Bayesian reconstruction of gravitational wave bursts using chirplets

NASA Astrophysics Data System (ADS)

Millhouse, Margaret; Cornish, Neil; Littenberg, Tyson

2017-01-01

The BayesWave algorithm has been shown to accurately reconstruct unmodeled short duration gravitational wave bursts and to distinguish between astrophysical signals and transient noise events. BayesWave does this by using a variable number of sine-Gaussian (Morlet) wavelets to reconstruct data in multiple interferometers. While the Morlet wavelets can be summed together to produce any possible waveform, there could be other wavelet functions that improve the performance. Because we expect most astrophysical gravitational wave signals to evolve in frequency, modified Morlet wavelets with linear frequency evolution - called chirplets - may better reconstruct signals with fewer wavelets. We compare the performance of BayesWave using Morlet wavelets and chirplets on a variety of simulated signals.

Method of detecting system function by measuring frequency response

NASA Technical Reports Server (NTRS)

Morrison, John L. (Inventor); Morrison, William H. (Inventor); Christophersen, Jon P. (Inventor)

2012-01-01

Real-time battery impedance spectrum is acquired using a one-time record. Fast Summation Transformation (FST) is a parallel method of acquiring a real-time battery impedance spectrum using a one-time record that enables battery diagnostics. An excitation current to a battery is a sum of equal amplitude sine waves of frequencies that are octave harmonics spread over a range of interest. A sample frequency is also octave and harmonically related to all frequencies in the sum. The time profile of this signal has a duration that is a few periods of the lowest frequency. The voltage response of the battery, average deleted, is the impedance of the battery in the time domain. Since the excitation frequencies are known and octave and harmonically related, a simple algorithm, FST, processes the time record by rectifying relative to the sine and cosine of each frequency. Another algorithm yields real and imaginary components for each frequency.

Method of detecting system function by measuring frequency response

DOEpatents

Morrison, John L [Butte, MT; Morrison, William H [Manchester, CT; Christophersen, Jon P [Idaho Falls, ID

2012-04-03

Real-time battery impedance spectrum is acquired using a one-time record. Fast Summation Transformation (FST) is a parallel method of acquiring a real-time battery impedance spectrum using a one-time record that enables battery diagnostics. An excitation current to a battery is a sum of equal amplitude sine waves of frequencies that are octave harmonics spread over a range of interest. A sample frequency is also octave and harmonically related to all frequencies in the sum. The time profile of this signal has a duration that is a few periods of the lowest frequency. The voltage response of the battery, average deleted, is the impedance of the battery in the time domain. Since the excitation frequencies are known and octave and harmonically related, a simple algorithm, FST, processes the time record by rectifying relative to the sine and cosine of each frequency. Another algorithm yields real and imaginary components for each frequency.

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.

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.

Systematics-insensitive Periodic Signal Search with K2

NASA Astrophysics Data System (ADS)

Angus, Ruth; Foreman-Mackey, Daniel; Johnson, John A.

2016-02-01

From pulsating stars to transiting exoplanets, the search for periodic signals in K2 data, Kepler’s two-wheeled extension, is relevant to a long list of scientific goals. Systematics affecting K2 light curves due to the decreased spacecraft pointing precision inhibit the easy extraction of periodic signals from the data. We here develop a method for producing periodograms of K2 light curves that are insensitive to pointing-induced systematics; the Systematics-insensitive Periodogram (SIP). Traditional sine-fitting periodograms use a generative model to find the frequency of a sinusoid that best describes the data. We extend this principle by including systematic trends, based on a set of “eigen light curves,” following Foreman-Mackey et al., in our generative model as well as a sum of sine and cosine functions over a grid of frequencies. Using this method we are able to produce periodograms with vastly reduced systematic features. The quality of the resulting periodograms are such that we can recover acoustic oscillations in giant stars and measure stellar rotation periods without the need for any detrending. The algorithm is also applicable to the detection of other periodic phenomena such as variable stars, eclipsing binaries and short-period exoplanet candidates. The SIP code is available at https://github.com/RuthAngus/SIPK2.

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.

Partitioning Pythagorean Triangles Using Pythagorean Angles

ERIC Educational Resources Information Center

Swenson, Carl E.; Yandl, Andre L.

2012-01-01

Inside any Pythagorean right triangle, it is possible to find a point M so that drawing segments from M to each vertex of the triangle yields angles whose sines and cosines are all rational. This article describes an algorithm that generates an infinite number of such points.

Method, system and computer-readable media for measuring impedance of an energy storage device

DOEpatents

Morrison, John L.; Morrison, William H.; Christophersen, Jon P.; Motloch, Chester G.

2016-01-26

Real-time battery impedance spectrum is acquired using a one-time record. Fast Summation Transformation (FST) is a parallel method of acquiring a real-time battery impedance spectrum using a one-time record that enables battery diagnostics. An excitation current to a battery is a sum of equal amplitude sine waves of frequencies that are octave harmonics spread over a range of interest. A sample frequency is also octave and harmonically related to all frequencies in the sum. A time profile of this sampled signal has a duration that is a few periods of the lowest frequency. A voltage response of the battery, average deleted, is an impedance of the battery in a time domain. Since the excitation frequencies are known and octave and harmonically related, a simple algorithm, FST, processes the time profile by rectifying relative to sine and cosine of each frequency. Another algorithm yields real and imaginary components for each frequency.

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.

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.

A Geometric View of Complex Trigonometric Functions

ERIC Educational Resources Information Center

Hammack, Richard

2007-01-01

Given that the sine and cosine functions of a real variable can be interpreted as the coordinates of points on the unit circle, the author of this article asks whether there is something similar for complex variables, and shows that indeed there is.

Boundary Conditions for Infinite Conservation Laws

NASA Astrophysics Data System (ADS)

Rosenhaus, V.; Bruzón, M. S.; Gandarias, M. L.

2016-12-01

Regular soliton equations (KdV, sine-Gordon, NLS) are known to possess infinite sets of local conservation laws. Some other classes of nonlinear PDE possess infinite-dimensional symmetries parametrized by arbitrary functions of independent or dependent variables; among them are Zabolotskaya-Khokhlov, Kadomtsev-Petviashvili, Davey-Stewartson equations and Born-Infeld equation. Boundary conditions were shown to play an important role for the existence of local conservation laws associated with infinite-dimensional symmetries. In this paper, we analyze boundary conditions for the infinite conserved densities of regular soliton equations: KdV, potential KdV, Sine-Gordon equation, and nonlinear Schrödinger equation, and compare them with boundary conditions for the conserved densities obtained from infinite-dimensional symmetries with arbitrary functions of independent and dependent variables.

Function algorithms for MPP scientific subroutines, volume 1

NASA Technical Reports Server (NTRS)

Gouch, J. G.

1984-01-01

Design documentation and user documentation for function algorithms for the Massively Parallel Processor (MPP) are presented. The contract specifies development of MPP assembler instructions to perform the following functions: natural logarithm; exponential (e to the x power); square root; sine; cosine; and arctangent. To fulfill the requirements of the contract, parallel array and solar implementations for these functions were developed on the PDP11/34 Program Development and Management Unit (PDMU) that is resident at the MPP testbed installation located at the NASA Goddard facility.

Fractal Music: The Mathematics Behind "Techno" Music

ERIC Educational Resources Information Center

Padula, Janice

2005-01-01

This article describes sound waves, their basis in the sine curve, Fourier's theorem of infinite series, the fractal equation and its application to the composition of music, together with algorithms (such as those employed by meteorologist Edward Lorenz in his discovery of chaos theory) that are now being used to compose fractal music on…

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.

Relationship among Demographic Variables and Pupils' Reasoning Ability

ERIC Educational Resources Information Center

Tella, Adeyinka; Tella, Adedeji; Adika, L. O.; Toyobo, Majekodunmi Oluwole

2008-01-01

Introduction: Pupils reasoning ability is a sine-qua-non to the evaluation of their performance in learning and an indicator of their potential predictors of future performance. Method: The study examined the relationship among demographic variables and reasoning ability of primary school pupils. It drew four hundred pupils from ten (10)…

Principal components and iterative regression analysis of geophysical series: Application to Sunspot number (1750 2004)

NASA Astrophysics Data System (ADS)

Nordemann, D. J. R.; Rigozo, N. R.; de Souza Echer, M. P.; Echer, E.

2008-11-01

We present here an implementation of a least squares iterative regression method applied to the sine functions embedded in the principal components extracted from geophysical time series. This method seems to represent a useful improvement for the non-stationary time series periodicity quantitative analysis. The principal components determination followed by the least squares iterative regression method was implemented in an algorithm written in the Scilab (2006) language. The main result of the method is to obtain the set of sine functions embedded in the series analyzed in decreasing order of significance, from the most important ones, likely to represent the physical processes involved in the generation of the series, to the less important ones that represent noise components. Taking into account the need of a deeper knowledge of the Sun's past history and its implication to global climate change, the method was applied to the Sunspot Number series (1750-2004). With the threshold and parameter values used here, the application of the method leads to a total of 441 explicit sine functions, among which 65 were considered as being significant and were used for a reconstruction that gave a normalized mean squared error of 0.146.

Color image encryption by using Yang-Gu mixture amplitude-phase retrieval algorithm in gyrator transform domain and two-dimensional Sine logistic modulation map

NASA Astrophysics Data System (ADS)

Sui, Liansheng; Liu, Benqing; Wang, Qiang; Li, Ye; Liang, Junli

2015-12-01

A color image encryption scheme is proposed based on Yang-Gu mixture amplitude-phase retrieval algorithm and two-coupled logistic map in gyrator transform domain. First, the color plaintext image is decomposed into red, green and blue components, which are scrambled individually by three random sequences generated by using the two-dimensional Sine logistic modulation map. Second, each scrambled component is encrypted into a real-valued function with stationary white noise distribution in the iterative amplitude-phase retrieval process in the gyrator transform domain, and then three obtained functions are considered as red, green and blue channels to form the color ciphertext image. Obviously, the ciphertext image is real-valued function and more convenient for storing and transmitting. In the encryption and decryption processes, the chaotic random phase mask generated based on logistic map is employed as the phase key, which means that only the initial values are used as private key and the cryptosystem has high convenience on key management. Meanwhile, the security of the cryptosystem is enhanced greatly because of high sensitivity of the private keys. Simulation results are presented to prove the security and robustness of the proposed scheme.

Centrifugal unbalance detection system

DOEpatents

Cordaro, Joseph V.; Reeves, George; Mets, Michael

2002-01-01

A system consisting of an accelerometer sensor attached to a centrifuge enclosure for sensing vibrations and outputting a signal in the form of a sine wave with an amplitude and frequency that is passed through a pre-amp to convert it to a voltage signal, a low pass filter for removing extraneous noise, an A/D converter and a processor and algorithm for operating on the signal, whereby the algorithm interprets the amplitude and frequency associated with the signal and once an amplitude threshold has been exceeded the algorithm begins to count cycles during a predetermined time period and if a given number of complete cycles exceeds the frequency threshold during the predetermined time period, the system shuts down the centrifuge.

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 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.

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

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.

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.

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.

Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export.

PubMed

Karijolich, John; Zhao, Yang; Alla, Ravi; Glaunsinger, Britt

2017-06-02

Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28 270 SINE loci, with ∼50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA-RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export

PubMed Central

Zhao, Yang; Alla, Ravi

2017-01-01

Abstract Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28 270 SINE loci, with ∼50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA–RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation. PMID:28334904

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.

Sine-Gordon Equation in (1+2) and (1+3) dimensions: Existence and Classification of Traveling-Wave Solutions.

PubMed

Zarmi, Yair

2015-01-01

The (1+1)-dimensional Sine-Gordon equation passes integrability tests commonly applied to nonlinear evolution equations. Its kink solutions (one-dimensional fronts) are obtained by a Hirota algorithm. In higher space-dimensions, the equation does not pass these tests. Although it has been derived over the years for quite a few physical systems that have nothing to do with Special Relativity, the Sine-Gordon equation emerges as a non-linear relativistic wave equation. This opens the way for exploiting the tools of the Theory of Special Relativity. Using no more than the relativistic kinematics of tachyonic momentum vectors, from which the solutions are constructed through the Hirota algorithm, the existence and classification of N-moving-front solutions of the (1+2)- and (1+3)-dimensional equations for all N ≥ 1 are presented. In (1+2) dimensions, each multi-front solution propagates rigidly at one velocity. The solutions are divided into two subsets: Solutions whose velocities are lower than a limiting speed, c = 1, or are greater than or equal to c. To connect with concepts of the Theory of Special Relativity, c will be called "the speed of light." In (1+3)-dimensions, multi-front solutions are characterized by spatial structure and by velocity composition. The spatial structure is either planar (rotated (1+2)-dimensional solutions), or genuinely three-dimensional--branes. Planar solutions, propagate rigidly at one velocity, which is lower than, equal to, or higher than c. Branes must contain clusters of fronts whose speed exceeds c = 1. Some branes are "hybrids": different clusters of fronts propagate at different velocities. Some velocities may be lower than c but some must be equal to, or exceed, c. Finally, the speed of light cannot be approached from within the subset of slower-than-light solutions in both (1+2) and (1+3) dimensions.

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).

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.

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.

A new compound control method for sine-on-random mixed vibration test

NASA Astrophysics Data System (ADS)

Zhang, Buyun; Wang, Ruochen; Zeng, Falin

2017-09-01

Vibration environmental test (VET) is one of the important and effective methods to provide supports for the strength design, reliability and durability test of mechanical products. A new separation control strategy was proposed to apply in multiple-input multiple-output (MIMO) sine on random (SOR) mixed mode vibration test, which is the advanced and intensive test type of VET. As the key problem of the strategy, correlation integral method was applied to separate the mixed signals which included random and sinusoidal components. The feedback control formula of MIMO linear random vibration system was systematically deduced in frequency domain, and Jacobi control algorithm was proposed in view of the elements, such as self-spectrum, coherence, and phase of power spectral density (PSD) matrix. Based on the excessive correction of excitation in sine vibration test, compression factor was introduced to reduce the excitation correction, avoiding the destruction to vibration table or other devices. The two methods were synthesized to be applied in MIMO SOR vibration test system. In the final, verification test system with the vibration of a cantilever beam as the control object was established to verify the reliability and effectiveness of the methods proposed in the paper. The test results show that the exceeding values can be controlled in the tolerance range of references accurately, and the method can supply theory and application supports for mechanical engineering.

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…

Robust control algorithms for Mars aerobraking

NASA Technical Reports Server (NTRS)

Shipley, Buford W., Jr.; Ward, Donald T.

1992-01-01

Four atmospheric guidance concepts have been adapted to control an interplanetary vehicle aerobraking in the Martian atmosphere. The first two offer improvements to the Analytic Predictor Corrector (APC) to increase its robustness to density variations. The second two are variations of a new Liapunov tracking exit phase algorithm, developed to guide the vehicle along a reference trajectory. These four new controllers are tested using a six degree of freedom computer simulation to evaluate their robustness. MARSGRAM is used to develop realistic atmospheres for the study. When square wave density pulses perturb the atmosphere all four controllers are successful. The algorithms are tested against atmospheres where the inbound and outbound density functions are different. Square wave density pulses are again used, but only for the outbound leg of the trajectory. Additionally, sine waves are used to perturb the density function. The new algorithms are found to be more robust than any previously tested and a Liapunov controller is selected as the most robust control algorithm overall examined.

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.

Computer simulator for a mobile telephone system

NASA Technical Reports Server (NTRS)

Schilling, D. L.

1981-01-01

A software simulator was developed to assist NASA in the design of the land mobile satellite service. Structured programming techniques were used by developing the algorithm using an ALCOL-like pseudo language and then encoding the algorithm into FORTRAN 4. The basic input data to the system is a sine wave signal although future plans call for actual sampled voice as the input signal. The simulator is capable of studying all the possible combinations of types and modes of calls through the use of five communication scenarios: single hop systems; double hop, signal gateway system; double hop, double gateway system; mobile to wireline system; and wireline to mobile system. The transmitter, fading channel, and interference source simulation are also discussed.

SPF/DB titanium concepts for structural efficiency foi HC

NASA Technical Reports Server (NTRS)

Wilson, V. E.

1982-01-01

Illustrations for a presentation on superplastic forming/diffusion bonding titanium design concepts are presented. Sandwich skin panels with hat section, semicircular corrugation, sine wave, and truss cores are shown. The fabrication of wing panels is illustrated, and applications to the design of advanced variable sweep bombers summarized.

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.

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.

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.

Discrete cosine and sine transforms generalized to honeycomb lattice

NASA Astrophysics Data System (ADS)

Hrivnák, Jiří; Motlochová, Lenka

2018-06-01

The discrete cosine and sine transforms are generalized to a triangular fragment of the honeycomb lattice. The honeycomb point sets are constructed by subtracting the root lattice from the weight lattice points of the crystallographic root system A2. The two-variable orbit functions of the Weyl group of A2, discretized simultaneously on the weight and root lattices, induce a novel parametric family of extended Weyl orbit functions. The periodicity and von Neumann and Dirichlet boundary properties of the extended Weyl orbit functions are detailed. Three types of discrete complex Fourier-Weyl transforms and real-valued Hartley-Weyl transforms are described. Unitary transform matrices and interpolating behavior of the discrete transforms are exemplified. Consequences of the developed discrete transforms for transversal eigenvibrations of the mechanical graphene model are discussed.

