERIC Educational Resources Information Center

DiSpezio, Michael A.

2010-01-01

Being flat, Mercator maps inherently misrepresent some aspects of Earth's geography. That's because there is absolutely no way to simultaneously conserve all of the elements of three-dimensional space in a two-dimensional model. To dispel misconceptions, check out the Activity Worksheet and the website resources included in this article. Along…

A New Class of SINEs with snRNA Gene-Derived Heads

PubMed Central

Kojima, Kenji K.

2015-01-01

Eukaryotic genomes are colonized by various transposons including short interspersed elements (SINEs). The 5′ region (head) of the majority of SINEs is derived from one of the three types of RNA genes—7SL RNA, transfer RNA (tRNA), or 5S ribosomal RNA (rRNA)—and the internal promoter inside the head promotes the transcription of the entire SINEs. Here I report a new group of SINEs whose heads originate from either the U1 or U2 small nuclear RNA gene. These SINEs, named SINEU, are distributed among crocodilians and classified into three families. The structures of the SINEU-1 subfamilies indicate the recurrent addition of a U1- or U2-derived sequence onto the 5′ end of SINEU-1 elements. SINEU-1 and SINEU-3 are ancient and shared among alligators, crocodiles, and gharials, while SINEU-2 is absent in the alligator genome. SINEU-2 is the only SINE family that was active after the split of crocodiles and gharials. All SINEU families, especially SINEU-3, are preferentially inserted into a family of Mariner DNA transposon, Mariner-N4_AMi. A group of Tx1 non-long terminal repeat retrotransposons designated Tx1-Mar also show target preference for Mariner-N4_AMi, indicating that SINEU was mobilized by Tx1-Mar. PMID:26019167

A New Class of SINEs with snRNA Gene-Derived Heads.

PubMed

Kojima, Kenji K

2015-05-27

Eukaryotic genomes are colonized by various transposons including short interspersed elements (SINEs). The 5' region (head) of the majority of SINEs is derived from one of the three types of RNA genes--7SL RNA, transfer RNA (tRNA), or 5S ribosomal RNA (rRNA)--and the internal promoter inside the head promotes the transcription of the entire SINEs. Here I report a new group of SINEs whose heads originate from either the U1 or U2 small nuclear RNA gene. These SINEs, named SINEU, are distributed among crocodilians and classified into three families. The structures of the SINEU-1 subfamilies indicate the recurrent addition of a U1- or U2-derived sequence onto the 5' end of SINEU-1 elements. SINEU-1 and SINEU-3 are ancient and shared among alligators, crocodiles, and gharials, while SINEU-2 is absent in the alligator genome. SINEU-2 is the only SINE family that was active after the split of crocodiles and gharials. All SINEU families, especially SINEU-3, are preferentially inserted into a family of Mariner DNA transposon, Mariner-N4_AMi. A group of Tx1 non-long terminal repeat retrotransposons designated Tx1-Mar also show target preference for Mariner-N4_AMi, indicating that SINEU was mobilized by Tx1-Mar. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Phylogenetic relationships among East African haplochromine fish as revealed by short interspersed elements (SINEs).

PubMed

Terai, Yohey; Takezaki, Naoko; Mayer, Werner E; Tichy, Herbert; Takahata, Naoyuki; Klein, Jan; Okada, Norihiro

2004-01-01

Genomic DNA libraries were prepared from two endemic species of Lake Victoria haplochromine (cichlid) fish and used to isolate and characterize a set of short interspersed elements (SINEs). The distribution and sequences of the SINEs were used to infer phylogenetic relationships among East African haplochromines. The SINE-based classification divides the fish into four groups, which, in order of their divergence from a stem lineage, are the endemic Lake Tanganyika flock (group 1); fish of the nonendemic, monotypic, widely distributed genus Astatoreochromis (group 2); the endemic Lake Malawi flock (group 3); and group 4, which contains fish from widely dispersed East African localities including Lakes Victoria, Edward, George, Albert, and Rukwa, as well as many rivers. The group 4 haplochromines are characterized by a subset of polymorphic SINEs, each of which is present in some individuals and absent in others of the same population at a given locality, the same morphologically defined species, and the same mtDNA-defined haplogroup. SINE-defined group 4 contains six of the seven previously described mtDNA haplogroups. One of the polymorphic SINEs appears to be fixed in the endemic Lake Victoria flock; four others display the presence-or-absence polymorphism within the species of this flock. These findings have implications for the origin of Lake Victoria cichlids and for their founding population sizes.

RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity

PubMed Central

2013-01-01

A substantial number of “retrogenes” that are derived from the mRNA of various intron-containing genes have been reported. A class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been shown to be involved in the reverse transcription of retrogenes (or processed pseudogenes) and non-autonomous short interspersed elements (SINEs). The 3′-end sequences of various SINEs originated from a corresponding LINE. As the 3′-untranslated regions of several LINEs are essential for retroposition, these LINEs presumably require “stringent” recognition of the 3′-end sequence of the RNA template. However, the 3′-ends of mammalian L1s do not exhibit any similarity to SINEs, except for the presence of 3′-poly(A) repeats. Since the 3′-poly(A) repeats of L1 and Alu SINE are critical for their retroposition, L1 probably recognizes the poly(A) repeats, thereby mobilizing not only Alu SINE but also cytosolic mRNA. Many flowering plants only harbor L1-clade LINEs and a significant number of SINEs with poly(A) repeats, but no homology to the LINEs. Moreover, processed pseudogenes have also been found in flowering plants. I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized a specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution. PMID:23984183

A Transposon in Comt Generates mRNA Variants and Causes Widespread Expression and Behavioral Differences among Mice

PubMed Central

Wang, Xusheng; Miles, Michael F.; Lu, Lu; Williams, Robert W.

2010-01-01

Background Catechol-O-methyltransferase (COMT) is a key enzyme responsible for the degradation of dopamine and norepinephrine. COMT activity influences cognitive and emotional states in humans and aggression and drug responses in mice. This study identifies the key sequence variant that leads to differences in Comt mRNA and protein levels among mice, and that modulates synaptic function and pharmacological and behavioral traits. Methodology/Principal Findings We examined Comt expression in multiple tissues in over 100 diverse strains and several genetic crosses. Differences in expression map back to Comt and are generated by a 230 nt insertion of a B2 short interspersed element (B2 SINE) in the proximal 3′ UTR of Comt in C57BL/6J. This transposon introduces a premature polyadenylation signal and creates a short 3′ UTR isoform. The B2 SINE is shared by a subset of strains, including C57BL/6J, A/J, BALB/cByJ, and AKR/J, but is absent in others, including DBA/2J, FVB/NJ, SJL/J, and wild subspecies. The short isoform is associated with increased protein expression in prefrontal cortex and hippocampus relative to the longer ancestral isoform. The Comt variant causes downstream differences in the expression of genes involved in synaptic function, and also modulates phenotypes such as dopamine D1 and D2 receptor binding and pharmacological responses to haloperidol. Conclusions/Significance We have precisely defined the B2 SINE as the source of variation in Comt and demonstrated that a transposon in a 3′ UTR can alter mRNA isoform use and modulate behavior. The recent fixation of the variant in a subset of strains may have contributed to the rapid divergence of inbred strains. PMID:20808911

Transcriptional activity of transposable elements in coelacanth.

PubMed

Forconi, Mariko; Chalopin, Domitille; Barucca, Marco; Biscotti, Maria Assunta; De Moro, Gianluca; Galiana, Delphine; Gerdol, Marco; Pallavicini, Alberto; Canapa, Adriana; Olmo, Ettore; Volff, Jean-Nicolas

2014-09-01

The morphological stasis of coelacanths has long suggested a slow evolutionary rate. General genomic stasis might also imply a decrease of transposable elements activity. To evaluate the potential activity of transposable elements (TEs) in "living fossil" species, transcriptomic data of Latimeria chalumnae and its Indonesian congener Latimeria menadoensis were compared through the RNA-sequencing mapping procedures in three different organs (liver, testis, and muscle). The analysis of coelacanth transcriptomes highlights a significant percentage of transcribed TEs in both species. Major contributors are LINE retrotransposons, especially from the CR1 family. Furthermore, some particular elements such as a LF-SINE and a LINE2 sequences seem to be more expressed than other elements. The amount of TEs expressed in testis suggests possible transposition burst in incoming generations. Moreover, significant amount of TEs in liver and muscle transcriptomes were also observed. Analyses of elements displaying marked organ-specific expression gave us the opportunity to highlight exaptation cases, that is, the recruitment of TEs as new cellular genes, but also to identify a new Latimeria-specific family of Short Interspersed Nuclear Elements called CoeG-SINEs. Overall, transcriptome results do not seem to be in line with a slow-evolving genome with poor TE activity. © 2013 Wiley Periodicals, Inc.

Short interspersed elements (SINEs) of squamate reptiles (Squam1 and Squam2): structure and phylogenetic significance.

PubMed

Grechko, Vernata V; Kosushkin, Sergei A; Borodulina, Olga R; Butaeva, Fatima G; Darevsky, Ilya S

2011-05-15

Short interspersed elements (SINEs) are important nuclear molecular markers of the evolution of many eukaryotes. However, the SINEs of squamate reptile genomes have been little studied. We first identified two families of SINEs, termed Squam1 and Squam2, in the DNA of meadow lizard Darevskia praticola (Lacertidae) by performing DNA hybridization and PCR. Later, the same families of retrotransposons were found using the same methods in members of another 25 lizard families (from Iguania, Scincomorpha, Gekkota, Varanoidea, and Diploglossa infraorders) and two snake families, but their abundances in these taxa varied greatly. Both SINEs were Squamata-specific and were absent from mammals, birds, crocodiles, turtles, amphibians, and fish. Squam1 possessed some characteristics common to tRNA-related SINEs from fish and mammals, while Squam2 belonged to the tRNA(Ala) group of SINEs and had a more unusual and divergent structure. Squam2-related sequences were found in several unannotated GenBank sequences of squamate reptiles. Squam1 abundance in the Polychrotidae, Agamidae, Leiolepididae, Chamaeleonidae, Scincidae, Lacertidae, Gekkonidae, Varanidae, Helodermatidae, and two snake families were 10(2) -10(4) times higher than those in other taxa (Corytophanidae, Iguanidae, Anguidae, Cordylidae, Gerrhosauridae, Pygopodidae, and Eublepharidae). A less dramatic degree of copy number variation was observed for Squam2 in different taxa. Several Squam1 copies from Lacertidae, Chamaeleonidae, Gekkonidae, Varanidae, and Colubridae were sequenced and found to have evident orthologous features, as well as taxa-specific autapomorphies. Squam1 from Lacertidae and Chamaeleonidae could be divided into several subgroups based on sequence differences. Possible applications of these SINEs as Squamata phylogeny markers are discussed. Copyright © 2010 Wiley-Liss, Inc., A Wiley Company.

Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs.

PubMed

López-Giráldez, Francesc; Andrés, Olga; Domingo-Roura, Xavier; Bosch, Montserrat

2006-10-23

The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the interspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes.Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNALys-derived SINEs, we recommend avoiding their use as genetic markers.

Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences.

PubMed

Chen, Zhuo; Xu, Shixia; Zhou, Kaiya; Yang, Guang

2011-10-27

A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales), and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae), and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae), whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving cetacean phylogenetic relationships in the future.

Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences

PubMed Central

2011-01-01

Background A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales), and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. Results An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae), and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. Conclusions Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae), whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving cetacean phylogenetic relationships in the future. PMID:22029548

[Hypochondria sine materia as a psychosomatic problem: a model of hypochondriac disorders realized in the cutaneous sphere].

PubMed

Smulevich, A B; Dorozhenok, I Iu; Romanov, D V; L'vov, A N

2012-01-01

Hypochondria sine materia is a disorder with physical complains corresponding to no any somatic diagnosis. Hypochondria sine materia is a more complicated psychopathological condition compared to hypochondria cum materia. Hypochondria sine materia could be diagnosed not only in psychiatry, but mainly in general medicine. It is especially prevalent in dermatology. As a result of analysis of hypochondriac disorders involving cutaneous sphere in patients without dermatological diseases, a binary model of psychodermatological syndromes presenting with hypochondria sine materia in dermatology was developed. The binary structure of the psychodermatological syndromes includes secondary psychiatric symptoms based on primary coenesthesiopathic phenomena. The heterogeneous psychodermatological syndromes (cutaneous organ neurosis, impulsive excoriations syndrome, circumscripta hypochondria, coenesthesiopathic paranoia) could be arranged in a continuum of consecutively worsening conditions from neurotic to psychotic severity register. The syndromes differ in clinical and social prognosis requiring different approach to diagnosis and treatment.

Study on W-band sheet-beam traveling-wave tube based on flat-roofed sine waveguide

NASA Astrophysics Data System (ADS)

Fang, Shuanzhu; Xu, Jin; Jiang, Xuebing; Lei, Xia; Wu, Gangxiong; Li, Qian; Ding, Chong; Yu, Xiang; Wang, Wenxiang; Gong, Yubin; Wei, Yanyu

2018-05-01

A W-band sheet electron beam (SEB) traveling-wave tube (TWT) based on flat-roofed sine waveguide slow-wave structure (FRSWG-SWS) is proposed. The sine wave of the metal grating is replaced by a flat-roofed sine wave around the electron beam tunnel. The slow-wave characteristics including the dispersion properties and interaction impedance have been investigated by using the eigenmode solver in the 3-D electromagnetic simulation software Ansoft HFSS. Through calculations, the FRSWG SWS possesses the larger average interaction impedance than the conventional sine waveguide (SWG) SWS in the frequency range of 86-110 GHz. The beam-wave interaction was studied and particle-in-cell simulation results show that the SEB TWT can produce output power over 120 W within the bandwidth ranging from 90 to 100 GHz, and the maximum output power is 226 W at typical frequency 94 GHz, corresponding electron efficiency of 5.89%.

Spiral Transformation for High-Resolution and Efficient Sorting of Optical Vortex Modes.

PubMed

Wen, Yuanhui; Chremmos, Ioannis; Chen, Yujie; Zhu, Jiangbo; Zhang, Yanfeng; Yu, Siyuan

2018-05-11

Mode sorting is an essential function for optical multiplexing systems that exploit the orthogonality of the orbital angular momentum mode space. The familiar log-polar optical transformation provides a simple yet efficient approach whose resolution is, however, restricted by a considerable overlap between adjacent modes resulting from the limited excursion of the phase along a complete circle around the optical vortex axis. We propose and experimentally verify a new optical transformation that maps spirals (instead of concentric circles) to parallel lines. As the phase excursion along a spiral in the wave front of an optical vortex is theoretically unlimited, this new optical transformation can separate orbital angular momentum modes with superior resolution while maintaining unity efficiency.

Spiral Transformation for High-Resolution and Efficient Sorting of Optical Vortex Modes

NASA Astrophysics Data System (ADS)

Wen, Yuanhui; Chremmos, Ioannis; Chen, Yujie; Zhu, Jiangbo; Zhang, Yanfeng; Yu, Siyuan

2018-05-01

Mode sorting is an essential function for optical multiplexing systems that exploit the orthogonality of the orbital angular momentum mode space. The familiar log-polar optical transformation provides a simple yet efficient approach whose resolution is, however, restricted by a considerable overlap between adjacent modes resulting from the limited excursion of the phase along a complete circle around the optical vortex axis. We propose and experimentally verify a new optical transformation that maps spirals (instead of concentric circles) to parallel lines. As the phase excursion along a spiral in the wave front of an optical vortex is theoretically unlimited, this new optical transformation can separate orbital angular momentum modes with superior resolution while maintaining unity efficiency.

X-Shaped Bulge in the Milky Way

NASA Image and Video Library

2016-07-19

In 2010, NASA's Wide-field Infrared Survey Explorer (WISE) mission observed the entire sky twice. Astronomers used these data to point out the X-shaped structure in the bulge of the Milky Way, contained in the small circle at center, as well as the inset image. The circled central portion covers roughly the area of sky that would be blocked by a basketball when held out at arm's length. Dustin Lang, an astronomer at the Dunlap Institute of the University of Toronto, used these data to make this map, which shows the full 360-degree panorama of the sky as seen by WISE. Lang collaborated with Melissa Ness, postdoctoral researcher at the Max Planck Institute for Astronomy in Germany, http://photojournal.jpl.nasa.gov/catalog/PIA20699

BoS: a large and diverse family of short interspersed elements (SINEs) in Brassica oleracea.

PubMed

Zhang, Xiaoyu; Wessler, Susan R

2005-05-01

Short interspersed elements (SINEs) are nonautonomous non-LTR retrotransposons that populate eukaryotic genomes. Numerous SINE families have been identified in animals, whereas only a few have been described in plants. Here we describe a new family of SINEs, named BoS, that is widespread in Brassicaceae and present at approximately 2000 copies in Brassica oleracea. In addition to sharing a modular structure and target site preference with previously described SINEs, BoS elements have several unusual features. First, the head regions of BoS RNAs can adopt a distinct hairpin-like secondary structure. Second, with 15 distinct subfamilies, BoS represents one of the most diverse SINE families described to date. Third, several of the subfamilies have a mosaic structure that has arisen through the exchange of sequences between existing subfamilies, possibly during retrotransposition. Analysis of BoS subfamilies indicate that they were active during various time periods through the evolution of Brassicaceae and that active elements may still reside in some Brassica species. As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family.

Talua SINE biology in the genome of the Reticulitermes subterranean termites (Isoptera, Rhinotermitidae).

PubMed

Luchetti, Andrea; Mantovani, Barbara

2009-12-01

Studies on transposable elements in termites are of interest because their genome is in a permanent condition of inbreeding. In this situation, an increase in transposon copy number should be mainly due to a Muller's ratchet effect, with selection against deleterious insertions playing a major role. Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, known to be stable components of eukaryotic genomes. The SINE Talua, first isolated from Reticulitermes lucifugus (Rhinotermitidae), is the only mobile element described so far in termites. In the present survey, Talua has been found widespread in the Isoptera order. In comparison with other non-termite SINEs, Talua diversity and distribution in the Reticulitermes genome demonstrate that Talua is an ancient component of termite genome and that it is significantly associated with other repeats. In particular, the element is found to be involved with microsatellite motifs either as their generator or because inserted in their nearby. Further, two new SINEs and a putative retrotranscriptase-like sequence were found linked to Talua. Talua's genomic distribution is discussed in the light of the available models on transposable element dynamics within inbred genomes, also taking into account SINE role as drivers of genetic diversity in counteracting inbreeding depression.

Mental transformations of spatial stimuli in humans and in monkeys: rotation vs. translocation.

PubMed

Nekovarova, Tereza; Nedvidek, Jan; Klement, Daniel; Rokyta, Richard; Bures, Jan

2013-03-01

We studied the ability of monkeys and humans to orient in one spatial frame ("response frame") according to abstract spatial stimuli presented in another spatial frame ("stimulus frame"). The stimuli were designed as simple maps of the "response space". We studied how the transformations of these stimuli affected the performance. The subjects were trained to choose a particular position in the response frame - either on a touch screen (monkeys) or on a keyboard (humans) - according to schematic spatial stimuli presented on the stimulus screen. The monkeys responded by touching one of four circles shown in corners of a rectangle displayed on the touch screen. The correct position was signaled by the stimulus ("map") presented on the stimulus screen. The map was a complementary rectangle, but only with one circle shown ("pointer"). The position of this circle indicated the correct position in the response frame. In the first experiment we only manipulated stimuli presented on the computer screen. The "map" was originally shown in the same position and orientation as the "response pattern" but later the position and the rotation of the map on the screen were changing. Such transformations of the stimuli allow us to study the mental operations that the animals performed and how particular mental transformations mutually differed. In the second experiment we tested whether the monkeys relied more on stimuli presented on the screen or on the surrounding stable environment and objects. We compared the performance of animals in tasks with rotated virtual maps in a stable surrounding environment with the performance in tasks where we rotated the surrounding frame (computer monitor), whereas the stimuli on the screen remained stable. In the third experiment we tested human subjects in analogous tests to compare the ability and cognitive strategies of monkeys and humans in this task. We showed that the mental strategies that monkeys used for orientation in one spatial frame according to the map presented in the other spatial frame depended on the type of stimulus manipulation. We demonstrated that for monkeys there was a difference between solving "mental rotation" and "mental translocation" in this experimental design. We showed that humans were able both to mentally rotate and translocate the displayed stimuli. However, the mental rotation was more difficult than mental translocation also for them. These experiments help us to understand how the monkeys perceive the abstract spatial information, create the representation of space and how they transform the information about the position obtained from one spatial frame into another. The comparison between humans and monkeys allows us to study this cognitive ability in phylogeny. Copyright © 2012 Elsevier B.V. All rights reserved.

Identification of a Recently Active Mammalian SINE Derived from Ribosomal RNA

PubMed Central

Longo, Mark S.; Brown, Judy D.; Zhang, Chu; O’Neill, Michael J.; O’Neill, Rachel J.

2015-01-01

Complex eukaryotic genomes are riddled with repeated sequences whose derivation does not coincide with phylogenetic history and thus is often unknown. Among such sequences, the capacity for transcriptional activity coupled with the adaptive use of reverse transcription can lead to a diverse group of genomic elements across taxa, otherwise known as selfish elements or mobile elements. Short interspersed nuclear elements (SINEs) are nonautonomous mobile elements found in eukaryotic genomes, typically derived from cellular RNAs such as tRNAs, 7SL or 5S rRNA. Here, we identify and characterize a previously unknown SINE derived from the 3′-end of the large ribosomal subunit (LSU or 28S rDNA) and transcribed via RNA polymerase III. This new element, SINE28, is represented in low-copy numbers in the human reference genome assembly, wherein we have identified 27 discrete loci. Phylogenetic analysis indicates these elements have been transpositionally active within primate lineages as recently as 6 MYA while modern humans still carry transcriptionally active copies. Moreover, we have identified SINE28s in all currently available assembled mammalian genome sequences. Phylogenetic comparisons indicate that these elements are frequently rederived from the highly conserved LSU rRNA sequences in a lineage-specific manner. We propose that this element has not been previously recognized as a SINE given its high identity to the canonical LSU, and that SINE28 likely represents one of possibly many unidentified, active transposable elements within mammalian genomes. PMID:25637222

Lineage-specific SoxR-mediated Regulation of an Endoribonuclease Protects Non-enteric Bacteria from Redox-active Compounds*

PubMed Central

Kim, Jisun; Park, Chulwoo; Imlay, James A.; Park, Woojun

2017-01-01

Bacteria use redox-sensitive transcription factors to coordinate responses to redox stress. The [2Fe-2S] cluster-containing transcription factor SoxR is particularly tuned to protect cells against redox-active compounds (RACs). In enteric bacteria, SoxR is paired with a second transcription factor, SoxS, that activates downstream effectors. However, SoxS is absent in non-enteric bacteria, raising questions as to how SoxR functions. Here, we first show that SoxR of Acinetobacter oleivorans displayed similar activation profiles in response to RACs as did its homolog from Escherichia coli but controlled a different set of target genes, including sinE, which encodes an endoribonuclease. Expression, gel mobility shift, and mutational analyses indicated that sinE is a direct target of SoxR. Redox potentials and permeability of RACs determined optimal sinE induction. Bioinformatics suggested that only a few γ- and β-proteobacteria might have SoxR-regulated sinE. Purified SinE, in the presence of Mg2+ ions, degrades rRNAs, thus inhibiting protein synthesis. Similarly, pretreatment of cells with RACs demonstrated a role for SinE in promoting persistence in the presence of antibiotics that inhibit protein synthesis. Our data improve our understanding of the physiology of soil microorganisms by suggesting that both non-enteric SoxR and its target SinE play protective roles in the presence of RACs and antibiotics. PMID:27895125

Anti-tumor activity of selective inhibitors of XPO1/CRM1-mediated nuclear export in diffuse malignant peritoneal mesothelioma: the role of survivin

PubMed Central

Doldi, Valentina; Lopergolo, Alessia; Deraco, Marcello; Gandellini, Paolo; Friedlander, Sharon; Landesman, Yosef; Kauffman, Michael G.; Shacham, Sharon

2015-01-01

Survivin, which is highly expressed and promotes cell survival in diffuse malignant peritoneal mesothelioma (DMPM), exclusively relies on exportin 1 (XPO1/CRM1) to be shuttled into the cytoplasm and perform its anti-apoptotic function. Here, we explored the efficacy of Selective Inhibitors of Nuclear Export (SINE), KPT-251, KPT-276 and the orally available, clinical stage KPT-330 (selinexor), in DMPM preclinical models. Exposure to SINE induced dose-dependent inhibition of cell growth, cell cycle arrest at G1-phase and caspase-dependent apoptosis, which were consequent to a decrease of XPO1/CRM1 protein levels and the concomitant nuclear accumulation of its cargo proteins p53 and CDKN1a. Cell exposure to SINE led to a time-dependent reduction of cytoplasmic survivin levels. In addition, after an initial accumulation, the nuclear protein abundance progressively decreased, as a consequence of an enhanced ubiquitination and proteasome-dependent degradation. SINE and the survivin inhibitor YM155 synergistically cooperated in reducing DMPM cell proliferation. Most importantly, orally administered SINE caused a significant anti-tumor effect in subcutaneous and orthotopic DMPM xenografts without appreciable toxicity. Overall, we have demonstrated a marked efficacy of SINE in DMPM preclinical models that may relay on the interference with survivin intracellular distribution and function. Our study suggests SINE-mediated XPO1/CRM1 inhibition as a novel therapeutic option for DMPM. PMID:25948791

The structure of mode-locking regions of piecewise-linear continuous maps: II. Skew sawtooth maps

NASA Astrophysics Data System (ADS)

Simpson, D. J. W.

2018-05-01

In two-parameter bifurcation diagrams of piecewise-linear continuous maps on , mode-locking regions typically have points of zero width known as shrinking points. Near any shrinking point, but outside the associated mode-locking region, a significant proportion of parameter space can be usefully partitioned into a two-dimensional array of annular sectors. The purpose of this paper is to show that in these sectors the dynamics is well-approximated by a three-parameter family of skew sawtooth circle maps, where the relationship between the skew sawtooth maps and the N-dimensional map is fixed within each sector. The skew sawtooth maps are continuous, degree-one, and piecewise-linear, with two different slopes. They approximate the stable dynamics of the N-dimensional map with an error that goes to zero with the distance from the shrinking point. The results explain the complicated radial pattern of periodic, quasi-periodic, and chaotic dynamics that occurs near shrinking points.

Berkeley Lab Scientists to Play Role in New Space Telescope

Science.gov Websites

circling distant suns, among other science aims. The Wide Field Infrared Survey Telescope (WFIRST) will Hubble Space Telescope's Wide Field Camera 3 infrared imager. A Hubble large-scale mapping survey of the survey of the M31 galaxy (shown here) required 432 "pointings" of its imager, while only two

From genes to landscapes: conserving biodiversity at multiple scales.

Treesearch

Sally Duncan

2000-01-01

Biodiversity has at last become a familiar term outside of scientific circles. Ways of measuring it and mapping it are advancing and becoming more complex, but ways of deciding how to conserve it remain mixed at best, and the resources available to manage dimishing biodiversity are themselves scarce. One significant problem is that policy decisions are frequently at...

Elastostatic stress analysis of orthotropic rectangular center-cracked plates

NASA Technical Reports Server (NTRS)

Gyekenyesi, G. S.; Mendelson, A.

1972-01-01

A mapping-collocation method was developed for the elastostatic stress analysis of finite, anisotropic plates with centrally located traction-free cracks. The method essentially consists of mapping the crack into the unit circle and satisfying the crack boundary conditions exactly with the help of Muskhelishvili's function extension concept. The conditions on the outer boundary are satisfied approximately by applying the method of least-squares boundary collocation. A parametric study of finite-plate stress intensity factors, employing this mapping-collocation method, is presented. It shows the effects of varying material properties, orientation angle, and crack-length-to-plate-width and plate-height-to-plate-width ratios for rectangular orthotropic plates under constant tensile and shear loads.

Gross-Pitaevski map as a chaotic dynamical system.

PubMed

Guarneri, Italo

2017-03-01

The Gross-Pitaevski map is a discrete time, split-operator version of the Gross-Pitaevski dynamics in the circle, for which exponential instability has been recently reported. Here it is studied as a classical dynamical system in its own right. A systematic analysis of Lyapunov exponents exposes strongly chaotic behavior. Exponential growth of energy is then shown to be a direct consequence of rotational invariance and for stationary solutions the full spectrum of Lyapunov exponents is analytically computed. The present analysis includes the "resonant" case, when the free rotation period is commensurate to 2π, and the map has countably many constants of the motion. Except for lowest-order resonances, this case exhibits an integrable-chaotic transition.

A rigorous computational approach to linear response

NASA Astrophysics Data System (ADS)

Bahsoun, Wael; Galatolo, Stefano; Nisoli, Isaia; Niu, Xiaolong

2018-03-01

We present a general setting in which the formula describing the linear response of the physical measure of a perturbed system can be obtained. In this general setting we obtain an algorithm to rigorously compute the linear response. We apply our results to expanding circle maps. In particular, we present examples where we compute, up to a pre-specified error in the L∞ -norm, the response of expanding circle maps under stochastic and deterministic perturbations. Moreover, we present an example where we compute, up to a pre-specified error in the L 1-norm, the response of the intermittent family at the boundary; i.e. when the unperturbed system is the doubling map. This work was mainly conducted during a visit of SG to Loughborough University. WB and SG would like to thank The Leverhulme Trust for supporting mutual research visits through the Network Grant IN-2014-021. SG thanks the Department of Mathematical Sciences at Loughborough University for hospitality. WB thanks Dipartimento di Matematica, Universita di Pisa. The research of SG and IN is partially supported by EU Marie-Curie IRSES ‘Brazilian-European partnership in Dynamical Systems’ (FP7-PEOPLE-2012-IRSES 318999 BREUDS). IN was partially supported by CNPq and FAPERJ. IN would like to thank the Department of Mathematics at Uppsala University and the support of the KAW grant 2013.0315.

Water impact shock test system

NASA Technical Reports Server (NTRS)

1977-01-01

The basic objective was to design, manufacture, and install a shock test system which, in part, would have the ability to subject test articles weighing up to 1,000 pounds to both half sine and/or full sine pulses having peak levels of up to 50 G's with half sine pulse durations of 100 milliseconds or full sine period duration of 200 milliseconds. The tolerances associated with the aforementioned pulses were +20% and -10% for the peak levels and plus or minus 10% for the pulse durations. The subject shock test system was to be capable of accepting test article sizes of up to 4 feet by 4 feet mounting surface by 4 feet in length.

Pulse-spreading harmonic complex as an alternative carrier for vocoder simulations of cochlear implants.

PubMed

Mesnildrey, Quentin; Hilkhuysen, Gaston; Macherey, Olivier

2016-02-01

Noise- and sine-carrier vocoders are often used to acoustically simulate the information transmitted by a cochlear implant (CI). However, sine-waves fail to mimic the broad spread of excitation produced by a CI and noise-bands contain intrinsic modulations that are absent in CIs. The present study proposes pulse-spreading harmonic complexes (PSHCs) as an alternative acoustic carrier in vocoders. Sentence-in-noise recognition was measured in 12 normal-hearing subjects for noise-, sine-, and PSHC-vocoders. Consistent with the amount of intrinsic modulations present in each vocoder condition, the average speech reception threshold obtained with the PSHC-vocoder was higher than with sine-vocoding but lower than with noise-vocoding.

Seismicity map tools for earthquake studies

NASA Astrophysics Data System (ADS)

Boucouvalas, Anthony; Kaskebes, Athanasios; Tselikas, Nikos

2014-05-01

We report on the development of new and online set of tools for use within Google Maps, for earthquake research. We demonstrate this server based and online platform (developped with PHP, Javascript, MySQL) with the new tools using a database system with earthquake data. The platform allows us to carry out statistical and deterministic analysis on earthquake data use of Google Maps and plot various seismicity graphs. The tool box has been extended to draw on the map line segments, multiple straight lines horizontally and vertically as well as multiple circles, including geodesic lines. The application is demonstrated using localized seismic data from the geographic region of Greece as well as other global earthquake data. The application also offers regional segmentation (NxN) which allows the studying earthquake clustering, and earthquake cluster shift within the segments in space. The platform offers many filters such for plotting selected magnitude ranges or time periods. The plotting facility allows statistically based plots such as cumulative earthquake magnitude plots and earthquake magnitude histograms, calculation of 'b' etc. What is novel for the platform is the additional deterministic tools. Using the newly developed horizontal and vertical line and circle tools we have studied the spatial distribution trends of many earthquakes and we here show for the first time the link between Fibonacci Numbers and spatiotemporal location of some earthquakes. The new tools are valuable for examining visualizing trends in earthquake research as it allows calculation of statistics as well as deterministic precursors. We plan to show many new results based on our newly developed platform.

The LINEs and SINEs of Entamoeba histolytica: comparative analysis and genomic distribution.

PubMed

Bakre, Abhijeet A; Rawal, Kamal; Ramaswamy, Ram; Bhattacharya, Alok; Bhattacharya, Sudha

2005-07-01

Autonomous non-long terminal repeat retrotransposons are commonly referred to as long interspersed elements (LINEs). Short non-autonomous elements that borrow the LINE machinery are called SINES. The Entamoeba histolytica genome contains three classes of LINEs and SINEs. Together the EhLINEs/SINEs account for about 6% of the genome. The recognizable functional domains in all three EhLINEs included reverse transcriptase and endonuclease. A novel feature was the presence of two types of members-some with a single long ORF (less frequent) and some with two ORFs (more frequent) in both EhLINE1 and 2. The two ORFs were generated by conserved changes leading to stop codon. Computational analysis of the immediate flanking sequences for each element showed that they inserted in AT-rich sequences, with a preponderance of Ts in the upstream site. The elements were very frequently located close to protein-coding genes and other EhLINEs/SINEs. The possible influence of these elements on expression of neighboring genes needs to be determined.

Stress induction of Bm1 RNA in silkworm larvae: SINEs, an unusual class of stress genes

PubMed Central

Kimura, Richard H.; Choudary, Prabhakara V.; Stone, Koni K.; Schmid, Carl W.

2001-01-01

This study surveys the induction of RNA polymerase III (Pol III)–directed expression of short interspersed element (SINE) transcripts by various stresses in an animal model, silkworm larvae. Sublethal heat shock and exposure to several toxic compounds increase the level of Bm1 RNA, the silkworm SINE transcript, while also transiently increasing expression of a well-characterized stress-induced transcript, Hsp70 messenger RNA (mRNA). In certain cases, the Bm1 RNA response coincides with that of Hsp70 mRNA, but more often Bm1 RNA responds later in recovery. Baculovirus infection and exposure to certain toxic compounds increase Bm1 RNA but not Hsp70 mRNA, showing that SINE induction is not necessarily coupled to transcription of this particular heat shock gene. SINEs behave as an additional class of stress-inducible genes in living animals but are unusual as stress genes because of their high copy number, genomic dispersion, and Pol III–directed transcription. PMID:11599568

Detecting the chaotic nature in a transitional boundary layer using symbolic information-theory quantifiers.

PubMed

Zhang, Wen; Liu, Peiqing; Guo, Hao; Wang, Jinjun

2017-11-01

The permutation entropy and the statistical complexity are employed to study the boundary-layer transition induced by the surface roughness. The velocity signals measured in the transition process are analyzed with these symbolic quantifiers, as well as the complexity-entropy causality plane, and the chaotic nature of the instability fluctuations is identified. The frequency of the dominant fluctuations has been found according to the time scales corresponding to the extreme values of the symbolic quantifiers. The laminar-turbulent transition process is accompanied by the evolution in the degree of organization of the complex eddy motions, which is also characterized with the growing smaller and flatter circles in the complexity-entropy causality plane. With the help of the permutation entropy and the statistical complexity, the differences between the chaotic fluctuations detected in the experiments and the classical Tollmien-Schlichting wave are shown and discussed. It is also found that the chaotic features of the instability fluctuations can be approximated with a number of regular sine waves superimposed on the fluctuations of the undisturbed laminar boundary layer. This result is related to the physical mechanism in the generation of the instability fluctuations, which is the noise-induced chaos.

Detecting the chaotic nature in a transitional boundary layer using symbolic information-theory quantifiers

NASA Astrophysics Data System (ADS)

Zhang, Wen; Liu, Peiqing; Guo, Hao; Wang, Jinjun

2017-11-01

The permutation entropy and the statistical complexity are employed to study the boundary-layer transition induced by the surface roughness. The velocity signals measured in the transition process are analyzed with these symbolic quantifiers, as well as the complexity-entropy causality plane, and the chaotic nature of the instability fluctuations is identified. The frequency of the dominant fluctuations has been found according to the time scales corresponding to the extreme values of the symbolic quantifiers. The laminar-turbulent transition process is accompanied by the evolution in the degree of organization of the complex eddy motions, which is also characterized with the growing smaller and flatter circles in the complexity-entropy causality plane. With the help of the permutation entropy and the statistical complexity, the differences between the chaotic fluctuations detected in the experiments and the classical Tollmien-Schlichting wave are shown and discussed. It is also found that the chaotic features of the instability fluctuations can be approximated with a number of regular sine waves superimposed on the fluctuations of the undisturbed laminar boundary layer. This result is related to the physical mechanism in the generation of the instability fluctuations, which is the noise-induced chaos.

Modification of the azimuth control system in the LLMC

NASA Astrophysics Data System (ADS)

Li, Binhua; Yang, Lei; Chen, Linfei; Mao, Wei

2000-10-01

A new control system of the azimuth transmission mechanism used in the Lower Latitude Meridian Circle (LLMC) is described in this paper. Because the original azimuth transmission mechanism causes too much vibration during the transposition of the horizontal axis of the instrument, we decided to modify the original system by two ways. One is to modify the lift mechanism and the azimuth transmission mechanism. The other is to replace the original stepper motors with a new type of stepper motor. According to the requirement of the new motor and its sine subdivided microstep driver, the original control system has been modified. The new system has an expansion output board and a new control program compared with the original one. The hardware architecture of the new system is described. The program in the single chip microcontroller is written in ASM, which is composed of 10 subroutines. The program in a host PC is written in C++. The methods using in controlling motors and skills in designing these programs are discussed. Two sketch flow charts of the control program are presented in the paper. Modification of the lift mechanism is also introduced. All this works make the vibration very slight.

Mapping soil erosion risk in Serra de Grândola (Portugal)

NASA Astrophysics Data System (ADS)

Neto Paixão, H. M.; Granja Martins, F. M.; Zavala, L. M.; Jordán, A.; Bellinfante, N.

2012-04-01

Geomorphological processes can pose environmental risks to people and economical activities. Information and a better knowledge of the genesis of these processes is important for environmental planning, since it allows to model, quantify and classify risks, what can mitigate the threats. The objective of this research is to assess the soil erosion risk in Serra de Grândola, which is a north-south oriented mountain ridge with an altitude of 383 m, located in southwest of Alentejo (southern Portugal). The study area is 675 km2, including the councils of Grândola, Santiago do Cacém and Sines. The process for mapping of erosive status was based on the guidelines for measuring and mapping the processes of erosion of coastal areas of the Mediterranean proposed by PAP/RAC (1997), developed and later modified by other authors in different areas. This method is based on the application of a geographic information system that integrates different types of spatial information inserted into a digital terrain model and in their derivative models. Erosive status are classified using information from soil erodibility, slope, land use and vegetation cover. The rainfall erosivity map was obtained using the modified Fournier index, calculated from the mean monthly rainfall, as recorded in 30 meteorological stations with influence in the study area. Finally, the soil erosion risk map was designed by ovelaying the erosive status map and the rainfall erosivity map.

Shape Memory Alloys for Vibration Isolation and Damping of Large-Scale Space Structures

DTIC Science & Technology

2010-08-04

Portugal (2007) Figure 24 – Comparison of martensitic SMA with steel in sine upsweep 3.2.2.4 Dwell Test Comparison with Sine Sweep Results...International Conference on Experimental Vibration Analysis for Civil Engineering Structures (EVACES), Porto, Portugal (2007) † Lammering, Rolf...a unique jump in amplitude during a sine sweep if sufficient pre- stretch is applied. These results were significant, but investigation of more

Factors Influencing Army Accessions.

DTIC Science & Technology

1982-12-01

partial autocorrelations were examined for significant lags or a recognizable pattern such as a damped exponential or a sine wave. The TSP prugrams...decreasing function indicating nonstation- *arity or a very long sine wave where only a small portion of the wave is plotted. The partial...plot of the raw data appeared (Appendix E-1) to be either the middle of a long sine wave or a linearly decreasing function. This pattern is recognized

Using SINEs to probe ancient explosive speciation: "hidden" radiation of African cichlids?

PubMed

Terai, Yohey; Takahashi, Kazuhiko; Nishida, Mutsumi; Sato, Tetsu; Okada, Norihiro

2003-06-01

Cichlid fishes of the east African Great Lakes represent a paradigm of adaptive radiation. We conducted a phylogenetic analysis of cichlids including pan-African and west African species by using insertion patterns of short interspersed elements (SINEs) at orthologous loci. The monophyly of the east African cichlids was consistently supported by seven independent insertions of SINE sequences that are uniquely shared by these species. In addition, data from four other loci indicated that the genera Tilapia (pan-African) and Steatocranus (west African) are the closest relatives to east African cichlids. However, relationships among Tilapia, Steatocranus, and the east African clade were ambiguous because of incongruencies among topologies suggested by insertion patterns of SINEs at six other loci. One plausible explanation for this phenomenon is incomplete lineage sorting of alleles containing or missing a SINE insertion at these loci during ancestral speciation. Such incomplete sorting may have taken place earlier than 14 MYA, followed by random and stochastic fixation of the alleles in subsequent lineages. These observations prompted us to consider the possibility that cichlid speciation occurred at an accelerated rate during this period when the African Great Lakes did not exist. The SINE method could be useful for detecting ancient exclusive speciation events that tend to remain hidden during conventional sequence analyses because of accumulated point mutations.

Selective inhibitors of nuclear export show that CRM1/XPO1 is a target in chronic lymphocytic leukemia

PubMed Central

Lapalombella, Rosa; Sun, Qingxiang; Williams, Katie; Tangeman, Larissa; Jha, Shruti; Zhong, Yiming; Goettl, Virginia; Mahoney, Emilia; Berglund, Caroline; Gupta, Sneha; Farmer, Alicia; Mani, Rajeswaran; Johnson, Amy J.; Lucas, David; Mo, Xiaokui; Daelemans, Dirk; Sandanayaka, Vincent; Shechter, Sharon; McCauley, Dilara; Shacham, Sharon; Kauffman, Michael

2012-01-01

The nuclear export protein XPO1 is overexpressed in cancer, leading to the cytoplasmic mislocalization of multiple tumor suppressor proteins. Existing XPO1-targeting agents lack selectivity and have been associated with significant toxicity. Small molecule selective inhibitors of nuclear export (SINEs) were designed that specifically inhibit XPO1. Genetic experiments and X-ray structures demonstrate that SINE covalently bind to a cysteine residue in the cargo-binding groove of XPO1, thereby inhibiting nuclear export of cargo proteins. The clinical relevance of SINEs was explored in chronic lymphocytic leukemia (CLL), a disease associated with recurrent XPO1 mutations. Evidence is presented that SINEs can restore normal regulation to the majority of the dysregulated pathways in CLL both in vitro and in vivo and induce apoptosis of CLL cells with a favorable therapeutic index, with enhanced killing of genomically high-risk CLL cells that are typically unresponsive to traditional therapies. More importantly, SINE slows disease progression, and improves overall survival in the Eμ-TCL1-SCID mouse model of CLL with minimal weight loss or other toxicities. Together, these findings demonstrate that XPO1 is a valid target in CLL with minimal effects on normal cells and provide a basis for the development of SINEs in CLL and related hematologic malignancies. PMID:23034282

Effects of Pump Pulsation on Hydrodynamic Properties and Dissolution Profiles in Flow-Through Dissolution Systems (USP 4).

PubMed

Yoshida, Hiroyuki; Kuwana, Akemi; Shibata, Hiroko; Izutsu, Ken-Ichi; Goda, Yukihiro

2016-06-01

To clarify the effects of pump pulsation and flow-through cell (FTC) dissolution system settings on the hydrodynamic properties and dissolution profiles of model formulations. Two FTC systems with different cell temperature control mechanisms were used. Particle image velocimetry (PIV) was used to analyze the hydrodynamic properties of test solutions in the flow-through dissolution test cell. Two pulsation pumps (semi-sine, full-sine) and a non-pulsatile pump were used to study the effects of varied flows on the dissolution profiles of United States Pharmacopeia standard tablets. PIV analysis showed periodic changes in the aligned upward fluid flow throughout the dissolution cell that was designed to reduce the temperature gradient during pump pulsation (0.5 s/pulse). The maximum instantaneous flow from the semi-sine pump was higher than that of the full-sine pump under all conditions. The flow from the semi-sine wave pump showed faster dissolution of salicylic acid and prednisone tablets than those from other pumps. The semi-sine wave pump flow showed similar dissolution profiles in the two FTC systems. Variations in instantaneous fluid flow caused by pump pulsation that meets the requirements of pharmacopoeias are a factor that affects the dissolution profiles of tablets in FTC systems.

Molecular characterization, genomic distribution and evolutionary dynamics of Short INterspersed Elements in the termite genome.

PubMed

Luchetti, Andrea; Mantovani, Barbara

2011-02-01

Short INterspersed Elements (SINEs) in invertebrates, and especially in animal inbred genomes such that of termites, are poorly known; in this paper we characterize three new SINE families (Talub, Taluc and Talud) through the analyses of 341 sequences, either isolated from the Reticulitermes lucifugus genome or drawn from EST Genbank collection. We further add new data to the only isopteran element known so far, Talua. These SINEs are tRNA-derived elements, with an average length ranging from 258 to 372 bp. The tails are made up by poly(A) or microsatellite motifs. Their copy number varies from 7.9 × 10(3) to 10(5) copies, well within the range observed for other metazoan genomes. Species distribution, age and target site duplication analysis indicate Talud as the oldest, possibly inactive SINE originated before the onset of Isoptera (~150 Myr ago). Taluc underwent to substantial sequence changes throughout the evolution of termites and data suggest it was silenced and then re-activated in the R. lucifugus lineage. Moreover, Taluc shares a conserved sequence block with other unrelated SINEs, as observed for some vertebrate and cephalopod elements. The study of genomic environment showed that insertions are mainly surrounded by microsatellites and other SINEs, indicating a biased accumulation within non-coding regions. The evolutionary dynamics of Talu~ elements is explained through selective mechanisms acting in an inbred genome; in this respect, the study of termites' SINEs activity may provide an interesting framework to address the (co)evolution of mobile elements and the host genome.

Haplotype diversity in the equine myostatin gene with focus on variants associated with race distance propensity and muscle fiber type proportions

PubMed Central

Petersen, Jessica L; Valberg, Stephanie J; Mickelson, James R; McCue, Molly E

2014-01-01

Summary Two variants in the equine myostatin gene (MSTN), including a T/C SNP substitution in the first intron and a 227-bp SINE insertion in the promoter, are associated with muscle fiber type proportions in the Quarter Horse (QH) and with the prediction of race distance propensity in the Thoroughbred (TB). Genotypes from these loci, along with 18 additional variants surrounding MSTN, were examined in 301 horses of 14 breeds to evaluate haplotype relationships and diversity. The C allele of intron 1 was found in 12 of 14 breeds at a frequency of 0.27; the SINE was observed in five breeds, but common in only the TB and QH (0.73 and 0.48 respectively). Haplotype data suggest the SINE insertion is contemporary to and arose upon a haplotype containing the intron 1 C allele. Gluteal muscle biopsies of TBs showed a significant association of the intron 1 C allele and SINE with a higher proportion of Type 2B and lower proportion of Type 1 fibers. However, in the Belgian horse, in which the SINE is not present, the intron 1 SNP was not associated with fiber type proportions, and evaluation of fiber type proportions across the Belgian, TB and QH breeds shows the significant effect of breed on fiber type proportions is negated when evaluating horses without the SINE variant. These data suggest the SINE, rather than the intron 1 SNP, is driving the observed muscle fiber type characteristics and is the variant targeted by selection for short-distance racing. PMID:25160752

Evolutionary diversity and potential recombinogenic role of integration targets of non-LTR retrotransposons

PubMed Central

Gentles, Andrew J.; Kohany, Oleksiy; Jurka, Jerzy

2005-01-01

Short interspersed elements (SINEs) make up a significant fraction of total DNA in mammalian genomes, providing a rich substrate for chromosomal rearrangements by SINE-SINE recombinations. Proliferation of mammalian SINEs is mediated primarily by LINE1 (L1) non-LTR retrotransposons that preferentially integrate at DNA sequence targets with average length ~15 bp and containing conserved endonucleolytic nicking signals at both ends. We report that sequence variations in the first of the two nicking signals, represented by a 5′TT-AAAA consensus sequence, affect the position of the second signal thus leading to target site duplications (TSDs) of different lengths. The length distribution of TSDs appears to be affected also by L1-encoded enzyme variants, since targets with the same 5′ nicking site can be of different average length in different mammalian species. Taking this into account, we re-analyzed the second nicking site and found that it is larger and includes more conserved sites than previously appreciated, with a consensus of 5′ANTNTN-AA. We also studied potential involvement of the nicking sites in stimulating recombinations between SINE elements. We determined that SINE elements retaining TSDs with perfect 5′TT-AAAA nicking sites appear to be lost relatively rapidly from the human and rat genomes, and less rapidly from dog. We speculate that the introduction of single-strand DNA breaks induced by recurring endonucleolytic attacks at these sites, combined with the ubiquitousness of SINEs, may significantly promote recombination between repetitive elements, leading to the observed losses. At the same time new L1 subfamilies may be selected for “incompatibility” with pre-existing targets. This provides a possible driving force for the continual emergence of new L1 subfamilies which, in turn, may affect selection of L1-dependent SINE subfamilies. PMID:15944437

Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs

PubMed Central

López-Giráldez, Francesc; Andrés, Olga; Domingo-Roura, Xavier; Bosch, Montserrat

2006-01-01

Background The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. Results We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the insterspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. Conclusion Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes. Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNALys-derived SINEs, we recommend avoiding their use as genetic markers. PMID:17059596

Aerodynamic loads on a Darrieus rotor blade

NASA Astrophysics Data System (ADS)

Wilson, R. E.; McKie, W. R.; Lissaman, P. B. S.; James, M.

1983-03-01

A method is presented for the free vortex analysis of a Darrieus rotor blade in nonsteady motion, which employs the circle theorem to map the moving rotor airfoil into the circle plane and models the wake generated in terms of point vortices. Nascent vortex strength and position are taken from the Kutta condition, so that the nascent vortex has the same strength as a vortex sheet of uniform strength. Pressure integration over the plate and wake vortex impulse methods yields the same numerical results. The numerical results presented for a one-bladed Darrieus rotor at a tip/speed ratio of three, and two different chord sizes, indicate that the moment on the blade can be adequately approximated by quasi-steady relationships, although the accurate determination of local velocity and circulation are still required.

Log polar image sensor in CMOS technology

NASA Astrophysics Data System (ADS)

Scheffer, Danny; Dierickx, Bart; Pardo, Fernando; Vlummens, Jan; Meynants, Guy; Hermans, Lou

1996-08-01

We report on the design, design issues, fabrication and performance of a log-polar CMOS image sensor. The sensor is developed for the use in a videophone system for deaf and hearing impaired people, who are not capable of communicating through a 'normal' telephone. The system allows 15 detailed images per second to be transmitted over existing telephone lines. This framerate is sufficient for conversations by means of sign language or lip reading. The pixel array of the sensor consists of 76 concentric circles with (up to) 128 pixels per circle, in total 8013 pixels. The interior pixels have a pitch of 14 micrometers, up to 250 micrometers at the border. The 8013-pixels image is mapped (log-polar transformation) in a X-Y addressable 76 by 128 array.

Permutation entropy with vector embedding delays

NASA Astrophysics Data System (ADS)

Little, Douglas J.; Kane, Deb M.

2017-12-01

Permutation entropy (PE) is a statistic used widely for the detection of structure within a time series. Embedding delay times at which the PE is reduced are characteristic timescales for which such structure exists. Here, a generalized scheme is investigated where embedding delays are represented by vectors rather than scalars, permitting PE to be calculated over a (D -1 ) -dimensional space, where D is the embedding dimension. This scheme is applied to numerically generated noise, sine wave and logistic map series, and experimental data sets taken from a vertical-cavity surface emitting laser exhibiting temporally localized pulse structures within the round-trip time of the laser cavity. Results are visualized as PE maps as a function of embedding delay, with low PE values indicating combinations of embedding delays where correlation structure is present. It is demonstrated that vector embedding delays enable identification of structure that is ambiguous or masked, when the embedding delay is constrained to scalar form.

System and method for calibrating a rotary absolute position sensor

NASA Technical Reports Server (NTRS)

Davis, Donald R. (Inventor); Permenter, Frank Noble (Inventor); Radford, Nicolaus A (Inventor)

2012-01-01

A system includes a rotary device, a rotary absolute position (RAP) sensor generating encoded pairs of voltage signals describing positional data of the rotary device, a host machine, and an algorithm. The algorithm calculates calibration parameters usable to determine an absolute position of the rotary device using the encoded pairs, and is adapted for linearly-mapping an ellipse defined by the encoded pairs to thereby calculate the calibration parameters. A method of calibrating the RAP sensor includes measuring the rotary position as encoded pairs of voltage signals, linearly-mapping an ellipse defined by the encoded pairs to thereby calculate the calibration parameters, and calculating an absolute position of the rotary device using the calibration parameters. The calibration parameters include a positive definite matrix (A) and a center point (q) of the ellipse. The voltage signals may include an encoded sine and cosine of a rotary angle of the rotary device.

Wide-range lock-in amplifier

DOEpatents

McNeilly, D.R.

1984-01-01

A lock-in amplifier is provided which allows detection of a signal buried in noise without preprocessing of the input signal. An analog signal multiplier is used to obtain a dc output which is the product of the signal being detected and a high-purity sine wave signal. A reference signal of a known selectable frequency is applied to a sine-wave generator to generate the sine wave of the same frequency. The sine wave is applied to a multiplier through a phase shift arrangement to allow the detection of both amplitude of the detected signal and the phases relative to the reference signal. The multiplier output is filtered by a low-pass filter to eliminate unwanted frequency components from the output signal.

Wide-range lock-in amplifier

DOEpatents

McNeilly, David R.

1985-01-01

A lock-in amplifier is provided which allows detection of a signal buried in noise without preprocessing of the input signal. An analog signal multiplier is used to obtain a dc output which is the product of the signal being detected and a high-purity sine wave signal. A reference signal of a known selectable frequency is applied to a sine-wave generator to generate the sine wave of the same frequency. The sine wave is applied to a multiplier through a phase shift arrangement to allow the detection of both amplitude of the detected signal and the phases relative to the reference signal. The multiplier output is filtered by a low-pass filter to eliminate unwanted frequency components from the output signal.

All Are Worthy to Know the Earth: Henry De la Beche and the Origin of Geological Literacy

ERIC Educational Resources Information Center

Clary, Renee M.; Wandersee, James H.

2009-01-01

Henry T. De la Beche (1796-1855) began his geological career within an elite circle (Geological Society of London, 1817; FRS, 1819), collaborating with influential gentlemen geologists and publishing original research. When his independent income dwindled, De la Beche managed to secure governmental funding for his mapping projects. This led to…

The Organization of Repetitive DNA in the Genomes of Amazonian Lizard Species in the Family Teiidae.

PubMed

Carvalho, Natalia D M; Pinheiro, Vanessa S S; Carmo, Edson J; Goll, Leonardo G; Schneider, Carlos H; Gross, Maria C

2015-01-01

Repetitive DNA is the largest fraction of the eukaryote genome and comprises tandem and dispersed sequences. It presents variations in relation to its composition, number of copies, distribution, dynamics, and genome organization, and participates in the evolutionary diversification of different vertebrate species. Repetitive sequences are usually located in the heterochromatin of centromeric and telomeric regions of chromosomes, contributing to chromosomal structures. Therefore, the aim of this study was to physically map repetitive DNA sequences (5S rDNA, telomeric sequences, tropomyosin gene 1, and retroelements Rex1 and SINE) of mitotic chromosomes of Amazonian species of teiids (Ameiva ameiva, Cnemidophorus sp. 1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin) to understand their genome organization and karyotype evolution. The mapping of repetitive sequences revealed a distinct pattern in Cnemidophorus sp. 1, whereas the other species showed all sequences interspersed in the heterochromatic region. Physical mapping of the tropomyosin 1 gene was performed for the first time in lizards and showed that in addition to being functional, this gene has a structural function similar to the mapped repetitive elements as it is located preferentially in centromeric regions and termini of chromosomes. © 2016 S. Karger AG, Basel.

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

Kwasniewski, Bartosz K

The construction of reversible extensions of dynamical systems presented in a previous paper by the author and A.V. Lebedev is enhanced, so that it applies to arbitrary mappings (not necessarily with open range). It is based on calculating the maximal ideal space of C*-algebras that extends endomorphisms to partial automorphisms via partial isometric representations, and involves a new set of 'parameters' (the role of parameters is played by chosen sets or ideals). As model examples, we give a thorough description of reversible extensions of logistic maps and a classification of systems associated with compression of unitaries generating homeomorphisms of themore » circle. Bibliography: 34 titles.« less

Heart rate variability as determinism with jump stochastic parameters.

PubMed

Zheng, Jiongxuan; Skufca, Joseph D; Bollt, Erik M

2013-08-01

We use measured heart rate information (RR intervals) to develop a one-dimensional nonlinear map that describes short term deterministic behavior in the data. Our study suggests that there is a stochastic parameter with persistence which causes the heart rate and rhythm system to wander about a bifurcation point. We propose a modified circle map with a jump process noise term as a model which can qualitatively capture such this behavior of low dimensional transient determinism with occasional (stochastically defined) jumps from one deterministic system to another within a one parameter family of deterministic systems.

A hybrid Q-learning sine-cosine-based strategy for addressing the combinatorial test suite minimization problem

PubMed Central

Zamli, Kamal Z.; Din, Fakhrud; Bures, Miroslav

2018-01-01

The sine-cosine algorithm (SCA) is a new population-based meta-heuristic algorithm. In addition to exploiting sine and cosine functions to perform local and global searches (hence the name sine-cosine), the SCA introduces several random and adaptive parameters to facilitate the search process. Although it shows promising results, the search process of the SCA is vulnerable to local minima/maxima due to the adoption of a fixed switch probability and the bounded magnitude of the sine and cosine functions (from -1 to 1). In this paper, we propose a new hybrid Q-learning sine-cosine- based strategy, called the Q-learning sine-cosine algorithm (QLSCA). Within the QLSCA, we eliminate the switching probability. Instead, we rely on the Q-learning algorithm (based on the penalty and reward mechanism) to dynamically identify the best operation during runtime. Additionally, we integrate two new operations (Lévy flight motion and crossover) into the QLSCA to facilitate jumping out of local minima/maxima and enhance the solution diversity. To assess its performance, we adopt the QLSCA for the combinatorial test suite minimization problem. Experimental results reveal that the QLSCA is statistically superior with regard to test suite size reduction compared to recent state-of-the-art strategies, including the original SCA, the particle swarm test generator (PSTG), adaptive particle swarm optimization (APSO) and the cuckoo search strategy (CS) at the 95% confidence level. However, concerning the comparison with discrete particle swarm optimization (DPSO), there is no significant difference in performance at the 95% confidence level. On a positive note, the QLSCA statistically outperforms the DPSO in certain configurations at the 90% confidence level. PMID:29771918

A hybrid Q-learning sine-cosine-based strategy for addressing the combinatorial test suite minimization problem.

PubMed

Zamli, Kamal Z; Din, Fakhrud; Ahmed, Bestoun S; Bures, Miroslav

2018-01-01

The sine-cosine algorithm (SCA) is a new population-based meta-heuristic algorithm. In addition to exploiting sine and cosine functions to perform local and global searches (hence the name sine-cosine), the SCA introduces several random and adaptive parameters to facilitate the search process. Although it shows promising results, the search process of the SCA is vulnerable to local minima/maxima due to the adoption of a fixed switch probability and the bounded magnitude of the sine and cosine functions (from -1 to 1). In this paper, we propose a new hybrid Q-learning sine-cosine- based strategy, called the Q-learning sine-cosine algorithm (QLSCA). Within the QLSCA, we eliminate the switching probability. Instead, we rely on the Q-learning algorithm (based on the penalty and reward mechanism) to dynamically identify the best operation during runtime. Additionally, we integrate two new operations (Lévy flight motion and crossover) into the QLSCA to facilitate jumping out of local minima/maxima and enhance the solution diversity. To assess its performance, we adopt the QLSCA for the combinatorial test suite minimization problem. Experimental results reveal that the QLSCA is statistically superior with regard to test suite size reduction compared to recent state-of-the-art strategies, including the original SCA, the particle swarm test generator (PSTG), adaptive particle swarm optimization (APSO) and the cuckoo search strategy (CS) at the 95% confidence level. However, concerning the comparison with discrete particle swarm optimization (DPSO), there is no significant difference in performance at the 95% confidence level. On a positive note, the QLSCA statistically outperforms the DPSO in certain configurations at the 90% confidence level.

Retroposition of the AFC family of SINEs (short interspersed repetitive elements) before and during the adaptive radiation of cichlid fishes in Lake Malawi and related inferences about phylogeny.

PubMed

Takahashi, K; Nishida, M; Yuma, M; Okada, N

2001-01-01

Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation. To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed repetitive elements) at orthologous loci. We identified six loci at which a SINE sequence had apparently been specifically inserted by retroposition in the common ancestor of all the investigated species of endemic cichlids in Lake Malawi. At another locus, unique sharing of a SINE sequence was evident among all the investigated species of endemic non-Mbuna cichlids with the exception of Rhamphochromis sp. The relationships were in good agreement with those deduced in previous studies with various different markers, demonstrating that the SINE method is useful for the elucidation of phylogenetic relationships among cichlids in Lake Malawi. We also characterized a locus that exhibited transspecies polymorphism with respect to the presence or absence of the SINE sequence among non-Mbuna species. This result suggests that incomplete lineage sorting and/or interspecific hybridization might have occurred or be occurring among the species in this group, which might potentially cause misinterpretation of phylogenetic data, in particular when a single-locus marker, such as a sequence in the mitochondrial DNA, is used for analysis.

Fatigue Damage Spectrum calculation in a Mission Synthesis procedure for Sine-on-Random excitations

NASA Astrophysics Data System (ADS)

Angeli, Andrea; Cornelis, Bram; Troncossi, Marco

2016-09-01

In many real-life environments, certain mechanical and electronic components may be subjected to Sine-on-Random vibrations, i.e. excitations composed of random vibrations superimposed on deterministic (sinusoidal) contributions, in particular sine tones due to some rotating parts of the system (e.g. helicopters, engine-mounted components,...). These components must be designed to withstand the fatigue damage induced by the “composed” vibration environment, and qualification tests are advisable for the most critical ones. In the case of an accelerated qualification test, a proper test tailoring which starts from the real environment (measured vibration signals) and which preserves not only the accumulated fatigue damage but also the “nature” of the excitation (i.e. sinusoidal components plus random process) is important to obtain reliable results. In this paper, the classic time domain approach is taken as a reference for the comparison of different methods for the Fatigue Damage Spectrum (FDS) calculation in case of Sine-on-Random vibration environments. Then, a methodology to compute a Sine-on-Random specification based on a mission FDS is proposed.

Constitutive behavior and processing maps of low-expansion GH909 superalloy

NASA Astrophysics Data System (ADS)

Yao, Zhi-hao; Wu, Shao-cong; Dong, Jian-xin; Yu, Qiu-ying; Zhang, Mai-cang; Han, Guang-wei

2017-04-01

The hot deformation behavior of GH909 superalloy was studied systematically using isothermal hot compression tests in a temperature range of 960 to 1040°C and at strain rates from 0.02 to 10 s-1 with a height reduction as large as 70%. The relations considering flow stress, temperature, and strain rate were evaluated via power-law, hyperbolic sine, and exponential constitutive equations under different strain conditions. An exponential equation was found to be the most appropriate for process modeling. The processing maps for the superalloy were constructed for strains of 0.2, 0.4, 0.6, and 0.8 on the basis of the dynamic material model, and a total processing map that includes all the investigated strains was proposed. Metallurgical instabilities in the instability domain mainly located at higher strain rates manifested as adiabatic shear bands and cracking. The stability domain occurred at 960-1040°C and at strain rates less than 0.2 s-1; these conditions are recommended for optimum hot working of GH909 superalloy.

Sines and Cosines. Part 3 of 3

NASA Technical Reports Server (NTRS)

Apostol, Tom M. (Editor)

1994-01-01

In this 'Project Mathematics' series video, the addition formulas of sines and cosines are explained and their real life applications are demonstrated. Both film footage and computer animation is used. Several mathematical concepts are discussed and include: Ptolemy's theorem concerned with quadrilaterals; the difference between a central angle and an inscribed angle; sines and chord lengths; special angles; subtraction formulas; and a application to simple harmonic motion. A brief history of the city Alexandria, its mathematicians, and their contribution to the field of mathematics is shown.

Location of Nearest Rocky Exoplanet Known

NASA Image and Video Library

2015-07-30

This sky map shows the location of the star HD 219134 (circle), host to the nearest confirmed rocky planet found to date outside of our solar system. The star lies just off the "W" shape of the constellation Cassiopeia and can be seen with the naked eye in dark skies. It actually has multiple planets, none of which are habitable. http://photojournal.jpl.nasa.gov/catalog/PIA19832

QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.

PubMed

Appelt, J-U; Giordano, F A; Ecker, M; Roeder, I; Grund, N; Hotz-Wagenblatt, A; Opelz, G; Zeller, W J; Allgayer, H; Fruehauf, S; Laufs, S

2009-07-01

Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles.

Ground vibration test results of a JetStar airplane using impulsive sine excitation

NASA Technical Reports Server (NTRS)

Kehoe, Michael W.; Voracek, David F.

1989-01-01

Structural excitation is important for both ground vibration and flight flutter testing. The structural responses caused by this excitation are analyzed to determine frequency, damping, and mode shape information. Many excitation waveforms have been used throughout the years. The use of impulsive sine (sin omega t)/omega t as an excitation waveform for ground vibration testing and the advantages of using this waveform for flight flutter testing are discussed. The ground vibration test results of a modified JetStar airplane using impulsive sine as an excitation waveform are compared with the test results of the same airplane using multiple-input random excitation. The results indicated that the structure was sufficiently excited using the impulsive sine waveform. Comparisons of input force spectrums, mode shape plots, and frequency and damping values for the two methods of excitation are presented.

Vibration and acoustic testing of TOPEX/Poseidon satellite

NASA Technical Reports Server (NTRS)

Boatman, Dave; Scharton, Terry; Hershfeld, Donald; Larkin, Paul

1992-01-01

The satellite was subjected to a 1.5G swept sine vibration test and a 146 dB overall level acoustic test, in accordance with Ariane launch vehicle requirements, at the NASA Goddard Space Flight Center. Extensive pretest analysis of the sine test was conducted to plan the input notching and to justify vibration testing the satellite only in the longitudinal axis. A unique measurement system was utilized to determine the six components of interface force between the shaker and the satellite in the sine vibration test. The satellite was heavily instrumented in both the sine vibration and acoustic test in order to insure that the launch loads were enveloped with appropriate margin and that satellite responses did not exceed the compatibilities of the structure and equipment. The test specification, objectives, instrumentation, and test results are described herein.

Gravity localization in sine-Gordon braneworlds

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

Cruz, W.T., E-mail: wilamicruz@gmail.com; Maluf, R.V., E-mail: r.v.maluf@fisica.ufc.br; Sousa, L.J.S., E-mail: luisjose@fisica.ufc.br

2016-01-15

In this work we study two types of five-dimensional braneworld models given by sine-Gordon potentials. In both scenarios, the thick brane is generated by a real scalar field coupled to gravity. We focus our investigation on the localization of graviton field and the behaviour of the massive spectrum. In particular, we analyse the localization of massive modes by means of a relative probability method in a Quantum Mechanics context. Initially, considering a scalar field sine-Gordon potential, we find a localized state to the graviton at zero mode. However, when we consider a double sine-Gordon potential, the brane structure is changedmore » allowing the existence of massive resonant states. The new results show how the existence of an internal structure can aid in the emergence of massive resonant modes on the brane.« less

Application of the sine-Poisson equation in solar magnetostatics

NASA Technical Reports Server (NTRS)

Webb, G. M.; Zank, G. P.

1990-01-01

Solutions of the sine-Poisson equations are used to construct a class of isothermal magnetostatic atmospheres, with one ignorable coordinate corresponding to a uniform gravitational field in a plane geometry. The distributed current in the model (j) is directed along the x-axis, where x is the horizontal ignorable coordinate; (j) varies as the sine of the magnetostatic potential and falls off exponentially with distance vertical to the base with an e-folding distance equal to the gravitational scale height. Solutions for the magnetostatic potential A corresponding to the one-soliton, two-soliton, and breather solutions of the sine-Gordon equation are studied. Depending on the values of the free parameters in the soliton solutions, horizontally periodic magnetostatic structures are obtained possessing either a single X-type neutral point, multiple neural X-points, or solutions without X-points.

Modified hyperbolic sine model for titanium dioxide-based memristive thin films

NASA Astrophysics Data System (ADS)

Abu Bakar, Raudah; Syahirah Kamarozaman, Nur; Fazlida Hanim Abdullah, Wan; Herman, Sukreen Hana

2018-03-01

Since the emergence of memristor as the newest fundamental circuit elements, studies on memristor modeling have been evolved. To date, the developed models were based on the linear model, linear ionic drift model using different window functions, tunnelling barrier model and hyperbolic-sine function based model. Although using hyperbolic-sine function model could predict the memristor electrical properties, the model was not well fitted to the experimental data. In order to improve the performance of the hyperbolic-sine function model, the state variable equation was modified. On the one hand, the addition of window function cannot provide an improved fitting. By multiplying the Yakopcic’s state variable model to Chang’s model on the other hand resulted in the closer agreement with the TiO2 thin film experimental data. The percentage error was approximately 2.15%.

Scenario Based Approach for Multiple Source Tsunami Hazard Assessment for Sines, Portugal

NASA Astrophysics Data System (ADS)

Wronna, Martin; Omira, Rachid; Baptista, Maria Ana

2015-04-01

In this paper, we present a scenario-based approach for tsunami hazard assessment for the city and harbour of Sines, Portugal one the test-sites of project ASTARTE. Sines holds one of the most important deep-water ports which contains oil-bearing, petrochemical, liquid bulk, coal and container terminals. The port and its industrial infrastructures are facing the ocean to the southwest facing the main seismogenic sources. This work considers two different seismic zones: the Southwest Iberian Margin and the Gloria Fault. Within these two regions, a total of five scenarios were selected to assess tsunami impact at the test site. These scenarios correspond to the worst-case credible scenario approach based upon the largest events of the historical and paleo tsunami catalogues. The tsunami simulations from the source area towards the coast is carried out using NSWING a Non-linear Shallow Water Model With Nested Grids. The code solves the non-linear shallow water equations using the discretization and explicit leap-frog finite difference scheme, in a Cartesian or Spherical frame. The initial sea surface displacement is assumed to be equal to the sea bottom deformation that is computed by Okada equations. Both uniform and non-uniform slip conditions are used. The presented results correspond to the models using non-uniform slip conditions. In this study, the static effect of tides is analysed for three different tidal stages MLLW (mean lower low water) MSL (mean sea level) and MHHW (mean higher high water). For each scenario, inundation is described by maximum values of wave height, flow depth, drawdown, run-up and inundation distance. Synthetic waveforms are computed at virtual tide gages at specific locations outside and inside the harbour. The final results consist of Aggregate Scenario Maps presented for the different inundation parameters. This work is funded by ASTARTE - Assessment, Strategy And Risk Reduction for Tsunamis in Europe - FP7-ENV2013 6.4-3, Grant 603839

On-sky calibration performance of a monolithic Michelson interferometer filtered source

NASA Astrophysics Data System (ADS)

Ge, Jian; Ma, Bo; Powell, Scott; Varosi, Frank; Schofield, Sidney; Grieves, Nolan; Liu, Jian

2014-07-01

In the new era of searching for Earth-like planets, new generation radial velocity (RV) high resolution spectrographs requires ~0.1 m/s Doppler calibration accuracy in the visible band and a similar calibration precision in the near infrared. The patented stable monolithic Michelson interferometer filtered source called the Sine source emerges as a very promising calibration device. This Sine source has the potential of covering the practical working wavelengths (~0.38- 2.5 μm) for Doppler measurements with high resolution optical and near infrared high resolution spectrographs at the ground-based telescopes. The single frame calibration precision can reach < 0.1 m/s for the state of the art spectrographs, and it can be easily designed to match the intrinsic sensitivities of future Doppler instruments. The Sine source also has the great practical advantages in compact (portable) size and low cost. Here we report early results from on-sky calibration of a Sine source measured with two state-of-the-art TOU optical high resolution spectrograph (R=100,000, 0.38-0.9 microns) and FIRST near infrared spectrograph (R=50,000, 0.8-1.8 microns) at a 2 meter robotic telescope at Fairborn Observatory in Arizona. The results with the TOU spectrograph monitoring over seven days show that the Sine source has produced ~3 times better calibration precision than the ThAr calibration (RMS = 2.7m/s vs. 7.4m/s) at 0.49-0.62 microns where calibration data have been processed by our preliminary data pipeline and ~1.4 times better than the iodine absorption spectra (RMS=3.6 m/s) at the same wavelength region. As both ThAr and Iodine have reached sub m/s calibration accuracy with existing Doppler instruments (such as HARPS and HIRES), it is likely that the sine source would provide similar improvement once a better data pipeline and an upgraded version of a Sine source are developed. It is totally possible to reach ~0.1 m/s in the optical wavelength region. In addition, this Sine source offers potential very accurate calibration at 0.7-0.9 μm where ThAr lines are totally dominated by strong and saturated Argon lines and the ThAr calibration data are nearly useless. The early measurements with the FIRST near infrared spectrograph show that this Sine source produces very homogenous fringe modulations over 0.8-1.8 μm which can potentially provide better precision than the UrNe lamp for instrument drift measurements.

The Alaskan Mineral Resource Assessment Program; background information to accompany folio of geologic and mineral resource maps of the Circle quadrangle, Alaska

USGS Publications Warehouse

Foster, Helen Laura; Menzie, W.D.; Cady, J.W.; Simpson, S.L.; Aleinikoff, J.N.; Wilson, Frederic H.; Tripp, R.B.