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

Dispersive optical solitons and modulation instability analysis of Schrödinger-Hirota equation with spatio-temporal dispersion and Kerr law nonlinearity

NASA Astrophysics Data System (ADS)

Inc, Mustafa; Aliyu, Aliyu Isa; Yusuf, Abdullahi; Baleanu, Dumitru

2018-01-01

This paper obtains the dark, bright, dark-bright or combined optical and singular solitons to the perturbed nonlinear Schrödinger-Hirota equation (SHE) with spatio-temporal dispersion (STD) and Kerr law nonlinearity in optical fibers. The integration algorithm is the Sine-Gordon equation method (SGEM). Furthermore, the modulation instability analysis (MI) of the equation is studied based on the standard linear-stability analysis and the MI gain spectrum is got.

An Experimental Study of an Ultra-Mobile Vehicle for Off-Road Transportation.

DTIC Science & Technology

1983-07-01

implemented. 2.2.3 Image Processing Algorithms The ultimate goal of a vision system is to understand the content of a scene and to extract useful...to extract useful information from it. Four existing robot-vision systems, the General Motors CONSIGHT system, the UNIVISIUN system, the Westinghouse...cos + C . sino A (5.48) By taking out a comon factor, Eq. (5.48) can be rewritten as /-- c. ( B coso + C sine) A (5.49) 203 !_ - Let Z B sie4 = : v, VB2

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.

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.

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.

Perceptual organization of speech signals by children with and without dyslexia

PubMed Central

Nittrouer, Susan; Lowenstein, Joanna H.

2013-01-01

Developmental dyslexia is a condition in which children encounter difficulty learning to read in spite of adequate instruction. Although considerable effort has been expended trying to identify the source of the problem, no single solution has been agreed upon. The current study explored a new hypothesis, that developmental dyslexia may be due to faulty perceptual organization of linguistically relevant sensory input. To test that idea, sentence-length speech signals were processed to create either sine-wave or noise-vocoded analogs. Seventy children between 8 and 11 years of age, with and without dyslexia participated. Children with dyslexia were selected to have phonological awareness deficits, although those without such deficits were retained in the study. The processed sentences were presented for recognition, and measures of reading, phonological awareness, and expressive vocabulary were collected. Results showed that children with dyslexia, regardless of phonological subtype, had poorer recognition scores than children without dyslexia for both kinds of degraded sentences. Older children with dyslexia recognized the sine-wave sentences better than younger children with dyslexia, but no such effect of age was found for the vocoded materials. Recognition scores were used as predictor variables in regression analyses with reading, phonological awareness, and vocabulary measures used as dependent variables. Scores for both sorts of sentence materials were strong predictors of performance on all three dependent measures when all children were included, but only performance for the sine-wave materials explained significant proportions of variance when only children with dyslexia were included. Finally, matching young, typical readers with older children with dyslexia on reading abilities did not mitigate the group difference in recognition of vocoded sentences. Conclusions were that children with dyslexia have difficulty organizing linguistically relevant sensory input, but learn to do so for the structure preserved by sine-wave signals before they do so for other sorts of signal structure. These perceptual organization deficits could account for difficulties acquiring refined linguistic representations, including those of a phonological nature, although ramifications are different across affected children. PMID:23702597

Perceptual organization of speech signals by children with and without dyslexia.

PubMed

Nittrouer, Susan; Lowenstein, Joanna H

2013-08-01

Developmental dyslexia is a condition in which children encounter difficulty learning to read in spite of adequate instruction. Although considerable effort has been expended trying to identify the source of the problem, no single solution has been agreed upon. The current study explored a new hypothesis, that developmental dyslexia may be due to faulty perceptual organization of linguistically relevant sensory input. To test that idea, sentence-length speech signals were processed to create either sine-wave or noise-vocoded analogs. Seventy children between 8 and 11 years of age, with and without dyslexia participated. Children with dyslexia were selected to have phonological awareness deficits, although those without such deficits were retained in the study. The processed sentences were presented for recognition, and measures of reading, phonological awareness, and expressive vocabulary were collected. Results showed that children with dyslexia, regardless of phonological subtype, had poorer recognition scores than children without dyslexia for both kinds of degraded sentences. Older children with dyslexia recognized the sine-wave sentences better than younger children with dyslexia, but no such effect of age was found for the vocoded materials. Recognition scores were used as predictor variables in regression analyses with reading, phonological awareness, and vocabulary measures used as dependent variables. Scores for both sorts of sentence materials were strong predictors of performance on all three dependent measures when all children were included, but only performance for the sine-wave materials explained significant proportions of variance when only children with dyslexia were included. Finally, matching young, typical readers with older children with dyslexia on reading abilities did not mitigate the group difference in recognition of vocoded sentences. Conclusions were that children with dyslexia have difficulty organizing linguistically relevant sensory input, but learn to do so for the structure preserved by sine-wave signals before they do so for other sorts of signal structure. These perceptual organization deficits could account for difficulties acquiring refined linguistic representations, including those of a phonological nature, although ramifications are different across affected children. Copyright © 2013 Elsevier Ltd. All rights reserved.

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.

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

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.

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.

Rocket measurements of electron density irregularities during MAC/SINE

NASA Technical Reports Server (NTRS)

Ulwick, J. C.

1989-01-01

Four Super Arcas rockets were launched at the Andoya Rocket Range, Norway, as part of the MAC/SINE campaign to measure electron density irregularities with high spatial resolution in the cold summer polar mesosphere. They were launched as part of two salvos: the turbulent/gravity wave salvo (3 rockets) and the EISCAT/SOUSY radar salvo (one rocket). In both salvos meteorological rockets, measuring temperature and winds, were also launched and the SOUSY radar, located near the launch site, measured mesospheric turbulence. Electron density irregularities and strong gradients were measured by the rocket probes in the region of most intense backscatter observed by the radar. The electron density profiles (8 to 4 on ascent and 4 on descent) show very different characteristics in the peak scattering region and show marked spatial and temporal variability. These data are intercompared and discussed.

Digital slip frequency generator and method for determining the desired slip frequency

DOEpatents

Klein, Frederick F.

1989-01-01

The output frequency of an electric power generator is kept constant with variable rotor speed by automatic adjustment of the excitation slip frequency. The invention features a digital slip frequency generator which provides sine and cosine waveforms from a look-up table, which are combined with real and reactive power output of the power generator.

Investigation Faculty of Education Students' Cyberloafing Behaviors in Terms of Various Variables

ERIC Educational Resources Information Center

Arabaci, I. Bakir

2017-01-01

Today, internet-based information technologies are sine qua non of effective learning and teaching. By the use of multiple multi-media tools in education, learning environment is enriched, persistence of learning is ensured and the boringness of the course is prevented. However, the purposeless use of internet in classrooms leads students to get…

Numerical results for near surface time domain electromagnetic exploration: a full waveform approach

NASA Astrophysics Data System (ADS)

Sun, H.; Li, K.; Li, X., Sr.; Liu, Y., Sr.; Wen, J., Sr.

2015-12-01

Time domain or Transient electromagnetic (TEM) survey including types with airborne, semi-airborne and ground play important roles in applicants such as geological surveys, ground water/aquifer assess [Meju et al., 2000; Cox et al., 2010], metal ore exploration [Yang and Oldenburg, 2012], prediction of water bearing structures in tunnels [Xue et al., 2007; Sun et al., 2012], UXO exploration [Pasion et al., 2007; Gasperikova et al., 2009] etc. The common practice is introducing a current into a transmitting (Tx) loop and acquire the induced electromagnetic field after the current is cut off [Zhdanov and Keller, 1994]. The current waveforms are different depending on instruments. Rectangle is the most widely used excitation current source especially in ground TEM. Triangle and half sine are commonly used in airborne and semi-airborne TEM investigation. In most instruments, only the off time responses are acquired and used in later analysis and data inversion. Very few airborne instruments acquire the on time and off time responses together. Although these systems acquire the on time data, they usually do not use them in the interpretation.This abstract shows a novel full waveform time domain electromagnetic method and our recent modeling results. The benefits comes from our new algorithm in modeling full waveform time domain electromagnetic problems. We introduced the current density into the Maxwell's equation as the transmitting source. This approach allows arbitrary waveforms, such as triangle, half-sine, trapezoidal waves or scatter record from equipment, being used in modeling. Here, we simulate the establishing and induced diffusion process of the electromagnetic field in the earth. The traditional time domain electromagnetic with pure secondary fields can also be extracted from our modeling results. The real time responses excited by a loop source can be calculated using the algorithm. We analyze the full time gates responses of homogeneous half space and two layered models with half sine current waveform as examples. We find the on time responses are quite sensitive to resistivity or depth changes. The results show the potential use of full waveform responses in time domain electromagnetic surveys.

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.

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.

[Molecular variability in the commom shrew Sorex araneus L. from European Russia and Siberia inferred from the length polymorphism of DNA regions flanked by short interspersed elements (Inter-SINE PCR) and the relationships between the Moscow and Seliger chromosome races].

PubMed

Bannikova, A A; Bulatova, N Sh; Kramerov, D A

2006-06-01

Genetic exchange among chromosomal races of the common shrew Sorex araneus and the problem of reproductive barriers have been extensively studied by means of such molecular markers as mtDNA, microsatellites, and allozymes. In the present study, the interpopulation and interracial polymorphism in the common shrew was derived, using fingerprints generated by amplified DNA regions flanked by short interspersed repeats (SINEs)-interSINE PCR (IS-PCR). We used primers, complementary to consensus sequences of two short retroposons: mammalian element MIR and the SOR element from the genome of Sorex araneus. Genetic differentiation among eleven populations of the common shrew from eight chromosome races was estimated. The NP and MJ analyses, as well as multidimensional scaling showed that all samples examined grouped into two main clusters, corresponding to European Russia and Siberia. The bootstrap support of the European Russia cluster in the NJ and MP analyses was respectively 76 and 61%. The bootstrap index for the Siberian cluster was 100% in both analyses; the Tomsk race, included into this cluster, was separated with the bootstrap support of NJ/MP 92/95%.

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

A generalized sine condition and performance comparison of Wolter type II and Wolter-Schwarzschild extreme ultraviolet telescopes

NASA Technical Reports Server (NTRS)

Saha, T. T.

1984-01-01

An equation similar to the Abbe sine condition is derived for a Wolter type II telescope. This equation and the sine condition are then combined to produce a so called generalized sine condition. Using the law of reflection, Fermat's principle, the generalized sine condition, and simple geometry the surface equations for a Wolter type II telescope and an equivalent Wolter-Schwarzschild telescope are calculated. The performances of the telescopes are compared in terms of rms blur circle radius at the Gaussian focal plane and at best focus.

Assessing the Association Between Asthma and Air Quality in the Presence of Wildfires

NASA Astrophysics Data System (ADS)

Young, L. J.; Al-Hamdan, M. Z.; Lopiano, K. K.; Crosson, W. L.; Gotway, C. A.; DuClos, C.; Jordan, M.; Estes, M. G.; Luvall, J. C.; Estes, S. M.; Xu, X.; Holt, N. M.; Leary, E.

2012-12-01

Asthma hospital/emergency room (patient) data are used as the foundation for creating a health outcome indicator of human response to environmental air quality. Daily U.S. Environmental Protection Agency (EPA) Air Quality System (AQS) fine particulates (PM2.5) ground data and the U.S. National Aeronautical Space Administration (NASA) MODIS aerosol optical depth (AOD) data were acquired and processed for years of 2007 and 2008. Figure 1 shows the PM2.5 annual mean composite of all the 2007 B-spline daily surfaces. Initial models for predicting the number of weekly asthma cases within a Florida county has focused on environmental variables. Weekly maximums of PM2.5, relative humidity, and the proportions of the county with smoke and fire were the environmental variables included in the model. Cosine and sine functions of time were used to account for seasonality in asthma cases. Counties were considered to be random effects, thereby adjusting for differences in socio-demographics and other factors. The 2007 predictions for Miami-Dade county when using B-splines PM2.5 are displayed in Figures 2.; PM2.5 annual mean composite of all the 2007 daily surfaces developed using Al-Hamdan et al (2009) B-spline fitting algorithm ; Predicted and observed weekly asthma cases presenting to hospitals or emergency rooms in Miami-Dade county in Florida during 2007

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.

Core-SINE blocks comprise a large fraction of monotreme genomes; implications for vertebrate chromosome evolution.

PubMed

Kirby, Patrick J; Greaves, Ian K; Koina, Edda; Waters, Paul D; Marshall Graves, Jennifer A

2007-01-01

The genomes of the egg-laying platypus and echidna are of particular interest because monotremes are the most basal mammal group. The chromosomal distribution of an ancient family of short interspersed repeats (SINEs), the core-SINEs, was investigated to better understand monotreme genome organization and evolution. Previous studies have identified the core-SINE as the predominant SINE in the platypus genome, and in this study we quantified, characterized and localized subfamilies. Dot blot analysis suggested that a very large fraction (32% of the platypus and 16% of the echidna genome) is composed of Mon core-SINEs. Core-SINE-specific primers were used to amplify PCR products from platypus and echidna genomic DNA. Sequence analysis suggests a common consensus sequence Mon 1-B, shared by platypus and echidna, as well as platypus-specific Mon 1-C and echidna specific Mon 1-D consensus sequences. FISH mapping of the Mon core-SINE products to platypus metaphase spreads demonstrates that the Mon-1C subfamily is responsible for the striking Mon core-SINE accumulation in the distal regions of the six large autosomal pairs and the largest X chromosome. This unusual distribution highlights the dichotomy between the seven large chromosome pairs and the 19 smaller pairs in the monotreme karyotype, which has some similarity to the macro- and micro-chromosomes of birds and reptiles, and suggests that accumulation of repetitive sequences may have enlarged small chromosomes in an ancestral vertebrate. In the forthcoming sequence of the platypus genome there are still large gaps, and the extensive Mon core-SINE accumulation on the distal regions of the six large autosomal pairs may provide one explanation for this missing sequence.

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.

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.

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.

A robust and accurate center-frequency estimation (RACE) algorithm for improving motion estimation performance of SinMod on tagged cardiac MR images without known tagging parameters.

PubMed

Liu, Hong; Wang, Jie; Xu, Xiangyang; Song, Enmin; Wang, Qian; Jin, Renchao; Hung, Chih-Cheng; Fei, Baowei

2014-11-01

A robust and accurate center-frequency (CF) estimation (RACE) algorithm for improving the performance of the local sine-wave modeling (SinMod) method, which is a good motion estimation method for tagged cardiac magnetic resonance (MR) images, is proposed in this study. The RACE algorithm can automatically, effectively and efficiently produce a very appropriate CF estimate for the SinMod method, under the circumstance that the specified tagging parameters are unknown, on account of the following two key techniques: (1) the well-known mean-shift algorithm, which can provide accurate and rapid CF estimation; and (2) an original two-direction-combination strategy, which can further enhance the accuracy and robustness of CF estimation. Some other available CF estimation algorithms are brought out for comparison. Several validation approaches that can work on the real data without ground truths are specially designed. Experimental results on human body in vivo cardiac data demonstrate the significance of accurate CF estimation for SinMod, and validate the effectiveness of RACE in facilitating the motion estimation performance of SinMod. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

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

Effective dimensional reduction algorithm for eigenvalue problems for thin elastic structures: A paradigm in three dimensions

PubMed Central

Ovtchinnikov, Evgueni E.; Xanthis, Leonidas S.

2000-01-01

We present a methodology for the efficient numerical solution of eigenvalue problems of full three-dimensional elasticity for thin elastic structures, such as shells, plates and rods of arbitrary geometry, discretized by the finite element method. Such problems are solved by iterative methods, which, however, are known to suffer from slow convergence or even convergence failure, when the thickness is small. In this paper we show an effective way of resolving this difficulty by invoking a special preconditioning technique associated with the effective dimensional reduction algorithm (EDRA). As an example, we present an algorithm for computing the minimal eigenvalue of a thin elastic plate and we show both theoretically and numerically that it is robust with respect to both the thickness and discretization parameters, i.e. the convergence does not deteriorate with diminishing thickness or mesh refinement. This robustness is sine qua non for the efficient computation of large-scale eigenvalue problems for thin elastic structures. PMID:10655469

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.

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

On the use of video projectors for three-dimensional scanning

NASA Astrophysics Data System (ADS)

Juarez-Salazar, Rigoberto; Diaz-Ramirez, Victor H.; Robledo-Sanchez, Carlos; Diaz-Gonzalez, Gerardo

2017-08-01

Structured light projection is one of the most useful methods for accurate three-dimensional scanning. Video projectors are typically used as the illumination source. However, because video projectors are not designed for structured light systems, some considerations such as gamma calibration must be taken into account. In this work, we present a simple method for gamma calibration of video projectors. First, the experimental fringe patterns are normalized. Then, the samples of the fringe patterns are sorted in ascending order. The sample sorting leads to a simple three-parameter sine curve that is fitted using the Gauss-Newton algorithm. The novelty of this method is that the sorting process removes the effect of the unknown phase. Thus, the resulting gamma calibration algorithm is significantly simplified. The feasibility of the proposed method is illustrated in a three-dimensional scanning experiment.