1987-01-01

The geology, geochemistry, geophysics, and Landsat imagery of the Circle quadrangle were investigated by an interdisciplinary research team for the purpose of assessing the mineral potential of the area. The quadrangle covers approximately 15,765 km2 in east-central Alaska; most of it is included in the mountainous Yukon-Tanana Upland physiographic division, but the northernmost part is in the low-lying Yukon Flats section. The Circle mining district, in the east-central part of the quadrangle, has been a major producing area of placer gold since its discovery in 1893. For descriptive purposes, the Circle quadrangle is divided into three areas: the northwest Circle quadrangle, the area north of the Tintina fault zone, and the area south of the Tintina fault zone. The Tintina fault zone extends northwesterly through the northern part of the quadrangle. The northwest Circle quadrangle contains mostly folded and faulted, slightly metamorphosed sedimentary rocks that are intruded by Tertiary granitic plutons. In the northern part of the area north of the Tintina fault zone (Little Crazy Mountains and northern east Crazy Mountains), the rocks consist primarily of the gabbro and basalt of the Circle Volcanics and minor associated chert, graywacke, and limestone. Elsewhere in this area (south of the Circle Volcanics and in the western Crazy Mountains), the rocks are mostly slightly metamorphosed Paleozoic sedimentary rocks that have been folded and faulted. Rocks in the largest part of the quadrangle, the area south of the Tintina fault zone, consist largely of pelitic rocks that are regionally metamorphosed to greenschist and amphibolite facies. Felsic plutons, mostly Tertiary in age, occur throughout the area. The metamorphic rocks are separated from sedimentary rocks on the northwest by thrust faulting. The aeromagnetic and gravity data show clear differences between the areas north and south of the Tintina fault zone. The metamorphic terrane to the south has low overall gravity and local gravity lows over exposed granitic plutons. It is hypothesized that magnetic chlorite schist infolded with nonmagnetic quartzite and schist account for east-northeast-trending magnetic highs that approximately parallel the regional strike of the most prominent foliation in the metamorphic rocks. North of the Tintina fault zone, the Circle Volcanics are characterized by high gravity and east-west-trending magnetic highs. The Tintina fault zone has an intense magnetic high near the western margin of the Circle quadrangle overlying the magnetic granodiorite of the Victoria Mountain pluton. A magnetic high near Circle Hot Springs is less intense, but broader, and could reflect a buried magnetic pluton similar to that of the Victoria Mountain pluton. Computer-enhanced Landsat images of the Circle quadrangle show trends and patterns of concentrations of linear features. Features trending northeast-southwest predominate throughout the quadrangle; northwest-southeast-trending linear features are found mostly south of the Tintina fault zone. High concentrations of linear features were not found to correspond to areas of known mineralization in any consistent or significant way that could presently be used in locating areas of mineralization. Geochemical and mineralogical studies of stream sediment and heavy-mineral concentrates from the Circle quadrangle identify areas of anomalous concentrations of metallic elements, including gold, silver, tin, tungsten, lead, antimony, zinc, thorium, uranium, and beryllium. The data delineate areas of known mineral occurrences and areas that may contain undiscovered mineral resources. To date, placer gold has been the only significant metallic mineral resource from the Circle quadrangle, but the general geologic setting, especially the presence of post-orogenic plutons, is similar to that of regions that contain tin greisen deposits, tungsten skarn deposits, lode gold deposits in metasedimentary roc

Error analysis of mechanical system and wavelength calibration of monochromator

NASA Astrophysics Data System (ADS)

Zhang, Fudong; Chen, Chen; Liu, Jie; Wang, Zhihong

2018-02-01

This study focuses on improving the accuracy of a grating monochromator on the basis of the grating diffraction equation in combination with an analysis of the mechanical transmission relationship between the grating, the sine bar, and the screw of the scanning mechanism. First, the relationship between the mechanical error in the monochromator with the sine drive and the wavelength error is analyzed. Second, a mathematical model of the wavelength error and mechanical error is developed, and an accurate wavelength calibration method based on the sine bar's length adjustment and error compensation is proposed. Based on the mathematical model and calibration method, experiments using a standard light source with known spectral lines and a pre-adjusted sine bar length are conducted. The model parameter equations are solved, and subsequent parameter optimization simulations are performed to determine the optimal length ratio. Lastly, the length of the sine bar is adjusted. The experimental results indicate that the wavelength accuracy is ±0.3 nm, which is better than the original accuracy of ±2.6 nm. The results confirm the validity of the error analysis of the mechanical system of the monochromator as well as the validity of the calibration method.

Needle-array to Plate DBD Plasma Using Sine AC and Nanosecond Pulse Excitations for Purpose of Improving Indoor Air Quality

PubMed Central

Zhang, Li; Yang, Dezheng; Wang, Wenchun; Wang, Sen; Yuan, Hao; Zhao, Zilu; Sang, Chaofeng; Jia, Li

2016-01-01

In this study, needle-array to plate electrode configuration was employed to generate an atmospheric air diffuse discharge using both nanosecond pulse and sine AC voltage as excitation voltage for the purpose of improving indoor air quality. Different types of voltage sources and electrode configurations are employed to optimize electrical field distribution and improve discharge stability. Discharge images, electrical characteristics, optical emission spectra, and plasma gas temperatures in both sine AC discharge and nanosecond pulse discharge were compared and the discharge stability during long operating time were discussed. Compared with the discharge excited by sine AC voltage, the nanosecond pulsed discharge is more homogenous and stable, besides, the plasma gas temperature of nanosecond pulse discharge is much lower. Using packed-bed structure, where γ- Al2O3 pellets are filled in the electrode gap, has obvious efficacy in the production of homogenous discharge. Furthermore, both sine AC discharge and nanosecond pulse discharge were used for removing formaldehyde from flowing air. It shows that nanosecond pulse discharge has a significant advantage in energy cost. And the main physiochemical processes for the generation of active species and the degradation of formaldehyde were discussed. PMID:27125663

Wide-band doubler and sine wave quadrature generator

NASA Technical Reports Server (NTRS)

Crow, R. B.

1969-01-01

Phase-locked loop with photoresistive control, which provides both sine and cosine outputs for subcarrier demodulation, serves as a telemetry demodulator signal conditioner with a second harmonic signal for synchronization with the locally generated code.

The role of extreme orbits in the global organization of periodic regions in parameter space for one dimensional maps

NASA Astrophysics Data System (ADS)

da Costa, Diogo Ricardo; Hansen, Matheus; Guarise, Gustavo; Medrano-T, Rene O.; Leonel, Edson D.

2016-04-01

We show that extreme orbits, trajectories that connect local maximum and minimum values of one dimensional maps, play a major role in the parameter space of dissipative systems dictating the organization for the windows of periodicity, hence producing sets of shrimp-like structures. Here we solve three fundamental problems regarding the distribution of these sets and give: (i) their precise localization in the parameter space, even for sets of very high periods; (ii) their local and global distributions along cascades; and (iii) the association of these cascades to complicate sets of periodicity. The extreme orbits are proved to be a powerful indicator to investigate the organization of windows of periodicity in parameter planes. As applications of the theory, we obtain some results for the circle map and perturbed logistic map. The formalism presented here can be extended to many other different nonlinear and dissipative systems.

Phoenix's New Neighborhood

NASA Technical Reports Server (NTRS)

2008-01-01

The center of the red circle on this map shows where NASA's Phoenix Mars Lander eased down to the surface of Mars, at approximately 68 degrees north latitude, 234 degrees east longitude. Before Phoenix landed, engineers had predicted it would land within the blue ellipse.

Phoenix touched down on the Red Planet at 4:53 p.m. Pacific Time (7:53 p.m. Eastern Time), May 25, 2008, in an arctic region called Vastitas Borealis.

The map shows a color-coded interpretation of geomorphic units categories based on the surface textures and contours. The geomorphic mapping is overlaid on a shaded relief map based on data from the Mars Orbiter Laser Altimeter on NASA's Mars Global Surveyor orbiter.

The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

Surface Design Based on Discrete Conformal Transformations

NASA Astrophysics Data System (ADS)

Duque, Carlos; Santangelo, Christian; Vouga, Etienne

Conformal transformations are angle-preserving maps from one domain to another. Although angles are preserved, the lengths between arbitrary points are not generally conserved. As a consequence there is always a given amount of distortion associated to any conformal map. Different uses of such transformations can be found in various fields, but have been used by us to program non-uniformly swellable gel sheets to buckle into prescribed three dimensional shapes. In this work we apply circle packings as a kind of discrete conformal map in order to find conformal maps from the sphere to the plane that can be used as nearly uniform swelling patterns to program non-Euclidean sheets to buckle into spheres. We explore the possibility of tuning the area distortion to fit the experimental range of minimum and maximum swelling by modifying the boundary of the planar domain through the introduction of different cutting schemes.

Universal precision sine bar attachment

NASA Technical Reports Server (NTRS)

Mann, Franklin D. (Inventor)

1989-01-01

This invention relates to an attachment for a sine bar which can be used to perform measurements during lathe operations or other types of machining operations. The attachment can be used for setting precision angles on vises, dividing heads, rotary tables and angle plates. It can also be used in the inspection of machined parts, when close tolerances are required, and in the layout of precision hardware. The novelty of the invention is believed to reside in a specific versatile sine bar attachment for measuring a variety of angles on a number of different types of equipment.

[SINEs in mammalian genomes can serve as additional signals in formation of facultative heterochromatin].

PubMed

Usmanova, N M; Kazakov, V I; Tomilin, N V

2008-01-01

Using computer-based methods we determined the global distribution of short interspersed nuclear elements (SINEs) in the human and mouse X chromosomes. It has been shown that this distributions is similar to the distributions of CpG islands and genes but is different from the distribution of LINE1 elements. Since SINEs (human Alu and mouse B2) may have binding sites for Polycomb protein YY1, we suggest that these repeats can serve as additional signals ("boosters") in Polycomb-dependent silencing of gene rich segments during X inactivation.

Dynamics of generalized sine-Gordon soliton in inhomogeneous media

NASA Astrophysics Data System (ADS)

Gharaati, A.; Khordad, R.

2011-03-01

In this paper we introduce a few novel generalized sine-Gordon equations and study the dynamics of its solitons in inhomogeneous media. We consider length, mass, gravitational acceleration and spring stiffness of a coupled pendulums chain as a function of position x. Then in the continuum limit we derive semi-analytical and numerical soliton solutions of the modified sine-Gordon equation in the inhomogeneous media. The obtained results confirm that the behavior of solitons in these media is similar to that of a classical point particle moved in an external potential.

The magnetic map of hatchling loggerhead sea turtles.

PubMed

Lohmann, Kenneth J; Putman, Nathan F; Lohmann, Catherine M F

2012-04-01

Young loggerhead sea turtles (Caretta caretta) from eastern Florida, U.S.A., undertake a transoceanic migration in which they gradually circle the North Atlantic Ocean before returning to the North American coast. Hatchlings in the open sea are guided at least partly by a 'magnetic map' in which regional magnetic fields function as navigational markers and elicit changes in swimming direction at crucial locations along the migratory route. The magnetic map exists in turtles that have never migrated and thus appears to be inherited. Turtles derive both longitudinal and latitudinal information from the Earth's field, most likely by exploiting unique combinations of field inclination and intensity that occur in different geographic areas. Similar mechanisms may function in the migrations of diverse animals. Copyright © 2011 Elsevier Ltd. All rights reserved.

Restrictive bare stent prevents distal stent graft-induced new entry in endovascular repair of type B aortic dissection.

PubMed

Zhao, Yang; Yin, Henghui; Chen, Yitian; Wang, Mian; Zheng, Liang; Li, Zilun; Chang, Guangqi

2018-01-01

Distal stent graft-induced new entry (SINE) can occur after thoracic endovascular aortic repair (TEVAR) of type B aortic dissection. This study investigated the mechanism of distal SINE and its prevention using a restrictive bare stent (RBS) technique. From January 2013 to December 2014, 68 consecutive type B aortic dissection patients received endovascular repair at our center. The RBS technique was used with distal oversizing (between the diameter of the thoracic stent graft and the descending aorta true lumen diameter at the level of the intended distal edge of the thoracic stent graft) >20%. Twenty-three patients received TEVAR with a single thoracic stent graft (TEVAR group, n = 23); the rest received TEVAR combined with the RBS technique (TEVAR + RBS group, n = 45). Four distal SINEs occurred in the TEVAR group. Distal oversizing (69.7% ± 35.5% vs 31.2% ± 24.5%; P = .005) and expansion mismatch ratio (132.2% ± 16.9% vs 106.5% ± 11.6%; P < .05) were significantly higher in the SINE patients. Compared with standard TEVAR, TEVAR + RBS was associated with significantly lower distal oversizing (TEVAR vs TEVAR + RBS group, 59.8% ± 24.7% vs 16.7% ± 7.6%; P < .05), lower expansion mismatch ratio (113.8% ± 14.6% vs 103.8% ± 11.7%; P = .012), and lower distal SINE rate (4/23 [17.4%] vs 0/45 [0%]; P = .011). Compared with the TEVAR group, the false lumen was reduced significantly at the level of the RBS distal edge (P = .029). Excessive distal oversizing and distal expansion mismatch ratio may contribute to the occurrence of distal SINE. The RBS technique reduced the incidence of distal SINE. Based on our midterm and long-term observations, implantation of an RBS may improve aortic remodeling. Copyright © 2017 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Map-invariant spectral analysis for the identification of DNA periodicities

PubMed Central

2012-01-01

Many signal processing based methods for finding hidden periodicities in DNA sequences have primarily focused on assigning numerical values to the symbolic DNA sequence and then applying spectral analysis tools such as the short-time discrete Fourier transform (ST-DFT) to locate these repeats. The key results pertaining to this approach are however obtained using a very specific symbolic to numerical map, namely the so-called Voss representation. An important research problem is to therefore quantify the sensitivity of these results to the choice of the symbolic to numerical map. In this article, a novel algebraic approach to the periodicity detection problem is presented and provides a natural framework for studying the role of the symbolic to numerical map in finding these repeats. More specifically, we derive a new matrix-based expression of the DNA spectrum that comprises most of the widely used mappings in the literature as special cases, shows that the DNA spectrum is in fact invariable under all these mappings, and generates a necessary and sufficient condition for the invariance of the DNA spectrum to the symbolic to numerical map. Furthermore, the new algebraic framework decomposes the periodicity detection problem into several fundamental building blocks that are totally independent of each other. Sophisticated digital filters and/or alternate fast data transforms such as the discrete cosine and sine transforms can therefore be always incorporated in the periodicity detection scheme regardless of the choice of the symbolic to numerical map. Although the newly proposed framework is matrix based, identification of these periodicities can be achieved at a low computational cost. PMID:23067324

Generation of dark hollow beam by focusing a sine-Gaussian beam using a cylindrical lens and a focusing lens

NASA Astrophysics Data System (ADS)

Tang, Huiqin; Zhu, Kaicheng

2013-12-01

Based on the generalized Huygens-Fresnel diffraction integral, a closed-form propagation equation related to sine-Gaussian beams through a cylindrical lens and a focusing lens is derived and illustrated with numerical methods. It is found that a sine-Gaussian beam through such a system may be converted into a dark hollow beam (DHB) with topological charge index one and its bright enclosure is approximately an elongated ellipse with very high ellipticity. Moreover, the parameter values at which the DHBs have perfect intensity patterns are designed. The optimal relative orientation between the dislocation line of the input sine-Gaussian beam and the axial orientation of the cylindrical lens is specified. And the ellipticity of the elliptical DHBs is mainly defined by the focal length of the cylindrical lens and the Fresnel number of the optical system.

On the correct use of stepped-sine excitations for the measurement of time-varying bioimpedance.

PubMed

Louarroudi, E; Sanchez, B

2017-02-01

When a linear time-varying (LTV) bioimpedance is measured using stepped-sine excitations, a compromise must be made: the temporal distortions affecting the data depend on the experimental time, which in turn sets the data accuracy and limits the temporal bandwidth of the system that needs to be measured. Here, the experimental time required to measure linear time-invariant bioimpedance with a specified accuracy is analyzed for different stepped-sine excitation setups. We provide simple equations that allow the reader to know whether LTV bioimpedance can be measured through repeated time- invariant stepped-sine experiments. Bioimpedance technology is on the rise thanks to a plethora of healthcare monitoring applications. The results presented can help to avoid distortions in the data while measuring accurately non-stationary physiological phenomena. The impact of the work presented is broad, including the potential of enhancing bioimpedance studies and healthcare devices using bioimpedance technology.

Tropisms of Avena coleoptiles: sine law for gravitropism, exponential law for photogravitropic equilibrium.

PubMed

Galland, Paul

2002-09-01

The quantitative relation between gravitropism and phototropism was analyzed for light-grown coleoptiles of Avena sativa (L.). With respect to gravitropism the coleoptiles obeyed the sine law. To study the interaction between light and gravity, coleoptiles were inclined at variable angles and irradiated for 7 h with unilateral blue light (466 nm) impinging at right angles relative to the axis of the coleoptile. The phototropic stimulus was applied from the side opposite to the direction of gravitropic bending. The fluence rate that was required to counteract the negative gravitropism increased exponentially with the sine of the inclination angle. To achieve balance, a linear increase in the gravitropic stimulus required compensation by an exponential increase in the counteracting phototropic stimulus. The establishment of photogravitropic equilibrium during continuous unilateral irradiation is thus determined by two different laws: the well-known sine law for gravitropism and a novel exponential law for phototropism described in this work.

Analysis of torsional spectra of molecules with two internal C/3v/ rotors. III - Far-infrared and gas phase Raman spectra of dimethylamine-d0, -d3, and -d6

NASA Technical Reports Server (NTRS)

Durig, J. R.; Griffin, M. G.; Groner, P.

1977-01-01

The Raman spectra of gaseous dimethylamine-d0, -d3, and -d6 have been recorded between 0 and 4000/cm. The far-infrared spectra have been recorded between 300 and 100/cm. Considerable torsional data are reported and used to characterize the torsional potential function based on a semi-rigid model. The average effective V3 for the dimethylamines was found to be 1052 plus or minus 12/cm. The cos-cos coupling term was approximately 15% of the effective V3, whereas the sine-sine coupling term was of an order of magnitude smaller for (CH3)2NH and (CD3)2NH. However, for the mixed isotope the sine-sine term was found to be negligible and the cos-cos about one-half the value obtained for the other two isotopes.

Power law asymptotics in the creation of strange attractors in the quasi-periodically forced quadratic family

NASA Astrophysics Data System (ADS)

Ohlson Timoudas, Thomas

2017-12-01

Let Φ be a quasi-periodically forced quadratic map, where the rotation constant ω is a Diophantine irrational. A strange non-chaotic attractor (SNA) is an invariant (under Φ) attracting graph of a nowhere continuous measurable function ψ from the circle {T} to [0, 1] . This paper investigates how a smooth attractor degenerates into a strange one, as a parameter \

Short interspersed DNA elements and miRNAs: a novel hidden gene regulation layer in zebrafish?

PubMed

Scarpato, Margherita; Angelini, Claudia; Cocca, Ennio; Pallotta, Maria M; Morescalchi, Maria A; Capriglione, Teresa

2015-09-01

In this study, we investigated by in silico analysis the possible correlation between microRNAs (miRNAs) and Anamnia V-SINEs (a superfamily of short interspersed nuclear elements), which belong to those retroposon families that have been preserved in vertebrate genomes for millions of years and are actively transcribed because they are embedded in the 3' untranslated region (UTR) of several genes. We report the results of the analysis of the genomic distribution of these mobile elements in zebrafish (Danio rerio) and discuss their involvement in generating miRNA gene loci. The computational study showed that the genes predicted to bear V-SINEs can be targeted by miRNAs with a very high hybridization E-value. Gene ontology analysis indicates that these genes are mainly involved in metabolic, membrane, and cytoplasmic signaling pathways. Nearly all the miRNAs that were predicted to target the V-SINEs of these genes, i.e., miR-338, miR-9, miR-181, miR-724, miR-735, and miR-204, have been validated in similar regulatory roles in mammals. The large number of genes bearing a V-SINE involved in metabolic and cellular processes suggests that V-SINEs may play a role in modulating cell responses to different stimuli and in preserving the metabolic balance during cell proliferation and differentiation. Although they need experimental validation, these preliminary results suggest that in the genome of D. rerio, as in other TE families in vertebrates, the preservation of V-SINE retroposons may also have been favored by their putative role in gene network modulation.

Efficient use of bit planes in the generation of motion stimuli

NASA Technical Reports Server (NTRS)

Mulligan, Jeffrey B.; Stone, Leland S.

1988-01-01

The production of animated motion sequences on computer-controlled display systems presents a technical problem because large images cannot be transferred from disk storage to image memory at conventional frame rates. A technique is described in which a single base image can be used to generate a broad class of motion stimuli without the need for such memory transfers. This technique was applied to the generation of drifting sine-wave gratings (and by extension, sine wave plaids). For each drifting grating, sine and cosine spatial phase components are first reduced to 1 bit/pixel using a digital halftoning technique. The resulting pairs of 1-bit images are then loaded into pairs of bit planes of the display memory. To animate the patterns, the display hardware's color lookup table is modified on a frame-by-frame basis; for each frame the lookup table is set to display a weighted sum of the spatial sine and cosine phase components. Because the contrasts and temporal frequencies of the various components are mutually independent in each frame, the sine and cosine components can be counterphase modulated in temporal quadrature, yielding a single drifting grating. Using additional bit planes, multiple drifting gratings can be combined to form sine-wave plaid patterns. A large number of resultant plaid motions can be produced from a single image file because the temporal frequencies of all the components can be varied independently. For a graphics device having 8 bits/pixel, up to four drifting gratings may be combined, each having independently variable contrast and speed.

Mapping Inherited Fractures in the Critical Zone Using Seismic Anisotropy From Circular Surveys

NASA Astrophysics Data System (ADS)

Novitsky, Christopher G.; Holbrook, W. Steven; Carr, Bradley J.; Pasquet, Sylvain; Okaya, David; Flinchum, Brady A.

2018-04-01

Weathering and hydrological processes in Earth's shallow subsurface are influenced by inherited bedrock structures, such as bedding planes, faults, joints, and fractures. However, these structures are difficult to observe in soil-mantled landscapes. Steeply dipping structures with a dominant orientation are detectable by seismic anisotropy, with fast wave speeds along the strike of structures. We measured shallow ( 2-4 m) seismic anisotropy using "circle shots," geophones deployed in a circle around a central shot point, in a weathered granite terrain in the Laramie Range of Wyoming. The inferred remnant fracture orientations agree with brittle fracture orientations measured at tens of meters depth in boreholes, demonstrating that bedrock fractures persist through the weathering process into the shallow critical zone. Seismic anisotropy positively correlates with saprolite thickness, suggesting that inherited bedrock fractures may control saprolite thickness by providing preferential pathways for corrosive meteoric waters to access the deep critical zone.

Gamma-Ray "Raindrops" from Flaring Blazar

NASA Image and Video Library

2017-12-08

This visualization shows gamma rays detected during 3C 279's big flare by the LAT instrument on NASA's Fermi satellite. Gamma rays are represented as expanding circles reminiscent of raindrops on water. The flare is an abrupt shower of "rain" that trails off toward the end of the movie. Both the maximum size of the circle and its color represent the energy of the gamma ray, with white lowest and magenta highest. In a second version of the visualization, a background map shows how the LAT detects 3C 279 and other sources by accumulating high-energy photons over time (brighter squares reflect higher numbers of gamma rays). The movie starts on June 14 and ends June 17. The area shown is a region of the sky five degrees on a side and centered on the position of 3C 279. Read more: go.nasa.gov/1TqximF Credits: NASA/DOE/Fermi LAT Collaboration

Subcritical Multiplicative Chaos for Regularized Counting Statistics from Random Matrix Theory

NASA Astrophysics Data System (ADS)

Lambert, Gaultier; Ostrovsky, Dmitry; Simm, Nick

2018-05-01

For an {N × N} Haar distributed random unitary matrix U N , we consider the random field defined by counting the number of eigenvalues of U N in a mesoscopic arc centered at the point u on the unit circle. We prove that after regularizing at a small scale {ɛN > 0}, the renormalized exponential of this field converges as N \\to ∞ to a Gaussian multiplicative chaos measure in the whole subcritical phase. We discuss implications of this result for obtaining a lower bound on the maximum of the field. We also show that the moments of the total mass converge to a Selberg-like integral and by taking a further limit as the size of the arc diverges, we establish part of the conjectures in Ostrovsky (Nonlinearity 29(2):426-464, 2016). By an analogous construction, we prove that the multiplicative chaos measure coming from the sine process has the same distribution, which strongly suggests that this limiting object should be universal. Our approach to the L 1-phase is based on a generalization of the construction in Berestycki (Electron Commun Probab 22(27):12, 2017) to random fields which are only asymptotically Gaussian. In particular, our method could have applications to other random fields coming from either random matrix theory or a different context.

Alternative Proofs for Inequalities of Some Trigonometric Functions

ERIC Educational Resources Information Center

Guo, Bai-Ni; Qi, Feng

2008-01-01

By using an identity relating to Bernoulli's numbers and power series expansions of cotangent function and logarithms of functions involving sine function, cosine function and tangent function, four inequalities involving cotangent function, sine function, secant function and tangent function are established.

Electro-mechanical sine/cosine generator

NASA Technical Reports Server (NTRS)

Flagge, B. (Inventor)

1972-01-01

An electromechanical device for generating both sine and cosine functions is described. A motor rotates a cylinder about an axis parallel to and a slight distance from the central axis of the cylinder. Two noncontacting displacement sensing devices are placed ninety degrees apart, equal distances from the axis of rotation of the cylinder and short distances above the surface of cylinder. Each of these sensing devices produces an electrical signal proportional to the distance that it is away from the cylinder. Consequently, as the cylinder is rotated the outputs from the two sensing devices are the sine and cosine functions.

On the Monge-Ampere equivalent of the sine-Gordon equation

NASA Astrophysics Data System (ADS)

Ferapontov, E. V.; Nutku, Y.

1994-12-01

Surfaces of constant negative curvature in Euclidean space can be described by either the sine-Gordon equation for the angle between asymptotic directions, or a Monge-Ampere equation for the graph of the surface. We present the explicit form of the correspondence between these two integrable non-linear partial differential equations using their well-known properties in differential geometry. We find that the cotangent of the angle between asymptotic directions is directly related to the mean curvature of the surface. This is a Backlund-type transformation between the sine-Gordon and Monge-Ampere equations.

Details of Retropositional Genome Dynamics That Provide a Rationale for a Generic Division: The Distinct Branching of All the Pacific Salmon and Trout (Oncorhynchus) from the Atlantic Salmon and Trout (Salmo)

PubMed Central

Murata, S.; Takasaki, N.; Saitoh, M.; Tachida, H.; Okada, N.

1996-01-01

Salmonid species contain numerous short interspersed repetitive elements (SINEs), known collectively as the HpaI family, in their genomes. Amplification and successive integration of individual SINEs into the genomes have occurred during the evolution of salmonids. We reported previously a strategy for determining the phylogenetic relationships among the Pacific salmonids in which these SINEs were used as temporal landmarks of evolution. Here, we provide evidence for extensive genomic rearrangements that involved retropositions and deletions in a common ancestor of all the Pacific salmon and trout. Our results provide genetic support for the recent phylogenetic reassignment of steelhead and related species from the genus Salmo to the genus Oncorhynchus. Several other informative loci identified by insertions of HpaI SINEs have been isolated, and previously proposed branching orders of the Oncorhynchus species have been confirmed. The authenticity of our phylogenetic tree is supported both by the isolation of more than two informative loci per branching point and by the congruence of all our data, which suggest that the period between succesive speciations was sufficiently long for each SINE that had been amplified in the original species to become fixed in all individuals of that species. PMID:8849897

Conjunctival amelanotic malignant melanoma arising in primary acquired melanosis sine pigmento.

PubMed

Jay, V; Font, R L

1998-01-01

The authors describe an amelanotic malignant melanoma of the conjunctiva in association with primary acquired melanosis (PAM) sine pigmento, and highlight the clinical and pathologic features of this rare entity. Histopathologic and immunohistochemical studies were performed on a conjunctival tumor in a 54-year-old white woman. Case report. Histopathologic examination revealed an invasive amelanotic melanoma of the conjunctiva, with anterior orbital extension arising from intraepithelial dysplastic melanocytes that lacked melanin pigment (PAM sine pigmento). Both the malignant melanoma cells and the intraepithelial dysplastic melanocytes in the areas of PAM exhibited S-100 and HMB-45 positivity. The patient underwent an orbital exenteration that disclosed tumor within the anterior orbit inferiorly. Amelanotic invasive malignant melanoma can arise in association with PAM sine pigmento, as seen in our patient who had orbital invasion necessitating exenteration. This aggressive form of conjunctival melanoma is often associated with a poor prognosis and risk of metastatic disease. Absence of conjunctival pigmentation in PAM sine pigmento prevents early clinical detection of this variant of PAM. This lack of pigmentation also makes clinical diagnosis virtually impossible, and diagnosis can only be established histopathologically. Awareness of this nonpigmented variety of PAM is crucial for early recognition and appropriate management of the associated melanoma.

Benjamin Banneker and the Law of Sines

ERIC Educational Resources Information Center

Mahoney, John F.

2005-01-01

Benjamin Banneker, a self-taught mathematician, surveyor and astronomer published annual almanacs containing his astronomical observations and predictions. Banneker who also used logarithms to apply the Law of Sines believed that the method used to solve a mathematical problem depends on the tools available.

Expansion of CORE-SINEs in the genome of the Tasmanian devil

PubMed Central

2012-01-01

Background The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons. Results The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago. Conclusions The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome. PMID:22559330

Expansion of CORE-SINEs in the genome of the Tasmanian devil.

PubMed

Nilsson, Maria A; Janke, Axel; Murchison, Elizabeth P; Ning, Zemin; Hallström, Björn M

2012-05-06

The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species' survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons. The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago. The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.

Pharmacological treatment with inhibitors of nuclear export enhances the antitumor activity of docetaxel in human prostate cancer

PubMed Central

Gravina, Giovanni Luca; Mancini, Andrea; Colapietro, Alessandro; Marampon, Francesco; Sferra, Roberta; Pompili, Simona; Biordi, Leda Assunta; Iorio, Roberto; Flati, Vincenzo; Argueta, Christian; Landesman, Yosef; Kauffman, Michael; Shacham, Sharon; Festuccia, Claudio

2017-01-01

Background and aims Docetaxel (DTX) modestly increases patient survival of metastatic castration-resistant prostate cancer (mCRPC) due to insurgence of pharmacological resistance. Deregulation of Chromosome Region Maintenance (CRM-1)/ exportin-1 (XPO-1)-mediated nuclear export may play a crucial role in this phenomenon. Material and methods Here, we evaluated the effects of two Selective Inhibitor of Nuclear Export (SINE) compounds, selinexor (KPT-330) and KPT-251, in association with DTX by using 22rv1, PC3 and DU145 cell lines with their. DTX resistant derivatives. Results and conclusions We show that DTX resistance may involve overexpression of β-III tubulin (TUBB3) and P-glycoprotein as well as increased cytoplasmic accumulation of Foxo3a. Increased levels of XPO-1 were also observed in DTX resistant cells suggesting that SINE compounds may modulate DTX effectiveness in sensitive cells as well as restore the sensitivity to DTX in resistant ones. Pretreatment with SINE compounds, indeed, sensitized to DTX through increased tumor shrinkage and apoptosis by preventing DTX-induced cell cycle arrest. Basally SINE compounds induce FOXO3a activation and nuclear accumulation increasing the expression of FOXO-responsive genes including p21, p27 and Bim causing cell cycle arrest. SINE compounds-catenin and survivin supporting apoptosis. βdown-regulated Cyclin D1, c-myc, Nuclear sequestration of p-Foxo3a was able to reduce ABCB1 and TUBB3 H2AX levels, prolonged γ expression. Selinexor treatment increased DTX-mediated double strand breaks (DSB), and reduced the levels of DNA repairing proteins including DNA PKc and Topo2A. Our results provide supportive evidence for the therapeutic use of SINE compounds in combination with DTX suggesting their clinical use in mCRPC patients. PMID:29340049

A Decision-Support System for Sustainable Water Distribution System Planning.

PubMed

Freund, Alina; Aydin, Nazli Yonca; Zeckzer, Dirk; Hagen, Hans

2017-01-01

An interactive decision-support system (DSS) can help experts prepare water resource management plans for decision makers and stakeholders. The design of the proposed prototype incorporates visualization techniques such as circle views, grid layout, small multiple maps, and node simplification to improve the data readability of water distribution systems. A case study with three urban water management and sanitary engineering experts revealed that the proposed DSS is satisfactory, efficient, and effective.

Basic Lessons in ORA and AutoMap 2011

DTIC Science & Technology

2011-06-13

A small legend also appears. Below is a screen capture showing the visualization of the agent x event graph from the Stargate Summit Meta-Network...4 The visualization displays the connections between all items in the Stargate Summit Meta-Network. The red circles represent the agents, the...It takes the examples I used for the Stargate dataset. 5 lessons - 201-207 A step by step run through of creating the Meta-Network from

The Stability of Periodic Orbits.

DTIC Science & Technology

1981-01-21

first class, the new stable orbit has a fundamental frequency equal to half that of the original orbit. Thesebifurcations (for which one real...eigenvalue of the Poincare map passes out through the unit circle at -1 : see Appendix 1) 9,10 are observed and are referred to as subharmonic or period...doubling bifurcations. At such a bifurcation componenns of x(t) with a frequency -8- equal to half that of the original longitudinal motion grow

Zernike analysis of all-sky night brightness maps.

PubMed

Bará, Salvador; Nievas, Miguel; Sánchez de Miguel, Alejandro; Zamorano, Jaime

2014-04-20

All-sky night brightness maps (calibrated images of the night sky with hemispherical field-of-view (FOV) taken at standard photometric bands) provide useful data to assess the light pollution levels at any ground site. We show that these maps can be efficiently described and analyzed using Zernike circle polynomials. The relevant image information can be compressed into a low-dimensional coefficients vector, giving an analytical expression for the sky brightness and alleviating the effects of noise. Moreover, the Zernike expansions allow us to quantify in a straightforward way the average and zenithal sky brightness and its variation across the FOV, providing a convenient framework to study the time course of these magnitudes. We apply this framework to analyze the results of a one-year campaign of night sky brightness measurements made at the UCM observatory in Madrid.

A new chaotic multi-verse optimization algorithm for solving engineering optimization problems

NASA Astrophysics Data System (ADS)

Sayed, Gehad Ismail; Darwish, Ashraf; Hassanien, Aboul Ella

2018-03-01

Multi-verse optimization algorithm (MVO) is one of the recent meta-heuristic optimization algorithms. The main inspiration of this algorithm came from multi-verse theory in physics. However, MVO like most optimization algorithms suffers from low convergence rate and entrapment in local optima. In this paper, a new chaotic multi-verse optimization algorithm (CMVO) is proposed to overcome these problems. The proposed CMVO is applied on 13 benchmark functions and 7 well-known design problems in the engineering and mechanical field; namely, three-bar trust, speed reduce design, pressure vessel problem, spring design, welded beam, rolling element-bearing and multiple disc clutch brake. In the current study, a modified feasible-based mechanism is employed to handle constraints. In this mechanism, four rules were used to handle the specific constraint problem through maintaining a balance between feasible and infeasible solutions. Moreover, 10 well-known chaotic maps are used to improve the performance of MVO. The experimental results showed that CMVO outperforms other meta-heuristic optimization algorithms on most of the optimization problems. Also, the results reveal that sine chaotic map is the most appropriate map to significantly boost MVO's performance.

Optimum aerodynamic design via boundary control

NASA Technical Reports Server (NTRS)

Jameson, Antony

1994-01-01

These lectures describe the implementation of optimization techniques based on control theory for airfoil and wing design. In previous studies it was shown that control theory could be used to devise an effective optimization procedure for two-dimensional profiles in which the shape is determined by a conformal transformation from a unit circle, and the control is the mapping function. Recently the method has been implemented in an alternative formulation which does not depend on conformal mapping, so that it can more easily be extended to treat general configurations. The method has also been extended to treat the Euler equations, and results are presented for both two and three dimensional cases, including the optimization of a swept wing.

Long-life electromechanical sine-cosine generator

NASA Technical Reports Server (NTRS)

Flagge, B.

1971-01-01

Sine-cosine generator with no sliding parts is capable of withstanding a 20 Hz oscillation for more than 14 hours. Tests show that generator is electrically equal to potentiometer and that it has excellent dynamic characteristics. Generator shows promise of higher-speed applications than was previously possible.

[Non-LTR retrotransposons: LINEs and SINEs in plant genome].

PubMed

Cheng, Xu-Dong; Ling, Hong-Qing

2006-06-01

Retrotransposons are one of the drivers of genome evolution. They include LTR (long terminal repeat) retrotransposons, which widespread in Eukaryotagenomes, show structural similarity to retroviruses. Non-LTR retrotransposons were first discovered in animal genomes and then identified as ubiquitous components of nuclear genomes in many species across the plant kingdom. They constitute a large fraction of the repetitive DNA. Non-LTR retrotransposons are divided into LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements). Transposition of non-LTR retrotransposons is rarely observed in plants indicating that most of them are inactive and/or under regulation of the host genome. Transposition is poorly understood, but experimental evidence from other genetic systems shows that LINEs are able to transpose autonomously while non-autonomous SINEs depend on the reverse transcription machinery of other retrotransposons. Phylogenic analysis shows LINEs are probably the most ancient class of retrotransposons in plant genomes, while the origin of SINEs is unknown. This review sums up the above data and wants to show readers a clear picture of non-LTR retrotransposons.

Removal of Stationary Sinusoidal Noise from Random Vibration Signals.

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

Johnson, Brian; Cap, Jerome S.

In random vibration environments, sinusoidal line noise may appear in the vibration signal and can affect analysis of the resulting data. We studied two methods which remove stationary sine tones from random noise: a matrix inversion algorithm and a chirp-z transform algorithm. In addition, we developed new methods to determine the frequency of the tonal noise. The results show that both of the removal methods can eliminate sine tones in prefabricated random vibration data when the sine-to-random ratio is at least 0.25. For smaller ratios down to 0.02 only the matrix inversion technique can remove the tones, but the metricsmore » to evaluate its effectiveness also degrade. We also found that using fast Fourier transforms best identified the tonal noise, and determined that band-pass-filtering the signals prior to the process improved sine removal. When applied to actual vibration test data, the methods were not as effective at removing harmonic tones, which we believe to be a result of mixed-phase sinusoidal noise.« less

Determinism and randomness in the evolution of introns and sine inserts in mouse and human mitochondrial solute carrier and cytokine receptor genes.

PubMed

Cianciulli, Antonia; Calvello, Rosa; Panaro, Maria A

2015-04-01

In the homologous genes studied, the exons and introns alternated in the same order in mouse and human. We studied, in both species: corresponding short segments of introns, whole corresponding introns and complete homologous genes. We considered the total number of nucleotides and the number and orientation of the SINE inserts. Comparisons of mouse and human data series showed that at the level of individual relatively short segments of intronic sequences the stochastic variability prevails in the local structuring, but at higher levels of organization a deterministic component emerges, conserved in mouse and human during the divergent evolution, despite the ample re-editing of the intronic sequences and the fact that processes such as SINE spread had taken place in an independent way in the two species. Intron conservation is negatively correlated with the SINE occupancy, suggesting that virus inserts interfere with the conservation of the sequences inherited from the common ancestor. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characterization of short interspersed elements (SINEs) in a red alga, Porphyra yezoensis.

PubMed

Zhang, Wenbo; Lin, Xiaofei; Peddigari, Suresh; Takechi, Katsuaki; Takano, Hiroyoshi; Takio, Susumu

2007-02-01

Short interspersed element (SINE)-like sequences referred to as PySN1 and PySN2 were identified in a red alga, Porphyra yezoensis. Both elements contained an internal promoter with motifs (A box and B box) recognized by RNA polymerase III, and target site duplications at both ends. Genomic Southern blot analysis revealed that both elements were widely and abundantly distributed on the genome. 3' and 5' RACE suggested that PySN1 was expressed as a chimera transcript with flanking SINE-unrelated sequences and possessed the poly-A tail at the same position near the 3' end of PySN1.

Sine-Bar Attachment For Machine Tools

NASA Technical Reports Server (NTRS)

Mann, Franklin D.

1988-01-01

Sine-bar attachment for collets, spindles, and chucks helps machinists set up quickly for precise angular cuts that require greater precision than provided by graduations of machine tools. Machinist uses attachment to index head, carriage of milling machine or lathe relative to table or turning axis of tool. Attachment accurate to 1 minute or arc depending on length of sine bar and precision of gauge blocks in setup. Attachment installs quickly and easily on almost any type of lathe or mill. Requires no special clamps or fixtures, and eliminates many trial-and-error measurements. More stable than improvised setups and not jarred out of position readily.

Structural Qualification Testing of the WindSat Payload Using Sine Bursts Near Structural Resonance

NASA Technical Reports Server (NTRS)

Pontius, Jim; Barnes, Donald; Broduer, Steve (Technical Monitor)

2001-01-01

Sine burst tests are often used for structural qualification of space flight hardware. In most instances, the driving frequency of the shaker is specified far below the structure's first resonant mode, such that the entire test article sees uniform acceleration. For large structures, this limits qualification testing to lower parts of the structure, or else it over-tests the lower structure to achieve qualification of the upper structure. The WindSat payload, a 10.5 foot tall graphite/epoxy, titanium, and aluminum radiometer, experiences accelerations at the six foot diameter reflector nearly four times that at the spacecraft interface. Due to size of the payload, the number of bonded joints, and the lightweight reflector support structure design and construction, using static pull testing to qualify all of the bonded joints in the upper structure would result in large, expensive, and extensive test fixturing. Sine burst testing near the first two structural resonant modes was performed on the WindSat payload to achieve the correct load factor distribution up the stack for structural qualification. In this presentation, how finite element method (FEM) sine burst predictions were used in conjunction with low level random and sine burst tests to achieve correct qualification test load factor distribution on the WindSat payload is discussed. Also presented is the risk mitigation approach for using the uncorrelated FEM in this procedure.

Short interspersed CAN SINE elements as prognostic markers in canine mammary neoplasia.

PubMed

Gelaleti, Gabriela B; Granzotto, Adriana; Leonel, Camila; Jardim, Bruna V; Moschetta, Marina G; Carareto, Claudia M A; Zuccari, Debora Ap P C

2014-01-01

The genome of mammals is characterized by a large number of non-LTR retrotransposons, and among them, the CAN SINEs are characteristics of the canine species. Small amounts of DNA freely circulate in normal blood serum and high amounts are found in human patients with cancer, characterizing it as a candidate tumor-biomarker. The aim of this study was to estimate, through its absolute expression, the number of copies of CAN SINE sequences present in free circulating DNA of female dogs with mammary cancer, in order to correlate with the clinical and pathological characteristics and the follow-up period. The copy number of CAN SINE sequences was estimated by qPCR in 28 female dogs with mammary neoplasia. The univariate analysis showed an increased number of copies in female dogs with mammary tumor in female dogs >10 years old (p=0.02) and tumor time >18 months (p<0.05). The Kaplan-Meier test demonstrated a negative correlation between an increased number of copies and survival time (p=0.03). High amounts of CAN SINE fragments can be good markers for the detection of tumor DNA in blood and may characterize it as a marker of poor prognosis, being related to female dogs with shorter survival times. This estimate can be used as a prognostic marker in non-invasive breast cancer research and is useful in predicting tumor progression and patient monitoring.

A method for quantification of exportin-1 (XPO1) occupancy by Selective Inhibitor of Nuclear Export (SINE) compounds

PubMed Central

Crochiere, Marsha L.; Baloglu, Erkan; Klebanov, Boris; Donovan, Scott; del Alamo, Diego; Lee, Margaret; Kauffman, Michael; Shacham, Sharon; Landesman, Yosef

2016-01-01

Selective Inhibitor of Nuclear Export (SINE) compounds are a family of small-molecules that inhibit nuclear export through covalent binding to cysteine 528 (Cys528) in the cargo-binding pocket of Exportin 1 (XPO1/CRM1) and promote cancer cell death. Selinexor is the lead SINE compound currently in phase I and II clinical trials for advanced solid and hematological malignancies. In an effort to understand selinexor-XPO1 interaction and to establish whether cancer cell response is a function of drug-target engagement, we developed a quantitative XPO1 occupancy assay. Biotinylated leptomycin B (b-LMB) was utilized as a tool compound to measure SINE-free XPO1. Binding to XPO1 was quantitated from SINE compound treated adherent and suspension cells in vitro, dosed ex vivo human peripheral blood mononuclear cells (PBMCs), and PBMCs from mice dosed orally with drug in vivo. Evaluation of a panel of selinexor sensitive and resistant cell lines revealed that resistance was not attributed to XPO1 occupancy by selinexor. Administration of a single dose of selinexor bound XPO1 for minimally 72 hours both in vitro and in vivo. While XPO1 inhibition directly correlates with selinexor pharmacokinetics, the biological outcome of this inhibition depends on modulation of pathways downstream of XPO1, which ultimately determines cancer cell responsiveness. PMID:26654943

Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts.

PubMed Central

Liu, W M; Chu, W M; Choudary, P V; Schmid, C W

1995-01-01

The abundance of Alu RNA is transiently increased by heat shock in human cell lines. This effect is specific to Alu repeats among Pol III transcribed genes, since the abundance of 7SL, 7SK, 5S and U6 RNAs is essentially unaffected by heat shock. The rapid induction of Alu expression precedes the heat shock induction of mRNAs for the ubiquitin and HSP 70 heat shock genes. Heat shock mimetics also transiently induce Alu expression indicating that increased Alu expression is a general cell-stress response. Cycloheximide treatment rapidly and transiently increases the abundance of Alu RNA. Again, compared with other genes transcribed by Pol III, this increase is specific to Alu. However, as distinguished from the cell stress response, cycloheximide does not induce expression of HSP 70 and ubiquitin mRNAs. Puromycin also increases Alu expression, suggesting that this response is generally caused by translational inhibition. The response of mammalian SINEs to cell stress and translational inhibition is not limited to SINEs which are Alu homologues. Heat shock and cycloheximide each transiently induce Pol III directed expression of B1 and B2 RNAs in mouse cells and C-element RNA in rabbit cells. Together, these three species exemplify the known SINE composition of placental mammals, suggesting that mammalian SINEs are similarly regulated and may serve a common function. Images PMID:7784180

Explicitly solvable complex Chebyshev approximation problems related to sine polynomials

NASA Technical Reports Server (NTRS)

Freund, Roland

1989-01-01

Explicitly solvable real Chebyshev approximation problems on the unit interval are typically characterized by simple error curves. A similar principle is presented for complex approximation problems with error curves induced by sine polynomials. As an application, some new explicit formulae for complex best approximations are derived.

Toward Universal Forward Genetics: Using a Draft Genome Sequence of the Nematode Oscheius tipulae To Identify Mutations Affecting Vulva Development

PubMed Central

Besnard, Fabrice; Koutsovoulos, Georgios; Dieudonné, Sana; Blaxter, Mark; Félix, Marie-Anne

2017-01-01

Mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations in model species. Here, we show that a fragmented draft assembly is sufficient to perform mapping-by-sequencing in nonmodel species. We generated a draft assembly and annotation of the genome of the free-living nematode Oscheius tipulae, a distant relative of the model Caenorhabditis elegans. We used this draft to identify the likely causative mutations at the O. tipulae cov-3 locus, which affect vulval development. The cov-3 locus encodes the O. tipulae ortholog of C. elegans mig-13, and we further show that Cel-mig-13 mutants also have an unsuspected vulval-development phenotype. In a virtuous circle, we were able to use the linkage information collected during mutant mapping to improve the genome assembly. These results showcase the promise of genome-enabled forward genetics in nonmodel species. PMID:28630114

Toward Universal Forward Genetics: Using a Draft Genome Sequence of the Nematode Oscheius tipulae To Identify Mutations Affecting Vulva Development.

PubMed

Besnard, Fabrice; Koutsovoulos, Georgios; Dieudonné, Sana; Blaxter, Mark; Félix, Marie-Anne

2017-08-01

Mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations in model species. Here, we show that a fragmented draft assembly is sufficient to perform mapping-by-sequencing in nonmodel species. We generated a draft assembly and annotation of the genome of the free-living nematode Oscheius tipulae , a distant relative of the model Caenorhabditis elegans We used this draft to identify the likely causative mutations at the O. tipulae cov -3 locus, which affect vulval development. The cov-3 locus encodes the O. tipulae ortholog of C. elegans mig-13 , and we further show that Cel-mig-13 mutants also have an unsuspected vulval-development phenotype. In a virtuous circle, we were able to use the linkage information collected during mutant mapping to improve the genome assembly. These results showcase the promise of genome-enabled forward genetics in nonmodel species. Copyright © 2017 by the Genetics Society of America.

A robust color image watermarking algorithm against rotation attacks

NASA Astrophysics Data System (ADS)

Han, Shao-cheng; Yang, Jin-feng; Wang, Rui; Jia, Gui-min

2018-01-01

A robust digital watermarking algorithm is proposed based on quaternion wavelet transform (QWT) and discrete cosine transform (DCT) for copyright protection of color images. The luminance component Y of a host color image in YIQ space is decomposed by QWT, and then the coefficients of four low-frequency subbands are transformed by DCT. An original binary watermark scrambled by Arnold map and iterated sine chaotic system is embedded into the mid-frequency DCT coefficients of the subbands. In order to improve the performance of the proposed algorithm against rotation attacks, a rotation detection scheme is implemented before watermark extracting. The experimental results demonstrate that the proposed watermarking scheme shows strong robustness not only against common image processing attacks but also against arbitrary rotation attacks.

Integrability and chemical potential in the (3 + 1)-dimensional Skyrme model

NASA Astrophysics Data System (ADS)

Alvarez, P. D.; Canfora, F.; Dimakis, N.; Paliathanasis, A.

2017-10-01

Using a remarkable mapping from the original (3 + 1)dimensional Skyrme model to the Sine-Gordon model, we construct the first analytic examples of Skyrmions as well as of Skyrmions-anti-Skyrmions bound states within a finite box in 3 + 1 dimensional flat space-time. An analytic upper bound on the number of these Skyrmions-anti-Skyrmions bound states is derived. We compute the critical isospin chemical potential beyond which these Skyrmions cease to exist. With these tools, we also construct topologically protected time-crystals: time-periodic configurations whose time-dependence is protected by their non-trivial winding number. These are striking realizations of the ideas of Shapere and Wilczek. The critical isospin chemical potential for these time-crystals is determined.

Dimensional synthesis of a 3-DOF parallel manipulator with full circle rotation

NASA Astrophysics Data System (ADS)

Ni, Yanbing; Wu, Nan; Zhong, Xueyong; Zhang, Biao

2015-07-01

Parallel robots are widely used in the academic and industrial fields. In spite of the numerous achievements in the design and dimensional synthesis of the low-mobility parallel robots, few research efforts are directed towards the asymmetric 3-DOF parallel robots whose end-effector can realize 2 translational and 1 rotational(2T1R) motion. In order to develop a manipulator with the capability of full circle rotation to enlarge the workspace, a new 2T1R parallel mechanism is proposed. The modeling approach and kinematic analysis of this proposed mechanism are investigated. Using the method of vector analysis, the inverse kinematic equations are established. This is followed by a vigorous proof that this mechanism attains an annular workspace through its circular rotation and 2 dimensional translations. Taking the first order perturbation of the kinematic equations, the error Jacobian matrix which represents the mapping relationship between the error sources of geometric parameters and the end-effector position errors is derived. With consideration of the constraint conditions of pressure angles and feasible workspace, the dimensional synthesis is conducted with a goal to minimize the global comprehensive performance index. The dimension parameters making the mechanism to have optimal error mapping and kinematic performance are obtained through the optimization algorithm. All these research achievements lay the foundation for the prototype building of such kind of parallel robots.

Demystifying rotors and their place in clinical translation of atrial fibrillation mechanisms.

PubMed

Nattel, Stanley; Xiong, Feng; Aguilar, Martin

2017-09-01

Treatment of atrial fibrillation (AF), the most common arrhythmia in clinical practice, remains challenging. Improved understanding of underlying mechanisms is needed to improve therapy. Functional re-entry is central to AF maintenance. The first detailed, quantitative theory of functional re-entry, the 'leading circle' model, was developed 40 years ago. Subsequently, an alternative paradigm based on 'spiral waves' has evolved. Spiral-wave generators, or 'rotors', have been identified using advanced mapping methods in experimental and clinical AF. A central tool in the analysis of spiral-wave rotors is the phase transformation, allowing for easier visualization of rotors and tracking of 'phase singularity' points at the rotor tip. In contrast to leading circle theory, which is expressed in terms familiar to (and easily understood by) cardiologists, the ideas needed to understand rotors are much more theoretical and harder for clinicians to apply. In this Review, we summarize the basic notions of phase mapping and spiral-wave rotors, and the ways in which rotor sources might be involved in AF maintenance. We discuss competing observations about the role of spatially confined rotors, short-lived rotors clustered at the edge of fibrotic zones, endocardial-epicardial interactive breeder properties and transmural re-entry, as well as studies underway to resolve them. We conclude with consideration of the clinical relevance of the issues discussed and their potential implications for the management of patients with AF.

The development of sine vibration test requirements for Viking lander capsule components

NASA Technical Reports Server (NTRS)

Barrett, S.

1974-01-01

In connection with the Viking project for exploring the planet Mars, two identical spacecraft, each consisting of an orbiter and a lander, will be launched in the third quarter of 1975. Upon arrival at the planet, the Viking lander will separate from the Viking orbiter and descend to a soft landing at a selected site on the Mars surface. It was decided to perform a sine vibration test on the Viking spacecraft, in its launch configuration, to qualify it for the booster-induced transient-dynamic environment. It is shown that component-level testing is a cost- and schedule-effective prerequisite to the system-level, sine-vibration test sequences.

Truncated Painlevé expansion: Tanh-traveling wave solutions and reduction of sine-Poisson equation to a quadrature for stationary and nonstationary three-dimensional collisionless cold plasma

NASA Astrophysics Data System (ADS)

Ibrahim, R. S.; El-Kalaawy, O. H.

2006-10-01

The relativistic nonlinear self-consistent equations for a collisionless cold plasma with stationary ions [R. S. Ibrahim, IMA J. Appl. Math. 68, 523 (2003)] are extended to 3 and 3+1 dimensions. The resulting system of equations is reduced to the sine-Poisson equation. The truncated Painlevé expansion and reduction of the partial differential equation to a quadrature problem (RQ method) are described and applied to obtain the traveling wave solutions of the sine-Poisson equation for stationary and nonstationary equations in 3 and 3+1 dimensions describing the charge-density equilibrium configuration model.

TU-H-CAMPUS-IeP3-02: Neurovascular 4D Parametric Imaging Using Co-Registration of Biplane DSA Sequences with 3D Vascular Geometry Obtained From Cone Beam CT

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

Balasubramoniam, A; Bednarek, D; Rudin, S

Purpose: To create 4D parametric images using biplane Digital Subtraction Angiography (DSA) sequences co-registered with the 3D vascular geometry obtained from Cone Beam-CT (CBCT). Methods: We investigated a method to derive multiple 4D Parametric Imaging (PI) maps using only one CBCT acquisition. During this procedure a 3D-DSA geometry is stored and used subsequently for all 4D images. Each time a biplane DSA is acquired, we calculate 2D parametric maps of Bolus Arrival Time (BAT), Mean Transit Time (MTT) and Time to Peak (TTP). Arterial segments which are nearly parallel with one of the biplane imaging planes in the 2D parametricmore » maps are co-registered with the 3D geometry. The values in the remaining vascular network are found using spline interpolation since the points chosen for co-registration on the vasculature are discrete and remaining regions need to be interpolated. To evaluate the method we used a patient CT volume data set for 3D printing a neurovascular phantom containing a complete Circle of Willis. We connected the phantom to a flow loop with a peristaltic pump, simulating physiological flow conditions. Contrast media was injected with an automatic injector at 10 ml/sec. Images were acquired with a Toshiba Infinix C-arm and 4D parametric image maps of the vasculature were calculated. Results: 4D BAT, MTT, and TTP parametric image maps of the Circle of Willis were derived. We generated color-coded 3D geometries which avoided artifacts due to vessel overlap or foreshortening in the projection direction. Conclusion: The software was tested successfully and multiple 4D parametric images were obtained from biplane DSA sequences without the need to acquire additional 3D-DSA runs. This can benefit the patient by reducing the contrast media and the radiation dose normally associated with these procedures. Partial support from NIH Grant R01-EB002873 and Toshiba Medical Systems Corp.« less

Linear response formula for piecewise expanding unimodal maps

NASA Astrophysics Data System (ADS)

Baladi, Viviane; Smania, Daniel

2008-04-01

The average R(t)=\\int \\varphi\\,\\rmd \\mu_t of a smooth function phiv with respect to the SRB measure μt of a smooth one-parameter family ft of piecewise expanding interval maps is not always Lipschitz (Baladi 2007 Commun. Math. Phys. 275 839-59, Mazzolena 2007 Master's Thesis Rome 2, Tor Vergata). We prove that if ft is tangent to the topological class of f, and if ∂t ft|t = 0 = X circle f, then R(t) is differentiable at zero, and R'(0) coincides with the resummation proposed (Baladi 2007) of the (a priori divergent) series \\sum_{n=0}^\\infty \\int X(y) \\partial_y (\\varphi \\circ f^n)(y)\\,\\rmd \\mu_0(y) given by Ruelle's conjecture. In fact, we show that t map μt is differentiable within Radon measures. Linear response is violated if and only if ft is transversal to the topological class of f.

Overview of multi-input frequency domain modal testing methods with an emphasis on sine testing

NASA Technical Reports Server (NTRS)

Rost, Robert W.; Brown, David L.

1988-01-01

An overview of the current state of the art multiple-input, multiple-output modal testing technology is discussed. A very brief review of the current time domain methods is given. A detailed review of frequency and spatial domain methods is presented with an emphasis on sine testing.

Prediction and phylogenetic analysis of mammalian short interspersed elements (SINEs).

PubMed

Rogozin, I B; Mayorov, V I; Lavrentieva, M V; Milanesi, L; Adkison, L R

2000-09-01

The presence of repetitive elements can create serious problems for sequence analysis, especially in the case of homology searches in nucleotide sequence databases. Repetitive elements should be treated carefully by using special programs and databases. In this paper, various aspects of SINE (short interspersed repetitive element) identification, analysis and evolution are discussed.

Remarks on the Non-Linear Differential Equation the Second Derivative of Theta Plus A Sine Theta Equals 0.

ERIC Educational Resources Information Center

Fay, Temple H.; O'Neal, Elizabeth A.

1985-01-01

The authors draw together a variety of facts concerning a nonlinear differential equation and compare the exact solution with approximate solutions. Then they provide an expository introduction to the elliptic sine function suitable for presentation in undergraduate courses on differential equations. (MNS)

The Sine Method: An Alternative Height Measurement Technique

Treesearch

Don C. Bragg; Lee E. Frelich; Robert T. Leverett; Will Blozan; Dale J. Luthringer

2011-01-01

Height is one of the most important dimensions of trees, but few observers are fully aware of the consequences of the misapplication of conventional height measurement techniques. A new approach, the sine method, can improve height measurement by being less sensitive to the requirements of conventional techniques (similar triangles and the tangent method). We studied...

Catalog of Non-Stellar Objects

DTIC Science & Technology

1977-09-12

multiplication with the matrix S", /l 0 " 0 V S" =10 cose -sine , (la) \\0 sine cose/ where e is the 1950.0 obliquity of the ecliptic , viz...helicocentric rectangular ecliptic coordinates. Let these be (x’", y"’, zŕ) = r;1". Then heliocentric rectangular equatorial coordinates are obtained by

A SINE in the genome of the cephalochordate amphioxus is an Alu element

PubMed Central

Holland, Linda Z.

2006-01-01

Transposable elements of about 300 bp, termed “short interspersed nucleotide elements or SINEs are common in eukaryotes. However, Alu elements, SINEs containing restriction sites for the AluI enzyme, have been known only from primates. Here I report the first SINE found in the genome of the cephalochordate, amphioxus. It is an Alu element of 375 bp that does not share substantial identity with any genomic sequences in vertebrates. It was identified because it was located in the FoxD regulatory region in a cosmid derived from one individual, but absent from the two FoxD alleles of BACs from a second individual. However, searches of sequences of BACs and genomic traces from this second individual gave an estimate of 50-100 copies in the amphioxus genome. The finding of an Alu element in amphioxus raises the question of whether Alu elements in amphioxus and primates arose by convergent evolution or by inheritance from a common ancestor. Genome-wide analyses of transposable elements in amphioxus and other chordates such as tunicates, agnathans and cartilaginous fishes could well provide the answer. PMID:16733535

Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins

PubMed Central

Nikaido, Masato; Matsuno, Fumio; Hamilton, Healy; Brownell, Robert L.; Cao, Ying; Ding, Wang; Zuoyan, Zhu; Shedlock, Andrew M.; Fordyce, R. Ewan; Hasegawa, Masami; Okada, Norihiro

2001-01-01

SINE (short interspersed element) insertion analysis elucidates contentious aspects in the phylogeny of toothed whales and dolphins (Odontoceti), especially river dolphins. Here, we characterize 25 informative SINEs inserted into unique genomic loci during evolution of odontocetes to construct a cladogram, and determine a total of 2.8 kb per taxon of the flanking sequences of these SINE loci to estimate divergence times among lineages. We demonstrate that: (i) Odontocetes are monophyletic; (ii) Ganges River dolphins, beaked whales, and ocean dolphins diverged (in this order) after sperm whales; (iii) three other river dolphin taxa, namely the Amazon, La Plata, and Yangtze river dolphins, form a monophyletic group with Yangtze River dolphins being the most basal; and (iv) the rapid radiation of extant cetacean lineages occurred some 28–33 million years B.P., in strong accord with the fossil record. The combination of SINE and flanking sequence analysis suggests a topology and set of divergence times for odontocete relationships, offering alternative explanations for several long-standing problems in cetacean evolution. PMID:11416211

Selective Inhibitor of Nuclear Export (SINE) Compounds Alter New World Alphavirus Capsid Localization and Reduce Viral Replication in Mammalian Cells.

PubMed

Lundberg, Lindsay; Pinkham, Chelsea; de la Fuente, Cynthia; Brahms, Ashwini; Shafagati, Nazly; Wagstaff, Kylie M; Jans, David A; Tamir, Sharon; Kehn-Hall, Kylene

2016-11-01

The capsid structural protein of the New World alphavirus, Venezuelan equine encephalitis virus (VEEV), interacts with the host nuclear transport proteins importin α/β1 and CRM1. Novel selective inhibitor of nuclear export (SINE) compounds, KPT-185, KPT-335 (verdinexor), and KPT-350, target the host's primary nuclear export protein, CRM1, in a manner similar to the archetypical inhibitor Leptomycin B. One major limitation of Leptomycin B is its irreversible binding to CRM1; which SINE compounds alleviate because they are slowly reversible. Chemically inhibiting CRM1 with these compounds enhanced capsid localization to the nucleus compared to the inactive compound KPT-301, as indicated by immunofluorescent confocal microscopy. Differences in extracellular versus intracellular viral RNA, as well as decreased capsid in cell free supernatants, indicated the inhibitors affected viral assembly, which led to a decrease in viral titers. The decrease in viral replication was confirmed using a luciferase-tagged virus and through plaque assays. SINE compounds had no effect on VEEV TC83_Cm, which encodes a mutated form of capsid that is unable to enter the nucleus. Serially passaging VEEV in the presence of KPT-185 resulted in mutations within the nuclear localization and nuclear export signals of capsid. Finally, SINE compound treatment also reduced the viral titers of the related eastern and western equine encephalitis viruses, suggesting that CRM1 maintains a common interaction with capsid proteins across the New World alphavirus genus.

Game Theory in Fleet Management

NASA Astrophysics Data System (ADS)

Dulai, Tibor; Jaskó, Szilárd; Muhi, Dániel

2008-11-01

In this survey we attempt to apply the results of cooperative game theory on fleet management problems. We deal with the aspect of a fleet where the members have their own goal, however the fleet has a common purpose too. These goals are to reach all destinations and get back to the center as quickly as possible. If we draw the map of the area-which contains the destination points and their environment-as a graph, we should determinate circles in it for each member of the fleet. Separating the nodes for each member, we should find Hamilton-circles of the sub-graphs. How to separate the destination points between the fleet members? How to route the members? What happens if there is an accident on a road which changes the way of a member? It may influence the other members' route too. What to communicate for getting the relevant information? How to change the routes in real time? We use cooperative game theory to find the solution.

Quantum communications system with integrated photonic devices

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

Nordholt, Jane E.; Peterson, Charles Glen; Newell, Raymond Thorson

Security is increased in quantum communication (QC) systems lacking a true single-photon laser source by encoding a transmitted optical signal with two or more decoy-states. A variable attenuator or amplitude modulator randomly imposes average photon values onto the optical signal based on data input and the predetermined decoy-states. By measuring and comparing photon distributions for a received QC signal, a single-photon transmittance is estimated. Fiber birefringence is compensated by applying polarization modulation. A transmitter can be configured to transmit in conjugate polarization bases whose states of polarization (SOPs) can be represented as equidistant points on a great circle on themore » Poincare sphere so that the received SOPs are mapped to equidistant points on a great circle and routed to corresponding detectors. Transmitters are implemented in quantum communication cards and can be assembled from micro-optical components, or transmitter components can be fabricated as part of a monolithic or hybrid chip-scale circuit.« less

Experiments Testing the Causes of Namibian Fairy Circles.

PubMed

Tschinkel, Walter R

2015-01-01

The grasslands on the sandy soils of the eastern edge of the Namib Desert of Namibia are strikingly punctuated by millions of mostly regularly-spaced circular bare spots 2 to 10 m or more in diameter, generally with a margin of taller grasses. The causes of these so called fairy circles are unknown, but several hypotheses have been advanced. In October 2009, we set up experiments that specifically tested four hypothesized causes, and monitored these 5 times between 2009 and 2015. Grass exclusion in circles due to seepage of subterranean vapors or gases was tested by burying an impermeable barrier beneath fairy circles, but seedling density and growth did not differ from barrier-less controls. Plant germination and growth inhibition by allelochemicals or nutrient deficiencies in fairy circle soils were tested by transferring fairy circle soil to artificially cleared circles in the grassy matrix, and matrix soil to fairy circles (along with circle to circle and matrix to matrix controls). None of the transfers changed the seedling density and growth from the control reference conditions. Limitation of plant growth due to micronutrient depletion within fairy circles was tested by supplementing circles with a micronutrient mixture, but did not result in differences in plant seedling density and growth. Short-range vegetation competitive feedbacks were tested by creating artificially-cleared circles of 2 or 4 m diameter located 2 or 6 m from a natural fairy circle. The natural circles remained bare and the artificial circles revegetated. These four experiments provided evidence that fairy circles were not caused by subterranean vapors, that fairy circle soil per se did not inhibit plant growth, and that the circles were not caused by micronutrient deficiency. There was also no evidence that vegetative feedbacks affected fairy circles on a 2 to 10 m scale. Landscape-scale vegetative self-organization is discussed as a more likely cause of fairy circles.

Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene

PubMed Central

Bumaschny, Viviana F; Low, Malcolm J; Rubinstein, Marcelo

2007-01-01

The proopiomelanocortin gene (POMC) is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5′ distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE) retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution. PMID:17922573

A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons

PubMed Central

Nakanishi, Akiko; Sasaki, Takeshi; Yan, Kuo; Tarabykin, Victor; Vigier, Lisa; Sumiyama, Kenta; Hirakawa, Mika; Nishihara, Hidenori; Pierani, Alessandra; Okada, Norihiro

2011-01-01

Short interspersed repetitive elements (SINEs) are highly repeated sequences that account for a significant proportion of many eukaryotic genomes and are usually considered “junk DNA”. However, we previously discovered that many AmnSINE1 loci are evolutionarily conserved across mammalian genomes, suggesting that they may have acquired significant functions involved in controlling mammalian-specific traits. Notably, we identified the AS021 SINE locus, located 390 kbp upstream of Satb2. Using transgenic mice, we showed that this SINE displays specific enhancer activity in the developing cerebral cortex. The transcription factor Satb2 is expressed by cortical neurons extending axons through the corpus callosum and is a determinant of callosal versus subcortical projection. Mouse mutants reveal a crucial function for Sabt2 in corpus callosum formation. In this study, we compared the enhancer activity of the AS021 locus with Satb2 expression during telencephalic development in the mouse. First, we showed that the AS021 enhancer is specifically activated in early-born Satb2+ neurons. Second, we demonstrated that the activity of the AS021 enhancer recapitulates the expression of Satb2 at later embryonic and postnatal stages in deep-layer but not superficial-layer neurons, suggesting the possibility that the expression of Satb2 in these two subpopulations of cortical neurons is under genetically distinct transcriptional control. Third, we showed that the AS021 enhancer is activated in neurons projecting through the corpus callosum, as described for Satb2+ neurons. Notably, AS021 drives specific expression in axons crossing through the ventral (TAG1−/NPY+) portion of the corpus callosum, confirming that it is active in a subpopulation of callosal neurons. These data suggest that exaptation of the AS021 SINE locus might be involved in enhancement of Satb2 expression, leading to the establishment of interhemispheric communication via the corpus callosum, a eutherian-specific brain structure. PMID:22174821

Geomorphic domains and linear features on Landsat images, Circle Quadrangle, Alaska

USGS Publications Warehouse

Simpson, S.L.

1984-01-01

A remote sensing study using Landsat images was undertaken as part of the Alaska Mineral Resource Assessment Program (AMRAP). Geomorphic domains A and B, identified on enhanced Landsat images, divide Circle quadrangle south of Tintina fault zone into two regional areas having major differences in surface characteristics. Domain A is a roughly rectangular, northeast-trending area of relatively low relief and simple, widely spaced drainages, except where igneous rocks are exposed. In contrast, domain B, which bounds two sides of domain A, is more intricately dissected showing abrupt changes in slope and relatively high relief. The northwestern part of geomorphic domain A includes a previously mapped tectonostratigraphic terrane. The southeastern boundary of domain A occurs entirely within the adjoining tectonostratigraphic terrane. The sharp geomorphic contrast along the southeastern boundary of domain A and the existence of known faults along this boundary suggest that the southeastern part of domain A may be a subdivision of the adjoining terrane. Detailed field studies would be necessary to determine the characteristics of the subdivision. Domain B appears to be divisible into large areas of different geomorphic terrains by east-northeast-trending curvilinear lines drawn on Landsat images. Segments of two of these lines correlate with parts of boundaries of mapped tectonostratigraphic terranes. On Landsat images prominent north-trending lineaments together with the curvilinear lines form a large-scale regional pattern that is transected by mapped north-northeast-trending high-angle faults. The lineaments indicate possible lithlogic variations and/or structural boundaries. A statistical strike-frequency analysis of the linear features data for Circle quadrangle shows that northeast-trending linear features predominate throughout, and that most northwest-trending linear features are found south of Tintina fault zone. A major trend interval of N.64-72E. in the linear feature data, corresponds to the strike of foliations in metamorphic rocks and magnetic anomalies reflecting compositional variations suggesting that most linear features in the southern part of the quadrangle probably are related to lithologic variations brought about by folding and foliation of metamorphic rocks. A second important trend interval, N.14-35E., may be related to thrusting south of the Tintina fault zone, as high concentrations of linear features within this interval are found in areas of mapped thrusts. Low concentrations of linear features are found in areas of most igneous intrusives. High concentrations of linear features do not correspond to areas of mineralization in any consistent or significant way that would allow concentration patterns to be easily used as an aid in locating areas of mineralization. The results of this remote sensing study indicate that there are several possibly important areas where further detailed studies are warranted.

Fast Drawing of Traffic Sign Using Mobile Mapping System

NASA Astrophysics Data System (ADS)

Yao, Q.; Tan, B.; Huang, Y.

2016-06-01

Traffic sign provides road users with the specified instruction and information to enhance traffic safety. Automatic detection of traffic sign is important for navigation, autonomous driving, transportation asset management, etc. With the advance of laser and imaging sensors, Mobile Mapping System (MMS) becomes widely used in transportation agencies to map the transportation infrastructure. Although many algorithms of traffic sign detection are developed in the literature, they are still a tradeoff between the detection speed and accuracy, especially for the large-scale mobile mapping of both the rural and urban roads. This paper is motivated to efficiently survey traffic signs while mapping the road network and the roadside landscape. Inspired by the manual delineation of traffic sign, a drawing strategy is proposed to quickly approximate the boundary of traffic sign. Both the shape and color prior of the traffic sign are simultaneously involved during the drawing process. The most common speed-limit sign circle and the statistic color model of traffic sign are studied in this paper. Anchor points of traffic sign edge are located with the local maxima of color and gradient difference. Starting with the anchor points, contour of traffic sign is drawn smartly along the most significant direction of color and intensity consistency. The drawing process is also constrained by the curvature feature of the traffic sign circle. The drawing of linear growth is discarded immediately if it fails to form an arc over some steps. The Kalman filter principle is adopted to predict the temporal context of traffic sign. Based on the estimated point,we can predict and double check the traffic sign in consecutive frames.The event probability of having a traffic sign over the consecutive observations is compared with the null hypothesis of no perceptible traffic sign. The temporally salient traffic sign is then detected statistically and automatically as the rare event of having a traffic sign.The proposed algorithm is tested with a diverse set of images that are taken inWuhan, China with theMMS ofWuhan University. Experimental results demonstrate that the proposed algorithm can detect traffic signs at the rate of over 80% in around 10 milliseconds. It is promising for the large-scale traffic sign survey and change detection using the mobile mapping system.

Emotional Intelligence: The Sine Qua Non for a Clinical Leadership Toolbox

ERIC Educational Resources Information Center

Rao, Paul R.

2006-01-01

Over the past decade, it has become increasingly clear that although IQ and technical skills are important, emotional intelligence is the Sine Qua Non of leadership. According to Goleman [Goleman, D. (1998). What makes a leader? "Harvard Business Review," 93-102] "effective leaders are alike in one crucial way: they all have a high degree of…

From sine-Gordon to vacuumless systems in flat and curved spacetimes

NASA Astrophysics Data System (ADS)

Bazeia, D.; Moreira, D. C.

2017-12-01

In this work we start from the Higgs prototype model to introduce a new model, which makes a smooth transition between systems with well-located minima and systems that support no minima at all. We implement this possibility using the deformation procedure, which allows the obtaining a sine-Gordon-like model, controlled by a real parameter that gives rise to a family of models, reproducing the sine-Gordon and the so-called vacuumless models. We also study the thick brane scenarios associated with these models and investigate their stability and renormalization group flow. In particular, it is shown how gravity can change from the 5-dimensional warped geometry with a single extra dimension of infinite extent to the conventional 5-dimensional Minkowski geometry.

Distinguishability notion based on Wootters statistical distance: Application to discrete maps

NASA Astrophysics Data System (ADS)

Gomez, Ignacio S.; Portesi, M.; Lamberti, P. W.