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.

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

A Novel Multilayer Correlation Maximization Model for Improving CCA-Based Frequency Recognition in SSVEP Brain-Computer Interface.

PubMed

Jiao, Yong; Zhang, Yu; Wang, Yu; Wang, Bei; Jin, Jing; Wang, Xingyu

2018-05-01

Multiset canonical correlation analysis (MsetCCA) has been successfully applied to optimize the reference signals by extracting common features from multiple sets of electroencephalogram (EEG) for steady-state visual evoked potential (SSVEP) recognition in brain-computer interface application. To avoid extracting the possible noise components as common features, this study proposes a sophisticated extension of MsetCCA, called multilayer correlation maximization (MCM) model for further improving SSVEP recognition accuracy. MCM combines advantages of both CCA and MsetCCA by carrying out three layers of correlation maximization processes. The first layer is to extract the stimulus frequency-related information in using CCA between EEG samples and sine-cosine reference signals. The second layer is to learn reference signals by extracting the common features with MsetCCA. The third layer is to re-optimize the reference signals set in using CCA with sine-cosine reference signals again. Experimental study is implemented to validate effectiveness of the proposed MCM model in comparison with the standard CCA and MsetCCA algorithms. Superior performance of MCM demonstrates its promising potential for the development of an improved SSVEP-based brain-computer interface.

A global optimization algorithm inspired in the behavior of selfish herds.

PubMed

Fausto, Fernando; Cuevas, Erik; Valdivia, Arturo; González, Adrián

2017-10-01

In this paper, a novel swarm optimization algorithm called the Selfish Herd Optimizer (SHO) is proposed for solving global optimization problems. SHO is based on the simulation of the widely observed selfish herd behavior manifested by individuals within a herd of animals subjected to some form of predation risk. In SHO, individuals emulate the predatory interactions between groups of prey and predators by two types of search agents: the members of a selfish herd (the prey) and a pack of hungry predators. Depending on their classification as either a prey or a predator, each individual is conducted by a set of unique evolutionary operators inspired by such prey-predator relationship. These unique traits allow SHO to improve the balance between exploration and exploitation without altering the population size. To illustrate the proficiency and robustness of the proposed method, it is compared to other well-known evolutionary optimization approaches such as Particle Swarm Optimization (PSO), Artificial Bee Colony (ABC), Firefly Algorithm (FA), Differential Evolution (DE), Genetic Algorithms (GA), Crow Search Algorithm (CSA), Dragonfly Algorithm (DA), Moth-flame Optimization Algorithm (MOA) and Sine Cosine Algorithm (SCA). The comparison examines several standard benchmark functions, commonly considered within the literature of evolutionary algorithms. The experimental results show the remarkable performance of our proposed approach against those of the other compared methods, and as such SHO is proven to be an excellent alternative to solve global optimization problems. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Transformation (normalization) of slope gradient and surface curvatures, automated for statistical analyses from DEMs

NASA Astrophysics Data System (ADS)

Csillik, O.; Evans, I. S.; Drăguţ, L.

2015-03-01

Automated procedures are developed to alleviate long tails in frequency distributions of morphometric variables. They minimize the skewness of slope gradient frequency distributions, and modify the kurtosis of profile and plan curvature distributions toward that of the Gaussian (normal) model. Box-Cox (for slope) and arctangent (for curvature) transformations are tested on nine digital elevation models (DEMs) of varying origin and resolution, and different landscapes, and shown to be effective. Resulting histograms are illustrated and show considerable improvements over those for previously recommended slope transformations (sine, square root of sine, and logarithm of tangent). Unlike previous approaches, the proposed method evaluates the frequency distribution of slope gradient values in a given area and applies the most appropriate transform if required. Sensitivity of the arctangent transformation is tested, showing that Gaussian-kurtosis transformations are acceptable also in terms of histogram shape. Cube root transformations of curvatures produced bimodal histograms. The transforms are applicable to morphometric variables and many others with skewed or long-tailed distributions. By avoiding long tails and outliers, they permit parametric statistics such as correlation, regression and principal component analyses to be applied, with greater confidence that requirements for linearity, additivity and even scatter of residuals (constancy of error variance) are likely to be met. It is suggested that such transformations should be routinely applied in all parametric analyses of long-tailed variables. Our Box-Cox and curvature automated transformations are based on a Python script, implemented as an easy-to-use script tool in ArcGIS.

Reliability of Leg and Vertical Stiffness During High Speed Treadmill Running.

PubMed

Pappas, Panagiotis; Dallas, Giorgos; Paradisis, Giorgos

2017-04-01

In research, the accurate and reliable measurement of leg and vertical stiffness could contribute to valid interpretations. The current study aimed at determining the intraparticipant variability (ie, intraday and interday reliabilities) of leg and vertical stiffness, as well as related parameters, during high speed treadmill running, using the "sine-wave" method. Thirty-one males ran on a treadmill at 6.67 m∙s -1 , and the contact and flight times were measured. To determine the intraday reliability, three 10-s running bouts with 10-min recovery were performed. In addition, to examine the interday reliability, three 10-s running bouts on 3 separate days with 48-h interbout intervals were performed. The reliability statistics included repeated-measure analysis of variance, average intertrial correlations, intraclass correlation coefficients (ICCs), Cronbach's α reliability coefficient, and the coefficient of variation (CV%). Both intraday and interday reliabilities were high for leg and vertical stiffness (ICC > 0.939 and CV < 4.3%), as well as related variables (ICC > 0.934 and CV < 3.9%). It was thus inferred that the measurements of leg and vertical stiffness, as well as the related parameters obtained using the "sine-wave" method during treadmill running at 6.67 m∙s -1 , were highly reliable, both within and across days.

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.

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

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.

Proposal for a trigonometric method to evaluate the abduction angle of the lower limbs in neonates.

PubMed

Lima, Thaís; Alves, Cyntia; Funayama, Carolina A R

2008-12-01

It is difficult to precisely measure articular arc movement in newborns using a goniometer. This article proposes an objective method based on trigonometry for the evaluation of lower limb abduction. With the newborn aligned in the dorsal decubitus position, 2 points are marked at the level of the medial malleolus, one on the sagittal line and the other at the end of the abduction. Using the right-sided line between these 2 points and a line from the medial malleolus to the reference point at the anterior superior iliac spine or umbilical scar, an isosceles triangle is drawn, and half of the inferential abduction angle is obtained by calculating the sine. Twenty healthy full-term newborns comprise the study cohort. Intersubject and intrasubject variability among the abduction angle values (mean [SD], 37 degrees [4] degrees) is low. This method is advantageous because the measurement is precise and because the sine can be used without approximation.

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

Comparison of least squares and exponential sine sweep methods for Parallel Hammerstein Models estimation

NASA Astrophysics Data System (ADS)

Rebillat, Marc; Schoukens, Maarten

2018-05-01

Linearity is a common assumption for many real-life systems, but in many cases the nonlinear behavior of systems cannot be ignored and must be modeled and estimated. Among the various existing classes of nonlinear models, Parallel Hammerstein Models (PHM) are interesting as they are at the same time easy to interpret as well as to estimate. One way to estimate PHM relies on the fact that the estimation problem is linear in the parameters and thus that classical least squares (LS) estimation algorithms can be used. In that area, this article introduces a regularized LS estimation algorithm inspired on some of the recently developed regularized impulse response estimation techniques. Another mean to estimate PHM consists in using parametric or non-parametric exponential sine sweeps (ESS) based methods. These methods (LS and ESS) are founded on radically different mathematical backgrounds but are expected to tackle the same issue. A methodology is proposed here to compare them with respect to (i) their accuracy, (ii) their computational cost, and (iii) their robustness to noise. Tests are performed on simulated systems for several values of methods respective parameters and of signal to noise ratio. Results show that, for a given set of data points, the ESS method is less demanding in computational resources than the LS method but that it is also less accurate. Furthermore, the LS method needs parameters to be set in advance whereas the ESS method is not subject to conditioning issues and can be fully non-parametric. In summary, for a given set of data points, ESS method can provide a first, automatic, and quick overview of a nonlinear system than can guide more computationally demanding and precise methods, such as the regularized LS one proposed here.

Modal identification of structures from the responses and random decrement signatures

NASA Technical Reports Server (NTRS)

Brahim, S. R.; Goglia, G. L.

1977-01-01

The theory and application of a method which utilizes the free response of a structure to determine its vibration parameters is described. The time-domain free response is digitized and used in a digital computer program to determine the number of modes excited, the natural frequencies, the damping factors, and the modal vectors. The technique is applied to a complex generalized payload model previously tested using sine sweep method and analyzed by NASTRAN. Ten modes of the payload model are identified. In case free decay response is not readily available, an algorithm is developed to obtain the free responses of a structure from its random responses, due to some unknown or known random input or inputs, using the random decrement technique without changing time correlation between signals. The algorithm is tested using random responses from a generalized payload model and from the space shuttle model.

A Fourier transform with speed improvements for microprocessor applications

NASA Technical Reports Server (NTRS)

Lokerson, D. C.; Rochelle, R.

1980-01-01

A fast Fourier transform algorithm for the RCA 1802microprocessor was developed for spacecraft instrument applications. The computations were tailored for the restrictions an eight bit machine imposes. The algorithm incorporates some aspects of Walsh function sequency to improve operational speed. This method uses a register to add a value proportional to the period of the band being processed before each computation is to be considered. If the result overflows into the DF register, the data sample is used in computation; otherwise computation is skipped. This operation is repeated for each of the 64 data samples. This technique is used for both sine and cosine portions of the computation. The processing uses eight bit data, but because of the many computations that can increase the size of the coefficient, floating point form is used. A method to reduce the alias problem in the lower bands is also described.

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.

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%.

Sine-Gordon equation and its application to tectonic stress transfer

NASA Astrophysics Data System (ADS)

Bykov, Victor G.

2014-07-01

An overview is given on remarkable progress that has been made in theoretical studies of solitons and other nonlinear wave patterns, excited during the deformation of fault block (fragmented) geological media. The models that are compliant with the classical and perturbed sine-Gordon equations have only been chosen. In these mathematical models, the rotation angle of blocks (fragments) and their translatory displacement of the medium are used as dynamic variables. A brief description of the known models and their geophysical and geodynamic applications is given. These models reproduce the kinematic and dynamic features of the traveling deformation front (kink, soliton) generated in the fragmented media. It is demonstrated that the sine-Gordon equation is applicable to the description of series of the observed seismic data, modeling of strain waves, as well as the features related to fault dynamics and the subduction slab, including slow earthquakes, periodicity of episodic tremor and slow slip (ETS) events, and migration pattern of tremors. The study shows that simple heuristic models and analytical and numerical computations can explain triggering of seismicity by transient processes, such as stress changes associated with solitary strain waves in crustal faults. The need to develop the above-mentioned new (nonlinear) mathematical models of the deformed fault and fragmented media was caused by the reason that it is impossible to explain a lot of the observed effects, particularly, slow redistribution and migration of stresses in the lithosphere, within the framework of the linear elasticity theory.

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.

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

Influence of cutting strains and magnetic anisotropy of electrical steel on the air gap flux distribution of an induction motor

NASA Astrophysics Data System (ADS)

Hribernik, Božo

1984-02-01

This paper describes an iterative algorithm for the simulation of various real magnetic materials in a small induction motor and their influence on the flux distribution in the air gap. Two standard materials, fully-, and semi-processed steel strips were used. The nonlinearity of the magnetization curve, the influence of cutting strains and magnetic anisotropy are also considered. All these influences bring out the facts that the uniformly rotated and sine form exitation causes a nonuniformly rotated and deformed magnetic field in the air gap of the machine and that the magnetization current is winding place dependent.

Parallel Fixed Point Implementation of a Radial Basis Function Network in an FPGA

PubMed Central

de Souza, Alisson C. D.; Fernandes, Marcelo A. C.

2014-01-01

This paper proposes a parallel fixed point radial basis function (RBF) artificial neural network (ANN), implemented in a field programmable gate array (FPGA) trained online with a least mean square (LMS) algorithm. The processing time and occupied area were analyzed for various fixed point formats. The problems of precision of the ANN response for nonlinear classification using the XOR gate and interpolation using the sine function were also analyzed in a hardware implementation. The entire project was developed using the System Generator platform (Xilinx), with a Virtex-6 xc6vcx240t-1ff1156 as the target FPGA. PMID:25268918

Optical solitons, explicit solutions and modulation instability analysis with second-order spatio-temporal dispersion

NASA Astrophysics Data System (ADS)

Inc, Mustafa; Isa Aliyu, Aliyu; Yusuf, Abdullahi; Baleanu, Dumitru

2017-12-01

This paper obtains the dark, bright, dark-bright or combined optical and singular solitons to the nonlinear Schrödinger equation (NLSE) with group velocity dispersion coefficient and second-order spatio-temporal dispersion coefficient, which arises in photonics and waveguide optics and in optical fibers. The integration algorithm is the sine-Gordon equation method (SGEM). Furthermore, the explicit solutions of the equation are derived by considering the power series solutions (PSS) theory and the convergence of the solutions is guaranteed. Lastly, the modulation instability analysis (MI) is studied based on the standard linear-stability analysis and the MI gain spectrum is obtained.

Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species

PubMed Central

Lorenzi, Hernan; Thiagarajan, Mathangi; Haas, Brian; Wortman, Jennifer; Hall, Neil; Caler, Elisabet

2008-01-01

Background Identification and mapping of repetitive elements is a key step for accurate gene prediction and overall structural annotation of genomes. During the assembly and annotation of three highly repetitive amoeba genomes, Entamoeba histolytica, Entamoeba dispar, and Entamoeba invadens, we performed comparative sequence analysis to identify and map all class I and class II transposable elements in their sequences. Results Here, we report the identification of two novel Entamoeba-specific repeats: ERE1 and ERE2; ERE1 is spread across the three genomes and associated with different repeats in a species-specific manner, while ERE2 is unique to E. histolytica. We also report the identification of two novel subfamilies of LINE and SINE retrotransposons in E. dispar and provide evidence for how the different LINE and SINE subfamilies evolved in these species. Additionally, we found a putative transposase-coding gene in E. histolytica and E. dispar related to the mariner transposon Hydargos from E. invadens. The distribution of transposable elements in these genomes is markedly skewed with a tendency of forming clusters. More than 70% of the three genomes have a repeat density below their corresponding average value indicating that transposable elements are not evenly distributed. We show that repeats and repeat-clusters are found at syntenic break points between E. histolytica and E. dispar and hence, could work as recombination hot spots promoting genome rearrangements. Conclusion The mapping of all transposable elements found in these parasites shows that repeat coverage is up to three times higher than previously reported. LINE, ERE1 and mariner elements were present in the common ancestor to the three Entamoeba species while ERE2 was likely acquired by E. histolytica after its separation from E. dispar. We demonstrate that E. histolytica and E. dispar share their entire repertoire of LINE and SINE retrotransposons and that Eh_SINE3/Ed_SINE1 originated as a chimeric SINE from Eh/Ed_SINE2 and Eh_SINE1/Ed_SINE3. Our work shows that transposable elements are organized in clusters, frequently found at syntenic break points providing insights into their contribution to chromosome instability and therefore, to genomic variation and speciation in these parasites. PMID:19077187

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.

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

Objective evaluation of slanted edge charts

NASA Astrophysics Data System (ADS)

Hornung, Harvey (.

2015-01-01

Camera objective characterization methodologies are widely used in the digital camera industry. Most objective characterization systems rely on a chart with specific patterns, a software algorithm measures a degradation or difference between the captured image and the chart itself. The Spatial Frequency Response (SFR) method, which is part of the ISO 122331 standard, is now very commonly used in the imaging industry, it is a very convenient way to measure a camera Modulation transfer function (MTF). The SFR algorithm can measure frequencies beyond the Nyquist frequency thanks to super-resolution, so it does provide useful information on aliasing and can provide modulation for frequencies between half Nyquist and Nyquist on all color channels of a color sensor with a Bayer pattern. The measurement process relies on a chart that is simple to manufacture: a straight transition from a bright reflectance to a dark one (black and white for instance), while a sine chart requires handling precisely shades of gray which can also create all sort of issues with printers that rely on half-toning. However, no technology can create a perfect edge, so it is important to assess the quality of the chart and understand how it affects the accuracy of the measurement. In this article, I describe a protocol to characterize the MTF of a slanted edge chart, using a high-resolution flatbed scanner. The main idea is to use the RAW output of the scanner as a high-resolution micro-densitometer, since the signal is linear it is suitable to measure the chart MTF using the SFR algorithm. The scanner needs to be calibrated in sharpness: the scanner MTF is measured with a calibrated sine chart and inverted to compensate for the modulation loss from the scanner. Then the true chart MTF is computed. This article compares measured MTF from commercial charts and charts printed on printers, and also compares how of the contrast of the edge (using different shades of gray) can affect the chart MTF, then concludes on what distance range and camera resolution the chart can reliably measure the camera MTF.