2017-08-01

We study the distinguishability notion given by Wootters for states represented by probability density functions. This presents the particularity that it can also be used for defining a statistical distance in chaotic unidimensional maps. Based on that definition, we provide a metric d ¯ for an arbitrary discrete map. Moreover, from d ¯ , we associate a metric space with each invariant density of a given map, which results to be the set of all distinguished points when the number of iterations of the map tends to infinity. Also, we give a characterization of the wandering set of a map in terms of the metric d ¯ , which allows us to identify the dissipative regions in the phase space. We illustrate the results in the case of the logistic and the circle maps numerically and analytically, and we obtain d ¯ and the wandering set for some characteristic values of their parameters. Finally, an extension of the metric space associated for arbitrary probability distributions (not necessarily invariant densities) is given along with some consequences. The statistical properties of distributions given by histograms are characterized in terms of the cardinal of the associated metric space. For two conjugate variables, the uncertainty principle is expressed in terms of the diameters of the associated metric space with those variables.

Soil temperature investigations using satellite acquired thermal-infrared data in semi-arid regions. Thesis. Final Report; [Utah

NASA Technical Reports Server (NTRS)

Day, R. L.; Petersen, G. W.

1983-01-01

Thermal-infrared data from the Heat Capacity Mapping Mission satellite were used to map the spatial distribution of diurnal surface temperatures and to estimate mean annual soil temperatures (MAST) and annual surface temperature amplitudes (AMP) in semi-arid east central Utah. Diurnal data with minimal snow and cloud cover were selected for five dates throughout a yearly period and geometrically co-registered. Rubber-sheet stretching was aided by the WARP program which allowed preview of image transformations. Daytime maximum and nighttime minimum temperatures were averaged to generation average daily temperature (ADT) data set for each of the five dates. Five ADT values for each pixel were used to fit a sine curve describing the theoretical annual surface temperature response as defined by a solution of a one-dimensinal heat flow equation. Linearization of the equation produced estimates of MAST and AMP plus associated confidence statistics. MAST values were grouped into classes and displayed on a color video screen. Diurnal surface temperatures and MAST were primarily correlated with elevation.

Minimally Invasive Electrochemotherapy Procedure for Treating Nasal Duct Tumors in Dogs using a Single Needle Electrode

PubMed Central

Maglietti, Felipe; Tellado, Matías; Olaiz, Nahuel; Michinski, Sebastian; Marshall, Guillermo

2017-01-01

Abstract Background Nasal cavity tumors are usually diagnosed late, when they already have infiltrated adjacent tissues thus requiring very aggressive treatments with serious side effects. Here we use electrochemotherapy (ECT), a well demonstrated treatment modality for superficial tumors. Materials and methods In the case of deep-seated tumors, the main limitation of ECT is reaching the tumor with an appropriate electric field. To overcome this limitation we introduce the single needle electrode (SiNE), a minimally invasive device that can deliver an appropriate electric field with a simple procedure. Twenty-one canine patients with spontaneous tumors were selected, eleven were treated using the SiNE with ECT, and ten with surgery plus adjuvant chemotherapy as a control group. Results In the SiNE group, 27% achieved a complete response, 64% had a partial response, and 9% had a stable disease. This means that 91% of objective responses were obtained. The mean overall survival was 16.86 months (4–32 months, median 16.5 months), with a survival rate significantly higher (p = 0.0008) when compared with control group. The only side effect observed was the inflammation of the treated nasal passage, which was controlled with corticosteroid therapy for one week. One year after the treatment, 60% of the canine of the SiNE group vs. 10% of the control group remained alive, and after the 32 months follow-up, the survival rate were 30% and 0%, respectively. Conclusions ECT with the SiNE can be safely used in canine to treat nasal tumors with encouraging results. PMID:29333121

The stationary sine-Gordon equation on metric graphs: Exact analytical solutions for simple topologies

NASA Astrophysics Data System (ADS)

Sabirov, K.; Rakhmanov, S.; Matrasulov, D.; Susanto, H.

2018-04-01

We consider the stationary sine-Gordon equation on metric graphs with simple topologies. Exact analytical solutions are obtained for different vertex boundary conditions. It is shown that the method can be extended for tree and other simple graph topologies. Applications of the obtained results to branched planar Josephson junctions and Josephson junctions with tricrystal boundaries are discussed.

Discovering Trigonometric Relationships Implied by the Law of Sines and the Law of Cosines

ERIC Educational Resources Information Center

Skurnick, Ronald; Javadi, Mohammad

2006-01-01

The Law of Sines and The Law of Cosines are of paramount importance in the field of trigonometry because these two theorems establish relationships satisfied by the three sides and the three angles of any triangle. In this article, the authors use these two laws to discover a host of other trigonometric relationships that exist within any…

Tachometer

NASA Technical Reports Server (NTRS)

Nola, F. J. (Inventor)

1977-01-01

A tachometer in which sine and cosine signals responsive to the angular position of a shaft as it rotates are each multiplied by like, sine or cosine, functions of a carrier signal, the products summed, and the resulting frequency signal converted to fixed height, fixed width pulses of a like frequency. These pulses are then integrated, and the resulting dc output is an indication of shaft speed.

Retroelements (LINEs and SINEs) in vole genomes: differential distribution in the constitutive heterochromatin.

PubMed

Acosta, M J; Marchal, J A; Fernández-Espartero, C H; Bullejos, M; Sánchez, A

2008-01-01

The chromosomal distribution of mobile genetic elements is scarcely known in Arvicolinae species, but could be of relevance to understand the origin and complex evolution of the sex chromosome heterochromatin. In this work we cloned two retrotransposon sequences, L1 and SINE-B1, from the genome of Chionomys nivalis and investigated their chromosomal distribution on several arvicoline species. Our results demonstrate first that both retroelements are the most abundant repeated DNA sequences in the genome of these species. L1 elements, in most species, are highly accumulated in the sex chromosomes compared to the autosomes. This favoured L1 insertion could have played an important role in the origin of the enlarged heterochromatic blocks existing in the sex chromosomes of some Microtus species. Also, we propose that L1 accumulation on the X heterochromatin could have been the consequence of different, independent and rapid amplification processes acting in each species. SINE elements, however, were completely lacking from the constitutive heterochromatin, either in autosomes or in the heterochromatic blocks of sex chromosomes. These data could indicate that some SINE elements are incompatible with the formation of heterochromatic complexes and hence are necessarily missing from the constitutive heterochromatin.

Instrument to synchronize Thomson scattering diagnostic measurements with MHD acitivity in a tokamak

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

Wintenberg, A.L.

1985-04-01

An instrument to synchronize the firing of a ruby laser for a Thomson scattering diagnostic with plasma oscillations was designed, developed, and evaluated. The instrument will fire the laser at a user-selected phase of an input sine or sawtooth wave with an accuracy of +-15/sup 0/. Allowable frequencies range from 20 to 500 Hz for a sawtooth and from 1 to 30 kHz for a sine wave. The instrument also allows synchronization with a sine wave to be enabled by a preselected sawtooth phase. The instrument uses analog signal processing circuits to separate the signal components, remove unwanted components, andmore » produce zero-phase synchronization pulses. The instrument measures the period between zero-phase pulses in order to produce phase synchronization pulses delayed a fraction of the period from the zero-phase pulses. The laser is fired by the phase synchronization pulse. Unwanted signal components are attenuated by bandpass filters. A digitally controlled self-adjusting bandpass filter for sine processing. The instrument was used to investigate the variation of the electron temperature profile with the phase of the x-ray signal from an Impurity Studies Experiment (ISX-B) plasma exhibiting magnetohydrodynamic (MHD) activity.« less

Introducing Nine-Point Circle to Junior High School Students

NASA Astrophysics Data System (ADS)

Fiangga, S.; Azizah, M. A. N.; Rini, R. N. K.; Hidayanti, A. N.

2018-01-01

The concept of circles is an ancient concept that has appeared since Ancient Egypt from which this concept gives many significant contributions in mathematics’ development until now. Nevertheless, the concept of circles hides many uncover mysterious features that are of applications in mathematics. One of the mysterious features is the Nine-Point Circle. This Nine-point circle is also known as Euler’s circle, six-point circle, Feuerbach’s circle, the twelve-point circle, and many others. Because of these different names, there have been misunderstand among mathematicians about the Nine-Point Circle’s history. Besides, the discussion of Nine-Point Circle can be used to be an initial material to explain elementary geometry topic in junior high school’s level curriculum of 2013. Therefore, this concept needs to be delivered to the students as a geometry introduction. A possible form of the integration historical aspect of Nine-point circle is suggested in this paper as well as its importance in the curriculum of 2013.

The research on multi-projection correction based on color coding grid array

NASA Astrophysics Data System (ADS)

Yang, Fan; Han, Cheng; Bai, Baoxing; Zhang, Chao; Zhao, Yunxiu

2017-10-01

There are many disadvantages such as lower timeliness, greater manual intervention in multi-channel projection system, in order to solve the above problems, this paper proposes a multi-projector correction technology based on color coding grid array. Firstly, a color structured light stripe is generated by using the De Bruijn sequences, then meshing the feature information of the color structured light stripe image. We put the meshing colored grid intersection as the center of the circle, and build a white solid circle as the feature sample set of projected images. It makes the constructed feature sample set not only has the perceptual localization, but also has good noise immunity. Secondly, we establish the subpixel geometric mapping relationship between the projection screen and the individual projectors by using the structure of light encoding and decoding based on the color array, and the geometrical mapping relation is used to solve the homography matrix of each projector. Lastly the brightness inconsistency of the multi-channel projection overlap area is seriously interfered, it leads to the corrected image doesn't fit well with the observer's visual needs, and we obtain the projection display image of visual consistency by using the luminance fusion correction algorithm. The experimental results show that this method not only effectively solved the problem of distortion of multi-projection screen and the issue of luminance interference in overlapping region, but also improved the calibration efficient of multi-channel projective system and reduced the maintenance cost of intelligent multi-projection system.

Specification and correlation of the sine vibration environment for Viking '75

NASA Technical Reports Server (NTRS)

Snyder, R. E.; Trummel, M.; Wada, B. K.; Pohlen, J. C.

1974-01-01

Two Viking spacecraft will be individually launched on a new Titan IIIE/Centaur D-1T launch vehicle in August 1975. The method for the establishment of spacecraft sine vibration test levels prior to availability of any Titan IIIE/Centaur D-1T flight data by use of both computer simulations and data from previous Titan and Atlas Centaur vehicles is described. The specification level is compared with actual flight data obtained from a proof flight launch of the Titan IIIE/Centaur D-1T and a Viking dynamic simulator in January 1974. An objective of the proof flight launch was to obtain estimates of the flight loads and environments. The criteria used to minimize the structural weight that would result from an unmodified application of a sine test environment are described.

Seismostratigraphic model of the Sines Contourite Drift (SW Portuguese Margin) - depositional evolution, structural control and paleoceanographic implications

NASA Astrophysics Data System (ADS)

Rodrigues, Sara; Roque, Cristina; Terrinha, Pedro; Hernández-Molina, Francisco J.; Llave, Estefania; Ercilla, Gemma; Casas, David; Farran, Marcelli

2017-04-01

The Sines Contourite Drift, located in the Southwest Portuguese margin, is a distal drift of the Contourite Depositional System of the Gulf of Cadiz, built by the influence of the Mediterranean Outflow Water (MOW). This drift is located between 1000 and 2000 m water depth on the Alentejo margin continental slope. The Sines Drift is bounded by four major morphologic features, the 1.4 km high Pereira de Sousa Fault escarpment to the west, the upper continental slope to the east and the Setúbal and São Vicente canyons to the north and south, respectively. This work presents a seismic stratigraphic analysis and proposes an evolutionary model for the Sines Drift, as well as the identification of its main driving mechanisms and constraints. We used new seismic reflection lines acquired during the MOWER/CONDRIBER cruise in September-October 2014, pre-existent multichannel seismic lines and lithostratigraphic and chronological data from Site U1391 of IODP Expedition 339 carried out in 2011-2012. Three evolutionary phases are identified for the Sines Drift development: 1) a sheeted-contourite-drift phase (<5.3-3.2 Ma) built since the Late Miocene by an initially weak flowing MOW; 2) a mounded-contourite-drift phase (3.2-0.7 Ma) from Late Pliocene to Early Quaternary times characterized by a mounded drift in the north and sheeted in the south, with a succession of sinuous N-S paleomoats in the east built as a result of a MOW enhancement; and 3) a plastered-contourite-drift phase from Mid-Pleistocene (0.7 Ma) till the present day, characterized by the present depositional (sandy-muddy drifts) and erosional (moats) contourite features associated with two major events of MOW intensification. The growth of the Sines Drift was constrained, in a long-term, by seafloor morphologies that resulted from the Mesozoic rifting processes of the Southwest Portuguese margin, inherited from the Mesozoic rifting phases. The paleomorphology provided accommodation space for drift growth and conditioned its overall architecture. The N-S horsts built during the Mesozoic rifting confined drift formation and did not allow lateral migration. The formation of the Sines Drift has also been influenced, in short-term, by climatic fluctuations and sea-level changes especially during the Quaternary. The succession of sinuous paleomoats beneath the present-day moat suggests a persistent and northward flowing MOW with several phases of enhancement. It was also perceived that the São Vicente and Setúbal canyons took most of the downslope sediment supply, as well as the occurrence of mass-movement processes in the west associated with the steep gradient of the Pereira de Sousa escarpment. All these results suggest the Sines Drift had a complex evolution controlled by several and varied factors at different scales.

Geophysical Data Sets in GeoMapApp

NASA Astrophysics Data System (ADS)

Goodwillie, A. M.

2017-12-01

GeoMapApp (http://www.geomapapp.org), a free map-based data tool developed at Lamont-Doherty Earth Observatory, provides access to hundreds of integrated geoscience data sets that are useful for geophysical studies. Examples include earthquake and volcano catalogues, gravity and magnetics data, seismic velocity tomographic models, geological maps, geochemical analytical data, lithospheric plate boundary information, geodetic velocities, and high-resolution bathymetry and land elevations. Users can also import and analyse their own data files. Data analytical functions provide contouring, shading, profiling, layering and transparency, allowing multiple data sets to be seamlessly compared. A new digitization and field planning portal allow stations and waypoints to be generated. Sessions can be saved and shared with colleagues and students. In this eLightning presentation we will demonstrate some of GeoMapApp's capabilities with a focus upon subduction zones and tectonics. In the attached screen shot of the Cascadia margin, the contoured depth to the top of the subducting Juan de Fuca slab is overlain on a shear wave velocity depth slice. Geochemical data coloured on Al2O3 and scaled on MgO content is shown as circles. The stack of data profiles was generated along the white line.

A Classroom Note on Generating Examples for the Laws of Sines and Cosines from Pythagorean Triangles

ERIC Educational Resources Information Center

Sher, Lawrence; Sher, David

2007-01-01

By selecting certain special triangles, students can learn about the laws of sines and cosines without wrestling with long decimal representations or irrational numbers. Since the law of cosines requires only one of the three angles of a triangle, there are many examples of triangles with integral sides and a cosine that can be represented exactly…

The sine method as a more accurate height predictor for hardwoods

Treesearch

Don C. Bragg

2007-01-01

Most hypsometers apply a mathematical technique that utilizes the tangent of angles and a horizontal distance to deliver the exact height of a tree under idealized circumstances. Unfortunately, these conditions are rarely met for hardwoods in the field. A “new” predictor based on sine and slope distance and discussed here does not require the same assumptions for...

Retinal detachment and retinal holes in retinitis pigmentosa sine pigmento.

PubMed

Csaky, K; Olk, R J; Mahl, C F; Bloom, S M

1991-01-01

Retinal detachment and retinal holes in two family members with retinitis pigmentosa sine pigmento are reported. We believe these are the first such cases reported in the literature. We describe the presenting symptoms and management, including cryotherapy, scleral buckling procedure, and sulfur hexafluoride injection (SF6), resulting in stable visual acuity in one case and retinal reattachment and improved visual acuity in the other case.

The Mediation of Tools in the Development of Formal Mathematical Concepts: The Compass and the Circle as an Example.

ERIC Educational Resources Information Center

Chassapis, Dimitris

1999-01-01

Focuses on the process by which children develop a formal mathematical concept of the circle by using various instruments to draw circles within the context of a goal-directed drawing task. Concludes that the use of the compass in circle drawing structures the circle-drawing operation in a radically different fashion than circle tracers and…

Circling motion and screen edges as an alternative input method for on-screen target manipulation.

PubMed

Ka, Hyun W; Simpson, Richard C

2017-04-01

To investigate a new alternative interaction method, called circling interface, for manipulating on-screen objects. To specify a target, the user makes a circling motion around the target. To specify a desired pointing command with the circling interface, each edge of the screen is used. The user selects a command before circling the target. To evaluate the circling interface, we conducted an experiment with 16 participants, comparing the performance on pointing tasks with different combinations of selection method (circling interface, physical mouse and dwelling interface) and input device (normal computer mouse, head pointer and joystick mouse emulator). A circling interface is compatible with many types of pointing devices, not requiring physical activation of mouse buttons, and is more efficient than dwell-clicking. Across all common pointing operations, the circling interface had a tendency to produce faster performance with a head-mounted mouse emulator than with a joystick mouse. The performance accuracy of the circling interface outperformed the dwelling interface. It was demonstrated that the circling interface has the potential as another alternative pointing method for selecting and manipulating objects in a graphical user interface. Implications for Rehabilitation A circling interface will improve clinical practice by providing an alternative pointing method that does not require physically activating mouse buttons and is more efficient than dwell-clicking. The Circling interface can also work with AAC devices.

A localization algorithm of adaptively determining the ROI of the reference circle in image

NASA Astrophysics Data System (ADS)

Xu, Zeen; Zhang, Jun; Zhang, Daimeng; Liu, Xiaomao; Tian, Jinwen

2018-03-01

Aiming at solving the problem of accurately positioning the detection probes underwater, this paper proposed a method based on computer vision which can effectively solve this problem. The theory of this method is that: First, because the shape information of the heat tube is similar to a circle in the image, we can find a circle which physical location is well known in the image, we set this circle as the reference circle. Second, we calculate the pixel offset between the reference circle and the probes in the picture, and adjust the steering gear through the offset. As a result, we can accurately measure the physical distance between the probes and the under test heat tubes, then we can know the precise location of the probes underwater. However, how to choose reference circle in image is a difficult problem. In this paper, we propose an algorithm that can adaptively confirm the area of reference circle. In this area, there will be only one circle, and the circle is the reference circle. The test results show that the accuracy of the algorithm of extracting the reference circle in the whole picture without using ROI (region of interest) of the reference circle is only 58.76% and the proposed algorithm is 95.88%. The experimental results indicate that the proposed algorithm can effectively improve the efficiency of the tubes detection.

Fourier modeling of the BOLD response to a breath-hold task: Optimization and reproducibility.

PubMed

Pinto, Joana; Jorge, João; Sousa, Inês; Vilela, Pedro; Figueiredo, Patrícia

2016-07-15

Cerebrovascular reactivity (CVR) reflects the capacity of blood vessels to adjust their caliber in order to maintain a steady supply of brain perfusion, and it may provide a sensitive disease biomarker. Measurement of the blood oxygen level dependent (BOLD) response to a hypercapnia-inducing breath-hold (BH) task has been frequently used to map CVR noninvasively using functional magnetic resonance imaging (fMRI). However, the best modeling approach for the accurate quantification of CVR maps remains an open issue. Here, we compare and optimize Fourier models of the BOLD response to a BH task with a preparatory inspiration, and assess the test-retest reproducibility of the associated CVR measurements, in a group of 10 healthy volunteers studied over two fMRI sessions. Linear combinations of sine-cosine pairs at the BH task frequency and its successive harmonics were added sequentially in a nested models approach, and were compared in terms of the adjusted coefficient of determination and corresponding variance explained (VE) of the BOLD signal, as well as the number of voxels exhibiting significant BOLD responses, the estimated CVR values, and their test-retest reproducibility. The brain average VE increased significantly with the Fourier model order, up to the 3rd order. However, the number of responsive voxels increased significantly only up to the 2nd order, and started to decrease from the 3rd order onwards. Moreover, no significant relative underestimation of CVR values was observed beyond the 2nd order. Hence, the 2nd order model was concluded to be the optimal choice for the studied paradigm. This model also yielded the best test-retest reproducibility results, with intra-subject coefficients of variation of 12 and 16% and an intra-class correlation coefficient of 0.74. In conclusion, our results indicate that a Fourier series set consisting of a sine-cosine pair at the BH task frequency and its two harmonics is a suitable model for BOLD-fMRI CVR measurements based on a BH task with preparatory inspiration, yielding robust estimates of this important physiological parameter. Copyright © 2016 Elsevier Inc. All rights reserved.

Are Namibian “Fairy Circles” the Consequence of Self-Organizing Spatial Vegetation Patterning?

PubMed Central

Cramer, Michael D.; Barger, Nichole N.

2013-01-01

Causes of over-dispersed barren “fairy circles” that are often surrounded by ca. 0.5 m tall peripheral grasses in a matrix of shorter (ca. 0.2 m tall) grasses in Namibian grasslands remain mysterious. It was hypothesized that the fairy circles are the consequence of self-organizing spatial vegetation patterning arising from resource competition and facilitation. We examined the edaphic properties of fairy circles and variation in fairy circle size, density and landscape occupancy (% land surface) with edaphic properties and water availability at a local scale (<50 km) and with climate and vegetation characteristics at a regional scale. Soil moisture in the barren fairy circles declines from the center towards the periphery and is inversely correlated with soil organic carbon, possibly indicating that the peripheral grass roots access soil moisture that persists into the dry season within fairy circles. Fairy circle landscape occupancy is negatively correlated with precipitation and soil [N], consistent with fairy circles being the product of resource-competition. Regional fairy circle presence/absence is highly predictable using an empirical model that includes narrow ranges of vegetation biomass, precipitation and temperature seasonality as predictor variables, indicating that fairy circles are likely a climate-dependent emergent phenomenon. This dependence of fairy circle occurrence on climate explains why fairy circles in some locations may appear and disappear over time. Fairy circles are only over-dispersed at high landscape occupancies, indicating that inter-circle competition may determine their spacing. We conclude that fairy circles are likely to be an emergent arid-grassland phenomenon that forms as a consequence of peripheral grass resource-competition and that the consequent barren circle may provide a resource-reservoir essential for the survival of the larger peripheral grasses and provides a habitat for fossicking fauna. PMID:23976962

Influence of waveform and current direction on short-interval intracortical facilitation: a paired-pulse TMS study.

PubMed

Delvendahl, Igor; Lindemann, Hannes; Jung, Nikolai H; Pechmann, Astrid; Siebner, Hartwig R; Mall, Volker

2014-01-01

Transcranial magnetic stimulation (TMS) of the human primary motor hand area (M1-HAND) can produce multiple descending volleys in fast-conducting corticospinal neurons, especially so-called indirect waves (I-waves) resulting from trans-synaptic excitation. Facilitatory interaction between these I-waves can be studied non-invasively using a paired-pulse paradigm referred to as short-interval intracortical facilitation (SICF). We examined whether SICF depends on waveform and current direction of the TMS pulses. In young healthy volunteers, we applied single- and paired-pulse TMS to M1-HAND. We probed SICF by pairs of monophasic or half-sine pulses at suprathreshold stimulation intensity and inter-stimulus intervals (ISIs) between 1.0 and 5.0 ms. For monophasic paired-pulse stimulation, both pulses had either a posterior-anterior (PA) or anterior-posterior (AP) current direction (AP-AP or PA-PA), whereas current direction was reversed between first and second pulse for half-sine paired-pulse stimulation (PA-AP and AP-PA). Monophasic AP-AP stimulation resulted in stronger early SICF at 1.4 ms relative to late SICF at 2.8 and 4.4 ms, whereas monophasic PA-PA stimulation produced SICF of comparable size at all three peaks. With half-sine stimulation the third SICF peak was reduced for PA-AP current orientation compared with AP-PA. SICF elicited using monophasic as well as half-sine pulses is affected by current direction at clearly suprathreshold intensities. The impact of current orientation is stronger for monophasic compared with half-sine pulses. The direction-specific effect of paired-pulse TMS on the strength of early versus late SICF shows that different cortical circuits mediate early and late SICF. Copyright © 2014 Elsevier Inc. All rights reserved.

An interactive GIS based tool on Chinese history and its topography

NASA Astrophysics Data System (ADS)

Konda, Ashish Reddy

The aim of the thesis is to demonstrate how China was attacked by the foreign powers, the rise and fall of the empires, the border conflicts with India, Russia, Vietnam and territorial disputes in South China Sea. This thesis is focused on creating a GIS tool showcasing the modern Chinese history, which includes the major wars fought during that period. This tool is developed using the features of Google Maps that shows the location of the wars. The topography of China is also represented on the interactive Google Map by creating layers for rivers, mountain ranges and deserts. The provinces with highest population are also represented on the Google Map with circles. The application also shows the historical events in chronological order using a timeline feature. This has been implemented using JQuery, JavaScript, HTML5 and CSS. Chinese culture and biographies of important leaders are also included in this thesis, which is embedded with pictures and videos.

Mapping the social determinants of substance use for pregnant-involved young Aboriginal women

PubMed Central

Shahram, Sana Z.; Bottorff, Joan L.; Oelke, Nelly D.; Kurtz, Donna L. M.; Thomas, Victoria; Spittal, Patricia M.

2017-01-01

ABSTRACT There is a dearth of knowledge about the social determinants of substance use among young pregnant-involved Indigenous women in Canada from their perspectives. As part of life history interviews, 17 young pregnant-involved Indigenous women with experiences with substances completed a participant-generated mapping activity CIRCLES (Charting Intersectional Relationships in the Context of Life). As women created their maps, they discussed how different social determinants impacted their experiences with pregnancy and substance use. The social determinants identified and used by women to explain determinants of their substance use were grouped into 10 themes: traumatic life histories; socioeconomic status; culture, identity and spirituality; shame and guilt; mental wellness; family connections; romantic and platonic relationships; strength and hope; mothering; and the intersections of determinants. We conclude that understanding the context and social determinants of substance use from a woman-informed perspective is paramount to informing effective and appropriate programs to support young Indigenous women who use substances. PMID:28140776

Janus configurations with SL(2, ℤ)-duality twists, strings on mapping tori and a tridiagonal determinant formula

NASA Astrophysics Data System (ADS)

Ganor, Ori J.; Moore, Nathan P.; Sun, Hao-Yu; Torres-Chicon, Nesty R.

2014-07-01

We develop an equivalence between two Hilbert spaces: (i) the space of states of U(1) n Chern-Simons theory with a certain class of tridiagonal matrices of coupling constants (with corners) on T 2; and (ii) the space of ground states of strings on an associated mapping torus with T 2 fiber. The equivalence is deduced by studying the space of ground states of SL(2, ℤ)-twisted circle compactifications of U(1) gauge theory, connected with a Janus configuration, and further compactified on T 2. The equality of dimensions of the two Hilbert spaces (i) and (ii) is equivalent to a known identity on determinants of tridiagonal matrices with corners. The equivalence of operator algebras acting on the two Hilbert spaces follows from a relation between the Smith normal form of the Chern-Simons coupling constant matrix and the isometry group of the mapping torus, as well as the torsion part of its first homology group.

EISCAT observations during MAC/SINE and MAC/Epsilon

NASA Technical Reports Server (NTRS)

Roettger, J.; Hoppe, U.-P.; Hall, C.

1989-01-01

The EISCAT incoherent scatter radar facility in Tromsoe, Norway was operated during the MAC/SINE campaign for 78 hours in the period 10 June to 17 July 1987, and during the MAC/Epsilon campaign for 90 hours in the period 15 October to 5 November 1987. The VHF (224 MHz) radar operations during MAC/SINE yielded most interesting observations of strong coherent echoes from the mesopause region. Characteristic data of these polar mesospheric summer echoes are presented. The UHF (933 MHz) radar operations during MAC/Epsilon were done with 18 deg off zenith beam and allows the deduction of meridonal and horizontal wind components as well as radial velocity spectra in addition to the usual electron density profiles in the D and lower E regions. Some results from the VHF and UHF radars indicating the presence of gravity waves are examined.

Conformal dynamics of precursors to fracture

NASA Astrophysics Data System (ADS)

Barra, F.; Herrera, M.; Procaccia, I.

2003-09-01

An exact integro-differential equation for the conformal map from the unit circle to the boundary of an evolving cavity in a stressed 2-dimensional solid is derived. This equation provides an accurate description of the dynamics of precursors to fracture when surface diffusion is important. The solution predicts the creation of sharp grooves that eventually lead to material failure via rapid fracture. Solutions of the new equation are demonstrated for the dynamics of an elliptical cavity and the stability of a circular cavity under biaxial stress, including the effects of surface stress.

Theoretical damping in roll and rolling moment due to differential wing incidence for slender cruciform wings and wing-body combinations

NASA Technical Reports Server (NTRS)

Adams, Gaynor J; DUGAN DUANE W

1952-01-01

A method of analysis based on slender-wing theory is developed to investigate the characteristics in roll of slender cruciform wings and wing-body combinations. The method makes use of the conformal mapping processes of classical hydrodynamics which transform the region outside a circle and the region outside an arbitrary arrangement of line segments intersecting at the origin. The method of analysis may be utilized to solve other slender cruciform wing-body problems involving arbitrarily assigned boundary conditions. (author)

Deciphering Stress State of Seismogenic Faults in Oklahoma and Kansas Based on High-resolution Stress Maps

NASA Astrophysics Data System (ADS)

Qin, Y.; Chen, X.; Haffener, J.; Trugman, D. T.; Carpenter, B.; Reches, Z.

2017-12-01

Induced seismicity in Oklahoma and Kansas delineates clear fault trends. It is assumed that fluid injection reactivates faults which are optimally oriented relative to the regional tectonic stress field. We utilized recently improved earthquake locations and more complete focal mechanism catalogs to quantitatively analyze the stress state of seismogenic faults with high-resolution stress maps. The steps of analysis are: (1) Mapping the faults by clustering seismicity using a nearest-neighbor approach, manually picking the fault in each cluster and calculating the fault geometry using principal component analysis. (2) Running a stress inversion with 0.2° grid spacing to produce an in-situ stress map. (3) The fault stress state is determined from fault geometry and a 3D Mohr circle. The parameter `understress' is calculated to quantify the criticalness of these faults. If it approaches 0, the fault is critically stressed; while understress=1 means there is no shear stress on the fault. Our results indicate that most of the active faults have a planar shape (planarity>0.8), and dip steeply (dip>70°). The fault trends are distributed mainly in conjugate set ranges of [50°,70°] and [100°,120°]. More importantly, these conjugate trends are consistent with mapped basement fractures in southern Oklahoma, suggesting similar basement features from regional tectonics. The fault length data shows a loglinear relationship with the maximum earthquake magnitude with an expected maximum magnitude range from 3.2 to 4.4 for most seismogenic faults. Based on 3D local Mohr circle, we find that 61% of the faults have low understress (<0.2); while several faults with high understress (>0.5) are located within highest-rate injection zones and therefore are likely to be influenced by high pore pressure. The faults that hosted the largest earthquakes, M5.7 Prague and M5.8 Pawnee are critically stressed (understress < 0.08), whereas the fault of M5 Fairview earthquake is only moderately stressed (understress > 0.2). These differences may help in understanding earthquake sequences, for example, the predominantly aftershock-type sequence for Prague and Pawnee earthquakes, compared to predominantly swarm-type behavior for Fairview earthquake. These results provide ways to quantitatively evaluate local earthquake hazard.

Procedure for normalization of cDNA libraries

DOEpatents

Bonaldo, Maria DeFatima; Soares, Marcelo Bento

1997-01-01

This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library.

The newest miracle drug: quality circles in hospitals.

PubMed

McKinney, M M

1984-01-01

In recent years, a number of hospitals throughout the United States have been exploring the use of Japanese-style quality circles to reduce their operating expenses, improve productivity, and enhance the quality of work life for hospital employees. This article examines the organizational climate necessary for quality circles, methods used to implement quality circles, and management's role in guiding and responding to circle activities. Ideas for building and maintaining staff support are presented along with a cost/benefit analysis of quality circle programs. The author concludes that quality circles are most successful in hospitals where they are part of a larger organizational development effort. When administrators believe in their employees' ability to contribute to the institution and are willing to invest necessary time and resources in employee education and the measurement of quality circle achievements, quality circles can produce creative solutions to perplexing institutional problems.

Amplification of telomeric arrays via rolling-circle mechanism.

PubMed

Nosek, Jozef; Rycovska, Adriana; Makhov, Alexander M; Griffith, Jack D; Tomaska, Lubomir

2005-03-18

Alternative (telomerase-independent) lengthening of telomeres mediated through homologous recombination is often accompanied by a generation of extrachromosomal telomeric circles (t-circles), whose role in direct promotion of recombinational telomere elongation has been recently demonstrated. Here we present evidence that t-circles in a natural telomerase-deficient system of mitochondria of the yeast Candida parapsilosis replicate independently of the linear chromosome via a rolling-circle mechanism. This is supported by an observation of (i) single-stranded DNA consisting of concatameric arrays of telomeric sequence, (ii) lasso-shaped molecules representing rolling-circle intermediates, and (iii) preferential incorporation of deoxyribonucleotides into telomeric fragments and t-circles. Analysis of naturally occurring variant t-circles revealed conserved motifs with potential function in driving the rolling-circle replication. These data indicate that extrachromosomal t-circles observed in a wide variety of organisms, including yeasts, plants, Xenopus laevis, and certain human cell lines, may represent independent replicons generating telomeric sequences and, thus, actively participating in telomere dynamics. Moreover, because of the promiscuous occurrence of t-circles across phyla, the results from yeast mitochondria have implications related to the primordial system of telomere maintenance, providing a paradigm for evolution of telomeres in nuclei of early eukaryotes.

Analog circuit for the measurement of phase difference between two noisy sine-wave signals

NASA Technical Reports Server (NTRS)

Shakkottai, P.; Kwack, E. Y.; Back, L. H.

1989-01-01

A simple circuit was designed to measure the phase difference between two noisy sine waves. It locks over a wide range of frequencies and produces an output proportional to the phase difference of rapidly varying signals. A square wave locked in frequency and phase to the first signal is produced by a phase-locked loop and is amplified by an operational amplifier.

Unilateral retinitis pigmentosa sine pigmento.

PubMed Central

Pearlman, J T; Saxton, J; Hoffman, G

1976-01-01

A patient presented with unilateral findings of night blindness shown by impaired rod function and dark adaptation, constricted visual fields with good central acuity, a barely recordable electro-retinographic b-wave, and a unilaterally impaired electro-oculogram. There were none of the pigmentary changes usually associated with retinitis pigmentosa. The unaffected right eye was normal in all respects. Therefore the case is most probably one of unilateral retinitis pigmentosa sine pigmento. Images PMID:952804

Unilateral retinitis pigmentosa sine pigmento.

PubMed

Pearlman, J T; Saxton, J; Hoffman, G

1976-05-01

A patient presented with unilateral findings of night blindness shown by impaired rod function and dark adaptation, constricted visual fields with good central acuity, a barely recordable electro-retinographic b-wave, and a unilaterally impaired electro-oculogram. There were none of the pigmentary changes usually associated with retinitis pigmentosa. The unaffected right eye was normal in all respects. Therefore the case is most probably one of unilateral retinitis pigmentosa sine pigmento.

The response of phospholipid-encapsulated microbubbles to chirp-coded excitation: Implications for high-frequency nonlinear imaging

PubMed Central

Shekhar, Himanshu; Doyley, Marvin M.

2013-01-01

The current excitation strategy for harmonic and subharmonic imaging (HI and SHI) uses short sine-bursts. However, alternate pulsing strategies may be useful for enhancing nonlinear emissions from ultrasound contrast agents. The goal of this study was to corroborate the hypothesis that chirp-coded excitation can improve the performance of high-frequency HI and SHI. A secondary goal was to understand the mechanisms that govern the response of ultrasound contrast agents to chirp-coded and sine-burst excitation schemes. Numerical simulations and acoustic measurements were conducted to evaluate the response of a commercial contrast agent (Targestar-P®) to chirp-coded and sine-burst excitation (10 MHz frequency, peak pressures 290 kPa). The results of the acoustic measurements revealed an improvement in signal-to-noise ratio by 4 to 14 dB, and a two- to threefold reduction in the subharmonic threshold with chirp-coded excitation. Simulations conducted with the Marmottant model suggest that an increase in expansion-dominated radial excursion of microbubbles was the mechanism responsible for the stronger nonlinear response. Additionally, chirp-coded excitation detected the nonlinear response for a wider range of agent concentrations than sine-bursts. Therefore, chirp-coded excitation could be a viable approach for enhancing the performance of HI and SHI. PMID:23654417

The response of phospholipid-encapsulated microbubbles to chirp-coded excitation: implications for high-frequency nonlinear imaging.

PubMed

Shekhar, Himanshu; Doyley, Marvin M

2013-05-01

The current excitation strategy for harmonic and subharmonic imaging (HI and SHI) uses short sine-bursts. However, alternate pulsing strategies may be useful for enhancing nonlinear emissions from ultrasound contrast agents. The goal of this study was to corroborate the hypothesis that chirp-coded excitation can improve the performance of high-frequency HI and SHI. A secondary goal was to understand the mechanisms that govern the response of ultrasound contrast agents to chirp-coded and sine-burst excitation schemes. Numerical simulations and acoustic measurements were conducted to evaluate the response of a commercial contrast agent (Targestar-P(®)) to chirp-coded and sine-burst excitation (10 MHz frequency, peak pressures 290 kPa). The results of the acoustic measurements revealed an improvement in signal-to-noise ratio by 4 to 14 dB, and a two- to threefold reduction in the subharmonic threshold with chirp-coded excitation. Simulations conducted with the Marmottant model suggest that an increase in expansion-dominated radial excursion of microbubbles was the mechanism responsible for the stronger nonlinear response. Additionally, chirp-coded excitation detected the nonlinear response for a wider range of agent concentrations than sine-bursts. Therefore, chirp-coded excitation could be a viable approach for enhancing the performance of HI and SHI.

Synchrony of two uncoupled neurons under half wave sine current stimulation

NASA Astrophysics Data System (ADS)

Peng, Yueping; Wang, Jue; Jian, Zhong

2009-04-01

Two uncoupled Hindmarsh-Rose neurons under different initial discharge patterns are stimulated by the half wave sine current; and the synchronization mechanism of the two neurons is discussed by analyzing their membrane potentials and their interspike interval (ISI) distribution. Under the half wave sine current stimulation, the two uncoupled neurons under different initial conditions, whose parameter r (the parameter r is related to the membrane penetration of calcium ion, and reflects the changing speed of the slow adaptation current) is different or the same, can realize discharge synchronization (phase synchronization) or the full synchronization (state synchronization). The synchronization characteristics are mainly related to the frequency and the amplitude of the half wave sine current, and are little related to the parameter r and the initial state of the two neurons. This investigation shows the mechanism of the current's amplitude and its frequency affecting the synchronization process of neurons, and the neurons' discharge patterns and synchronization process can be adjusted and controlled by the current's amplitude and its frequency. This result is of far reaching importance to study synchronization and encode of many neurons or neural network, and provides the theoretic basis for studying the mechanism of some nervous diseases such as epilepsy and Alzheimer's disease by the slow wave of EEG.

Hole-assisted fiber based fiber fuse terminator supporting 22 W input

NASA Astrophysics Data System (ADS)

Tsujikawa, Kyozo; Kurokawa, Kenji; Hanzawa, Nobutomo; Nozoe, Saki; Matsui, Takashi; Nakajima, Kazuhide

2018-05-01

We investigated the air hole structure in hole-assisted fiber (HAF) with the aim of terminating fiber fuse propagation. We focused on two structural parameters c/MFD and S1/S2, which are related respectively to the position and area of the air holes, and mapped their appropriate values for terminating fiber fuse propagation. Here, MFD is the mode field diameter, c is the diameter of an inscribed circle linking the air holes, S1 is the total area of the air holes, and S2 is the area of a circumscribed circle linking the air holes. On the basis of these results, we successfully realized a compact fiber fuse terminator consisting of a 1.35 mm-long HAF, which can terminate fiber fuse propagation even with a 22 W input. In addition, we observed fiber fuse termination using a high-speed camera. We additionally confirmed that the HAF-based fiber fuse terminator is effective under various input power conditions. The penetration length of the optical discharge in the HAF was only less than 300 μm when the input power was from 2 to 22 W.

A Cross-Sectional Study of the Effect of Quality Circles on Twelve Attitudinal Variables.

DTIC Science & Technology

1985-09-01

task of rebuilding its industrial capabilities which had been largely destroyed during the war. Japanese leaders had a goal of making their country an...members, providing support when necessary, and acting as a liaison between the circles and other organizations. The circle leader or supervisor...34" " .-.-- • .- .".-",,-, . -.- -,: ".’-"’ -. -. .,-’,: Top & Middle - Management Steering Committee Supervisors . . . ....- Circle Circle Leaders Facilitator Employees Circle Members Source

Circles of support and accountability: The characteristics of core members in England and Wales.

PubMed

Clarke, Martin; Warwick, Leah; Völlm, Birgit

2017-04-01

Circles of support and accountability, or Circles, use community volunteers to help reintegrate sex offenders at risk of reoffending in the community. The aims of this study are to describe the first 275 male sex offenders ('core members') in England and Wales supported by a Circle and to compare those attending the five largest Circles. As part of their monitoring activity, 10 Circles extracted data from case files, anonymised it and submitted it to Circles UK, the national oversight body. Circles have expanded rapidly with 165 (60%) of Circles commencing in the three years 2011-2013 compared with 110 in the nine years 2002-2010. Most core members were referred from the Probation Service (82%). Circles were provided to men with a range of predicted risks of reoffending - from low (26%) to very high (12%). There were some positive changes between the beginning and end of Circles, such as fewer men being unemployed and more living in their own chosen accommodation. Circles have been used to support the reintegration of a wide range of sex offenders. Given their rapid growth and flexibility, consistent recording standards are required across. These standards should be reviewed periodically to ensure all important fields of change are captured, including frequency of attendance, length per session and quality of engagement in the work. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Three Concentric Circles: Young Chinese English Learners' Perceptions of Purposeful Audiences

ERIC Educational Resources Information Center

Liu, Jack Jinghui

2015-01-01

English learners have more access to communicate with different purposeful audiences across the Three Concentric Circles of English (Kachu, 1985): the Inner Circle, the Outer Circle and the Expanding Circle. However, young language learners' purposeful audience as a focus of communication has not been emphasized as much as other linguistic…

Procedure for normalization of cDNA libraries

DOEpatents

Bonaldo, M.D.; Soares, M.B.

1997-12-30

This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library. 1 fig.

Closed Circular Chains

ERIC Educational Resources Information Center

Caglayan, Günhan

2016-01-01

A Steiner chain is defined as the sequence of n circles that are all tangent to two given non-intersecting circles. A closed chain, in particular, is one in which every circle in the sequence is tangent to the previous and next circles of the chain. In a closed Steiner chain the first and the "n"th circles of the chain are also tangent…

The Director Circle of a Central Conic Section

ERIC Educational Resources Information Center

Ayoub, Ayoub B.

2007-01-01

Each ellipse and hyperbola has a circle associated with it called the director circle. In this article, the author derives the equations of the circle for the ellipse and hyperbola through a different approach. Then the author concentrates on the director circle of the central conic given by the general quadratic equation. The content of this…

[Short interspersed repetitive sequences (SINEs) and their use as a phylogenetic tool].

PubMed

Kramerov, D A; Vasetskiĭ, N S

2009-01-01

The data on one of the most common repetitive elements of eukaryotic genomes, short interspersed elements (SINEs), are reviewed. Their structure, origin, and functioning in the genome are discussed. The variation and abundance of these neutral genomic markers makes them a convenient and reliable tool for phylogenetic analysis. The main methods of such analysis are presented, and the potential and limitations of this approach are discussed using specific examples.

On the solution of the generalized wave and generalized sine-Gordon equations

NASA Technical Reports Server (NTRS)

Ablowitz, M. J.; Beals, R.; Tenenblat, K.

1986-01-01

The generalized wave equation and generalized sine-Gordon equations are known to be natural multidimensional differential geometric generalizations of the classical two-dimensional versions. In this paper, a system of linear differential equations is associated with these equations, and it is shown how the direct and inverse problems can be solved for appropriately decaying data on suitable lines. An initial-boundary value problem is solved for these equations.

B-spline goal-oriented error estimators for geometrically nonlinear rods

DTIC Science & Technology

2011-04-01

respectively, for the output functionals q2–q4 (linear and nonlinear with the trigonometric functions sine and cosine) in all the tests considered...of the errors resulting from the linear, quadratic and nonlinear (with trigonometric functions sine and cosine) outputs and for p = 1, 2. If the... Portugal . References [1] A.T. Adams. Sobolev Spaces. Academic Press, Boston, 1975. [2] M. Ainsworth and J.T. Oden. A posteriori error estimation in

Formation of Large-Amplitude Wave Groups in an Experimental Model Basin

DTIC Science & Technology

2008-08-01

varying parameters, including amplitude, frequency, and signal duration. Superposition of thes finite regular waves produced repeatable wave groups at a...19 Regular Waves 20 Irregular Waves 21 Senix Wave Gages 21 GLRP 23 Instrumentation Calibration and Uncertainty 26 Senix Ultrasonic Wave Gages... signal output from sine wave superposition, two sine waves combined: x] + x2 (top) and x3 + x4 (middle), all four waves (x, + x2 + x, + xA

The long (LINEs) and the short (SINEs) of it: altered methylation as a precursor to toxicity.

PubMed

Carnell, Ammie N; Goodman, Jay I

2003-10-01

Although once thought of as "junk" DNA, the importance of interspersed elements in the genome has become increasingly appreciated in recent years. In a broad sense these are collectively referred to as transposable elements, which encompass both transposons and retrotransposons. The latter include long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). Expression of these elements leads to genetic instability. Therefore, it is important that they remain transcriptionally silenced, and DNA methylation plays a key role in this regard. A framework for understanding the possible interplay between altered DNA methylation, an epigenetic change, and mutational events is presented. A case is made as to how retrotransposable elements, specifically LINEs and SINEs, are likely to emerge as key players in furthering our understanding of mechanisms underlying a variety of toxicities, including carcinogenesis but not limited to this endpoint.

Generation and propagation of a sine-azimuthal wavefront modulated Gaussian beam

PubMed Central

Lao, Guanming; Zhang, Zhaohui; Luo, Meilan; Zhao, Daomu

2016-01-01

We introduce a method for modulating the Gaussian beam by means of sine-azimuthal wavefront and carry out the experimental generation. The analytical propagation formula of such a beam passing through a paraxial ABCD optical system is derived, by which the intensity properties of the sine-azimuthal wavefront modulated Gaussian (SWMG) beam are examined both theoretically and experimentally. Both of the experimental and theoretical results show that the SWMG beam goes through the process from beam splitting to a Gaussian-like profile, which is closely determined by the phase factor and the propagation distance. Appropriate phase factor and short distance are helpful for the splitting of beam. However, in the cases of large phase factor and focal plane, the intensity distributions tend to take a Gaussian form. Such unique features may be of importance in particle trapping and medical applications. PMID:27443798

Vibration testing of the JE-M-604-4-IUE rocket motor (Thiokol P/N E 28639-03)

NASA Technical Reports Server (NTRS)

Alt, R. E.; Tosh, J. T.

1976-01-01

The NASA International Ultraviolet Explorer (IUE) rocket motor (TE-M-604-4), a solid fuel, spherical rocket motor, was vibration tested in the Impact, Vibration, and Acceleration (IVA) Test Unit of the von Karman Gas Dynamics Facility (VKF). The objective of the test program was to subject the motor to qualification levels of sinusoidal and random vibration prior to the altitude firing of the motor in the Propulsion Development Test Cell (T-3), Engine Test Facility (ETF), AEDC. The vibration testing consisted of a low level sine survey from 5 to 2,000 Hz, followed by a qualification level sine sweep and qualification level random vibration. A second low level sine survey followed the qualification level testing. This sequence of testing was accomplished in each of three orthogonal axes. No motor problems were observed due to the imposition of these dynamic environments.

Qualitative and semiquantitative Fourier transformation using a noncoherent system.

PubMed

Rogers, G L

1979-09-15

A number of authors have pointed out that a system of zone plates combined with a diffuse source, transparent input, lens, and focusing screen will display on the output screen the Fourier transform of the input. Strictly speaking, the transform normally displayed is the cosine transform, and the bipolar output is superimposed on a dc gray level to give a positive-only intensity variation. By phase-shifting one zone plate the sine transform is obtained. Temporal modulation is possible. It is also possible to redesign the system to accept a diffusely reflecting input at the cost of introducing a phase gradient in the output. Results are given of the sine and cosine transforms of a small circular aperture. As expected, the sine transform is a uniform gray. Both transforms show unwanted artifacts beyond 0.1 rad off-axis. An analysis shows this is due to unwanted circularly symmetrical moire patterns between the zone plates.

Dark Circles under Eyes

MedlinePlus

Symptoms Dark circles under eyes By Mayo Clinic Staff Dark circles under your eyes generally implies that the darkening ... eye. Fatigue is the most common cause of dark circles under your eyes. Sometimes, what appear to ...

Visual motion transforms visual space representations similarly throughout the human visual hierarchy.

PubMed

Harvey, Ben M; Dumoulin, Serge O

2016-02-15

Several studies demonstrate that visual stimulus motion affects neural receptive fields and fMRI response amplitudes. Here we unite results of these two approaches and extend them by examining the effects of visual motion on neural position preferences throughout the hierarchy of human visual field maps. We measured population receptive field (pRF) properties using high-field fMRI (7T), characterizing position preferences simultaneously over large regions of the visual cortex. We measured pRFs properties using sine wave gratings in stationary apertures, moving at various speeds in either the direction of pRF measurement or the orthogonal direction. We find direction- and speed-dependent changes in pRF preferred position and size in all visual field maps examined, including V1, V3A, and the MT+ map TO1. These effects on pRF properties increase up the hierarchy of visual field maps. However, both within and between visual field maps the extent of pRF changes was approximately proportional to pRF size. This suggests that visual motion transforms the representation of visual space similarly throughout the visual hierarchy. Visual motion can also produce an illusory displacement of perceived stimulus position. We demonstrate perceptual displacements using the same stimulus configuration. In contrast to effects on pRF properties, perceptual displacements show only weak effects of motion speed, with far larger speed-independent effects. We describe a model where low-level mechanisms could underlie the observed effects on neural position preferences. We conclude that visual motion induces similar transformations of visuo-spatial representations throughout the visual hierarchy, which may arise through low-level mechanisms. Copyright © 2015 Elsevier Inc. All rights reserved.

Development of Maps of Simple and Complex Cells in the Primary Visual Cortex

PubMed Central

Antolík, Ján; Bednar, James A.

2011-01-01

Hubel and Wiesel (1962) classified primary visual cortex (V1) neurons as either simple, with responses modulated by the spatial phase of a sine grating, or complex, i.e., largely phase invariant. Much progress has been made in understanding how simple-cells develop, and there are now detailed computational models establishing how they can form topographic maps ordered by orientation preference. There are also models of how complex cells can develop using outputs from simple cells with different phase preferences, but no model of how a topographic orientation map of complex cells could be formed based on the actual connectivity patterns found in V1. Addressing this question is important, because the majority of existing developmental models of simple-cell maps group neurons selective to similar spatial phases together, which is contrary to experimental evidence, and makes it difficult to construct complex cells. Overcoming this limitation is not trivial, because mechanisms responsible for map development drive receptive fields (RF) of nearby neurons to be highly correlated, while co-oriented RFs of opposite phases are anti-correlated. In this work, we model V1 as two topographically organized sheets representing cortical layer 4 and 2/3. Only layer 4 receives direct thalamic input. Both sheets are connected with narrow feed-forward and feedback connectivity. Only layer 2/3 contains strong long-range lateral connectivity, in line with current anatomical findings. Initially all weights in the model are random, and each is modified via a Hebbian learning rule. The model develops smooth, matching, orientation preference maps in both sheets. Layer 4 units become simple cells, with phase preference arranged randomly, while those in layer 2/3 are primarily complex cells. To our knowledge this model is the first explaining how simple cells can develop with random phase preference, and how maps of complex cells can develop, using only realistic patterns of connectivity. PMID:21559067

Planning-free cerebral blood flow territory mapping in patients with intracranial arterial stenosis

PubMed Central

Arteaga, Daniel F; Strother, Megan K; Davis, L Taylor; Fusco, Matthew R; Faraco, Carlos C; Roach, Brent A; Scott, Allison O

2016-01-01

A noninvasive method for quantifying cerebral blood flow and simultaneously visualizing cerebral blood flow territories is vessel-encoded pseudocontinuous arterial spin labeling MRI. However, obstacles to acquiring such information include limited access to the methodology in clinical centers and limited work on how clinically acquired vessel-encoded pseudocontinuous arterial spin labeling data correlate with gold-standard methods. The purpose of this work is to develop and validate a semiautomated pipeline for the online quantification of cerebral blood flow maps and cerebral blood flow territories from planning-free vessel-encoded pseudocontinuous arterial spin labeling MRI with gold-standard digital subtraction angiography. Healthy controls (n = 10) and intracranial atherosclerotic disease patients (n = 34) underwent 3.0 T MRI imaging including vascular (MR angiography) and hemodynamic (cerebral blood flow-weighted arterial spin labeling) MRI. Patients additionally underwent catheter and/or CT angiography. Variations in cross-territorial filling were grouped according to diameters of circle of Willis vessels in controls. In patients, Cohen’s k-statistics were computed to quantify agreement in perfusion patterns between vessel-encoded pseudocontinuous arterial spin labeling and angiography. Cross-territorial filling patterns were consistent with circle of Willis anatomy. The intraobserver Cohen's k-statistics for cerebral blood flow territory and digital subtraction angiography perfusion agreement were 0.730 (95% CI = 0.593–0.867; reader one) and 0.708 (95% CI = 0.561–0.855; reader two). These results support the feasibility of a semiautomated pipeline for evaluating major neurovascular cerebral blood flow territories in patients with intracranial atherosclerotic disease. PMID:27389177

A Measurement of the Galaxy Group-Thermal Sunyaev-Zel’dovich Effect Cross-Correlation Function

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

Vikram, Vinu; Lidz, Adam; Jain, Bhuvnesh

2017-01-09

Stacking cosmic microwave background maps around known galaxy clusters and groups provides a powerful probe of the distribution of hot gas in these systems via the Sunyaev-Zel'dovich (SZ) effect. A stacking analysis allows one to detect the average SZ signal around low-mass haloes, to extend measurements out to large scales and measure the redshift dependence of the SZ background. Motivated by these exciting prospects, we measure the two-point cross-correlation function between similar to 380 000 galaxy groups (at z = 0.01-0.2) from the Sloan Digital Sky Survey and Compton-y parameter maps constructed by the Planck collaboration. We find statistically significantmore » correlations in each of six separate mass bins, with halo masses ranging from 1011.5 to 1015.5 M(circle dot)h(-1). We compare with halo models of the SZ signal, which describe the stacked measurement in terms of one-halo and two-halo contributions. The onehalo term quantifies the average pressure profile around the groups in a mass bin, while the two-halo term describes the contribution of correlated neighbouring haloes. For the massive groups, we find clear evidence for the one-and two-halo regimes, while groups with mass below 1013M(circle dot)h(-1) are dominated by the two-halo term, given the resolution of Planck data. We use the signal in the two-halo regime to determine the bias-weighted electron pressure of the Universe: < bPe > = 1.50 +/- 0.226 x 10(-7) keV cm(-3) (sigma) at z approximate to 0.15.« less

Study of the surface wave off-great-circle propagation based on dense seismic array: a case study in Northeast China

NASA Astrophysics Data System (ADS)

Chen, H.; Chong, J.

2016-12-01

The traditional surface wave tomography is based on the ray theory, which assumes that surface wave propagates along the great-circle. The great-circle assumption is valid only when the size of the anomaly is larger than the width of the Fresnel zone and the lateral variation is relatively smooth. However, off-great-circle propagation may occur when the surface wave travels across tectonic boundaries with strong heterogeneity and sharp velocity change, e.g., continental margin, mid-ridge and sea trench, resulting in arrival angle anomaly and multi-pathing effect. The off-great-circle propagation may deviate the result of surface wave tomography based on great-circle approximation, so it is of great importance to study the off-great-circle propagation. In this study, we used the teleseismic waveforms from September 2009 to August 2011, recorded by the NECESSArray in Northeast China, to study the off-great-circle propagation of Rayleigh wave by the Beamforming method. Our results show that the off-great-circle effect increases with decreasing period. At the period of 60 s, the off-great-circle effect is relatively weak and the Rayleigh wave propagates approximately along the great-circle. While at the period of 20 s, the off-great-circle effect becomes strong, the arrival angle anomaly measured from some events can be as large as 20º, and obvious multi-pathing effect is also observed. Lateral variations of the arrival angle anomaly and phase velocity have also been found in the study region, which may be correlated with the lithosphere heterogeneity in Northeast China. Our results demonstrate the necessity to study the surface wave off-great-circle propagation. Acknowledgement: This study is financially supported by National Natural Science Foundation of China under Grant No. 41590854.

Classification by causes of dark circles and appropriate evaluation method of dark circles.

PubMed

Park, S R; Kim, H J; Park, H K; Kim, J Y; Kim, N S; Byun, K S; Moon, T K; Byun, J W; Moon, J H; Choi, G S

2016-08-01

Dark circles refer to a symptom that present darkness under the eyes. Because of improvement in the quality of life, the dark circles have been recognized as one of major cosmetic concerns. However, it is not easy to classify the dark circles because they have various causes. To select suitable instruments and detailed evaluation items, the dark circles were classified according to the causes through visual assessment, Wood's lamp test, and medical history survey for 100 subjects with dark circles. After the classification, were newly recruited for instrument conformity assessment. Through this, suitable instruments for dark circle evaluation were selected. We performed a randomized clinical trial for dark circles, a placebo-controlled double-blind study, using effective parameters of the instruments selected from the preliminary test. Dark circles of vascular type (35%) and mixed type (54%), a combination of pigmented and vascular types, were the most common. Twenty four subjects with the mixed type dark circles applied the test product (Vitamin C 3%, Vitamin A 0.1%, Vitamin E 0.5%) and placebo on randomized split-face for 8 weeks. The effective parameters (L*, a, M.I., E.I., quasi L*, quasi a* and dermal thickness) were measured during the study period. Result showed that the L* value of Chromameter(®) , Melanin index (M.I.) of Mexameter(®) and quasi L* value obtained by image analysis improved with statistical significance after applying the test product compared with the placebo product. We classified the dark circles according to the causes of the dark circles and verified the reliability of the parameter obtained by the instrument conformity assessment used in this study through the efficacy evaluation. Also based on this study, we were to suggest newly established methods which can be applied to the evaluation of efficacy of functional cosmetics for dark circles. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Arctic Circle Traverse 2010 (ACT-10): South East Greenland snow accumulation variability from firn coring and ice sounding radar

NASA Astrophysics Data System (ADS)

Forster, R. R.; Miege, C.; Box, J. E.; McConnell, J.; Spikes, V. B.; Burgess, E. W.

2010-12-01

The Greenland Ice Sheet plays an important role in Earth’s climate system evolution. The snow accumulation rate is the largest single mass budget term. With only 14% of the ice sheet area, Southeast Greenland contains the highest accumulation rates, accounting for one third of the total snow accumulation and annual variability. The high accumulation rates have made the region less desirable for long climate record ice cores and therefore, contain relatively very few in situ measurements to constrain the ice sheet mass budget. We present annual snow accumulation rates from the Arctic Circle Traverse 2010 (ACT-10). During April and May 2010 we acquired three 50 m firn cores connected by surface-based 400 MHz ground penetrating radar (GPR) in Southeast Greenland. The traverse repeated and extended the original Arctic Circle Traverse in 2004 (Spikes et al., 2004). Dating is achieved using geochemical analysis of the cores to identify isochronal layers detected by the GPR yielding annual accumulation estimates along the traverse between the core sites. The 300 km ACT-10 GPR snowmobile traverse extended the ACT-04 path 80 km to the lowest elevation core site at 1776 m. Meanwhile, airborne radars, operating as part of NASA’s Operation IceBridge also acquired data over the full length of the ACT-10 path, simultaneously with a portion of the traverse and within days for the remaining segments. The IceBridge and ACT-10 data are to be combined in a calibration effort such that snow accumulation rates may be mapped elsewhere in Greenland and even in Antarctica.

Comparison of sine dwell and broadband methods for modal testing

NASA Technical Reports Server (NTRS)

Chen, Jay-Chung

1989-01-01

The objectives of modal tests for large complex spacecraft structural systems are outlined. The comparison criteria for the modal test methods, namely, the broadband excitation and the sine dwell methods, are established. Using the Galileo spacecraft modal test and the Centaur G Prime upper stage vehicle modal test as examples, the relative advantage or disadvantage of each method is examined. The usefulness or shortcomings of the methods are given from a practical engineering viewpoint.

Electrostatic bonding of thin (cycle sine 3 mil) 7070 cover glass to Ta2O5 AR-coated thin (cycle sine 2 mil) silicon wafers and solar cells

NASA Technical Reports Server (NTRS)

Egelkrout, D. W.

1981-01-01

Electrostatic bonding of thin cover glass to thin solar cells was researched. Silicon solar cells, wafers, and Corning 7070 glass of from about 0.002" to about 0.003" in thickness were used in the investigation to establish optimum parameters for producing mechanically acceptable bonds while minimizing thermal stresses and resultant solar cell electrical parameter degradation.

Resonant circuit which provides dual-frequency excitation for rapid cycling of an electromagnet

DOEpatents

Praeg, W.F.

1982-03-09

Disclosed is a novel ring-magnet control circuit that permits synchrotron repetition rates much higher than the frequency of the sinusoidal guide field of the ring magnet during particle acceleration. The control circuit generates sinusoidal excitation currents of different frequencies in the half waves. During radio-frequency acceleration of the synchrotron, the control circuit operates with a lower frequency sine wave and, thereafter, the electromagnets are reset with a higher-frequency half sine wave.

Remote-Controlled Rotorcraft Blade Vibration and Modal Analysis at Low Frequencies

DTIC Science & Technology

2016-02-01

modal analysis, remote-controlled helicopter , remote-controlled rotorcraft, HUMS for rotorcraft 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...Experimental Setup 1 4. Results 4 4.1 Rotor Blade Acceleration 4 4.2 Modal Analysis: Using an Impact Hammer 7 4.3 Dynamic Response Revisited 8 5... Rotor blade response to shaker outputting 1-V sine wave at 100 Hz ....5 Fig. 6 Rotor blade response to shaker outputting 1-V sine sweep from 20- to 100

L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells.

PubMed

Dewannieux, Marie; Heidmann, Thierry

2005-06-03

SINEs are short interspersed nucleotide elements with transpositional activity, present at a high copy number (up to a million) in mammalian genomes. They are 80-400 bp long, non-coding sequences which derive either from the 7SL RNA (e.g. human Alus, murine B1s) or tRNA (e.g. murine B2s) polymerase III-driven genes. We have previously demonstrated that Alus very efficiently divert the enzymatic machinery of the autonomous L1 LINE (long interspersed nucleotide element) retrotransposons to transpose at a high rate. Here we show, using an ex vivo assay for transposition, that both B1 and B2 SINEs can be mobilized by murine LINEs, with the hallmarks of a bona fide retrotransposition process, including target site duplications of varying lengths and integrations into A-rich sequences. Despite different phylogenetic origins, transposition of the tRNA-derived B2 sequences is as efficient as that of the human Alus, whereas that of B1s is 20-100-fold lower despite a similar high copy number of these elements in the mouse genome. We provide evidence, via an appropriate nucleotide substitution within the B1 sequence in a domain essential for its intracellular targeting, that the current B1 SINEs are not optimal for transposition, a feature most probably selected for the host sake in the course of evolution.

Effects of Different Waveforms on the Performance of Active Capillary Dielectric Barrier Discharge Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Dumlao, Morphy C.; Xiao, Dan; Zhang, Daming; Fletcher, John; Donald, William A.

2017-04-01

Active capillary dielectric barrier discharge ionization (DBDI) is emerging as a compact, low-cost, and robust method to form intact ions of small molecules for detection in near real time by portable mass spectrometers. Here, we demonstrate that by using a 10 kHz, 2.5 kVp-p high-voltage square-wave alternating current plasma, active capillary DBDI can consume less than 1 μW of power. In contrast, the power consumed using a sine and triangle alternating current waveform is more than two orders of magnitude higher than that for the square waveform to obtain a similar voltage for plasma generation. Moreover, the plasma obtained using a square waveform can be significantly more homogenous than that obtained using sine and triangle waveforms. Protonated dimethyl methylphosphonate (DMMP) and deprotonated perfluorooctanoic acid (PFOA) can be detected at about the same or higher abundances using square-wave DBDI mass spectrometry compared with the use of sine and triangle waveforms. By use of benzylammonium thermometer ions, the extent of internal energy deposition using square, sine, or triangle waveform excited plasmas are essentially the same at the optimum voltages for ion detection. Using an H-bridge circuit driving a transformer optimized to reduce losses, square-wave active capillary DBDI can be continuously powered for 50 h by common 9 V-battery (PP3).

Gene conversion as a secondary mechanism of short interspersed element (SINE) evolution

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

Kass, D.H.; Batzer, M.A.; Deininger, P.L.

The Alu repetitive family of short interspersed elements (SINEs) in primates can be subdivided into distinct subfamilies by specific diagnostic nucleotide changes. The older subfamilies are generally very abundant, while the younger subfamilies have fewer copies. Some of the youngest Alu elements are absent in the orthologous loci of nonhuman primates, indicative of recent retroposition events, the primary mode of SINE evolutions. PCR analysis of one young Alu subfamily (Sb2) member found in the low-density lipoprotein receptor gene apparently revealed the presence of this element in the green monkey, orangutan, gorilla, and chimpanzee genomes, as well as the human genome.more » However, sequence analysis of these genomes revealed a highly mutated, older, primate-specific Alu element was present at this position in the nonhuman primates. Comparison of the flanking DNA sequences upstream of this Alu insertion corresponded to evolution expected for standard primate phylogeny, but comparison of the Alu repeat sequences revealed that the human element departed from this phylogeny. The change in the human sequence apparently occurred by a gene conversion event only within the Alu element itself, converting it from one of the oldest to one of the youngest Alu subfamilies. Although gene conversions of Alu elements are clearly very rare, this finding shows that such events can occur and contribute to specific cases of SINE subfamily evolution.« less

ComVisMD - compact visualization of multidimensional data: experimenting with cricket players data

NASA Astrophysics Data System (ADS)

Dandin, Shridhar B.; Ducassé, Mireille

2018-03-01

Database information is multidimensional and often displayed in tabular format (row/column display). Presented in aggregated form, multidimensional data can be used to analyze the records or objects. Online Analytical database Processing (OLAP) proposes mechanisms to display multidimensional data in aggregated forms. A choropleth map is a thematic map in which areas are colored in proportion to the measurement of a statistical variable being displayed, such as population density. They are used mostly for compact graphical representation of geographical information. We propose a system, ComVisMD inspired by choropleth map and the OLAP cube to visualize multidimensional data in a compact way. ComVisMD displays multidimensional data like OLAP Cube, where we are mapping an attribute a (first dimension, e.g. year started playing cricket) in vertical direction, object coloring based on b (second dimension, e.g. batting average), mapping varying-size circles based on attribute c (third dimension, e.g. highest score), mapping numbers based on attribute d (fourth dimension, e.g. matches played). We illustrate our approach on cricket players data, namely on two tables Country and Player. They have a large number of rows and columns: 246 rows and 17 columns for players of one country. ComVisMD’s visualization reduces the size of the tabular display by a factor of about 4, allowing users to grasp more information at a time than the bare table display.

Quality circles: Organizational adaptations, improvements and results

NASA Technical Reports Server (NTRS)

Tortorich, R.

1985-01-01

The effective application in industry and government of quality circles work was demonstrated. The results achieved in quality and productivity improvements and cost savings are impressive. The circle process should be institutionalized within industry and government. The stages of circle program growth, innovations that help achieve circle process institutionalization, and the result achieved at Martin Marietta's Michoud Division and within the National Aeronautics and Space Administration (NASA) are addressed.

A Nuclear Attack on Traumatic Brain Injury: Sequestration of Cell Death in the Nucleus.

PubMed

Tajiri, Naoki; De La Peña, Ike; Acosta, Sandra A; Kaneko, Yuji; Tamir, Sharon; Landesman, Yosef; Carlson, Robert; Shacham, Sharon; Borlongan, Cesar V

2016-04-01

Exportin 1 (XPO1/CRM1) plays prominent roles in the regulation of nuclear protein export. Selective inhibitors of nuclear export (SINE) are small orally bioavailable molecules that serve as drug-like inhibitors of XPO1, with potent anti-cancer properties. Traumatic brain injury (TBI) presents with a secondary cell death characterized by neuroinflammation that is putatively regulated by nuclear receptors. Here, we report that the SINE compounds (KPT-350 or KPT-335) sequestered TBI-induced neuroinflammation-related proteins (NF-(k)B, AKT, FOXP1) within the nucleus of cultured primary rat cortical neurons, which coincided with protection against TNF-α (20 ng/mL)-induced neurotoxicity as shown by at least 50% and 100% increments in preservation of cell viability and cellular enzymatic activity, respectively, compared to non-treated neuronal cells (P's < 0.05). In parallel, using an in vivo controlled cortical impact (CCI) model of TBI, we demonstrate that adult Sprague-Dawley rats treated post-injury with SINE compounds exhibited significant reductions in TBI-induced behavioral and histological deficits. Animals that received KPT-350 orally starting at 2 h post-TBI and once a day thereafter over the next 4 days exhibited significantly better motor coordination, and balance in the rotorod test and motor asymmetry test by 100-200% improvements, as early as 4 h after initial SINE compound injection that was sustained during subsequent KPT-350 dosing, and throughout the 18-day post-TBI study period compared to vehicle treatment (P's < 0.05). Moreover, KPT-350 reduced cortical core impact area and peri-impact cell death compared to vehicle treatment (P's < 0.05). Both in vitro and in vivo experiments revealed that KPT-350 increased XPO1, AKT, and FOXP1 nuclear expression and relegated NF-(k)B expression within the neuronal nuclei. Altogether, these findings advance the utility of SINE compounds to stop trafficking of cell death proteins within the nucleus as an efficacious treatment for TBI. © 2016 John Wiley & Sons Ltd.

Participant Experiences of Talking Circles on Type 2 Diabetes in Two Northern Plains American Indian Tribes

PubMed Central

Struthers, Roxanne; Hodge, Felicia Schanche; Geishirt-Cantrell, Betty; De Cora, Lorelei

2011-01-01

The Talking Circle, a culturally appropriate, 12-week educational intervention, was employed on two Northern Plains American Indian reservations to provide information on type 2 diabetes. In a phenomenological study, funded as a minority supplement to the Talking Circle intervention, the authors asked 8 American Indian participants of the Talking Circle to describe their experience of being an American Indian Talking Circle participant. Seven common themes describe the phenomenon of participating in a Talking Circle diabetic intervention. The Talking Circle technique was effective in providing information on type 2 diabetes through culturally appropriate community sharing. Type 2 diabetes is viewed by both outsiders and those involved as a chronic disease of the utmost concern in American Indian communities. PMID:14556421

Elements of the quality management in the materials' industry

NASA Astrophysics Data System (ADS)

Ioana, Adrian; Semenescu, Augustin; Costoiu, Mihnea; Marcu, Dragoş

2017-12-01

The criteria function concept consists of transforming the criteria function (CF) in a quality-economical matrix math MQE. The levels of prescribing the criteria function was obtained by using a composition algorithm for three vectors: T¯ vector - technical parameters' vector (ti); Ē vector - economical parameters' vector (ej) and P¯ vector - weight vector (p1). For each product or service, the area of the circle represents the value of its sales. The BCG Matrix thus offers a very useful map of the organization's service strengths and weaknesses, at least in terms of current profitability, as well as the likely cash flows.

Angle measures, general rotations, and roulettes in normed planes

NASA Astrophysics Data System (ADS)

Balestro, Vitor; Horváth, Ákos G.; Martini, Horst

2017-12-01

In this paper a special group of bijective maps of a normed plane (or, more generally, even of a plane with a suitable Jordan curve as unit circle) is introduced which we call the group of general rotations of that plane. It contains the isometry group as a subgroup. The concept of general rotations leads to the notion of flexible motions of the plane, and to the concept of Minkowskian roulettes. As a nice consequence of this new approach to motions the validity of strong analogues to the Euler-Savary equations for Minkowskian roulettes is proved.

ERRATUM: 'MAPPING THE GAS TURBULENCE IN THE COMA CLUSTER: PREDICTIONS FOR ASTRO-H'

NASA Technical Reports Server (NTRS)

Zuhone, J. A.; Markevitch, M.; Zhuravleva, I.

2016-01-01

The published version of this paper contained an error in Figure 5. This figure is intended to show the effect on the structure function of subtracting the bias induced by the statistical and systematic errors on the line shift. The filled circles show the bias-subtracted structure function. The positions of these points in the left panel of the original figure were calculated incorrectly. The figure is reproduced below (with the original caption) with the correct values for the bias-subtracted structure function. No other computations or figures in the original manuscript are affected.

The business of relief work: a Victorian Quaker in Constantinople and her circle.

PubMed

Tusan, Michelle

2009-01-01

This article explores how Victorian notions of charity translated to evangelical mission projects in the Near East. Focusing on Quaker philanthropist Ann Mary Burgess, it traces the trade networks that she established to serve the Armenian community living in the Ottoman Empire. Burgess's vast network of supporters throughout Britain, Europe, and the Near East enabled her to fund relief projects using profits from goods produced by the orphans and widows served by the Friends' Constantinople Mission. The mapping of these networks reveals the evolving relationship between evangelicalism, the humanitarian movement, and the marketplace in imperial Britain.

Made-in-USA Quality Circles Become People-Building Tool.

ERIC Educational Resources Information Center

Cohen, Larry

1983-01-01

Discusses the use of quality circles as a human resources development tool in Middlesex Community College's Career-Oriented Peer Services tutoring center. Delineates rules for circle participants and follows the activities of two circles comprised of business-oriented and engineering-oriented students. (DMM)

Operational improvements at traffic circles : safety analysis, final report, December 2008.

DOT National Transportation Integrated Search

2008-12-01

The purpose of this study was to improve the safety and operation at three traffic circles in New : Jersey. To do this, data were collected at the traffic circles to allow researchers to model the : circles using the PARAMICS software simulation pack...

On sine dwell or broadband methods for modal testing

NASA Technical Reports Server (NTRS)

Chen, Jay-Chung; Wada, Ben K.

1987-01-01

For large, complex spacecraft structural systems, the objectives of the modal test are outlined. Based on these objectives, the comparison criteria for the modal test methods, namely, the broadband excitation and the sine dwell methods are established. Using the Galileo spacecraft modal test and the Centaur G Prime upper stage vehicle modal test as examples, the relative advantages or disadvantages of each method are examined. The usefulness or shortcoming of the methods are given from a practicing engineer's view point.

Sines and Cosines. Part 2 of 3

NASA Technical Reports Server (NTRS)

Apostol, Tom M. (Editor)

1993-01-01

The Law of Sines and the Law of Cosines are introduced and demonstrated in this 'Project Mathematics' series video using both film footage and computer animation. This video deals primarily with the mathematical field of Trigonometry and explains how these laws were developed and their applications. One significant use is geographical and geological surveying. This includes both the triangulation method and the spirit leveling method. With these methods, it is shown how the height of the tallest mountain in the world, Mt. Everest, was determined.