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

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.

An Autonomous Navigation Algorithm for High Orbit Satellite Using Star Sensor and Ultraviolet Earth Sensor

PubMed Central

Baohua, Li; Wenjie, Lai; Yun, Chen; Zongming, Liu

2013-01-01

An autonomous navigation algorithm using the sensor that integrated the star sensor (FOV1) and ultraviolet earth sensor (FOV2) is presented. The star images are sampled by FOV1, and the ultraviolet earth images are sampled by the FOV2. The star identification algorithm and star tracking algorithm are executed at FOV1. Then, the optical axis direction of FOV1 at J2000.0 coordinate system is calculated. The ultraviolet image of earth is sampled by FOV2. The center vector of earth at FOV2 coordinate system is calculated with the coordinates of ultraviolet earth. The autonomous navigation data of satellite are calculated by integrated sensor with the optical axis direction of FOV1 and the center vector of earth from FOV2. The position accuracy of the autonomous navigation for satellite is improved from 1000 meters to 300 meters. And the velocity accuracy of the autonomous navigation for satellite is improved from 100 m/s to 20 m/s. At the same time, the period sine errors of the autonomous navigation for satellite are eliminated. The autonomous navigation for satellite with a sensor that integrated ultraviolet earth sensor and star sensor is well robust. PMID:24250261

An autonomous navigation algorithm for high orbit satellite using star sensor and ultraviolet earth sensor.

PubMed

Baohua, Li; Wenjie, Lai; Yun, Chen; Zongming, Liu

2013-01-01

An autonomous navigation algorithm using the sensor that integrated the star sensor (FOV1) and ultraviolet earth sensor (FOV2) is presented. The star images are sampled by FOV1, and the ultraviolet earth images are sampled by the FOV2. The star identification algorithm and star tracking algorithm are executed at FOV1. Then, the optical axis direction of FOV1 at J2000.0 coordinate system is calculated. The ultraviolet image of earth is sampled by FOV2. The center vector of earth at FOV2 coordinate system is calculated with the coordinates of ultraviolet earth. The autonomous navigation data of satellite are calculated by integrated sensor with the optical axis direction of FOV1 and the center vector of earth from FOV2. The position accuracy of the autonomous navigation for satellite is improved from 1000 meters to 300 meters. And the velocity accuracy of the autonomous navigation for satellite is improved from 100 m/s to 20 m/s. At the same time, the period sine errors of the autonomous navigation for satellite are eliminated. The autonomous navigation for satellite with a sensor that integrated ultraviolet earth sensor and star sensor is well robust.

Soliton and periodic solutions for time-dependent coefficient non-linear equation

NASA Astrophysics Data System (ADS)

Guner, Ozkan

2016-01-01

In this article, we establish exact solutions for the generalized (3+1)-dimensional variable coefficient Kadomtsev-Petviashvili (GVCKP) equation. Using solitary wave ansatz in terms of ? functions and the modified sine-cosine method, we find exact analytical bright soliton solutions and exact periodic solutions for the considered model. The physical parameters in the soliton solutions are obtained as function of the dependent model coefficients. The effectiveness and reliability of the method are shown by its application to the GVCKP equation.

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.

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.

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.

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.

Impact of Reconstruction Algorithms on CT Radiomic Features of Pulmonary Tumors: Analysis of Intra- and Inter-Reader Variability and Inter-Reconstruction Algorithm Variability.

PubMed

Kim, Hyungjin; Park, Chang Min; Lee, Myunghee; Park, Sang Joon; Song, Yong Sub; Lee, Jong Hyuk; Hwang, Eui Jin; Goo, Jin Mo

2016-01-01

To identify the impact of reconstruction algorithms on CT radiomic features of pulmonary tumors and to reveal and compare the intra- and inter-reader and inter-reconstruction algorithm variability of each feature. Forty-two patients (M:F = 19:23; mean age, 60.43±10.56 years) with 42 pulmonary tumors (22.56±8.51mm) underwent contrast-enhanced CT scans, which were reconstructed with filtered back projection and commercial iterative reconstruction algorithm (level 3 and 5). Two readers independently segmented the whole tumor volume. Fifteen radiomic features were extracted and compared among reconstruction algorithms. Intra- and inter-reader variability and inter-reconstruction algorithm variability were calculated using coefficients of variation (CVs) and then compared. Among the 15 features, 5 first-order tumor intensity features and 4 gray level co-occurrence matrix (GLCM)-based features showed significant differences (p<0.05) among reconstruction algorithms. As for the variability, effective diameter, sphericity, entropy, and GLCM entropy were the most robust features (CV≤5%). Inter-reader variability was larger than intra-reader or inter-reconstruction algorithm variability in 9 features. However, for entropy, homogeneity, and 4 GLCM-based features, inter-reconstruction algorithm variability was significantly greater than inter-reader variability (p<0.013). Most of the radiomic features were significantly affected by the reconstruction algorithms. Inter-reconstruction algorithm variability was greater than inter-reader variability for entropy, homogeneity, and GLCM-based features.

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.

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.

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.

Stereo reconstruction from multiperspective panoramas.

PubMed

Li, Yin; Shum, Heung-Yeung; Tang, Chi-Keung; Szeliski, Richard

2004-01-01

A new approach to computing a panoramic (360 degrees) depth map is presented in this paper. Our approach uses a large collection of images taken by a camera whose motion has been constrained to planar concentric circles. We resample regular perspective images to produce a set of multiperspective panoramas and then compute depth maps directly from these resampled panoramas. Our panoramas sample uniformly in three dimensions: rotation angle, inverse radial distance, and vertical elevation. The use of multiperspective panoramas eliminates the limited overlap present in the original input images and, thus, problems as in conventional multibaseline stereo can be avoided. Our approach differs from stereo matching of single-perspective panoramic images taken from different locations, where the epipolar constraints are sine curves. For our multiperspective panoramas, the epipolar geometry, to the first order approximation, consists of horizontal lines. Therefore, any traditional stereo algorithm can be applied to multiperspective panoramas with little modification. In this paper, we describe two reconstruction algorithms. The first is a cylinder sweep algorithm that uses a small number of resampled multiperspective panoramas to obtain dense 3D reconstruction. The second algorithm, in contrast, uses a large number of multiperspective panoramas and takes advantage of the approximate horizontal epipolar geometry inherent in multiperspective panoramas. It comprises a novel and efficient 1D multibaseline matching technique, followed by tensor voting to extract the depth surface. Experiments show that our algorithms are capable of producing comparable high quality depth maps which can be used for applications such as view interpolation.

Digital algorithms for parallel pipelined single-detector homodyne fringe counting in laser interferometry

NASA Astrophysics Data System (ADS)

Rerucha, Simon; Sarbort, Martin; Hola, Miroslava; Cizek, Martin; Hucl, Vaclav; Cip, Ondrej; Lazar, Josef

2016-12-01

The homodyne detection with only a single detector represents a promising approach in the interferometric application which enables a significant reduction of the optical system complexity while preserving the fundamental resolution and dynamic range of the single frequency laser interferometers. We present the design, implementation and analysis of algorithmic methods for computational processing of the single-detector interference signal based on parallel pipelined processing suitable for real time implementation on a programmable hardware platform (e.g. the FPGA - Field Programmable Gate Arrays or the SoC - System on Chip). The algorithmic methods incorporate (a) the single detector signal (sine) scaling, filtering, demodulations and mixing necessary for the second (cosine) quadrature signal reconstruction followed by a conic section projection in Cartesian plane as well as (a) the phase unwrapping together with the goniometric and linear transformations needed for the scale linearization and periodic error correction. The digital computing scheme was designed for bandwidths up to tens of megahertz which would allow to measure the displacements at the velocities around half metre per second. The algorithmic methods were tested in real-time operation with a PC-based reference implementation that employed the advantage pipelined processing by balancing the computational load among multiple processor cores. The results indicate that the algorithmic methods are suitable for a wide range of applications [3] and that they are bringing the fringe counting interferometry closer to the industrial applications due to their optical setup simplicity and robustness, computational stability, scalability and also a cost-effectiveness.

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.

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.

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.

Geosat crossover analysis in the tropical Pacific. Part 1: Constrained sinusoidal crossover adjustment

NASA Technical Reports Server (NTRS)

Tai, Chang-Kou

1988-01-01

A new method (constrained sinusoidal crossover adjustment) for removing the orbit error in satellite altimetry is tested (using crossovers accumulated in the first 91 days of the Geosat non-repeat era in the tropical Pacific) and found to have excellent qualities. Two features distinguish the new method from the conventional bias-and-tilt crossover adjustment. First, a sine wave (with wavelength equaling the circumference of the Earth) is used to represent the orbit error for each satellite revolution, instead of the bias-and-tilt (and curvature, if necessary) approach for each segment of the satellite ground track. Secondly, the indeterminacy of the adjustment process is removed by a simple constraint minimizing the amplitudes of the sine waves, rather than by fixing selected tracks. Overall the new method is more accurate, more efficient, and much less cumbersome than the old. The idea of restricting the crossover adjustment to crossovers between tracks that are less than certain days apart in order to preserve the large-scale long-term oceanic variability is also tested with inconclusive results because the orbit error was unusually nonstationary in the initial 91 days of the GEOSAT mission.

Detection of briefly flashed sine-gratings in dark-adapted vision.

PubMed

Hofmann, M I; Barnes, C S; Hallett, P E

1990-01-01

Scotopic contrast sensitivity was measured near 20 deg retinal eccentricity for briefly flashed (10 or 20 msec) sine-wave gratings presented in darkness to dark-adapted subjects. For very low spatial frequencies (0.2-0.5 c/deg), curves of contrast sensitivity vs luminous energy show evidence of a low rod plateau and a high scotopic region, with an intervening transition at around -2 to -2.5 log scot td sec. Similar measurements made using long flashed or flickering gratings do not show a plateau. The results suggest that vision in the low rod region is impaired for brief flashes. For the briefly flashed stimuli, curves of contrast sensitivity versus spatial frequency in the low region were best fit by simple Gaussian functions with a variable centre size (sigma c = 0.5----0.25 deg), size decreasing with increasing flash energy. Difference-of-Gaussian functions with constant centre size (sigma c = 0.25 deg) provided the best fit in the high region. Overt input from the cones and grating area artefacts are excluded by appropriate tests. Calculation of photon flux into the receptive field centres suggests that signal compression in P alpha ganglion cells contributes to the low rod plateau.

[A family of short retroposons (Squaml) from squamate reptiles (Reptilia: Squamata): structure, evolution and correlation with phylogeny].

PubMed

Kosushkin, S A; Borodulina, O R; Solov'eva, E N; Grechko, V V

2008-01-01

We have isolated and characterised sequences of a SINE family specific for squamate reptiles from a genome of lacertid lizard that we called Squam1. Copies are 360-390 bp in length and share a significant similarity with tRNA gene sequence on its 5'-end. This family was also detected by us in DNA of representatives of varanids, iguanids (anolis), gekkonids, and snakes. No signs of it were found in DNA of mammals, birds, amphibians, and crocodiles. Detailed analysis of primary structure of the retroposons obtained by us from genomic libraries or GenBank sequences was carried out. Most taxa possess 2-3 subfamilies of the SINE in their genomes with specific diagnostic features in their primary structure. Individual variability of copies in different families is about 85% and is just slightly lower on the genera level. Comparison of consensus sequences on family level reveals a high degree of structural similarity with a number of specific apomorphic features which makes it a useful marker of phylogeny for this group of reptiles. Snakes do not show specific affinity to varanids when compared to other lizards, as it was suggested earlier.

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.

AU-FREDI - AUTONOMOUS FREQUENCY DOMAIN IDENTIFICATION

NASA Technical Reports Server (NTRS)

Yam, Y.

1994-01-01

The Autonomous Frequency Domain Identification program, AU-FREDI, is a system of methods, algorithms and software that was developed for the identification of structural dynamic parameters and system transfer function characterization for control of large space platforms and flexible spacecraft. It was validated in the CALTECH/Jet Propulsion Laboratory's Large Spacecraft Control Laboratory. Due to the unique characteristics of this laboratory environment, and the environment-specific nature of many of the software's routines, AU-FREDI should be considered to be a collection of routines which can be modified and reassembled to suit system identification and control experiments on large flexible structures. The AU-FREDI software was originally designed to command plant excitation and handle subsequent input/output data transfer, and to conduct system identification based on the I/O data. Key features of the AU-FREDI methodology are as follows: 1. AU-FREDI has on-line digital filter design to support on-orbit optimal input design and data composition. 2. Data composition of experimental data in overlapping frequency bands overcomes finite actuator power constraints. 3. Recursive least squares sine-dwell estimation accurately handles digitized sinusoids and low frequency modes. 4. The system also includes automated estimation of model order using a product moment matrix. 5. A sample-data transfer function parametrization supports digital control design. 6. Minimum variance estimation is assured with a curve fitting algorithm with iterative reweighting. 7. Robust root solvers accurately factorize high order polynomials to determine frequency and damping estimates. 8. Output error characterization of model additive uncertainty supports robustness analysis. The research objectives associated with AU-FREDI were particularly useful in focusing the identification methodology for realistic on-orbit testing conditions. Rather than estimating the entire structure, as is typically done in ground structural testing, AU-FREDI identifies only the key transfer function parameters and uncertainty bounds that are necessary for on-line design and tuning of robust controllers. AU-FREDI's system identification algorithms are independent of the JPL-LSCL environment, and can easily be extracted and modified for use with input/output data files. The basic approach of AU-FREDI's system identification algorithms is to non-parametrically identify the sampled data in the frequency domain using either stochastic or sine-dwell input, and then to obtain a parametric model of the transfer function by curve-fitting techniques. A cross-spectral analysis of the output error is used to determine the additive uncertainty in the estimated transfer function. The nominal transfer function estimate and the estimate of the associated additive uncertainty can be used for robust control analysis and design. AU-FREDI's I/O data transfer routines are tailored to the environment of the CALTECH/ JPL-LSCL which included a special operating system to interface with the testbed. Input commands for a particular experiment (wideband, narrowband, or sine-dwell) were computed on-line and then issued to respective actuators by the operating system. The operating system also took measurements through displacement sensors and passed them back to the software for storage and off-line processing. In order to make use of AU-FREDI's I/O data transfer routines, a user would need to provide an operating system capable of overseeing such functions between the software and the experimental setup at hand. The program documentation contains information designed to support users in either providing such an operating system or modifying the system identification algorithms for use with input/output data files. It provides a history of the theoretical, algorithmic and software development efforts including operating system requirements and listings of some of the various special purpose subroutines which were developed and optimized for Lahey FORTRAN compilers on IBM PC-AT computers before the subroutines were integrated into the system software. Potential purchasers are encouraged to purchase and review the documentation before purchasing the AU-FREDI software. AU-FREDI is distributed in DEC VAX BACKUP format on a 1600 BPI 9-track magnetic tape (standard media) or a TK50 tape cartridge. AU-FREDI was developed in 1989 and is a copyrighted work with all copyright vested in NASA.

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

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.

Detecting Disease in Radiographs with Intuitive Confidence

PubMed Central

2015-01-01

This paper argues in favor of a specific type of confidence for use in computer-aided diagnosis and disease classification, namely, sine/cosine values of angles represented by points on the unit circle. The paper shows how this confidence is motivated by Chinese medicine and how sine/cosine values are directly related with the two forces Yin and Yang. The angle for which sine and cosine are equal (45°) represents the state of equilibrium between Yin and Yang, which is a state of nonduality that indicates neither normality nor abnormality in terms of disease classification. The paper claims that the proposed confidence is intuitive and can be readily understood by physicians. The paper underpins this thesis with theoretical results in neural signal processing, stating that a sine/cosine relationship between the actual input signal and the perceived (learned) input is key to neural learning processes. As a practical example, the paper shows how to use the proposed confidence values to highlight manifestations of tuberculosis in frontal chest X-rays. PMID:26495433

Classical and adaptive control of ex vivo skeletal muscle contractions using Functional Electrical Stimulation (FES)

PubMed Central

Shoemaker, Adam; Grange, Robert W.; Abaid, Nicole; Leonessa, Alexander

2017-01-01

Functional Electrical Stimulation is a promising approach to treat patients by stimulating the peripheral nerves and their corresponding motor neurons using electrical current. This technique helps maintain muscle mass and promote blood flow in the absence of a functioning nervous system. The goal of this work is to control muscle contractions from FES via three different algorithms and assess the most appropriate controller providing effective stimulation of the muscle. An open-loop system and a closed-loop system with three types of model-free feedback controllers were assessed for tracking control of skeletal muscle contractions: a Proportional-Integral (PI) controller, a Model Reference Adaptive Control algorithm, and an Adaptive Augmented PI system. Furthermore, a mathematical model of a muscle-mass-spring system was implemented in simulation to test the open-loop case and closed-loop controllers. These simulations were carried out and then validated through experiments ex vivo. The experiments included muscle contractions following four distinct trajectories: a step, sine, ramp, and square wave. Overall, the closed-loop controllers followed the stimulation trajectories set for all the simulated and tested muscles. When comparing the experimental outcomes of each controller, we concluded that the Adaptive Augmented PI algorithm provided the best closed-loop performance for speed of convergence and disturbance rejection. PMID:28273101

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.