Quantum corrections to quasi-periodic solution of Sine-Gordon model and periodic solution of phi4 model

NASA Astrophysics Data System (ADS)

Kwiatkowski, G.; Leble, S.

2014-03-01

Analytical form of quantum corrections to quasi-periodic solution of Sine-Gordon model and periodic solution of phi4 model is obtained through zeta function regularisation with account of all rest variables of a d-dimensional theory. Qualitative dependence of quantum corrections on parameters of the classical systems is also evaluated for a much broader class of potentials u(x) = b2f(bx) + C with b and C as arbitrary real constants.

Hilbertian sine as an absolute measure of Bayesian inference in ISR, homeland security, medicine, and defense

NASA Astrophysics Data System (ADS)

Jannson, Tomasz; Wang, Wenjian; Hodelin, Juan; Forrester, Thomas; Romanov, Volodymyr; Kostrzewski, Andrew

2016-05-01

In this paper, Bayesian Binary Sensing (BBS) is discussed as an effective tool for Bayesian Inference (BI) evaluation in interdisciplinary areas such as ISR (and, C3I), Homeland Security, QC, medicine, defense, and many others. In particular, Hilbertian Sine (HS) as an absolute measure of BI, is introduced, while avoiding relativity of decision threshold identification, as in the case of traditional measures of BI, related to false positives and false negatives.

Frequency Response Evaluation of Multiple Accelerometers Using a Modal Data Acquisition System

DTIC Science & Technology

1988-01-01

Computedi PCB @80 HZ 49mv/g 1@500 HZ 9.3mv/g lImp-sine Ifrom Imp-sine SN (2)V/g figureIV/g figure jV/g l(V/ gpk )xl.414(2)1 857 1 1.17 42 1 1.17 3 1.20 1.20...per g rms, V/ gpk = volts rms per g peak. 15 II Laboratory Transfer Function Procedures - 1. Setup and Power up equipment. a. Setup equipment per

A fast Karhunen-Loeve transform for a class of random processes

NASA Technical Reports Server (NTRS)

Jain, A. K.

1976-01-01

It is shown that for a class of finite first-order Markov signals, the Karhunen-Loeve (KL) transform for data compression is a set of periodic sine functions if the boundary values of the signal are fixed or known. These sine functions are shown to be related to the Fourier transform so that a fast Fourier transform algorithm can be used to implement the KL transform. Extension to two dimensions with reference to images with separable contravariance function is shown.

Labor Resource Audit and Analysis: A Tool for Management Planning and Control

DTIC Science & Technology

1989-06-01

RM(onn17 COSA~ CODES B 5OBJECT TERMS (Continge pn rev@rj !~cea and f, entfa y.block R V FIELD GROUP SUB-GROUP re-; P anning; labor; ugLr og; a e...David 1 hplr., chairman Department of Admi srtv Sine KnealeT-Mg;fi Dea ofInformation and-ln sine ii ABSTRACT This study was conducted in an effort to...Audit ---------------------------------- 84 viii ACKNOWLEDGMENTS A wide variety of authorities in their field have contributed material to this study. I

Multifocal amelanotic conjunctival melanoma and acquired melanosis sine pigmento.

PubMed Central

Paridaens, A D; McCartney, A C; Hungerford, J L

1992-01-01

Clinical and histopathological features of four cases of multifocal amelanotic malignant melanoma of the conjunctiva in association with 'acquired melanosis sine pigmento' are reported. The absence of conjunctival pigmentation in this extremely rare combination of lesions prevented early diagnosis and clinical monitoring. As a result orbital exenteration was required in three cases. This multicentric non-pigmented variety of conjunctival malignant melanoma tends to present later than pigmented forms and may require exenteration of the orbit as a primary procedure. Images PMID:1540561

Multifocal amelanotic conjunctival melanoma and acquired melanosis sine pigmento.

PubMed

Paridaens, A D; McCartney, A C; Hungerford, J L

1992-03-01

Clinical and histopathological features of four cases of multifocal amelanotic malignant melanoma of the conjunctiva in association with 'acquired melanosis sine pigmento' are reported. The absence of conjunctival pigmentation in this extremely rare combination of lesions prevented early diagnosis and clinical monitoring. As a result orbital exenteration was required in three cases. This multicentric non-pigmented variety of conjunctival malignant melanoma tends to present later than pigmented forms and may require exenteration of the orbit as a primary procedure.

Numerical analysis of soliton solutions of the modified Korteweg-de Vries-sine-Gordon equation

NASA Astrophysics Data System (ADS)

Popov, S. P.

2015-03-01

Multisoliton solutions of the modified Korteweg-de Vries-sine-Gordon equation (mKdV-SG) are found numerically by applying the quasi-spectral Fourier method and the fourth-order Runge-Kutta method. The accuracy and features of the approach are determined as applied to problems with initial data in the form of various combinations of perturbed soliton distributions. Three-soliton solutions are obtained, and the generation of kinks, breathers, wobblers, perturbed kinks, and nonlinear oscillatory waves is studied.

Evaluation of quasi-square wave inverter as a power source for induction motors

NASA Technical Reports Server (NTRS)

Guynes, B. V.; Haggard, R. L.; Lanier, J. R., Jr.

1977-01-01

The relative merits of quasi-square wave inverter-motor technology versus a sine wave inverter-motor system were investigated. The empirical results of several tests on various sizes of wye-wound induction motors are presented with mathematical analysis to support the conclusions of the study. It was concluded that, within the limitations presented, the quasi-square wave inverter-motor system is superior to the more complex sine wave system for most induction motor applications in space.

Soil Biota and Litter Decay in High Arctic Ecosystems

NASA Astrophysics Data System (ADS)

González, G.; Rivera, F.; Makarova, O.; Gould, W. A.

2006-12-01

Frost heave action contributes to the formation of non-sorted circles in the High Arctic. Non-sorted circles tend to heave more than the surrounding tundra due to deeper thaw and the formation of ice lenses. Thus, the geomorphology, soils and vegetation on the centers of the patterned-ground feature (non-sorted circles) as compared to the surrounding soils (inter-circles) can be different. We established a decomposition experiment to look at in situ decay rates of the most dominant graminoid species on non-sorted circles and adjacent inter-circle soils along a climatic gradient in the Canadian High Arctic as a component of a larger study looking at the biocomplexity of small-featured patterned ground ecosystems. Additionally, we investigated variation in soil chemical properties and biota, including soil microarthropods and microbial composition and biomass, as they relate to climate, topographic position, and litter decay rates. Our three sites locations, from coldest to warmest, are Isachsen, Ellef Ringnes Island (ER), NU (bioclimatic subzone A); Mould Bay (MB), Prince Patrick Island, NT (bioclimatic subzone B), and Green Cabin (GC), Aulavik National Park, Thomsen River, Banks Island, NT (bioclimatic subzone C). Our sample design included the selection of 15 non-sorted circles and adjacent inter-circle areas within the zonal vegetation at each site (a total of 90 sites), and a second set of 3 non-sorted circles and adjacent inter-circle areas in dry, mesic and wet tundra at each of the sites. Soil invertebrates were sampled at each site using both pitfall traps, soil microbial biomass was determined using substrate induced respiration and bacterial populations were determined using the most probable number method. Decomposition rates were measured using litterbags and as the percent of mass remaining of Carex misandra, Luzula nivalis and Alopecuris alpinus in GC, MB and ER, respectively. Our findings indicate these graminoid species decayed significantly over time at a rate of 10-15 % mass loss / yr during the first year of decay. Decay rates are different in non-sorted circles vs. inter-circle soils along the climatic gradient. In MB, L. nivalis seems to decay faster in the inter-circle soils than in non-sorted circles (0.05

Journey to the Edges: Social Structures and Neural Maps of Intergroup Processes

PubMed Central

Fiske, Susan T.

2013-01-01

This article explores boundaries of the intellectual map of intergroup processes, going to the macro (social structure) boundary and the micro (neural systems) boundary. Both are illustrated by with my own and others’ work on social structures and on neural structures related to intergroup processes. Analyzing the impact of social structures on intergroup processes led to insights about distinct forms of sexism and underlies current work on forms of ageism. The stereotype content model also starts with the social structure of intergroup relations (interdependence and status) and predicts images, emotions, and behaviors. Social structure has much to offer the social psychology of intergroup processes. At the other, less explored boundary, social neuroscience addresses the effects of social contexts on neural systems relevant to intergroup processes. Both social structural and neural analyses circle back to traditional social psychology as converging indicators of intergroup processes. PMID:22435843

Control theory based airfoil design for potential flow and a finite volume discretization

NASA Technical Reports Server (NTRS)

Reuther, J.; Jameson, A.

1994-01-01

This paper describes the implementation of optimization techniques based on control theory for airfoil design. In previous studies it was shown that control theory could be used to devise an effective optimization procedure for two-dimensional profiles in which the shape is determined by a conformal transformation from a unit circle, and the control is the mapping function. The goal of our present work is to develop a method which does not depend on conformal mapping, so that it can be extended to treat three-dimensional problems. Therefore, we have developed a method which can address arbitrary geometric shapes through the use of a finite volume method to discretize the potential flow equation. Here the control law serves to provide computationally inexpensive gradient information to a standard numerical optimization method. Results are presented, where both target speed distributions and minimum drag are used as objective functions.

M-theory superstrata and the MSW string

DOE PAGES

Bena, Iosif; Martinec, Emil; Turton, David; ...

2017-06-26

The low-energy description of wrapped M5 branes in compactifications of M-theory on a Calabi-Yau threefold times a circle is given by a conformal field theory studied by Maldacena, Strominger and Witten and known as the MSW CFT. Taking the threefold to be T 6 or K3×T 2, we construct a map between a sub-sector of this CFT and a sub-sector of the D1-D5 CFT. We demonstrate this map by considering a set of D1-D5 CFT states that have smooth horizonless bulk duals, and explicitly constructing the supergravity solutions dual to the corresponding states of the MSW CFT. We thus obtainmore » the largest known class of solutions dual to MSW CFT microstates, and demonstrate that five-dimensional ungauged supergravity admits much larger families of smooth horizonless solutions than previously known.« less

Europa Plumes Located near Warm Spot on Europa

NASA Image and Video Library

2017-04-13

These images of the surface of the Jovian moon Europa, taken by NASA's Galileo spacecraft, focus on a "region of interest" on the icy moon. The image at left traces the location of the erupting plumes of material, observed by NASA's Hubble Space Telescope in 2014 and again in 2016. The plumes are located inside the area surrounded by the green oval. The green oval also corresponds to a warm region on Europa's surface, as identified by the temperature map at right. The map is based on observations by the Galileo spacecraft. The warmest area is colored bright red. Researchers speculate these data offer circumstantial evidence for unusual activity that may be related to a subsurface ocean on Europa. The dark circle just below center in both images is a crater and is not thought to be related to the warm spot or the plume activity. https://photojournal.jpl.nasa.gov/catalog/PIA21444

Quality/Performance Circles Three Years after Implementation.

ERIC Educational Resources Information Center

Ladwig, Dennis J.

An overview is provided of the development of quality/performance circles at Lakeshore Technical Institute (LTI), Wisconsin, and of the projects undertaken through the quality/performance circle program during its 3-year history. First, background information is provided on the use of quality circles in Japan and the United States, including…

Fostering Classroom Communities through Circling with Teacher Candidates

ERIC Educational Resources Information Center

Bouchard, Karen L.; Hollweck, Trista; Smith, J. David

2016-01-01

Classroom circles have been recognized as a valuable pedagogical approach to develop students' social-emotional learning and to establish a sense of community within a classroom. Until recently, there has been little consideration that teachers, themselves, may benefit from circling experiences. To garner a deeper understanding of circling for…

Making Morning Circle Meaningful

ERIC Educational Resources Information Center

Bruce, Susan; Fasy, Cara; Gulick, Jessica; Jones, Jill; Pike, Elizabeth

2006-01-01

Morning Circle, also known as Morning Meeting, is often a daily lesson in both general education and special education classrooms. The primary purpose of the Circle is to support each child to establish membership in the class while developing a classroom community and culture. The Responsive Classroom Approach recommends four Circle components:…

Transaction Circles with Digital Texts as a Foundation for Democratic Practices

ERIC Educational Resources Information Center

Brown, Sally

2015-01-01

Transaction circles weave together elements of guided reading and literature circles in an open conversational structure that supports students as agentive learners. Discourse within these circles utilizing digital informational texts assist in the development of democratic practices even in a time when federal mandates limit curricula and…

Perceptual Differences in Attitudes on Quality Circles.

ERIC Educational Resources Information Center

Holcomb, Lynn; Berger, Leonard

1986-01-01

A study was conducted to determine any perceptual differences toward quality circles in a chemical plant. It also tried to determine if any perceptual differences that might be found could be related to attitudes toward the circles themselves or the attitudes toward circle members. Length of service was also a factor. (CT)

A Short Interspersed Nuclear Element (SINE)-Based Real-Time PCR Approach to Detect and Quantify Porcine Component in Meat Products.

PubMed

Zhang, Chi; Fang, Xin; Qiu, Haopu; Li, Ning

2015-01-01

Real-time PCR amplification of mitochondria gene could not be used for DNA quantification, and that of single copy DNA did not allow an ideal sensitivity. Moreover, cross-reactions among similar species were commonly observed in the published methods amplifying repetitive sequence, which hindered their further application. The purpose of this study was to establish a short interspersed nuclear element (SINE)-based real-time PCR approach having high specificity for species detection that could be used in DNA quantification. After massive screening of candidate Sus scrofa SINEs, one optimal combination of primers and probe was selected, which had no cross-reaction with other common meat species. LOD of the method was 44 fg DNA/reaction. Further, quantification tests showed this approach was practical in DNA estimation without tissue variance. Thus, this study provided a new tool for qualitative detection of porcine component, which could be promising in the QC of meat products.

Nonlinear aspects of infrasonic pressure transfer into the perilymph.

PubMed

Krukowski, B; Carlborg, B; Densert, O

1980-06-01

The perilymphatic pressure was studied in response to various low frequency pressure changes in the ear canal. The pressure transfer was analysed and found to be nonlinear in many aspects. The pressure response was found to contain two time constants representing the inner ear pressure regulating mechanisms. The time constants showed an asymmetry in response to positive and negative going inputs--the effects to some extent proportional to input levels. Further nonlinearities were found when infrasonic sine waves were applied to the ear. Harmonic distortion and modulation appeared. When short bursts of infrasound were introduced a clear d.c. shift was observed as a consequence of an asymmetry in the response to positive and negative going pressure inputs. A temporary change in mean perilymphatic pressure was thus achieved and continued throughout the duration of the signal. At very low frequencies a distinct phase shift was detected in the sine waves. This appeared as a phase lead, breaking the continuity of the output sine wave.

The automatic extraction of pitch perturbation using microcomputers: some methodological considerations.

PubMed

Deem, J F; Manning, W H; Knack, J V; Matesich, J S

1989-09-01

A program for the automatic extraction of jitter (PAEJ) was developed for the clinical measurement of pitch perturbations using a microcomputer. The program currently includes 12 implementations of an algorithm for marking the boundary criteria for a fundamental period of vocal fold vibration. The relative sensitivity of these extraction procedures for identifying the pitch period was compared using sine waves. Data obtained to date provide information for each procedure concerning the effects of waveform peakedness and slope, sample duration in cycles, noise level of the analysis system with both direct and tape recorded input, and the influence of interpolation. Zero crossing extraction procedures provided lower jitter values regardless of sine wave frequency or sample duration. The procedures making use of positive- or negative-going zero crossings with interpolation provided the lowest measures of jitter with the sine wave stimuli. Pilot data obtained with normal-speaking adults indicated that jitter measures varied as a function of the speaker, vowel, and sample duration.

Linear sine wave profiling to machine instability targets

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

Schmidt, Derek William; Martinez, John Israel

2016-08-01

Specialized machining processes and programming have been developed to deliver thin tin and copper Richtmyer-Meshkov instability targets that have different amplitude perturbations across the face of one 4-in.-diameter target. Typical targets have anywhere from two to five different regions of sine waves that have different amplitudes varying from 4 to 200 μm across the face of the target. The puck is composed of multiple rings that are zero press fit together and diamond turned to create a flat platform with a tolerance of 2 μm for the shock experiment. A custom software program was written in Labview to write themore » point-to-point program for the diamond-turning profiler through the X-Y-Z movements to cut the pure planar straight sine wave geometry. As a result, the software is optimized to push the profile of the whole part into the face while eliminating any unneeded passes that do not cut any material.« less

Natural convection heat transfer in an oscillating vertical cylinder

PubMed Central

Ali Shah, Nehad; Tassaddiq, Asifa; Mustapha, Norzieha; Kechil, Seripah Awang

2018-01-01

This paper studies the heat transfer analysis caused due to free convection in a vertically oscillating cylinder. Exact solutions are determined by applying the Laplace and finite Hankel transforms. Expressions for temperature distribution and velocity field corresponding to cosine and sine oscillations are obtained. The solutions that have been obtained for velocity are presented in the forms of transient and post-transient solutions. Moreover, these solutions satisfy both the governing differential equation and all imposed initial and boundary conditions. Numerical computations and graphical illustrations are used in order to study the effects of Prandtl and Grashof numbers on velocity and temperature for various times. The transient solutions for both cosine and sine oscillations are also computed in tables. It is found that, the transient solutions are of considerable interest up to the times t = 15 for cosine oscillations and t = 1.75 for sine oscillations. After these moments, the transient solutions can be neglected and, the fluid moves according with the post-transient solutions. PMID:29304161

Natural convection heat transfer in an oscillating vertical cylinder.

PubMed

Khan, Ilyas; Ali Shah, Nehad; Tassaddiq, Asifa; Mustapha, Norzieha; Kechil, Seripah Awang

2018-01-01

This paper studies the heat transfer analysis caused due to free convection in a vertically oscillating cylinder. Exact solutions are determined by applying the Laplace and finite Hankel transforms. Expressions for temperature distribution and velocity field corresponding to cosine and sine oscillations are obtained. The solutions that have been obtained for velocity are presented in the forms of transient and post-transient solutions. Moreover, these solutions satisfy both the governing differential equation and all imposed initial and boundary conditions. Numerical computations and graphical illustrations are used in order to study the effects of Prandtl and Grashof numbers on velocity and temperature for various times. The transient solutions for both cosine and sine oscillations are also computed in tables. It is found that, the transient solutions are of considerable interest up to the times t = 15 for cosine oscillations and t = 1.75 for sine oscillations. After these moments, the transient solutions can be neglected and, the fluid moves according with the post-transient solutions.

Quality Circles: Determination of Significant Factors for Success an a General Model for Implementing a Quality Circle Process.

DTIC Science & Technology

1981-06-01

receive for contributions to quality and productivity /4:Apdx-47. The initiative for the Quality Circle concept came from Dr Kaoru Ishikawa , a...eloquently summarized by the "Father of Quality Circles", Dr Kaoru Ishikawa . He sees that, although Japan started with the worst quality reputation among...Perceptions of Influence, Academy of Management Journal. December 1974, pp 649-bz. 49. Ishikawa , Kaoru . S.C. Circle Activities. Union of Japanese Scientists and

GENERATING FRACTAL PATTERNS BY USING p-CIRCLE INVERSION

NASA Astrophysics Data System (ADS)

Ramírez, José L.; Rubiano, Gustavo N.; Zlobec, Borut Jurčič

2015-10-01

In this paper, we introduce the p-circle inversion which generalizes the classical inversion with respect to a circle (p = 2) and the taxicab inversion (p = 1). We study some basic properties and we also show the inversive images of some basic curves. We apply this new transformation to well-known fractals such as Sierpinski triangle, Koch curve, dragon curve, Fibonacci fractal, among others. Then we obtain new fractal patterns. Moreover, we generalize the method called circle inversion fractal be means of the p-circle inversion.

Computational approach to compact Riemann surfaces

NASA Astrophysics Data System (ADS)

Frauendiener, Jörg; Klein, Christian

2017-01-01

A purely numerical approach to compact Riemann surfaces starting from plane algebraic curves is presented. The critical points of the algebraic curve are computed via a two-dimensional Newton iteration. The starting values for this iteration are obtained from the resultants with respect to both coordinates of the algebraic curve and a suitable pairing of their zeros. A set of generators of the fundamental group for the complement of these critical points in the complex plane is constructed from circles around these points and connecting lines obtained from a minimal spanning tree. The monodromies are computed by solving the defining equation of the algebraic curve on collocation points along these contours and by analytically continuing the roots. The collocation points are chosen to correspond to Chebychev collocation points for an ensuing Clenshaw-Curtis integration of the holomorphic differentials which gives the periods of the Riemann surface with spectral accuracy. At the singularities of the algebraic curve, Puiseux expansions computed by contour integration on the circles around the singularities are used to identify the holomorphic differentials. The Abel map is also computed with the Clenshaw-Curtis algorithm and contour integrals. As an application of the code, solutions to the Kadomtsev-Petviashvili equation are computed on non-hyperelliptic Riemann surfaces.

Polypteridae (Actinopterygii: Cladistia) and DANA-SINEs insertions.

PubMed

Morescalchi, Maria Alessandra; Barucca, Marco; Stingo, Vincenzo; Capriglione, Teresa

2010-06-01

SINE sequences are interspersed throughout virtually all eukaryotic genomes and greatly outnumber the other repetitive elements. These sequences are of increasing interest for phylogenetic studies because of their diagnostic power for establishing common ancestry among taxa, once properly characterized. We identified and characterized a peculiar family of composite tRNA-derived short interspersed SINEs, DANA-SINEs, associated with mutational activities in Danio rerio, in a group of species belonging to one of the most basal bony fish families, the Polypteridae, in order to investigate their own inner specific phylogenetic relationships. DANA sequences were identified, sequenced and then localized, by means of fluorescent in situ hybridization (FISH), in six Polypteridae species (Polypterus delhezi, P. ornatipinnis, P. palmas, P. buettikoferi P. senegalus and Erpetoichthys calabaricus) After cloning, the sequences obtained were aligned for phylogenetic analysis, comparing them with three Dipnoan lungfish species (Protopterus annectens, P. aethiopicus, Lepidosiren paradoxa), and Lethenteron reissneri (Petromyzontidae)was used as outgroup. The obtained overlapping MP, ML and NJ tree clustered together the species belonging to the two taxonomically different Osteichthyans groups: the Polypteridae, by one side, and the Protopteridae by the other, with the monotypic genus Erpetoichthys more distantly related to the Polypterus genus comprising three distinct groups: P. palmas and P. buettikoferi, P. delhezi and P. ornatipinnis and P. senegalus. In situ hybridization with DANA probes marked along the whole chromosome arms in the metaphases of all the Polypteridae species examined. Copyright © 2010 Elsevier B.V. All rights reserved.

Short interspersed elements (SINEs) are a major source of canine genomic diversity.

PubMed

Wang, Wei; Kirkness, Ewen F

2005-12-01

SINEs are retrotransposons that have enjoyed remarkable reproductive success during the course of mammalian evolution, and have played a major role in shaping mammalian genomes. Previously, an analysis of survey-sequence data from an individual dog (a poodle) indicated that canine genomes harbor a high frequency of alleles that differ only by the absence or presence of a SINEC_Cf repeat. Comparison of this survey-sequence data with a draft genome sequence of a distinct dog (a boxer) has confirmed this prediction, and revealed the chromosomal coordinates for >10,000 loci that are bimorphic for SINEC_Cf insertions. Analysis of SINE insertion sites from the genomes of nine additional dogs indicates that 3%-5% are absent from either the poodle or boxer genome sequences--suggesting that an additional 10,000 bimorphic loci could be readily identified in the general dog population. We describe a methodology that can be used to identify these loci, and could be adapted to exploit these bimorphic loci for genotyping purposes. Approximately half of all annotated canine genes contain SINEC_Cf repeats, and these elements are occasionally transcribed. When transcribed in the antisense orientation, they provide splice acceptor sites that can result in incorporation of novel exons. The high frequency of bimorphic SINE insertions in the dog population is predicted to provide numerous examples of allele-specific transcription patterns that will be valuable for the study of differential gene expression among multiple dog breeds.

Scenario based approach for multiple source Tsunami Hazard assessment for Sines, Portugal

NASA Astrophysics Data System (ADS)

Wronna, M.; Omira, R.; Baptista, M. A.

2015-08-01

In this paper, we present a scenario-based approach for tsunami hazard assessment for the city and harbour of Sines - Portugal, one of the test-sites of project ASTARTE. Sines holds one of the most important deep-water ports which contains oil-bearing, petrochemical, liquid bulk, coal and container terminals. The port and its industrial infrastructures are facing the ocean southwest towards the main seismogenic sources. This work considers two different seismic zones: the Southwest Iberian Margin and the Gloria Fault. Within these two regions, we selected a total of six scenarios to assess the tsunami impact at the test site. The tsunami simulations are computed using NSWING a Non-linear Shallow Water Model With Nested Grids. In this study, the static effect of tides is analysed for three different tidal stages MLLW (mean lower low water), MSL (mean sea level) and MHHW (mean higher high water). For each scenario, inundation is described by maximum values of wave height, flow depth, drawback, runup and inundation distance. Synthetic waveforms are computed at virtual tide gauges at specific locations outside and inside the harbour. The final results describe the impact at Sines test site considering the single scenarios at mean sea level, the aggregate scenario and the influence of the tide on the aggregate scenario. The results confirm the composite of Horseshoe and Marques Pombal fault as the worst case scenario. It governs the aggregate scenario with about 60 % and inundates an area of 3.5 km2.

piRNA-associated proteins and retrotransposons are differentially expressed in murine testis and ovary of aryl hydrocarbon receptor deficient mice

PubMed Central

Rico-Leo, Eva M.; Moreno-Marín, Nuria; González-Rico, Francisco J.; Barrasa, Eva; Ortega-Ferrusola, Cristina; Martín-Muñoz, Patricia; Sánchez-Guardado, Luis O.; Llano, Elena; Alvarez-Barrientos, Alberto; Infante-Campos, Ascensión; Catalina-Fernández, Inmaculada; Hidalgo-Sánchez, Matías; de Rooij, Dirk G.; Pendás, Alberto M.; Peña, Fernando J.; Merino, Jaime M.

2016-01-01

Previous studies suggested that the aryl hydrocarbon receptor (AhR) contributes to mice reproduction and fertility. However, the mechanisms involved remain mostly unknown. Retrotransposon silencing by Piwi-interacting RNAs (piRNAs) is essential for germ cell maturation and, remarkably, AhR has been identified as a regulator of murine B1-SINE retrotransposons. Here, using littermate AhR+/+ and AhR−/− mice, we report that AhR regulates the general course of spermatogenesis and oogenesis by a mechanism likely to be associated with piRNA-associated proteins, piRNAs and retrotransposons. piRNA-associated proteins MVH and Miwi are upregulated in leptotene to pachytene spermatocytes with a more precocious timing in AhR−/− than in AhR+/+ testes. piRNAs and transcripts from B1-SINE, LINE-1 and IAP retrotransposons increased at these meiotic stages in AhR-null testes. Moreover, B1-SINE transcripts colocalize with MVH and Miwi in leptonema and pachynema spermatocytes. Unexpectedly, AhR−/− males have increased sperm counts, higher sperm functionality and enhanced fertility than AhR+/+ mice. In contrast, piRNA-associated proteins and B1-SINE and IAP-derived transcripts are reduced in adult AhR−/− ovaries. Accordingly, AhR-null female mice have lower numbers of follicles when compared with AhR+/+ mice. Thus, AhR deficiency differentially affects testis and ovary development possibly by a process involving piRNA-associated proteins, piRNAs and transposable elements. PMID:28003471

Native American Values and Management Education: Envisioning an Inclusive Virtuous Circle

ERIC Educational Resources Information Center

Verbos, Amy Klemm; Gladstone, Joe S.; Kennedy, Deanna M.

2011-01-01

Circles are symbols of interconnectedness. Behavioral circles can be vicious or virtuous. Many American Indians are caught in a vicious circle of exclusion from the purported benefits of Westernization, entrapment in its negative elements, and the ongoing undermining of their culture and thus their identities. Yet Native Americans, along with many…

The Value of the Math Circle for Gifted Middle School Students

ERIC Educational Resources Information Center

Burns, Barbara; Henry, Julie; McCarthy, Dianne; Tripp, Jennifer

2017-01-01

Math Circles are designed to allow students to explore mathematics using a problem-solving/inquiry approach. Many of the students attending our Math Circle are mathematically talented and curious. This study examines the perspectives of the students and their families in determining why students attend Math Circle, what they enjoy about Math…

Expanding the Reach of Extension to Underserved Audiences through Study Circles in Rural Idaho

ERIC Educational Resources Information Center

Cummins, Melissa; Petty, Barbara; Hansen, Lyle; Hoffman, Katie; Wittman, Grace

2012-01-01

Extension educators expanded the reach of their programming to underserved audiences through the implementation of Study Circles in rural Southern Idaho. Study Circles gave educators entry into communities by establishing relationships necessary for long-term change. Study Circle discussions in rural Southern Idaho led to stronger relationships…

The Acoustic Reality of the Kachruvian Circles: A Rhythmic Perspective

ERIC Educational Resources Information Center

Low, Ee Ling

2010-01-01

This paper investigates whether the rhythmic properties of varieties of English found in each of the concentric circles of Kachru's model can, in any way, be elucidated by the "Three Circles" model. A measurement and comparison of the rhythm of three varieties of English: British English (from the Inner Circle), Singapore English (from…

The Relationship of Communication to Productivity: Quality Circles as a Mediating Variable.

ERIC Educational Resources Information Center

Creagh, Sara; Smeltzer, Larry

Quality circles, small groups of employees working voluntarily toward performance improvement, have become a popular business strategy in the past decade. When effective, the quality circle may be linked directly to the increased productivity of the work group. The quality circle process may be divided into four components: identification and…

Quality Circles: Involvement, Problem-Solving, and Recognition.

ERIC Educational Resources Information Center

Moretz, H. Lynn

1983-01-01

The media production department of Central Piedmont Community College (CPCC) began quality circle meetings in January 1981 after studying the process of quality circles and obtaining the understanding and support of the college administration. A quality circle is a small group of people doing similar work who voluntarily meet on a regular basis to…

The "Us" in Discuss: Grouping in Literature Circles

ERIC Educational Resources Information Center

Batchelor, Katherine

2012-01-01

This article describes one middle school teacher's use of literature circles using heterogeneous grouping. It begins with a brief rationale for using literature circles in the language arts classroom. Next, it describes techniques to form literature circles. Then, it shares how to build and establish a supportive environment within each group. It…

A Round Is a Circle...

ERIC Educational Resources Information Center

Boyarsky, Terry L.

2006-01-01

Circles are everywhere and endlessly intriguing. We know, sense, and feel them in time, space, sound, and the cycles of nature. A person's life contains spirals, repetitions, going out and coming back. Poets write of circles; composers write song cycles. Circles are at the root of the curriculum, concepts deep yet accessible, infinite in their…

Accuracy of tree diameter estimation from terrestrial laser scanning by circle-fitting methods

NASA Astrophysics Data System (ADS)

Koreň, Milan; Mokroš, Martin; Bucha, Tomáš

2017-12-01

This study compares the accuracies of diameter at breast height (DBH) estimations by three initial (minimum bounding box, centroid, and maximum distance) and two refining (Monte Carlo and optimal circle) circle-fitting methods The circle-fitting algorithms were evaluated in multi-scan mode and a simulated single-scan mode on 157 European beech trees (Fagus sylvatica L.). DBH measured by a calliper was used as reference data. Most of the studied circle-fitting algorithms significantly underestimated the mean DBH in both scanning modes. Only the Monte Carlo method in the single-scan mode significantly overestimated the mean DBH. The centroid method proved to be the least suitable and showed significantly different results from the other circle-fitting methods in both scanning modes. In multi-scan mode, the accuracy of the minimum bounding box method was not significantly different from the accuracies of the refining methods The accuracy of the maximum distance method was significantly different from the accuracies of the refining methods in both scanning modes. The accuracy of the Monte Carlo method was significantly different from the accuracy of the optimal circle method in only single-scan mode. The optimal circle method proved to be the most accurate circle-fitting method for DBH estimation from point clouds in both scanning modes.

COMPLETENESS OF CIRCLE OF WILLIS IN ASYMPTOMATIC AND SYMPTOMATIC EXTRACRANIAL CAROTID DISEASE.

PubMed

Manojlovic, Vladimir; Popovic, Vlandan; Nikoloc, Dragan; Milosevic, Dorde; Pasternak, Janko; Budakov, Nebojsa

2016-11-01

This research has been aimed at determining whether incomplete Circle of Willis in patients with significant extracranial carotid stenosis is associated with a higher incidence of neurological symptomatology and/or ischemnic cerebral lesions. The research was conducted as a prospective study which comprised 211 patients who underwent surgical treatment of extracranial carotid disease at the Department of Vascular Surgery in Novi Sad and 102 patients in the control group. Each patient underwent preoperative magnetic resonance imaging and magnetic resonance angiography with visualization of cerebral parenchyma. extracranial and intracranial cerebral circulation. Assessment of Circle of Willis morphology was performed by 3D time-of-fight magnetic resonance angiogram sequence analysis. The patients were divided into two groups: group I - the patients with'complete Circle of Willis and group II - the patients with incomplete Circle of Willis i.e. with the disruption of anterior and/ or ipsilateral posterior circulation - regarding the side of signif icant carotid stenosis. Out of 211 patients who -were operated during a two-year period, 133 had the complete Circle of Willis. while 78 patients had the incomplete Circle of Willis. Out of 111 patients with symptomatic carotid disease or silent cerebral infarction, 52.5% (58) had the complete Circle of' Willis and 47.5% (53) had the incomplete Circle of Willis. It was shown to be statistically different (P = 0.0146) in relation with the asymptomatic group of patients (100), where the frequency of the complete Circle of Willis was 75% (75) while the insufficiency of anterior or ipsilateral posterior collateral ization was found in 25% (25). In the control group there were significantly fewer cases of developed collateral flow and the complete Circle of Willis (41%) compared to the operated patients with extracranial carotid stenosis (63%) (P= 0.0003). Incompleteness of Circle of Willis is associated with more frequent occurrence of neurological symptomatology or ischemic lesions of brain parenchyma in operated patients with significant extracranial carotid stenosis. The control group without extracranial carotid stenosis had less developed collaterals of Circle of Willis compared to extracranial carotid patients.

Correlation Between the Integrity of the Circle of Willis and the Severity of Initial Noncardiac Cerebral Infarction and Clinical Prognosis

PubMed Central

Zhou, Houshi; Sun, Jian; Ji, Xiaotan; Lin, Jing; Tang, Shujin; Zeng, Jinsheng; Fan, Yu-hua

2016-01-01

Abstract The quality of collateral circulation affects the severity and prognosis of stroke patients. The effect of the circle of Willis, which is the primary collateral circulation, on ischemic stroke has attracted significant attention. This study was designed to investigate the effect of different circles of Willis types on stroke severity and prognosis in patients with noncardiac stroke. A total of 376 patients with noncardiac ischemic stroke, who were treated by the specialty team of cerebrovascular diseases at the First Affiliated Hospital of Sun Yat-sen Hospital, were successively enrolled in this study. The detailed clinical characteristics of the patients were recorded upon admission, including risk factors of vascular disease and National Institutes of Health Stroke Scale (NIHSS) scores. The patients were divided into groups of different circles of Willis types based on magnetic resonance angiography (MRA) that was performed within 3 days of admission—type I: complete circle of Willis; type II: complete anterior half of the circle of Willis and incomplete posterior half of the circle of Willis; type III: incomplete anterior half of the circle of Willis and complete posterior half of the circle of Willis; and type IV: incomplete anterior and posterior halves of the circle of Willis. Patients were re-evaluated for NIHSS scores at discharge and after discharge. The modified Rankin score (mRS) was recorded for 90 days, and stroke recurrence and death after 90 days were also recorded until the end of the study. The 376 patients were divided into 4 groups based on the MRA—type I group: 92 patients (24.5%); type II group: 215 patients (57.2%); type III group: 12 patients (3.2%), and type IV group: 57 patients (15.2%). NIHSS scores at admission and discharge were significantly lower for the type I group compared with those for the type II and type IV groups (P < 0.05). NIHSS scores were higher in the groups with an incomplete circle of Willis compared with the group with a complete circle of Willis. A poor recovery rate was highest for the type IV group, whereas a good recovery rate was highest for the type I group. The logistic regression analysis showed that a complete circle of Willis was one of the predictors of suitable recovery (odds ratio [OR] = 0.708, 95% confidence interval [CI]: 0.554–0.906). Circle of Willis type was associated with stroke severity and patient prognosis, whereas an incomplete circle of Willis was associated with more severe conditions and a higher 90-day poor diagnosis rate. A complete circle of Willis was an independent predictor of good prognosis. PMID:26962785

What Works: Study Circles in the Real World. Best Practices for Producing Community-Wide Study Circles.

ERIC Educational Resources Information Center

Mengual, Gloria

This document, which is based on information gathered during a 1998 study of how study circle programs contribute to community problem solving, presents best practices for producing community-wide study circles. The best practices are illustrated through stories that are grouped into five sections on the following themes: (1) creating a…

"Quality Circles": A Strategy for Personal and Curriculum Development. Coombe Lodge Working Paper. Information Bank Number 1803.

ERIC Educational Resources Information Center

Field, M. J.; Harrison, A. B.