Swept sine testing of rotor-bearing system for damping estimation

NASA Astrophysics Data System (ADS)

Chandra, N. Harish; Sekhar, A. S.

2014-01-01

Many types of rotating components commonly operate above the first or second critical speed and they are subjected to run-ups and shutdowns frequently. The present study focuses on developing FRF of rotor bearing systems for damping estimation from swept-sine excitation. The principle of active vibration control states that with increase in angular acceleration, the amplitude of vibration due to unbalance will reduce and the FRF envelope will shift towards the right (or higher frequency). The frequency response function (FRF) estimated by tracking filters or Co-Quad analyzers was proved to induce an error into the FRF estimate. Using Fast Fourier Transform (FFT) algorithm and stationary wavelet transform (SWT) decomposition FRF distortion can be reduced. To obtain a theoretical clarity, the shifting of FRF envelope phenomenon is incorporated into conventional FRF expressions and validation is performed with the FRF estimated using the Fourier Transform approach. The half-power bandwidth method is employed to extract damping ratios from the FRF estimates. While deriving half-power points for both types of responses (acceleration and displacement), damping ratio (ζ) is estimated with different approximations like classical definition (neglecting damping ratio of order higher than 2), third order (neglecting damping ratios with order higher than 4) and exact (no assumptions on damping ratio). The use of stationary wavelet transform to denoise the noise corrupted FRF data is explained. Finally, experiments are performed on a test rotor excited with different sweep rates to estimate the damping ratio.

AITRAC: Augmented Interactive Transient Radiation Analysis by Computer. User's information manual

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

Not Available

1977-10-01

AITRAC is a program designed for on-line, interactive, DC, and transient analysis of electronic circuits. The program solves linear and nonlinear simultaneous equations which characterize the mathematical models used to predict circuit response. The program features 100 external node--200 branch capability; conversional, free-format input language; built-in junction, FET, MOS, and switch models; sparse matrix algorithm with extended-precision H matrix and T vector calculations, for fast and accurate execution; linear transconductances: beta, GM, MU, ZM; accurate and fast radiation effects analysis; special interface for user-defined equations; selective control of multiple outputs; graphical outputs in wide and narrow formats; and on-line parametermore » modification capability. The user describes the problem by entering the circuit topology and part parameters. The program then automatically generates and solves the circuit equations, providing the user with printed or plotted output. The circuit topology and/or part values may then be changed by the user, and a new analysis, requested. Circuit descriptions may be saved on disk files for storage and later use. The program contains built-in standard models for resistors, voltage and current sources, capacitors, inductors including mutual couplings, switches, junction diodes and transistors, FETS, and MOS devices. Nonstandard models may be constructed from standard models or by using the special equations interface. Time functions may be described by straight-line segments or by sine, damped sine, and exponential functions. 42 figures, 1 table. (RWR)« less

Modulation-format-free and automatic bias control for optical IQ modulators based on dither-correlation detection.

PubMed

Li, Xiaolei; Deng, Lei; Chen, Xiaoman; Cheng, Mengfan; Fu, Songnian; Tang, Ming; Liu, Deming

2017-04-17

A novel automatic bias control (ABC) method for optical in-phase and quadrature (IQ) modulator is proposed and experimentally demonstrated. In the proposed method, two different low frequency sine wave dither signals are generated and added on to the I/Q bias signal respectively. Instead of power monitoring of the harmonics of the dither signal, dither-correlation detection is proposed and used to adjust the bias voltages of the optical IQ modulator. By this way, not only frequency spectral analysis isn't required but also the directional bias adjustment could be realized, resulting in the decrease of algorithm complexity and the growth of convergence rate of ABC algorithm. The results show that the sensitivity of the proposed ABC method outperforms that of the traditional dither frequency monitoring method. Moreover, the proposed ABC method is proved to be modulation-format-free, and the transmission penalty caused by this method for both 10 Gb/s optical QPSK and 17.9 Gb/s optical 16QAM-OFDM signal transmission are negligible in our experiment.

[Optimization of the pseudorandom input signals used for the forced oscillation technique].

PubMed

Liu, Xiaoli; Zhang, Nan; Liang, Hong; Zhang, Zhengbo; Li, Deyu; Wang, Weidong

2017-10-01

The forced oscillation technique (FOT) is an active pulmonary function measurement technique that was applied to identify the mechanical properties of the respiratory system using external excitation signals. FOT commonly includes single frequency sine, pseudorandom and periodic impulse excitation signals. Aiming at preventing the time-domain amplitude overshoot that might exist in the acquisition of combined multi sinusoidal pseudorandom signals, this paper studied the phase optimization of pseudorandom signals. We tried two methods including the random phase combination and time-frequency domain swapping algorithm to solve this problem, and used the crest factor to estimate the effect of optimization. Furthermore, in order to make the pseudorandom signals met the requirement of the respiratory system identification in 4-40 Hz, we compensated the input signals' amplitudes at the low frequency band (4-18 Hz) according to the frequency-response curve of the oscillation unit. Resuts showed that time-frequency domain swapping algorithm could effectively optimize the phase combination of pseudorandom signals. Moreover, when the amplitudes at low frequencies were compensated, the expected stimulus signals which met the performance requirements were obtained eventually.

Rigid body mode identification of the PAH-2 helicopter using the eigensystem realization algorithm

NASA Technical Reports Server (NTRS)

Schenk, Axel; Pappa, Richard S.

1992-01-01

The rigid body modes of the PAH-2 'Tiger' helicopter were identified using the Eigensystem Realization Algorithm (ERA). This work complements ground vibration tests performed using DLR's traditional phase resonance technique and the ISSPA (Identification of Structural System Parameters) method. Rigid body modal parameters are important for ground resonance prediction. Time-domain data for ERA were obtained by inverse Fourier transformation of frequency response functions measured with stepped-sine excitation. Mode purity (based on the Phase Resonance Criterion) was generally equal to or greater than corresponding results obtained in the ground vibration tests. All identified natural frequencies and mode shapes correlate well with corresponding ground vibration test results. The modal identification approach discussed in this report has become increasingly attractive in recent years due to the steadily declining cost and increased performance of scientific computers. As illustrated in this application, modern time-domain methods can be successfully applied to data acquired using DLR's existing test equipment. Some suggestions are made for future applications of time domain modal identification in this manner.

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.

Dedifferentiated Chondrosarcoma of the Larynx.

PubMed

Fidai, Shiraz S; Ginat, Daniel T; Langerman, Alexander J; Cipriani, Nicole A

2016-09-01

Primary dedifferentiated chondrosarcoma occurring in the larynx is a rare head and neck malignancy. The cases reported in the literature suggest male gender predilection and variable clinical outcomes ranging from disease-free survival to disease-related death. Although a calcified matrix is suggestive of chondrosarcoma, the dedifferentiated component is not readily appreciated on conventional imaging modalities and thorough tissue sampling is necessary for confirming the diagnosis. Histologically, there is an abrupt transition from a well-differentiated chondrosarcoma to a high-grade spindle cell component, which can show focal heterologous differentiation. These features are exemplified in this sine qua non radiology-pathology correlation article.

Dynamical complexity changes during two forms of meditation

NASA Astrophysics Data System (ADS)

Li, Jin; Hu, Jing; Zhang, Yinhong; Zhang, Xiaofeng

2011-06-01

Detection of dynamical complexity changes in natural and man-made systems has deep scientific and practical meaning. We use the base-scale entropy method to analyze dynamical complexity changes for heart rate variability (HRV) series during specific traditional forms of Chinese Chi and Kundalini Yoga meditation techniques in healthy young adults. The results show that dynamical complexity decreases in meditation states for two forms of meditation. Meanwhile, we detected changes in probability distribution of m-words during meditation and explained this changes using probability distribution of sine function. The base-scale entropy method may be used on a wider range of physiologic signals.

Large-Scale Multiantenna Multisine Wireless Power Transfer

NASA Astrophysics Data System (ADS)

Huang, Yang; Clerckx, Bruno

2017-11-01

Wireless Power Transfer (WPT) is expected to be a technology reshaping the landscape of low-power applications such as the Internet of Things, Radio Frequency identification (RFID) networks, etc. Although there has been some progress towards multi-antenna multi-sine WPT design, the large-scale design of WPT, reminiscent of massive MIMO in communications, remains an open challenge. In this paper, we derive efficient multiuser algorithms based on a generalizable optimization framework, in order to design transmit sinewaves that maximize the weighted-sum/minimum rectenna output DC voltage. The study highlights the significant effect of the nonlinearity introduced by the rectification process on the design of waveforms in multiuser systems. Interestingly, in the single-user case, the optimal spatial domain beamforming, obtained prior to the frequency domain power allocation optimization, turns out to be Maximum Ratio Transmission (MRT). In contrast, in the general weighted sum criterion maximization problem, the spatial domain beamforming optimization and the frequency domain power allocation optimization are coupled. Assuming channel hardening, low-complexity algorithms are proposed based on asymptotic analysis, to maximize the two criteria. The structure of the asymptotically optimal spatial domain precoder can be found prior to the optimization. The performance of the proposed algorithms is evaluated. Numerical results confirm the inefficiency of the linear model-based design for the single and multi-user scenarios. It is also shown that as nonlinear model-based designs, the proposed algorithms can benefit from an increasing number of sinewaves.

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.

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

A GPU-Based Implementation of the Firefly Algorithm for Variable Selection in Multivariate Calibration Problems

PubMed Central

de Paula, Lauro C. M.; Soares, Anderson S.; de Lima, Telma W.; Delbem, Alexandre C. B.; Coelho, Clarimar J.; Filho, Arlindo R. G.

2014-01-01

Several variable selection algorithms in multivariate calibration can be accelerated using Graphics Processing Units (GPU). Among these algorithms, the Firefly Algorithm (FA) is a recent proposed metaheuristic that may be used for variable selection. This paper presents a GPU-based FA (FA-MLR) with multiobjective formulation for variable selection in multivariate calibration problems and compares it with some traditional sequential algorithms in the literature. The advantage of the proposed implementation is demonstrated in an example involving a relatively large number of variables. The results showed that the FA-MLR, in comparison with the traditional algorithms is a more suitable choice and a relevant contribution for the variable selection problem. Additionally, the results also demonstrated that the FA-MLR performed in a GPU can be five times faster than its sequential implementation. PMID:25493625

A GPU-Based Implementation of the Firefly Algorithm for Variable Selection in Multivariate Calibration Problems.

PubMed

de Paula, Lauro C M; Soares, Anderson S; de Lima, Telma W; Delbem, Alexandre C B; Coelho, Clarimar J; Filho, Arlindo R G

2014-01-01

Several variable selection algorithms in multivariate calibration can be accelerated using Graphics Processing Units (GPU). Among these algorithms, the Firefly Algorithm (FA) is a recent proposed metaheuristic that may be used for variable selection. This paper presents a GPU-based FA (FA-MLR) with multiobjective formulation for variable selection in multivariate calibration problems and compares it with some traditional sequential algorithms in the literature. The advantage of the proposed implementation is demonstrated in an example involving a relatively large number of variables. The results showed that the FA-MLR, in comparison with the traditional algorithms is a more suitable choice and a relevant contribution for the variable selection problem. Additionally, the results also demonstrated that the FA-MLR performed in a GPU can be five times faster than its sequential implementation.

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.

Accurate estimation of normal incidence absorption coefficients with confidence intervals using a scanning laser Doppler vibrometer

NASA Astrophysics Data System (ADS)

Vuye, Cedric; Vanlanduit, Steve; Guillaume, Patrick

2009-06-01

When using optical measurements of the sound fields inside a glass tube, near the material under test, to estimate the reflection and absorption coefficients, not only these acoustical parameters but also confidence intervals can be determined. The sound fields are visualized using a scanning laser Doppler vibrometer (SLDV). In this paper the influence of different test signals on the quality of the results, obtained with this technique, is examined. The amount of data gathered during one measurement scan makes a thorough statistical analysis possible leading to the knowledge of confidence intervals. The use of a multi-sine, constructed on the resonance frequencies of the test tube, shows to be a very good alternative for the traditional periodic chirp. This signal offers the ability to obtain data for multiple frequencies in one measurement, without the danger of a low signal-to-noise ratio. The variability analysis in this paper clearly shows the advantages of the proposed multi-sine compared to the periodic chirp. The measurement procedure and the statistical analysis are validated by measuring the reflection ratio at a closed end and comparing the results with the theoretical value. Results of the testing of two building materials (an acoustic ceiling tile and linoleum) are presented and compared to supplier data.

Comparison of two parametric methods to estimate pesticide mass loads in California's Central Valley

USGS Publications Warehouse

Saleh, Dina K.; Lorenz, David L.; Domagalski, Joseph L.

2011-01-01

Mass loadings were calculated for four pesticides in two watersheds with different land uses in the Central Valley, California, by using two parametric models: (1) the Seasonal Wave model (SeaWave), in which a pulse signal is used to describe the annual cycle of pesticide occurrence in a stream, and (2) the Sine Wave model, in which first-order Fourier series sine and cosine terms are used to simulate seasonal mass loading patterns. The models were applied to data collected during water years 1997 through 2005. The pesticides modeled were carbaryl, diazinon, metolachlor, and molinate. Results from the two models show that the ability to capture seasonal variations in pesticide concentrations was affected by pesticide use patterns and the methods by which pesticides are transported to streams. Estimated seasonal loads compared well with results from previous studies for both models. Loads estimated by the two models did not differ significantly from each other, with the exceptions of carbaryl and molinate during the precipitation season, where loads were affected by application patterns and rainfall. However, in watersheds with variable and intermittent pesticide applications, the SeaWave model is more suitable for use on the basis of its robust capability of describing seasonal variation of pesticide concentrations.

Pain modality- and sex-specific effects of COMT genetic functional variants

PubMed Central

Belfer, Inna; Segall, Samantha K.; Lariviere, William R.; Smith, Shad B.; Dai, Feng; Slade, Gary G.; Rashid, Naim U.; Mogil, Jeffrey S.; Campbell, Claudia; Edwards, Robert; Liu, Qian; Bair, Eric; Maixner, William; Diatchenko, Luda

2013-01-01

The enzyme catechol-O-methyltransferase (COMT) metabolizes catecholamine neurotransmitters involved in a number of physiological functions including pain perception. Both human and mouse COMT genes possess functional polymorphisms contributing to inter-individual variability in pain phenotypes such as sensitivity to noxious stimuli, severity of clinical pain and response to pain treatment. In this study, we found that the effects of Comt functional variation in mice are modality-specific. Spontaneous inflammatory nociception and thermal nociception behaviors were correlated the most with the presence of the B2 SINE transposon insertion residing in the 3’UTR mRNA region. Similarly, in humans, COMT functional haplotypes were associated with thermal pain perception and with capsaicin-induced pain. Furthermore, COMT genetic variations contributed to pain behaviors in mice and pain ratings in humans in a sex-specific manner. The ancestral Comt variant, without a B2 SINE insertion, was more strongly associated with sensitivity to capsaicin in female versus male mice. In humans, the haplotype coding for low COMT activity increased capsaicin-induced pain perception in women, but not men. These findings reemphasize the fundamental contribution of COMT to pain processes, and provide a fine-grained resolution of this contribution at the genetic level that can be used to guide future studies in the area of pain genetics. PMID:23701723

Persistent quasiplanar nematic texture: Its properties and topological defects

NASA Astrophysics Data System (ADS)

Pieranski, Pawel; Godinho, Maria Helena; Čopar, Simon

2016-10-01

In the so-called quasiplanar texture of a nematic layer confined between parallel plates with homeotropic anchoring conditions, the director field rotates by π between limit surfaces so that field lines have the shape of a dowsing Y-shaped wooden tool. The orientation of the director field at midheight of the layer is arbitrary for symmetry reasons and is thus very sensitive to perturbations. We point out that contrary to accepted ideas the quasiplanar texture can be preserved infinitely in spite of its metastability with respect to the homogeneous homeotropic texture. We propose to call such a long-lived version of the quasiplanar texture the dowser texture. We demonstrate both experimentally and theoretically that in samples of variable thickness, the director field is sensitive to the gradient of the sample thickness through a linear coupling term. As a result, it has a tendency to follow the direction of the thickness gradient. Because of its sensitivity to perturbations we propose to call the midplane director field the dowser field and its tendency to follow the thickness gradient cuneitropism. Under effect of the gradient field, the dowser field obeys the sine-Gordon equation and exhibits domain walls that correspond to the well-known solitonic solutions of the sine-Gordon model.

Learning to perceptually organize speech signals in native fashion.

PubMed

Nittrouer, Susan; Lowenstein, Joanna H

2010-03-01

The ability to recognize speech involves sensory, perceptual, and cognitive processes. For much of the history of speech perception research, investigators have focused on the first and third of these, asking how much and what kinds of sensory information are used by normal and impaired listeners, as well as how effective amounts of that information are altered by "top-down" cognitive processes. This experiment focused on perceptual processes, asking what accounts for how the sensory information in the speech signal gets organized. Two types of speech signals processed to remove properties that could be considered traditional acoustic cues (amplitude envelopes and sine wave replicas) were presented to 100 listeners in five groups: native English-speaking (L1) adults, 7-, 5-, and 3-year-olds, and native Mandarin-speaking adults who were excellent second-language (L2) users of English. The L2 adults performed more poorly than L1 adults with both kinds of signals. Children performed more poorly than L1 adults but showed disproportionately better performance for the sine waves than for the amplitude envelopes compared to both groups of adults. Sentence context had similar effects across groups, so variability in recognition was attributed to differences in perceptual organization of the sensory information, presumed to arise from native language experience.

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

Analysis of nitrate in near-surface aquifers in the midcontinental United States: An application of the inverse hyperbolic sine Tobit model

USGS Publications Warehouse

Yen, Steven T.; Liu, Shiping; Kolpin, Dana W.

1996-01-01

A nonnormal and heteroscedastic Tobit model is used to determine the primary factors that affect nitrate concentrations in near-surface aquifers, using data from the U.S. Geological Survey collected in 1991. Both normality and homoscedasticity of errors are rejected, justifying the use of a nonnormal and heteroscedastic model. The following factors are found to have significant impacts on nitrate concentrations in groundwater: well screen interval, depth to top of aquifers, percentages of urban residential, forest land, and pasture within 3.2 km, dissolved oxygen concentration level, and presence of a chemical facility and feedlot. The effects of explanatory variables on nitrate concentration are explored further by calculating elasticities. Dissolved oxygen concentration level has more notable effects on nitrate concentrations in groundwater than other variables.

Transfer matrix spectrum for cyclic representations of the 6-vertex reflection algebra by quantum separation of variables

NASA Astrophysics Data System (ADS)

Pezelier, Baptiste

2018-02-01

In this proceeding, we recall the notion of quantum integrable systems on a lattice and then introduce the Sklyanin’s Separation of Variables method. We sum up the main results for the transfer matrix spectral problem for the cyclic representations of the trigonometric 6-vertex reflection algebra associated to the Bazanov-Stroganov Lax operator. These results apply as well to the spectral analysis of the lattice sine-Gordon model with open boundary conditions. The transfer matrix spectrum (both eigenvalues and eigenstates) is completely characterized in terms of the set of solutions to a discrete system of polynomial equations. We state an equivalent characterization as the set of solutions to a Baxter’s like T-Q functional equation, allowing us to rewrite the transfer matrix eigenstates in an algebraic Bethe ansatz form.

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.

Simple and practical approach for computing the ray Hessian matrix in geometrical optics.

PubMed

Lin, Psang Dain

2018-02-01

A method is proposed for simplifying the computation of the ray Hessian matrix in geometrical optics by replacing the angular variables in the system variable vector with their equivalent cosine and sine functions. The variable vector of a boundary surface is similarly defined in such a way as to exclude any angular variables. It is shown that the proposed formulations reduce the computation time of the Hessian matrix by around 10 times compared to the previous method reported by the current group in Advanced Geometrical Optics (2016). Notably, the method proposed in this study involves only polynomial differentiation, i.e., trigonometric function calls are not required. As a consequence, the computation complexity is significantly reduced. Five illustrative examples are given. The first three examples show that the proposed method is applicable to the determination of the Hessian matrix for any pose matrix, irrespective of the order in which the rotation and translation motions are specified. The last two examples demonstrate the use of the proposed Hessian matrix in determining the axial and lateral chromatic aberrations of a typical optical system.

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

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.

Series: Utilization of Differential Equations and Methods for Solving Them in Medical Physics (4).

PubMed

Murase, Kenya

2016-01-01

Partial differential equations are often used in the field of medical physics. In this (final) issue, the methods for solving the partial differential equations were introduced, which include separation of variables, integral transform (Fourier and Fourier-sine transforms), Green's function, and series expansion methods. Some examples were also introduced, in which the integral transform and Green's function methods were applied to solving Pennes' bioheat transfer equation and the Fourier series expansion method was applied to Navier-Stokes equation for analyzing the wall shear stress in blood vessels.Finally, the author hopes that this series will be helpful for people who engage in medical physics.

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.

An information-theoretic approach to the gravitational-wave burst detection problem

NASA Astrophysics Data System (ADS)

Katsavounidis, E.; Lynch, R.; Vitale, S.; Essick, R.; Robinet, F.

2016-03-01

The advanced era of gravitational-wave astronomy, with data collected in part by the LIGO gravitational-wave interferometers, has begun as of fall 2015. One potential type of detectable gravitational waves is short-duration gravitational-wave bursts, whose waveforms can be difficult to predict. We present the framework for a new detection algorithm - called oLIB - that can be used in relatively low-latency to turn calibrated strain data into a detection significance statement. This pipeline consists of 1) a sine-Gaussian matched-filter trigger generator based on the Q-transform - known as Omicron -, 2) incoherent down-selection of these triggers to the most signal-like set, and 3) a fully coherent analysis of this signal-like set using the Markov chain Monte Carlo (MCMC) Bayesian evidence calculator LALInferenceBurst (LIB). We optimally extract this information by using a likelihood-ratio test (LRT) to map these search statistics into a significance statement. Using representative archival LIGO data, we show that the algorithm can detect gravitational-wave burst events of realistic strength in realistic instrumental noise with good detection efficiencies across different burst waveform morphologies. With support from the National Science Foundation under Grant PHY-0757058.

Improved Evolutionary Programming with Various Crossover Techniques for Optimal Power Flow Problem

NASA Astrophysics Data System (ADS)

Tangpatiphan, Kritsana; Yokoyama, Akihiko

This paper presents an Improved Evolutionary Programming (IEP) for solving the Optimal Power Flow (OPF) problem, which is considered as a non-linear, non-smooth, and multimodal optimization problem in power system operation. The total generator fuel cost is regarded as an objective function to be minimized. The proposed method is an Evolutionary Programming (EP)-based algorithm with making use of various crossover techniques, normally applied in Real Coded Genetic Algorithm (RCGA). The effectiveness of the proposed approach is investigated on the IEEE 30-bus system with three different types of fuel cost functions; namely the quadratic cost curve, the piecewise quadratic cost curve, and the quadratic cost curve superimposed by sine component. These three cost curves represent the generator fuel cost functions with a simplified model and more accurate models of a combined-cycle generating unit and a thermal unit with value-point loading effect respectively. The OPF solutions by the proposed method and Pure Evolutionary Programming (PEP) are observed and compared. The simulation results indicate that IEP requires less computing time than PEP with better solutions in some cases. Moreover, the influences of important IEP parameters on the OPF solution are described in details.

Automatic Detection of Galaxy Type From Datasets of Galaxies Image Based on Image Retrieval Approach.

PubMed

Abd El Aziz, Mohamed; Selim, I M; Xiong, Shengwu

2017-06-30

This paper presents a new approach for the automatic detection of galaxy morphology from datasets based on an image-retrieval approach. Currently, there are several classification methods proposed to detect galaxy types within an image. However, in some situations, the aim is not only to determine the type of galaxy within the queried image, but also to determine the most similar images for query image. Therefore, this paper proposes an image-retrieval method to detect the type of galaxies within an image and return with the most similar image. The proposed method consists of two stages, in the first stage, a set of features is extracted based on shape, color and texture descriptors, then a binary sine cosine algorithm selects the most relevant features. In the second stage, the similarity between the features of the queried galaxy image and the features of other galaxy images is computed. Our experiments were performed using the EFIGI catalogue, which contains about 5000 galaxies images with different types (edge-on spiral, spiral, elliptical and irregular). We demonstrate that our proposed approach has better performance compared with the particle swarm optimization (PSO) and genetic algorithm (GA) methods.

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.

Creep strain and creep-life prediction for alloy 718 using the omega method

NASA Astrophysics Data System (ADS)

Yeom, Jong-Taek; Kim, Jong-Yup; Na, Young-Sang; Park, Nho-Kwang

2003-12-01

The creep behavior of Alloy 718 was investigated in relation to the MPCs omega (Ω) method. To evaluate the creep model and determine material parameters, constant load creep tests were performed at different initial stresses in a temperature range between 550°C and 700°C. The imaginary initial strain rate ɛ limits^. _0 and omega (Ω), considered to be important variables in the model, were expressed as a function of initial stress and temperature. For these variables, power-law and hyperbolic sine-law equations were used as constitutive equations for the creep of Alloy 718. To consider the effect of γ″ coarsening leading to a radical drop of tensile strength and creep strength at temperatures above 650°C, different material constants at the temperatures above 650°C were applied. The reliability of the models was investigated in relation to the creep curve and creep life.

Multi-Objective Sliding Mode Control on Vehicle Cornering Stability with Variable Gear Ratio Actuator-Based Active Front Steering Systems.

PubMed

Ma, Xinbo; Wong, Pak Kin; Zhao, Jing; Xie, Zhengchao

2016-12-28

Active front steering (AFS) is an emerging technology to improve the vehicle cornering stability by introducing an additional small steering angle to the driver's input. This paper proposes an AFS system with a variable gear ratio steering (VGRS) actuator which is controlled by using the sliding mode control (SMC) strategy to improve the cornering stability of vehicles. In the design of an AFS system, different sensors are considered to measure the vehicle state, and the mechanism of the AFS system is also modelled in detail. Moreover, in order to improve the cornering stability of vehicles, two dependent objectives, namely sideslip angle and yaw rate, are considered together in the design of SMC strategy. By evaluating the cornering performance, Sine with Dwell and accident avoidance tests are conducted, and the simulation results indicate that the proposed SMC strategy is capable of improving the cornering stability of vehicles in practice.

Cardiopulmonary readjustments in passive tilt

NASA Technical Reports Server (NTRS)

Matalon, S. V.; Farhi, L. E.

1979-01-01

The readjustment of cardiopulmonary variables in human volunteers at various tilt angles on a tilt board is studied. Five healthy subjects (18-31 yr) with thorough knowledge of the experimental protocol are tested, passively tilted from the supine to the upright position in 15-deg increments in random sequence. The parameters measured are cardiac output (Q), heart rate (HR), stroke volume (SV), minute and alveolar ventilation /V(E) and V(A)/, functional residual capacity (FRC), and arterial-end-tidal P(CO2) pressure difference. It is found that changes in Q and FRC are linearly related to the sine of the tilt angle, indicating that either reflexes are absent or their net effect is proportional to the effects of gravity. This is clearly not the case for other variables /HR, SV, V(E), V(A)/, where it is possible to demonstrate threshold values for the appearance of secondary changes.

Atlas of the Light Curves and Phase Plane Portraits of Selected Long-Period Variables

NASA Astrophysics Data System (ADS)

Kudashkina, L. S.; Andronov, I. L.

2017-12-01

For a group of the Mira-type stars, semi-regular variables and some RV Tau - type stars the limit cycles were computed and plotted using the phase plane diagrams. As generalized coordinates x and x', we have used φ - the brightness of the star and its phase derivative. We have used mean phase light curves using observations of various authors from the databases of AAVSO, AFOEV, VSOLJ, ASAS and approximated using a trigonometric polynomial of statistically optimal degree. For a simple sine-like light curve, the limit cycle is a simple ellipse. In a case of more complicated light curve, in which harmonics are statistically significant, the limit cycle has deviations from the ellipse. In an addition to a classical analysis, we use the error estimates of the smoothing function and its derivative to constrain an "error corridor" in the phase plane.

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.

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.

Comparison of Two Parametric Methods to Estimate Pesticide Mass Loads in California's Central Valley

USGS Publications Warehouse

Saleh, D.K.; Lorenz, D.L.; Domagalski, Joseph L.

2011-01-01

Mass loadings were calculated for four pesticides in two watersheds with different land uses in the Central Valley, California, by using two parametric models: (1) the Seasonal Wave model (SeaWave), in which a pulse signal is used to describe the annual cycle of pesticide occurrence in a stream, and (2) the Sine Wave model, in which first-order Fourier series sine and cosine terms are used to simulate seasonal mass loading patterns. The models were applied to data collected during water years 1997 through 2005. The pesticides modeled were carbaryl, diazinon, metolachlor, and molinate. Results from the two models show that the ability to capture seasonal variations in pesticide concentrations was affected by pesticide use patterns and the methods by which pesticides are transported to streams. Estimated seasonal loads compared well with results from previous studies for both models. Loads estimated by the two models did not differ significantly from each other, with the exceptions of carbaryl and molinate during the precipitation season, where loads were affected by application patterns and rainfall. However, in watersheds with variable and intermittent pesticide applications, the SeaWave model is more suitable for use on the basis of its robust capability of describing seasonal variation of pesticide concentrations. ?? 2010 American Water Resources Association. This article is a US Government work and is in the public domain in the USA.

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.

Jeffries Matusita-Spectral Angle Mapper (JM-SAM) spectral matching for species level mapping at Bhitarkanika, Muthupet and Pichavaram mangroves

NASA Astrophysics Data System (ADS)

Padma, S.; Sanjeevi, S.

2014-12-01

This paper proposes a novel hyperspectral matching algorithm by integrating the stochastic Jeffries-Matusita measure (JM) and the deterministic Spectral Angle Mapper (SAM), to accurately map the species and the associated landcover types of the mangroves of east coast of India using hyperspectral satellite images. The JM-SAM algorithm signifies the combination of a qualitative distance measure (JM) and a quantitative angle measure (SAM). The spectral capabilities of both the measures are orthogonally projected using the tangent and sine functions to result in the combined algorithm. The developed JM-SAM algorithm is implemented to discriminate the mangrove species and the landcover classes of Pichavaram (Tamil Nadu), Muthupet (Tamil Nadu) and Bhitarkanika (Odisha) mangrove forests along the Eastern Indian coast using the Hyperion image dat asets that contain 242 bands. The developed algorithm is extended in a supervised framework for accurate classification of the Hyperion image. The pixel-level matching performance of the developed algorithm is assessed by the Relative Spectral Discriminatory Probability (RSDPB) and Relative Spectral Discriminatory Entropy (RSDE) measures. From the values of RSDPB and RSDE, it is inferred that hybrid JM-SAM matching measure results in improved discriminability of the mangrove species and the associated landcover types than the individual SAM and JM algorithms. This performance is reflected in the classification accuracies of species and landcover map of Pichavaram mangrove ecosystem. Thus, the JM-SAM (TAN) matching algorithm yielded an accuracy better than SAM and JM measures at an average difference of 13.49 %, 7.21 % respectively, followed by JM-SAM (SIN) at 12.06%, 5.78% respectively. Similarly, in the case of Muthupet, JM-SAM (TAN) yielded an increased accuracy than SAM and JM measures at an average difference of 12.5 %, 9.72 % respectively, followed by JM-SAM (SIN) at 8.34 %, 5.55% respectively. For Bhitarkanika, the combined JM-SAM (TAN) and (SIN) measures improved the performance of individual SAM by (16.1 %, 15%) and of JM by (10.3%, 9.2%) respectively.

A Partitioning and Bounded Variable Algorithm for Linear Programming

ERIC Educational Resources Information Center

Sheskin, Theodore J.

2006-01-01

An interesting new partitioning and bounded variable algorithm (PBVA) is proposed for solving linear programming problems. The PBVA is a variant of the simplex algorithm which uses a modified form of the simplex method followed by the dual simplex method for bounded variables. In contrast to the two-phase method and the big M method, the PBVA does…

A two-stage approach to removing noise from recorded music

NASA Astrophysics Data System (ADS)

Berger, Jonathan; Goldberg, Maxim J.; Coifman, Ronald C.; Goldberg, Maxim J.; Coifman, Ronald C.

2004-05-01

A two-stage algorithm for removing noise from recorded music signals (first proposed in Berger et al., ICMC, 1995) is described and updated. The first stage selects the ``best'' local trigonometric basis for the signal and models noise as the part having high entropy [see Berger et al., J. Audio Eng. Soc. 42(10), 808-818 (1994)]. In the second stage, the original source and the model of the noise obtained from the first stage are expanded into dyadic trees of smooth local sine bases. The best basis for the source signal is extracted using a relative entropy function (the Kullback-Leibler distance) to compare the sum of the costs of the children nodes to the cost of their parent node; energies of the noise in corresponding nodes of the model noise tree are used as weights. The talk will include audio examples of various stages of the method and proposals for further research.

Costas loop lock detection in the advanced receiver

NASA Technical Reports Server (NTRS)

Mileant, A.; Hinedi, S.

1989-01-01

The advanced receiver currently being developed uses a Costas digital loop to demodulate the subcarrier. Previous analyses of lock detector algorithms for Costas loops have ignored the effects of the inherent correlation between the samples of the phase-error process. Accounting for this correlation is necessary to achieve the desired lock-detection probability for a given false-alarm rate. Both analysis and simulations are used to quantify the effects of phase correlation on lock detection for the square-law and the absolute-value type detectors. Results are obtained which depict the lock-detection probability as a function of loop signal-to-noise ratio for a given false-alarm rate. The mathematical model and computer simulation show that the square-law detector experiences less degradation due to phase jitter than the absolute-value detector and that the degradation in detector signal-to-noise ratio is more pronounced for square-wave than for sine-wave signals.

Exact solutions for unsteady free convection flow over an oscillating plate due to non-coaxial rotation.