Quality circles attempt to satisfy both task and personal needs through staff involvement in solving work-related problems. This paper summarizes quality circle theory, applies it to school settings, and suggests a framework for introducing the process to educational institutions. After briefly defining quality circles, the article presents two…

Mismanagement and Quality Circles: How Middle Managers Influence Direct Participation.

ERIC Educational Resources Information Center

Brennan, Maire

1991-01-01

Case studies of five Scottish companies found that four of their quality circles programs had ceased. Essential to the success of quality circles were changes in the systems of reward, communication, and decision making and the cooperation and support of middle managers, who may see quality circles as a threat and who control the resources they…

Expanding-Circle Students Learning "Standard English" in the Outer-Circle Asia

ERIC Educational Resources Information Center

Kobayashi, Yoko

2011-01-01

Drawing upon Kachru's concentric circles of English, the present study explores whether middle-class Japanese students who chose to study English solo at private language schools in Singapore diverge from many others who (wish to) study inner-circle English. The study is stimulated by the repeated interdisciplinary findings that, in spite of the…

Circles of Support and Personalization: Exploring the Economic Case

ERIC Educational Resources Information Center

Wistow, Gerald; Perkins, Margaret; Knapp, Martin; Bauer, Annette; Bonin, Eva-Maria

2016-01-01

Circles of Support aim to enable people with learning disabilities (and others) to live full lives as part of their communities. As part of a wider study of the economic case for community capacity building conducted from 2012 to 2014, we conducted a mixed methods study of five Circles in North West England. Members of these Circles were…

Children with Autism and Peer Group Support: "Using Circles of Friends".

ERIC Educational Resources Information Center

Whitaker, Philip; Barratt, Penny; Joy, Helen; Potter, Mo; Thomas, George

1998-01-01

Explains the "circle of friends approach" as one strategy aimed at using peer group support to promote the inclusion of children with autism into mainstream schools. It describes use of the approach with six autistic children in years 3 to 10 of British mainstream schools. Evaluation comments by the circle leaders, circle members, and…

The Chicken and the Egg: Inviting Response and Talk through Socratic Circles

ERIC Educational Resources Information Center

Styslinger, Mary E.; Pollock, Timothy

2010-01-01

This collaborative inquiry answers the following questions: 1) What is the nature of talk during Socratic Circles? 2) What is student response to talk? 3) How might knowing more about student response to talk and the nature of talk improve teaching during Socratic Circles? The article first describes the process of implementing Socratic Circles,…

Getting Started with Literature Circles. The Bill Harp Professional Teachers Library Series.

ERIC Educational Resources Information Center

Noe, Katherine L. Schlick; Johnson, Nancy J.

Designed to help teachers get started using literature circles in their classrooms, this book gives teachers a boost to begin, offers some insights from other teachers, and helps teachers clarify where to go next. It notes that literature circles (or literature study groups, book clubs, or discussion circles) take many forms and engage students in…

Guided Discovery of the Nine-Point Circle Theorem and Its Proof

ERIC Educational Resources Information Center

Buchbinder, Orly

2018-01-01

The nine-point circle theorem is one of the most beautiful and surprising theorems in Euclidean geometry. It establishes an existence of a circle passing through nine points, all of which are related to a single triangle. This paper describes a set of instructional activities that can help students discover the nine-point circle theorem through…

Integrated use of spatial and semantic relationships for extracting road networks from floating car data

NASA Astrophysics Data System (ADS)

Li, Jun; Qin, Qiming; Xie, Chao; Zhao, Yue

2012-10-01

The update frequency of digital road maps influences the quality of road-dependent services. However, digital road maps surveyed by probe vehicles or extracted from remotely sensed images still have a long updating circle and their cost remain high. With GPS technology and wireless communication technology maturing and their cost decreasing, floating car technology has been used in traffic monitoring and management, and the dynamic positioning data from floating cars become a new data source for updating road maps. In this paper, we aim to update digital road maps using the floating car data from China's National Commercial Vehicle Monitoring Platform, and present an incremental road network extraction method suitable for the platform's GPS data whose sampling frequency is low and which cover a large area. Based on both spatial and semantic relationships between a trajectory point and its associated road segment, the method classifies each trajectory point, and then merges every trajectory point into the candidate road network through the adding or modifying process according to its type. The road network is gradually updated until all trajectories have been processed. Finally, this method is applied in the updating process of major roads in North China and the experimental results reveal that it can accurately derive geometric information of roads under various scenes. This paper provides a highly-efficient, low-cost approach to update digital road maps.

Statistical properties of two sine waves in Gaussian noise.

NASA Technical Reports Server (NTRS)

Esposito, R.; Wilson, L. R.

1973-01-01

A detailed study is presented of some statistical properties of a stochastic process that consists of the sum of two sine waves of unknown relative phase and a normal process. Since none of the statistics investigated seem to yield a closed-form expression, all the derivations are cast in a form that is particularly suitable for machine computation. Specifically, results are presented for the probability density function (pdf) of the envelope and the instantaneous value, the moments of these distributions, and the relative cumulative density function (cdf).

(RTO) Characterization of the Time-dependent Behaviour of Dielectric Barrier Discharge Plasma Actuators

DTIC Science & Technology

2014-06-19

excited by a sine -wave signal with peak- to-peak amplitudes between 7.2 kV and 10 kV, and frequencies of 2.5 kHz and 4 kHz. The results indicate that the...side length of 0.68 m, made of transparent PMMA, to isolate it from ambient disturbances. The plasma actuator was excited by a sine -wave signal, which... Portugal , 2008. 6Hanson, R., Houser, N., and Lavoie, P., “Dielectric material degradation monitoring of dielectric barrier discharge plasma actuators

Exact Mass-Coupling Relation for the Homogeneous Sine-Gordon Model.

PubMed

Bajnok, Zoltán; Balog, János; Ito, Katsushi; Satoh, Yuji; Tóth, Gábor Zsolt

2016-05-06

We derive the exact mass-coupling relation of the simplest multiscale quantum integrable model, i.e., the homogeneous sine-Gordon model with two mass scales. The relation is obtained by comparing the perturbed conformal field theory description of the model valid at short distances to the large distance bootstrap description based on the model's integrability. In particular, we find a differential equation for the relation by constructing conserved tensor currents, which satisfy a generalization of the Θ sum rule Ward identity. The mass-coupling relation is written in terms of hypergeometric functions.

Optical solitons to the resonance nonlinear Schrödinger equation by Sine-Gordon equation method

NASA Astrophysics Data System (ADS)

Inc, Mustafa; Aliyu, Aliyu Isa; Yusuf, Abdullahi; Baleanu, Dumitru

2018-01-01

In this paper, we examined the optical solitons to the resonant nonlinear Schrödinger equation (R-NLSE) which describes the propagation of solitons through optical fibers. Three types of nonlinear media fibers are studied. They are; quadratic-cubic law, Kerr law and parabolic law. Dark, bright, dark-bright or combined optical and singular soliton solutions are derived using the sine-Gordon equation method (SGEM). The constraint conditions that naturally fall out of the solution structure which guarantee the existence of these solitons are also reported.

Chronic active VZV infection manifesting as zoster sine herpete, zoster paresis and myelopathy.

PubMed

Morita, Y; Osaki, Y; Doi, Y; Forghani, B; Gilden, D H

2003-08-15

After lumbar-distribution zoster, an HTLV-1-seropositive woman developed chronic radicular sacral-distribution pain (zoster sine herpete), cervical-distribution zoster paresis and thoracic-distribution myelopathy. Detection of anti-varicella zoster virus (VZV) IgM and VZV IgG antibody in cerebrospinal fluid (CSF), with reduced serum/CSF ratios of anti-VZV IgG compared to normal serum/CSF ratios for albumin and total IgG, proved that VZV caused the protracted neurological complications. Diagnosis by antibody testing led to aggressive antiviral treatment and a favorable outcome.

Angular measurement system

NASA Technical Reports Server (NTRS)

Currie, J. R.; Kissel, R. R.

1986-01-01

A system for the measurement of shaft angles is disclosed wherein a synchro resolver is sequentially pulsed, and alternately, a sine and then a cosine representative voltage output of it are sampled. Two like type, sine or cosine, succeeding outputs (V sub S1, V sub S2) are averaged and algebraically related to the opposite type output pulse (V sub c) occurring between the averaged pulses to provide a precise indication of the angle of a shaft coupled to the resolver at the instant of the occurrence of the intermediately occurring pulse (V sub c).

Ecohydrological interactions within "fairy circles" in the Namib Desert: Revisiting the self-organization hypothesis

NASA Astrophysics Data System (ADS)

Ravi, Sujith; Wang, Lixin; Kaseke, Kudzai Farai; Buynevich, Ilya V.; Marais, Eugene

2017-02-01

Vegetation patterns such as rings, bands, and spots are recurrent characteristics of resource-limited arid and semiarid ecosystems. One of the most recognizable vegetation patterns is the millions of circular patches, often referred to as "fairy circles," within the arid grassland matrix extending over hundreds of kilometers in the Namib Desert. Several modeling studies have highlighted the role of plant-soil interactions in the formation of these fairy circles. However, little is known about the spatial and temporal variabilities of hydrological processes inside a fairy circle. In particular, a detailed field assessment of hydrological and soil properties inside and outside the fairy circles is limited. We conducted extensive measurements of infiltration rate, soil moisture, grass biometric, and sediment grain-size distribution from multiple circles and interspaces in the Namib Desert. Our results indicate that considerable heterogeneity in hydrological processes exists within the fairy circles, resulting from the presence of coarser particles in the inner bare soil areas, whereas concentration of fine soil occurs on the vegetated edges. The trapping of aeolian and water-borne sediments by plants may result in the observed soil textural changes beneath the vegetation, which in turn, explains the heterogeneity in hydrological processes such as infiltration and runoff. Our investigation provides new insights and experimental data on the ecohydrological processes associated with fairy circles, from a less studied location devoid of sand termite activity within the circles. The results seem to provide support to the "self-organization hypothesis" of fairy circle formation attributed to the antiphase spatial biomass-water distributions.

A Spring Playscape Project: Building a Tree Circle

ERIC Educational Resources Information Center

Keeler, Rusty

2009-01-01

The Tree Circle is a green gathering area for children made by planting trees in a circle. For children, the Tree Circle becomes a magical place for dramatic play, quiet retreat, or lively nature exploration. For teachers and parents it becomes a shady grove for snacks and stories. The trees create a sweet spot that changes during the seasons and…

National Forest System working circles: a question of size and ownership composition

Treesearch

Robert J. Hrubes

1976-01-01

Allowable-cut (potential yield) levels on National Forest land are determined for planning units called working circles. The size of working circles has been increased over the past 30 years to the present scale which is often coincident with National Forest boundaries. Larger working circles have recently been considered because of the anticipated impacts on timber...

Hot deformation behaviors and processing maps of B{sub 4}C/Al6061 neutron absorber composites

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

Li, Yu-Li

In this study, the hot deformation behaviors of 30 wt.% B{sub 4}C/Al6061 neutron absorber composites (NACs) have been investigated by conducting isothermal compression tests at temperatures ranging from 653 K to 803 K and strain rates from 0.01 to 10 s{sup −1}. It was found that, during hot compression, the B{sub 4}C/Al6061 NACs exhibited a steady flow characteristic which can be expressed by the Zener-Hollomon parameter as a hyperbolic-sine function of flow stress. High average activation energy (185.62 kJ/mol) of B{sub 4}C/Al6061 NACs is noted in current study owing to the high content of B{sub 4}C particle. The optimum hotmore » working conditions for B{sub 4}C/Al6061 NACs are found to be 760–803 K/0.01–0.05 s{sup −1} based on processing map and microstructure evolution. Typical material instabilities are thought to be attributed to void formation, adiabatic shear bands (ASB), particle debonding, and matrix cracking. Finally, the effect of the plastic deformation zones (PDZs) on the microstructure evolution in this 30 wt.% B{sub 4}C/Al6061 composite is found to be very important. - Highlights: •The hot deformation behavior of the 30 wt.% B{sub 4}C/Al6061 NACs was first analyzed. •The 3D efficiency map and the instability map are developed. •The optimum hot working conditions were identified and validated by SEM and TEM. •The hot deformation schematic diagram of 30 wt.% B{sub 4}C/Al6061 NACs is developed.« less

The combination of circle topology and leaky integrator neurons remarkably improves the performance of echo state network on time series prediction.

PubMed

Xue, Fangzheng; Li, Qian; Li, Xiumin

2017-01-01

Recently, echo state network (ESN) has attracted a great deal of attention due to its high accuracy and efficient learning performance. Compared with the traditional random structure and classical sigmoid units, simple circle topology and leaky integrator neurons have more advantages on reservoir computing of ESN. In this paper, we propose a new model of ESN with both circle reservoir structure and leaky integrator units. By comparing the prediction capability on Mackey-Glass chaotic time series of four ESN models: classical ESN, circle ESN, traditional leaky integrator ESN, circle leaky integrator ESN, we find that our circle leaky integrator ESN shows significantly better performance than other ESNs with roughly 2 orders of magnitude reduction of the predictive error. Moreover, this model has stronger ability to approximate nonlinear dynamics and resist noise than conventional ESN and ESN with only simple circle structure or leaky integrator neurons. Our results show that the combination of circle topology and leaky integrator neurons can remarkably increase dynamical diversity and meanwhile decrease the correlation of reservoir states, which contribute to the significant improvement of computational performance of Echo state network on time series prediction.

Fabrication and characteristics of thin disc piezoelectric transformers based on piezoelectric buzzers with gap circles.

PubMed

Chang, Kuo-Tsai; Lee, Chun-Wei

2008-04-01

This paper investigates design, fabrication and test of thin disc piezoelectric transformers (PTs) based on piezoelectric buzzers with gap circles at different diameters of the gap circles. The performance test is focused on characteristics of voltage gains, including maximum voltage gains and maximum-gain frequencies, for each piezoelectric transformer under different load conditions. Both a piezoelectric buzzer and a gap circle on a silver electrode of the buzzer are needed to build any type of the PTs. Here, the gap circle is used to form a ring-shaped input electrode and a circle-shaped output electrode for each piezoelectric transformer. To do so, both structure and connection of a PT are first expressed. Then, operating principle of a PT and its related vibration mode observed by a carbon-power imaging technique are described. Moreover, an experimental setup for characterizing each piezoelectric transformer is constructed. Finally, effects of diameters of the gap circles on characteristics of voltage gains at different load resistances are discussed.

A programmable systolic array correlator as a trigger processor for electron pairs in rich (ring image Cherenkov) counters

NASA Astrophysics Data System (ADS)

Männer, R.

1989-12-01

This paper describes a systolic array processor for a ring image Cherenkov counter which is capable of identifying pairs of electron circles with a known radius and a certain minimum distance within 15 μs. The processor is a very flexible and fast device. It consists of 128 x 128 processing elements (PEs), where one PE is assigned to each pixel of the image. All PEs run synchronously at 40 MHz. The identification of electron circles is done by correlating the detector image with the proper circle circumference. Circle centers are found by peak detection in the correlation result. A second correlation with a circle disc allows circles of closed electron pairs to be rejected. The trigger decision is generated if a pseudo adder detects at least two remaining circles. The device is controlled by a freely programmable sequencer. A VLSI chip containing 8 x 8 PEs is being developed using a VENUS design system and will be produced in 2μ CMOS technology.

Circles South East: the first 10 years 2002-2012.

PubMed

Bates, Andrew; Williams, Dominic; Wilson, Chris; Wilson, Robin J

2014-07-01

This article describes the first 10 years of the implementation of Circles of Support and Accountability (Circles) in the management of sexual offenders in South-East England by Circles South East (CSE). The Circles of 71 core members are reviewed in detail, with reference to demographic data, offense and sentencing histories, risk assessment data, and considerations regarding Multi-Agency Public Protection Arrangements. A group of 71 comparison subjects who were referred to CSE and deemed suitable for but did not receive the service was identified. Follow-up behaviors of both groups are examined (including all forms of reconviction, breach of orders, and prison recall). Over a comparable follow-up period of 55 months, the incidence of violent and contact sexual reconviction in the comparison group was significantly higher than for the Circles cohort. Comparisons are made between expected and actual levels of sexual reconviction, with the Circles cohort showing lower than expected rate of sexual reconviction but not to a statistically significant degree. © The Author(s) 2013.

Wear simulation of apex seal in rotary engine under mixed lubrication

NASA Astrophysics Data System (ADS)

Jiang, Hanying; Zuo, Zhengxing; Liu, Jinxiang

2018-05-01

In this work, the wear of apex seal's running face under mixed lubrication is studied. Numerical simulation is carried out by employing the couple model of Reynolds equation, Greenwood and Tripp model and Archard's wear law. The simulation is performed both for one circle and multi circle. In the multi circle simulation, the change of contact position due to wear is considered. A method that is able to find the new contact position based on the updated apex seal's contour profile is proposed, validated and used. The result of multi circle simulation indicates that contact position changes obviously around the maximum swing angles both on leading and trailing sides with the increase number of circles. The wear depth distribution becomes more uniform with the increase of operation circle number.

Algebraic criteria for positive realness relative to the unit circle.

NASA Technical Reports Server (NTRS)

Siljak, D. D.

1973-01-01

A definition is presented of the circle positive realness of real rational functions relative to the unit circle in the complex variable plane. The problem of testing this kind of positive reality is reduced to the algebraic problem of determining the distribution of zeros of a real polynomial with respect to and on the unit circle. Such reformulation of the problem avoids the search for explicit information about imaginary poles of rational functions. The stated algebraic problem is solved by applying the polynomial criteria of Marden (1966) and Jury (1964), and a completely recursive algorithm for circle positive realness is obtained.

Stereoscopic Machine-Vision System Using Projected Circles

NASA Technical Reports Server (NTRS)

Mackey, Jeffrey R.

2010-01-01

A machine-vision system capable of detecting obstacles large enough to damage or trap a robotic vehicle is undergoing development. The system includes (1) a pattern generator that projects concentric circles of laser light forward onto the terrain, (2) a stereoscopic pair of cameras that are aimed forward to acquire images of the circles, (3) a frame grabber and digitizer for acquiring image data from the cameras, and (4) a single-board computer that processes the data. The system is being developed as a prototype of machine- vision systems to enable robotic vehicles ( rovers ) on remote planets to avoid craters, large rocks, and other terrain features that could capture or damage the vehicles. Potential terrestrial applications of systems like this one could include terrain mapping, collision avoidance, navigation of robotic vehicles, mining, and robotic rescue. This system is based partly on the same principles as those of a prior stereoscopic machine-vision system in which the cameras acquire images of a single stripe of laser light that is swept forward across the terrain. However, this system is designed to afford improvements over some of the undesirable features of the prior system, including the need for a pan-and-tilt mechanism to aim the laser to generate the swept stripe, ambiguities in interpretation of the single-stripe image, the time needed to sweep the stripe across the terrain and process the data from many images acquired during that time, and difficulty of calibration because of the narrowness of the stripe. In this system, the pattern generator does not contain any moving parts and need not be mounted on a pan-and-tilt mechanism: the pattern of concentric circles is projected steadily in the forward direction. The system calibrates itself by use of data acquired during projection of the concentric-circle pattern onto a known target representing flat ground. The calibration- target image data are stored in the computer memory for use as a template in processing terrain images. During operation on terrain, the images acquired by the left and right cameras are analyzed. The analysis includes (1) computation of the horizontal and vertical dimensions and the aspect ratios of rectangles that bound the circle images and (2) comparison of these aspect ratios with those of the template. Coordinates of distortions of the circles are used to identify and locate objects. If the analysis leads to identification of an object of significant size, then stereoscopicvision algorithms are used to estimate the distance to the object. The time taken in performing this analysis on a single pair of images acquired by the left and right cameras in this system is a fraction of the time taken in processing the many pairs of images acquired in a sweep of the laser stripe across the field of view in the prior system. The results of the analysis include data on sizes and shapes of, and distances and directions to, objects. Coordinates of objects are updated as the vehicle moves so that intelligent decisions regarding speed and direction can be made. The results of the analysis are utilized in a computational decision-making process that generates obstacle-avoidance data and feeds those data to the control system of the robotic vehicle.

Learning effects of dynamic postural control by auditory biofeedback versus visual biofeedback training.

PubMed

Hasegawa, Naoya; Takeda, Kenta; Sakuma, Moe; Mani, Hiroki; Maejima, Hiroshi; Asaka, Tadayoshi

2017-10-01

Augmented sensory biofeedback (BF) for postural control is widely used to improve postural stability. However, the effective sensory information in BF systems of motor learning for postural control is still unknown. The purpose of this study was to investigate the learning effects of visual versus auditory BF training in dynamic postural control. Eighteen healthy young adults were randomly divided into two groups (visual BF and auditory BF). In test sessions, participants were asked to bring the real-time center of pressure (COP) in line with a hidden target by body sway in the sagittal plane. The target moved in seven cycles of sine curves at 0.23Hz in the vertical direction on a monitor. In training sessions, the visual and auditory BF groups were required to change the magnitude of a visual circle and a sound, respectively, according to the distance between the COP and target in order to reach the target. The perceptual magnitudes of visual and auditory BF were equalized according to Stevens' power law. At the retention test, the auditory but not visual BF group demonstrated decreased postural performance errors in both the spatial and temporal parameters under the no-feedback condition. These findings suggest that visual BF increases the dependence on visual information to control postural performance, while auditory BF may enhance the integration of the proprioceptive sensory system, which contributes to motor learning without BF. These results suggest that auditory BF training improves motor learning of dynamic postural control. Copyright © 2017 Elsevier B.V. All rights reserved.

Optical coherence tomography detection of shear wave propagation in inhomogeneous tissue equivalent phantoms and ex-vivo carotid artery samples

PubMed Central

Razani, Marjan; Luk, Timothy W.H.; Mariampillai, Adrian; Siegler, Peter; Kiehl, Tim-Rasmus; Kolios, Michael C.; Yang, Victor X.D.

2014-01-01

In this work, we explored the potential of measuring shear wave propagation using optical coherence elastography (OCE) in an inhomogeneous phantom and carotid artery samples based on a swept-source optical coherence tomography (OCT) system. Shear waves were generated using a piezoelectric transducer transmitting sine-wave bursts of 400 μs duration, applying acoustic radiation force (ARF) to inhomogeneous phantoms and carotid artery samples, synchronized with a swept-source OCT (SS-OCT) imaging system. The phantoms were composed of gelatin and titanium dioxide whereas the carotid artery samples were embedded in gel. Differential OCT phase maps, measured with and without the ARF, detected the microscopic displacement generated by shear wave propagation in these phantoms and samples of different stiffness. We present the technique for calculating tissue mechanical properties by propagating shear waves in inhomogeneous tissue equivalent phantoms and carotid artery samples using the ARF of an ultrasound transducer, and measuring the shear wave speed and its associated properties in the different layers with OCT phase maps. This method lays the foundation for future in-vitro and in-vivo studies of mechanical property measurements of biological tissues such as vascular tissues, where normal and pathological structures may exhibit significant contrast in the shear modulus. PMID:24688822

Using the Convergent Cross Mapping method to test causality between Arctic Oscillation / North Atlantic Oscillation and Atlantic Multidecadal Oscillation

NASA Astrophysics Data System (ADS)

Gutowska, Dorota; Piskozub, Jacek

2017-04-01

There is a vast literature body on the climate indices and processes they represent. A large part of it deals with "teleconnections" or causal relations between them. However until recently time lagged correlations was the best tool of studying causation. However no correlation (even lagged) proves causation. We use a recently developed method of studying casual relations between short time series, Convergent Cross Mapping (CCM), to search for causation between the atmospheric (AO and NAO) and oceanic (AMO) indices. The version we have chosen (available as an R language package rEDM) allows for comparing time series with time lags. This work builds on previous one, showing with time-lagged correlations that AO/NAO precedes AMO by about 15 years and at the same time is preceded by AMO (but with an inverted sign) also by the same amount of time. This behaviour is identical to the relationship of a sine and cosine with the same period. This may suggest that the multidecadal oscillatory parts of the atmospheric and oceanic indices represent the same global-scale set of processes. In other words they may be symptoms of the same oscillation. The aim of present study is to test this hypothesis with a tool created specially for discovering causal relationships in dynamic systems.

Conformal Nets II: Conformal Blocks

NASA Astrophysics Data System (ADS)

Bartels, Arthur; Douglas, Christopher L.; Henriques, André

2017-08-01

Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

Possible Detection of Pi(exp 0)-Decay Gamma-Ray Emission from Cyg OB2 by EGRET

NASA Technical Reports Server (NTRS)

Chen, W.; White, R. L.; Bertsch, D.

1996-01-01

We report possible detection of pi (exp 0) decay radiation from Cyg OB2, a nearby (1.7 kpc) massive OB star association. The EGRET flux (greater than 100 MeV) maps clearly indicate a point source whose error circle includes both Cyg OB2 and Cyg X-3. We show that Cyg X-3 is unlikely to be the counterpart for the EGRET source, because of the marginal spatial consistency and the lack of the 4.8 hour modulation seen in other high energy emissions from Cyg X-3. If confirmed, this will be the first detection by EGRET of massive stars.

OCT Expanded Clinical Data Analysis

NASA Technical Reports Server (NTRS)

Van Baalen, Mary; Tafreshi, Ali; Patel, Nimesh; Young, Millennia; Mason, Sara; Otto, Christian; Samuels, Brian; Koslovsky, Matthew; Schaefer, Caroline; Taiym, Wafa;

Possible detection of π^0^-decay γ-ray emission from CYG OB2 by EGRET.

NASA Astrophysics Data System (ADS)

Chen, W.; White, R. L.; Bertsch, D.

1996-12-01

We report possible detection of π^0^-decay radiation from Cyg OB2, a nearby (1.7kpc) massive OB star association. The EGRET flux (>100MeV) maps clearly indicate a point source whose error circle includes both Cyg OB2 and Cyg X-3. We show that Cyg X-3 is unlikely to be the counterpart for the EGRET source, because of the marginal spatial consistency and the lack of the 4.8-hour modulation seen in other high energy emissions from Cyg X-3. If confirmed, this will be the first detection by EGRET of massive stars.

Influence of off-great-circle propagation of Rayleigh waves on event-based surface wave tomography in Northeast China

NASA Astrophysics Data System (ADS)

Chen, Haopeng; Ni, Sidao; Chu, Risheng; Chong, Jiajun; Liu, Zhikun; Zhu, Liangbao

2018-05-01

Surface waves are generally assumed to propagate along great-circle paths in most surface-wave tomography. However, when lateral heterogeneity is strong, off-great-circle propagation may occur and deteriorate surface wave tomography results based on the great-circle assumption. In this study, we used teleseismic waveforms recorded by the NECESSArray in Northeast China to study off-great-circle propagation of Rayleigh waves using the beamforming method and evaluated the influence of off-great-circle propagation on event-based surface wave tomography. The results show that arrival angle anomalies generally increase with decreasing period. The arrival angle anomalies at 60 and 50 s periods are smaller than that at 40 and 30 s periods, which indicates that the off-great-circle propagation is relatively weak for longer periods. At 30 s period, the arrival angle anomalies are relatively larger and some of the measurements can exceed 20°, which represents a strong off-great-circle propagation effect. In some areas, the arrival angle anomalies of adjacent events differ significantly, which may be attributed to multipathing propagation of surface waves. To evaluate the influence of off-great-circle propagation on event-based surface wave tomography, we used measured arrival angle anomalies to correct two-station phase velocity measurements, and performed azimuthal anisotropy tomography using dispersion datasets with and without the arrival angle correction. At longer periods, such as 60 s, the influence of off-great-circle propagation on surface wave tomography is weak even though the corrected model has better data fit than the uncorrected model. However, the influence of off-great-circle propagation is non-negligible at short periods. The tomography results at 30 s period show that the differences in phase velocity, the strength of anisotropy and the fast direction can be as large as 1.5 per cent, 1.0 per cent and 30°, respectively. Furthermore, the corrected phase velocity is systematically lower than that without correction. This study illustrates the necessity of studying the off-great-circle propagation of surface waves to improve the accuracy of event-based surface wave tomography, especially for shorter periods.

Bov-tA short interspersed nucleotide element sequences in circulating nucleic acids from sera of cattle with bovine spongiform encephalopathy (BSE) and sera of cattle exposed to BSE.

PubMed

Schütz, Ekkehard; Urnovitz, Howard B; Iakoubov, Leonid; Schulz-Schaeffer, Walter; Wemheuer, Wilhelm; Brenig, Bertram

2005-07-01

Circulating nucleic acids (CNA) are known to be enriched in repetitive DNA sequences in humans. Here, bovine sera CNA were analyzed to determine if cell stress-related short interspersed nucleotide elements (SINEs) could be detected in sera from cattle associated with bovine spongiform encephalopathy (BSE). Nucleic acids were extracted, amplified, cloned, and sequenced from the sera of protease-resistant prion protein (PrP(res))-positive cattle (n = 2) and sera from BSE-cohort cows (n = 6); 150 out of 163 clones revealed the presence of, on average, an 80-bp sequence from the 3' region of Bov-tA SINE. A PCR protocol was developed that differentially identified SINE-associated CNA in BSE-exposed versus normal cattle. CNA were extracted from a serum vesicular fraction after controlled blood collection and processing procedures. Sera from four confirmed cases of BSE, 137 BSE-exposed cohort animals associated with eight confirmed BSE cases, and 845 healthy, PrP(res)-negative control cows were tested. All four sera from confirmed BSE cases were repeatedly reactive in the assay. BSE-exposed cohorts had a 100-fold higher occurrence of repeatedly reactive individuals per cohort (average = 63%; range = 33% to 91%), compared to healthy controls (average = 0.6%; P < 0.001). This study shows that BSE-confirmed and cohort animals possess a unique profile of SINE-associated serum CNA that can be utilized as a marker that highly correlates to BSE exposure.

Bov-tA Short Interspersed Nucleotide Element Sequences in Circulating Nucleic Acids from Sera of Cattle with Bovine Spongiform Encephalopathy (BSE) and Sera of Cattle Exposed to BSE

PubMed Central

Schütz, Ekkehard; Urnovitz, Howard B.; Iakoubov, Leonid; Schulz-Schaeffer, Walter; Wemheuer, Wilhelm; Brenig, Bertram

2005-01-01

Circulating nucleic acids (CNA) are known to be enriched in repetitive DNA sequences in humans. Here, bovine sera CNA were analyzed to determine if cell stress-related short interspersed nucleotide elements (SINEs) could be detected in sera from cattle associated with bovine spongiform encephalopathy (BSE). Nucleic acids were extracted, amplified, cloned, and sequenced from the sera of protease-resistant prion protein (PrPres)-positive cattle (n = 2) and sera from BSE-cohort cows (n = 6); 150 out of 163 clones revealed the presence of, on average, an 80-bp sequence from the 3′ region of Bov-tA SINE. A PCR protocol was developed that differentially identified SINE-associated CNA in BSE-exposed versus normal cattle. CNA were extracted from a serum vesicular fraction after controlled blood collection and processing procedures. Sera from four confirmed cases of BSE, 137 BSE-exposed cohort animals associated with eight confirmed BSE cases, and 845 healthy, PrPres-negative control cows were tested. All four sera from confirmed BSE cases were repeatedly reactive in the assay. BSE-exposed cohorts had a 100-fold higher occurrence of repeatedly reactive individuals per cohort (average = 63%; range = 33% to 91%), compared to healthy controls (average = 0.6%; P < 0.001). This study shows that BSE-confirmed and cohort animals possess a unique profile of SINE-associated serum CNA that can be utilized as a marker that highly correlates to BSE exposure. PMID:16002628

A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla).

PubMed

Gallus, S; Kumar, V; Bertelsen, M F; Janke, A; Nilsson, M A

2015-10-25

Ruminantia, the ruminating, hoofed mammals (cow, deer, giraffe and allies) are an unranked artiodactylan clade. Around 50-60 million years ago the BovB retrotransposon entered the ancestral ruminantian genome through horizontal gene transfer. A survey genome screen using 454-pyrosequencing of the Java mouse deer (Tragulus javanicus) and the lesser kudu (Tragelaphus imberbis) was done to investigate and to compare the landscape of transposable elements within Ruminantia. The family Tragulidae (mouse deer) is the only representative of Tragulina and phylogenetically important, because it represents the earliest divergence in Ruminantia. The data analyses show that, relative to other ruminantian species, the lesser kudu genome has seen an expansion of BovB Long INterspersed Elements (LINEs) and BovB related Short INterspersed Elements (SINEs) like BOVA2. In comparison the genome of Java mouse deer has fewer BovB elements than other ruminants, especially Bovinae, and has in addition a novel CHR-3 SINE most likely propagated by LINE-1. By contrast the other ruminants have low amounts of CHR SINEs but high numbers of actively propagating BovB-derived and BovB-propagated SINEs. The survey sequencing data suggest that the transposable element landscape in mouse deer (Tragulina) is unique among Ruminantia, suggesting a lineage specific evolutionary trajectory that does not involve BovB mediated retrotransposition. This shows that the genomic landscape of mobile genetic elements can rapidly change in any lineage. Copyright © 2015 Elsevier B.V. All rights reserved.

Advanced Sine Wave Modulation of Continuous Wave Laser System for Atmospheric CO2 Differential Absorption Measurements

NASA Technical Reports Server (NTRS)

Campbell, Joel F.; Lin, Bing; Nehrir, Amin R.

2014-01-01

NASA Langley Research Center in collaboration with ITT Exelis have been experimenting with Continuous Wave (CW) laser absorption spectrometer (LAS) as a means of performing atmospheric CO2 column measurements from space to support the Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS) mission.Because range resolving Intensity Modulated (IM) CW lidar techniques presented here rely on matched filter correlations, autocorrelation properties without side lobes or other artifacts are highly desirable since the autocorrelation function is critical for the measurements of lidar return powers, laser path lengths, and CO2 column amounts. In this paper modulation techniques are investigated that improve autocorrelation properties. The modulation techniques investigated in this paper include sine waves modulated by maximum length (ML) sequences in various hardware configurations. A CW lidar system using sine waves modulated by ML pseudo random noise codes is described, which uses a time shifting approach to separate channels and make multiple, simultaneous online/offline differential absorption measurements. Unlike the pure ML sequence, this technique is useful in hardware that is band pass filtered as the IM sine wave carrier shifts the main power band. Both amplitude and Phase Shift Keying (PSK) modulated IM carriers are investigated that exibit perfect autocorrelation properties down to one cycle per code bit. In addition, a method is presented to bandwidth limit the ML sequence based on a Gaussian filter implemented in terms of Jacobi theta functions that does not seriously degrade the resolution or introduce side lobes as a means of reducing aliasing and IM carrier bandwidth.

Endogenous Cortical Oscillations Constrain Neuromodulation by Weak Electric Fields

PubMed Central

Schmidt, Stephen L.; Iyengar, Apoorva K.; Foulser, A. Alban; Boyle, Michael R.; Fröhlich, Flavio

2014-01-01

Background Transcranial alternating current stimulation (tACS) is a non-invasive brain stimulation modality that may modulate cognition by enhancing endogenous neocortical oscillations with the application of sine-wave electric fields. Yet, the role of endogenous network activity in enabling and shaping the effects of tACS has remained unclear. Objective We combined optogenetic stimulation and multichannel slice electrophysiology to elucidate how the effect of weak sine-wave electric field depends on the ongoing cortical oscillatory activity. We hypothesized that the structure of the response to stimulation depended on matching the stimulation frequency to the endogenous cortical oscillation. Methods We studied the effect of weak sine-wave electric fields on oscillatory activity in mouse neocortical slices. Optogenetic control of the network activity enabled the generation of in vivo like cortical oscillations for studying the temporal relationship between network activity and sine-wave electric field stimulation. Results Weak electric fields enhanced endogenous oscillations but failed to induce a frequency shift of the ongoing oscillation for stimulation frequencies that were not matched to the endogenous oscillation. This constraint on the effect of electric field stimulation imposed by endogenous network dynamics was limited to the case of weak electric fields targeting in vivo-like network dynamics. Together, these results suggest that the key mechanism of tACS may be enhancing but not overriding of intrinsic network dynamics. Conclusion Our results contribute to understanding the inconsistent tACS results from human studies and propose that stimulation precisely adjusted in frequency to the endogenous oscillations is key to rational design of non-invasive brain stimulation paradigms. PMID:25129402

Surface wave tomography of North America and the Caribbean using global and regional broad-band networks: Phase velocity maps and limitations of ray theory

USGS Publications Warehouse

Godey, S.; Snieder, R.; Villasenor, A.; Benz, H.M.

2003-01-01

We present phase velocity maps of fundamental mode Rayleigh waves across the North American and Caribbean plates. Our data set consists of 1846 waveforms from 172 events recorded at 91 broad-band stations operating in North America. We compute phase velocity maps in four narrow period bands between 50 and 150 s using a non-linear waveform inversion method that solves for phase velocity perturbations relative to a reference Earth model (PREM). Our results show a strong velocity contrast between high velocities beneath the stable North American craton, and lower velocities in the tectonically active western margin, in agreement with other regional and global surface wave tomography studies. We perform detailed comparisons with global model results, which display good agreement between phase velocity maps in the location and amplitude of the anomalies. However, forward modelling shows that regional maps are more accurate for predicting waveforms. In addition, at long periods, the amplitude of the velocity anomalies imaged in our regional phase velocity maps is three time larger than in global phase velocity models. This amplitude factor is necessary to explain the data accurately, showing that regional models provide a better image of velocity structures. Synthetic tests show that the raypath coverage used in this study enables one to resolve velocity features of the order of 800-1000 km. However, only larger length-scale features are observed in the phase velocity maps. The limitation in resolution of our maps can be attributed to the wave propagation theory used in the inversion. Ray theory does not account for off-great-circle ray propagation effects, such as ray bending or scattering. For wavelengths less than 1000 km, scattering effects are significant and may need to be considered.