PubMed

Mohamad, Ahmad Qushairi; Khan, Ilyas; Ismail, Zulkhibri; Shafie, Sharidan

2016-01-01

Non-coaxial rotation has wide applications in engineering devices, e.g. in food processing such as mixer machines and stirrers with a two-axis kneader, in cooling turbine blades, jet engines, pumps and vacuum cleaners, in designing thermal syphon tubes, and in geophysical flows. Therefore, this study aims to investigate unsteady free convection flow of viscous fluid due to non-coaxial rotation and fluid at infinity over an oscillating vertical plate with constant wall temperature. The governing equations are modelled by a sudden coincidence of the axes of a disk and the fluid at infinity rotating with uniform angular velocity, together with initial and boundary conditions. Some suitable non-dimensional variables are introduced. The Laplace transform method is used to obtain the exact solutions of the corresponding non-dimensional momentum and energy equations with conditions. Solutions of the velocity for cosine and sine oscillations as well as for temperature fields are obtained and displayed graphically for different values of time ( t ), the Grashof number ( Gr ), the Prandtl number ([Formula: see text]), and the phase angle ([Formula: see text]). Skin friction and the Nusselt number are also evaluated. The exact solutions are obtained and in limiting cases, the present solutions are found to be identical to the published results. Further, the obtained exact solutions also validated by comparing with results obtained by using Gaver-Stehfest algorithm. The interested physical property such as velocity, temperature, skin friction and Nusselt number are affected by the embedded parameters time ( t ), the Grashof number ( Gr ), the Prandtl number ([Formula: see text]), and the phase angle ([Formula: see text]).

More complicated than it looks: The vagaries of calculating intra-abdominal pressure

PubMed Central

Hamad, Nadia M.; Shaw, Janet M.; Nygaard, Ingrid E.; Coleman, Tanner J.; Hsu, Yvonne; Egger, Marlene; Hitchcock, Robert W.

2013-01-01

Activities thought to induce high intra-abdominal pressure (IAP), such as lifting weights, are restricted in women with pelvic floor disorders. Standardized procedures to assess IAP during activity are lacking and typically only focus on maximal IAP, variably defined. Our intent in this methods paper is to establish the best strategies for calculating maximal IAP and to add area under the curve and first moment of the area as potentially useful measures in understanding biologic effects of IAP. Thirteen women completed a range of activities while wearing an intra-vaginal pressure transducer. We first analyzed various strategies heuristically using data from 3 women. The measure that appeared to best represent maximal IAP was an average of the three, five or ten highest values, depending on activity, determined using a top down approach, with peaks at least 1 second apart using algorithms written for Matlab computer software, we then compared this strategy with others commonly reported in the literature quantitatively using data from 10 additional volunteers. Maximal IAP calculated using the top down approach differed for some, but not all, activities compared to the single highest peak or to averaging all peaks. We also calculated area under the curve, which allows for a time component, and first moment of the area, which maintains the time component while weighting pressure amplitude. We validated methods of assessing IAP using computer-generated sine waves. We offer standardized methods for assessing maximal, area under the curve and first moment of the area for IAP to improve future reporting and application of this clinically relevant measure in exercise science. PMID:23439349

[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

On the efficiency of the image encryption and decryption by using logistic-sine chaotic system and logistic-tent chaotic system

NASA Astrophysics Data System (ADS)

Chiun, Lee Chia; Mandangan, Arif; Daud, Muhamad Azlan; Hussin, Che Haziqah Che

2017-04-01

We may secure the content of text, audio, image and video during their transmission from one party to another party via an open channel such as the internet by using cryptograph. Logistic-Sine System (LSS) is a combination on two 1D chaotic maps which are Logistic Map and Sine Map. By applying the LSS into cryptography, the image encryption and decryption can be performed. This study is focusing on the performance test of the image encryption and decryption processes by using the LSS. For comparison purpose, we compare the performance of the encryption and decryption by using two different chaotic systems, which are the LSS and Logistic-Tent System (LTS). The result shows that system with LSS is less efficient than LTS in term of encryption time but both systems have similar efficiency in term of decryption time.

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.

PI-line-based image reconstruction in helical cone-beam computed tomography with a variable pitch.

PubMed

Zou, Yu; Pan, Xiaochuan; Xia, Dan; Wang, Ge

2005-08-01

Current applications of helical cone-beam computed tomography (CT) involve primarily a constant pitch where the translating speed of the table and the rotation speed of the source-detector remain constant. However, situations do exist where it may be more desirable to use a helical scan with a variable translating speed of the table, leading a variable pitch. One of such applications could arise in helical cone-beam CT fluoroscopy for the determination of vascular structures through real-time imaging of contrast bolus arrival. Most of the existing reconstruction algorithms have been developed only for helical cone-beam CT with constant pitch, including the backprojection-filtration (BPF) and filtered-backprojection (FBP) algorithms that we proposed previously. It is possible to generalize some of these algorithms to reconstruct images exactly for helical cone-beam CT with a variable pitch. In this work, we generalize our BPF and FBP algorithms to reconstruct images directly from data acquired in helical cone-beam CT with a variable pitch. We have also performed a preliminary numerical study to demonstrate and verify the generalization of the two algorithms. The results of the study confirm that our generalized BPF and FBP algorithms can yield exact reconstruction in helical cone-beam CT with a variable pitch. It should be pointed out that our generalized BPF algorithm is the only algorithm that is capable of reconstructing exactly region-of-interest image from data containing transverse truncations.

Improved multivariate polynomial factoring algorithm

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

Wang, P.S.

1978-10-01

A new algorithm for factoring multivariate polynomials over the integers based on an algorithm by Wang and Rothschild is described. The new algorithm has improved strategies for dealing with the known problems of the original algorithm, namely, the leading coefficient problem, the bad-zero problem and the occurrence of extraneous factors. It has an algorithm for correctly predetermining leading coefficients of the factors. A new and efficient p-adic algorithm named EEZ is described. Bascially it is a linearly convergent variable-by-variable parallel construction. The improved algorithm is generally faster and requires less store then the original algorithm. Machine examples with comparative timingmore » are included.« less

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

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

A provisional effective evaluation when errors are present in independent variables

NASA Technical Reports Server (NTRS)

Gurin, L. S.

1983-01-01

Algorithms are examined for evaluating the parameters of a regression model when there are errors in the independent variables. The algorithms are fast and the estimates they yield are stable with respect to the correlation of errors and measurements of both the dependent variable and the independent variables.

Efficient scatter distribution estimation and correction in CBCT using concurrent Monte Carlo fitting

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

Bootsma, G. J., E-mail: Gregory.Bootsma@rmp.uhn.on.ca; Verhaegen, F.; Medical Physics Unit, Department of Oncology, McGill University, Montreal, Quebec H3G 1A4

2015-01-15

Purpose: X-ray scatter is a significant impediment to image quality improvements in cone-beam CT (CBCT). The authors present and demonstrate a novel scatter correction algorithm using a scatter estimation method that simultaneously combines multiple Monte Carlo (MC) CBCT simulations through the use of a concurrently evaluated fitting function, referred to as concurrent MC fitting (CMCF). Methods: The CMCF method uses concurrently run MC CBCT scatter projection simulations that are a subset of the projection angles used in the projection set, P, to be corrected. The scattered photons reaching the detector in each MC simulation are simultaneously aggregated by an algorithmmore » which computes the scatter detector response, S{sub MC}. S{sub MC} is fit to a function, S{sub F}, and if the fit of S{sub F} is within a specified goodness of fit (GOF), the simulations are terminated. The fit, S{sub F}, is then used to interpolate the scatter distribution over all pixel locations for every projection angle in the set P. The CMCF algorithm was tested using a frequency limited sum of sines and cosines as the fitting function on both simulated and measured data. The simulated data consisted of an anthropomorphic head and a pelvis phantom created from CT data, simulated with and without the use of a compensator. The measured data were a pelvis scan of a phantom and patient taken on an Elekta Synergy platform. The simulated data were used to evaluate various GOF metrics as well as determine a suitable fitness value. The simulated data were also used to quantitatively evaluate the image quality improvements provided by the CMCF method. A qualitative analysis was performed on the measured data by comparing the CMCF scatter corrected reconstruction to the original uncorrected and corrected by a constant scatter correction reconstruction, as well as a reconstruction created using a set of projections taken with a small cone angle. Results: Pearson’s correlation, r, proved to be a suitable GOF metric with strong correlation with the actual error of the scatter fit, S{sub F}. Fitting the scatter distribution to a limited sum of sine and cosine functions using a low-pass filtered fast Fourier transform provided a computationally efficient and accurate fit. The CMCF algorithm reduces the number of photon histories required by over four orders of magnitude. The simulated experiments showed that using a compensator reduced the computational time by a factor between 1.5 and 1.75. The scatter estimates for the simulated and measured data were computed between 35–93 s and 114–122 s, respectively, using 16 Intel Xeon cores (3.0 GHz). The CMCF scatter correction improved the contrast-to-noise ratio by 10%–50% and reduced the reconstruction error to under 3% for the simulated phantoms. Conclusions: The novel CMCF algorithm significantly reduces the computation time required to estimate the scatter distribution by reducing the statistical noise in the MC scatter estimate and limiting the number of projection angles that must be simulated. Using the scatter estimate provided by the CMCF algorithm to correct both simulated and real projection data showed improved reconstruction image quality.« less

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.

A study on the application of Fourier series in IMRT treatment planning.

PubMed

Almeida-Trinidad, R; Garnica-Garza, H M

2007-12-01

In intensity-modulated radiotherapy, a set of x-ray fluence profiles is iteratively adjusted until a desired absorbed dose distribution is obtained. The purpose of this article is to present a method that allows the optimization of fluence profiles based on the Fourier series decomposition of an initial approximation to the profile. The method has the advantage that a new fluence profile can be obtained in a precise and controlled way with the tuning of only two parameters, namely the phase of the sine and cosine terms of one of the Fourier components, in contrast to the point-by-point tuning of the profile. Also, because the method uses analytical functions, the resultant profiles do not exhibit numerical artifacts. A test case consisting of a mathematical phantom with a target wrapped around a critical structure is discussed to illustrate the algorithm. It is shown that the degree of conformality of the absorbed dose distribution can be tailored by varying the number of Fourier terms made available to the optimization algorithm. For the test case discussed here, it is shown that the number of Fourier terms to be modified depends on the number of radiation beams incident on the target but it is in general in the order of 10 terms.

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.

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

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.

A Generic 1D Forward Modeling and Inversion Algorithm for TEM Sounding with an Arbitrary Horizontal Loop

NASA Astrophysics Data System (ADS)

Li, Zhanhui; Huang, Qinghua; Xie, Xingbing; Tang, Xingong; Chang, Liao

2016-08-01

We present a generic 1D forward modeling and inversion algorithm for transient electromagnetic (TEM) data with an arbitrary horizontal transmitting loop and receivers at any depth in a layered earth. Both the Hankel and sine transforms required in the forward algorithm are calculated using the filter method. The adjoint-equation method is used to derive the formulation of data sensitivity at any depth in non-permeable media. The inversion algorithm based on this forward modeling algorithm and sensitivity formulation is developed using the Gauss-Newton iteration method combined with the Tikhonov regularization. We propose a new data-weighting method to minimize the initial model dependence that enhances the convergence stability. On a laptop with a CPU of i7-5700HQ@3.5 GHz, the inversion iteration of a 200 layered input model with a single receiver takes only 0.34 s, while it increases to only 0.53 s for the data from four receivers at a same depth. For the case of four receivers at different depths, the inversion iteration runtime increases to 1.3 s. Modeling the data with an irregular loop and an equal-area square loop indicates that the effect of the loop geometry is significant at early times and vanishes gradually along the diffusion of TEM field. For a stratified earth, inversion of data from more than one receiver is useful in noise reducing to get a more credible layered earth. However, for a resistive layer shielded below a conductive layer, increasing the number of receivers on the ground does not have significant improvement in recovering the resistive layer. Even with a down-hole TEM sounding, the shielded resistive layer cannot be recovered if all receivers are above the shielded resistive layer. However, our modeling demonstrates remarkable improvement in detecting the resistive layer with receivers in or under this layer.

A chaos wolf optimization algorithm with self-adaptive variable step-size

NASA Astrophysics Data System (ADS)

Zhu, Yong; Jiang, Wanlu; Kong, Xiangdong; Quan, Lingxiao; Zhang, Yongshun

2017-10-01

To explore the problem of parameter optimization for complex nonlinear function, a chaos wolf optimization algorithm (CWOA) with self-adaptive variable step-size was proposed. The algorithm was based on the swarm intelligence of wolf pack, which fully simulated the predation behavior and prey distribution way of wolves. It possessed three intelligent behaviors such as migration, summons and siege. And the competition rule as "winner-take-all" and the update mechanism as "survival of the fittest" were also the characteristics of the algorithm. Moreover, it combined the strategies of self-adaptive variable step-size search and chaos optimization. The CWOA was utilized in parameter optimization of twelve typical and complex nonlinear functions. And the obtained results were compared with many existing algorithms, including the classical genetic algorithm, the particle swarm optimization algorithm and the leader wolf pack search algorithm. The investigation results indicate that CWOA possess preferable optimization ability. There are advantages in optimization accuracy and convergence rate. Furthermore, it demonstrates high robustness and global searching ability.

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.

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.

Multi-Objective Sliding Mode Control on Vehicle Cornering Stability with Variable Gear Ratio Actuator-Based Active Front Steering Systems

PubMed Central

Ma, Xinbo; Wong, Pak Kin; Zhao, Jing; Xie, Zhengchao

2016-01-01

Active front steering (AFS) is an emerging technology to improve the vehicle cornering stability by introducing an additional small steering angle to the driver’s input. This paper proposes an AFS system with a variable gear ratio steering (VGRS) actuator which is controlled by using the sliding mode control (SMC) strategy to improve the cornering stability of vehicles. In the design of an AFS system, different sensors are considered to measure the vehicle state, and the mechanism of the AFS system is also modelled in detail. Moreover, in order to improve the cornering stability of vehicles, two dependent objectives, namely sideslip angle and yaw rate, are considered together in the design of SMC strategy. By evaluating the cornering performance, Sine with Dwell and accident avoidance tests are conducted, and the simulation results indicate that the proposed SMC strategy is capable of improving the cornering stability of vehicles in practice. PMID:28036037

Teaching a Machine to Feel Postoperative Pain: Combining High-Dimensional Clinical Data with Machine Learning Algorithms to Forecast Acute Postoperative Pain

PubMed Central

Tighe, Patrick J.; Harle, Christopher A.; Hurley, Robert W.; Aytug, Haldun; Boezaart, Andre P.; Fillingim, Roger B.

2015-01-01

Background Given their ability to process highly dimensional datasets with hundreds of variables, machine learning algorithms may offer one solution to the vexing challenge of predicting postoperative pain. Methods Here, we report on the application of machine learning algorithms to predict postoperative pain outcomes in a retrospective cohort of 8071 surgical patients using 796 clinical variables. Five algorithms were compared in terms of their ability to forecast moderate to severe postoperative pain: Least Absolute Shrinkage and Selection Operator (LASSO), gradient-boosted decision tree, support vector machine, neural network, and k-nearest neighbor, with logistic regression included for baseline comparison. Results In forecasting moderate to severe postoperative pain for postoperative day (POD) 1, the LASSO algorithm, using all 796 variables, had the highest accuracy with an area under the receiver-operating curve (ROC) of 0.704. Next, the gradient-boosted decision tree had an ROC of 0.665 and the k-nearest neighbor algorithm had an ROC of 0.643. For POD 3, the LASSO algorithm, using all variables, again had the highest accuracy, with an ROC of 0.727. Logistic regression had a lower ROC of 0.5 for predicting pain outcomes on POD 1 and 3. Conclusions Machine learning algorithms, when combined with complex and heterogeneous data from electronic medical record systems, can forecast acute postoperative pain outcomes with accuracies similar to methods that rely only on variables specifically collected for pain outcome prediction. PMID:26031220

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

Li, Na; Wu, Yu-Ping; Min, Hao

A radio-frequency (RF) source designed for cold atom experiments is presented. The source uses AD9858, a direct digital synthesizer, to generate the sine wave directly, up to 400 MHz, with sub-Hz resolution. An amplitude control circuit consisting of wideband variable gain amplifier and high speed digital to analog converter is integrated into the source, capable of 70 dB off isolation and 4 ns on-off keying. A field programmable gate array is used to implement a versatile frequency and amplitude co-sweep logic. Owing to modular design, the RF sources have been used on many cold atom experiments to generate various complicatedmore » RF sequences, enriching the operation schemes of cold atoms, which cannot be done by standard RF source instruments.« less

System simulation for an untreated sewage source heat pump (USSHP) in winter

NASA Astrophysics Data System (ADS)

Qin, Na; Hao, Peng Z.

2017-01-01

The paper discusses the system characteristics of an untreated sewage source heat pump in winter. In this system, the sewage enters into the evaporator directly. The variable parameters to control the system contain the sewage temperature at evaporator inlet and the water temperature at condenser inlet. It is found that most parameters, except the condensation heat transfer coefficient, change in the form of sine wave the same as the sewage temperature at inlet. The heating load and consumed power are 12.9kW and 3.45kW when the sewage temperature at inlet is 13°C. COP is about 3.75 in the range of the sewage temperature at inlet of 12-13°C.

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

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.

Inverse Ising problem in continuous time: A latent variable approach

NASA Astrophysics Data System (ADS)

Donner, Christian; Opper, Manfred

2017-12-01

We consider the inverse Ising problem: the inference of network couplings from observed spin trajectories for a model with continuous time Glauber dynamics. By introducing two sets of auxiliary latent random variables we render the likelihood into a form which allows for simple iterative inference algorithms with analytical updates. The variables are (1) Poisson variables to linearize an exponential term which is typical for point process likelihoods and (2) Pólya-Gamma variables, which make the likelihood quadratic in the coupling parameters. Using the augmented likelihood, we derive an expectation-maximization (EM) algorithm to obtain the maximum likelihood estimate of network parameters. Using a third set of latent variables we extend the EM algorithm to sparse couplings via L1 regularization. Finally, we develop an efficient approximate Bayesian inference algorithm using a variational approach. We demonstrate the performance of our algorithms on data simulated from an Ising model. For data which are simulated from a more biologically plausible network with spiking neurons, we show that the Ising model captures well the low order statistics of the data and how the Ising couplings are related to the underlying synaptic structure of the simulated network.

The artificial-free technique along the objective direction for the simplex algorithm

NASA Astrophysics Data System (ADS)

Boonperm, Aua-aree; Sinapiromsaran, Krung

2014-03-01

The simplex algorithm is a popular algorithm for solving linear programming problems. If the origin point satisfies all constraints then the simplex can be started. Otherwise, artificial variables will be introduced to start the simplex algorithm. If we can start the simplex algorithm without using artificial variables then the simplex iterate will require less time. In this paper, we present the artificial-free technique for the simplex algorithm by mapping the problem into the objective plane and splitting constraints into three groups. In the objective plane, one of variables which has a nonzero coefficient of the objective function is fixed in terms of another variable. Then it can split constraints into three groups: the positive coefficient group, the negative coefficient group and the zero coefficient group. Along the objective direction, some constraints from the positive coefficient group will form the optimal solution. If the positive coefficient group is nonempty, the algorithm starts with relaxing constraints from the negative coefficient group and the zero coefficient group. We guarantee the feasible region obtained from the positive coefficient group to be nonempty. The transformed problem is solved using the simplex algorithm. Additional constraints from the negative coefficient group and the zero coefficient group will be added to the solved problem and use the dual simplex method to determine the new optimal solution. An example shows the effectiveness of our algorithm.

Global Convergence of the EM Algorithm for Unconstrained Latent Variable Models with Categorical Indicators

ERIC Educational Resources Information Center

Weissman, Alexander

2013-01-01

Convergence of the expectation-maximization (EM) algorithm to a global optimum of the marginal log likelihood function for unconstrained latent variable models with categorical indicators is presented. The sufficient conditions under which global convergence of the EM algorithm is attainable are provided in an information-theoretic context by…

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

Tumuluru, Jaya Shankar; McCulloch, Richard Chet James

In this work a new hybrid genetic algorithm was developed which combines a rudimentary adaptive steepest ascent hill climbing algorithm with a sophisticated evolutionary algorithm in order to optimize complex multivariate design problems. By combining a highly stochastic algorithm (evolutionary) with a simple deterministic optimization algorithm (adaptive steepest ascent) computational resources are conserved and the solution converges rapidly when compared to either algorithm alone. In genetic algorithms natural selection is mimicked by random events such as breeding and mutation. In the adaptive steepest ascent algorithm each variable is perturbed by a small amount and the variable that caused the mostmore » improvement is incremented by a small step. If the direction of most benefit is exactly opposite of the previous direction with the most benefit then the step size is reduced by a factor of 2, thus the step size adapts to the terrain. A graphical user interface was created in MATLAB to provide an interface between the hybrid genetic algorithm and the user. Additional features such as bounding the solution space and weighting the objective functions individually are also built into the interface. The algorithm developed was tested to optimize the functions developed for a wood pelleting process. Using process variables (such as feedstock moisture content, die speed, and preheating temperature) pellet properties were appropriately optimized. Specifically, variables were found which maximized unit density, bulk density, tapped density, and durability while minimizing pellet moisture content and specific energy consumption. The time and computational resources required for the optimization were dramatically decreased using the hybrid genetic algorithm when compared to MATLAB's native evolutionary optimization tool.« less

Sensitivity Analysis on Remote Sensing Evapotranspiration Algorithm of Surface Energy Balance for Land

NASA Astrophysics Data System (ADS)

Wang, J.; Samms, T.; Meier, C.; Simmons, L.; Miller, D.; Bathke, D.

2005-12-01

Spatial evapotranspiration (ET) is usually estimated by Surface Energy Balance Algorithm for Land. The average accuracy of the algorithm is 85% on daily basis and 95% on seasonable basis. However, the accuracy of the algorithm varies from 67% to 95% on instantaneous ET estimates and, as reported in 18 studies, 70% to 98% on 1 to 10-day ET estimates. There is a need to understand the sensitivity of the ET calculation with respect to the algorithm variables and equations. With an increased understanding, information can be developed to improve the algorithm, and to better identify the key variables and equations. A Modified Surface Energy Balance Algorithm for Land (MSEBAL) was developed and validated with data from a pecan orchard and an alfalfa field. The MSEBAL uses ground reflectance and temperature data from ASTER sensors along with humidity, wind speed, and solar radiation data from a local weather station. MSEBAL outputs hourly and daily ET with 90 m by 90 m resolution. A sensitivity analysis was conducted for MSEBAL on ET calculation. In order to observe the sensitivity of the calculation to a particular variable, the value of that variable was changed while holding the magnitudes of the other variables. The key variables and equations to which the ET calculation most sensitive were determined in this study. href='http://weather.nmsu.edu/pecans/SEBALFolder/San%20Francisco%20AGU%20meeting/ASensitivityAnalysisonMSE">http://weather.nmsu.edu/pecans/SEBALFolder/San%20Francisco%20AGU%20meeting/ASensitivityAnalysisonMSE

Detecting Anomalies in Process Control Networks

NASA Astrophysics Data System (ADS)

Rrushi, Julian; Kang, Kyoung-Don

This paper presents the estimation-inspection algorithm, a statistical algorithm for anomaly detection in process control networks. The algorithm determines if the payload of a network packet that is about to be processed by a control system is normal or abnormal based on the effect that the packet will have on a variable stored in control system memory. The estimation part of the algorithm uses logistic regression integrated with maximum likelihood estimation in an inductive machine learning process to estimate a series of statistical parameters; these parameters are used in conjunction with logistic regression formulas to form a probability mass function for each variable stored in control system memory. The inspection part of the algorithm uses the probability mass functions to estimate the normalcy probability of a specific value that a network packet writes to a variable. Experimental results demonstrate that the algorithm is very effective at detecting anomalies in process control networks.

Variable-spot ion beam figuring

NASA Astrophysics Data System (ADS)

Wu, Lixiang; Qiu, Keqiang; Fu, Shaojun

2016-03-01

This paper introduces a new scheme of ion beam figuring (IBF), or rather variable-spot IBF, which is conducted at a constant scanning velocity with variable-spot ion beam collimated by a variable diaphragm. It aims at improving the reachability and adaptation of the figuring process within the limits of machine dynamics by varying the ion beam spot size instead of the scanning velocity. In contrast to the dwell time algorithm in the conventional IBF, the variable-spot IBF adopts a new algorithm, which consists of the scan path programming and the trajectory optimization using pattern search. In this algorithm, instead of the dwell time, a new concept, integral etching time, is proposed to interpret the process of variable-spot IBF. We conducted simulations to verify its feasibility and practicality. The simulation results indicate the variable-spot IBF is a promising alternative to the conventional approach.

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).

Functional Entropy Variables: A New Methodology for Deriving Thermodynamically Consistent Algorithms for Complex Fluids, with Particular Reference to the Isothermal Navier-Stokes-Korteweg Equations

DTIC Science & Technology

2012-11-01

multicorrector algorithm . Predictor stage: Set Cρn+1,(0) = C ρ n, (157) Cun+1,(0) = C u n, (158) Cvn+1,(0) = C v n. (159) Multicorrector stage: Repeat the... corrector algorithm given by (157)-(178). Remark 20. We adopt the preconditioned GMRES algorithm [53] from PETSc [2] to solve the linear system given by (175...ICES REPORT 12-43 November 2012 Functional Entropy Variables: A New Methodology for Deriving Thermodynamically Consistent Algorithms for Complex

Variable-Metric Algorithm For Constrained Optimization

NASA Technical Reports Server (NTRS)

Frick, James D.

1989-01-01

Variable Metric Algorithm for Constrained Optimization (VMACO) is nonlinear computer program developed to calculate least value of function of n variables subject to general constraints, both equality and inequality. First set of constraints equality and remaining constraints inequalities. Program utilizes iterative method in seeking optimal solution. Written in ANSI Standard FORTRAN 77.

[Formula: see text]-regularized recursive total least squares based sparse system identification for the error-in-variables.

PubMed

Lim, Jun-Seok; Pang, Hee-Suk

2016-01-01

In this paper an [Formula: see text]-regularized recursive total least squares (RTLS) algorithm is considered for the sparse system identification. Although recursive least squares (RLS) has been successfully applied in sparse system identification, the estimation performance in RLS based algorithms becomes worse, when both input and output are contaminated by noise (the error-in-variables problem). We proposed an algorithm to handle the error-in-variables problem. The proposed [Formula: see text]-RTLS algorithm is an RLS like iteration using the [Formula: see text] regularization. The proposed algorithm not only gives excellent performance but also reduces the required complexity through the effective inversion matrix handling. Simulations demonstrate the superiority of the proposed [Formula: see text]-regularized RTLS for the sparse system identification setting.

Multiple-variable neighbourhood search for the single-machine total weighted tardiness problem

NASA Astrophysics Data System (ADS)

Chung, Tsui-Ping; Fu, Qunjie; Liao, Ching-Jong; Liu, Yi-Ting

2017-07-01

The single-machine total weighted tardiness (SMTWT) problem is a typical discrete combinatorial optimization problem in the scheduling literature. This problem has been proved to be NP hard and thus provides a challenging area for metaheuristics, especially the variable neighbourhood search algorithm. In this article, a multiple variable neighbourhood search (m-VNS) algorithm with multiple neighbourhood structures is proposed to solve the problem. Special mechanisms named matching and strengthening operations are employed in the algorithm, which has an auto-revising local search procedure to explore the solution space beyond local optimality. Two aspects, searching direction and searching depth, are considered, and neighbourhood structures are systematically exchanged. Experimental results show that the proposed m-VNS algorithm outperforms all the compared algorithms in solving the SMTWT problem.

An improved VSS NLMS algorithm for active noise cancellation

NASA Astrophysics Data System (ADS)

Sun, Yunzhuo; Wang, Mingjiang; Han, Yufei; Zhang, Congyan

2017-08-01

In this paper, an improved variable step size NLMS algorithm is proposed. NLMS has fast convergence rate and low steady state error compared to other traditional adaptive filtering algorithm. But there is a contradiction between the convergence speed and steady state error that affect the performance of the NLMS algorithm. Now, we propose a new variable step size NLMS algorithm. It dynamically changes the step size according to current error and iteration times. The proposed algorithm has simple formulation and easily setting parameters, and effectively solves the contradiction in NLMS. The simulation results show that the proposed algorithm has a good tracking ability, fast convergence rate and low steady state error simultaneously.

Development and Testing of Data Mining Algorithms for Earth Observation

NASA Technical Reports Server (NTRS)

Glymour, Clark

2005-01-01

The new algorithms developed under this project included a principled procedure for classification of objects, events or circumstances according to a target variable when a very large number of potential predictor variables is available but the number of cases that can be used for training a classifier is relatively small. These "high dimensional" problems require finding a minimal set of variables -called the Markov Blanket-- sufficient for predicting the value of the target variable. An algorithm, the Markov Blanket Fan Search, was developed, implemented and tested on both simulated and real data in conjunction with a graphical model classifier, which was also implemented. Another algorithm developed and implemented in TETRAD IV for time series elaborated on work by C. Granger and N. Swanson, which in turn exploited some of our earlier work. The algorithms in question learn a linear time series model from data. Given such a time series, the simultaneous residual covariances, after factoring out time dependencies, may provide information about causal processes that occur more rapidly than the time series representation allow, so called simultaneous or contemporaneous causal processes. Working with A. Monetta, a graduate student from Italy, we produced the correct statistics for estimating the contemporaneous causal structure from time series data using the TETRAD IV suite of algorithms. Two economists, David Bessler and Kevin Hoover, have independently published applications using TETRAD style algorithms to the same purpose. These implementations and algorithmic developments were separately used in two kinds of studies of climate data: Short time series of geographically proximate climate variables predicting agricultural effects in California, and longer duration climate measurements of temperature teleconnections.

Diversified models for portfolio selection based on uncertain semivariance

NASA Astrophysics Data System (ADS)

Chen, Lin; Peng, Jin; Zhang, Bo; Rosyida, Isnaini

2017-02-01

Since the financial markets are complex, sometimes the future security returns are represented mainly based on experts' estimations due to lack of historical data. This paper proposes a semivariance method for diversified portfolio selection, in which the security returns are given subjective to experts' estimations and depicted as uncertain variables. In the paper, three properties of the semivariance of uncertain variables are verified. Based on the concept of semivariance of uncertain variables, two types of mean-semivariance diversified models for uncertain portfolio selection are proposed. Since the models are complex, a hybrid intelligent algorithm which is based on 99-method and genetic algorithm is designed to solve the models. In this hybrid intelligent algorithm, 99-method is applied to compute the expected value and semivariance of uncertain variables, and genetic algorithm is employed to seek the best allocation plan for portfolio selection. At last, several numerical examples are presented to illustrate the modelling idea and the effectiveness of the algorithm.

A Program Complexity Metric Based on Variable Usage for Algorithmic Thinking Education of Novice Learners

ERIC Educational Resources Information Center

Fuwa, Minori; Kayama, Mizue; Kunimune, Hisayoshi; Hashimoto, Masami; Asano, David K.

2015-01-01

We have explored educational methods for algorithmic thinking for novices and implemented a block programming editor and a simple learning management system. In this paper, we propose a program/algorithm complexity metric specified for novice learners. This metric is based on the variable usage in arithmetic and relational formulas in learner's…

Efficient Variable Selection Method for Exposure Variables on Binary Data

NASA Astrophysics Data System (ADS)

Ohno, Manabu; Tarumi, Tomoyuki

In this paper, we propose a new variable selection method for "robust" exposure variables. We define "robust" as property that the same variable can select among original data and perturbed data. There are few studies of effective for the selection method. The problem that selects exposure variables is almost the same as a problem that extracts correlation rules without robustness. [Brin 97] is suggested that correlation rules are possible to extract efficiently using chi-squared statistic of contingency table having monotone property on binary data. But the chi-squared value does not have monotone property, so it's is easy to judge the method to be not independent with an increase in the dimension though the variable set is completely independent, and the method is not usable in variable selection for robust exposure variables. We assume anti-monotone property for independent variables to select robust independent variables and use the apriori algorithm for it. The apriori algorithm is one of the algorithms which find association rules from the market basket data. The algorithm use anti-monotone property on the support which is defined by association rules. But independent property does not completely have anti-monotone property on the AIC of independent probability model, but the tendency to have anti-monotone property is strong. Therefore, selected variables with anti-monotone property on the AIC have robustness. Our method judges whether a certain variable is exposure variable for the independent variable using previous comparison of the AIC. Our numerical experiments show that our method can select robust exposure variables efficiently and precisely.

THE MULTI-WAVELENGTH CHARACTERISTICS OF THE TeV BINARY LS I+61°303

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

Saha, L.; Chitnis, V. R.; Shukla, A.

2016-06-01

We study the characteristics of the TeV binary LS I+61°303 in radio, soft X-ray, hard X-ray, and gamma-ray (GeV and TeV) energies. The long-term variability characteristics are examined as a function of the phase of the binary period of 26.496 days as well as the phase of the superorbital period of 1626 days, dividing the observations into a matrix of 10 × 10 phases of these two periods. We find that the long-term variability can be described by a sine function of the superorbital period, with the phase and amplitude systematically varying with the binary period phase. We also findmore » a definite wavelength-dependent change in this variability description. To understand the radiation mechanism, we define three states in the orbital/superorbital phase matrix and examine the wideband spectral energy distribution. The derived source parameters indicate that the emission geometry is dominated by a jet structure showing a systematic variation with the orbital/superorbital period. We suggest that LS I+61°303 is likely a microquasar with a steady jet.« less

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.

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

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

Study on distributed generation algorithm of variable precision concept lattice based on ontology heterogeneous database

NASA Astrophysics Data System (ADS)

WANG, Qingrong; ZHU, Changfeng

2017-06-01

Integration of distributed heterogeneous data sources is the key issues under the big data applications. In this paper the strategy of variable precision is introduced to the concept lattice, and the one-to-one mapping mode of variable precision concept lattice and ontology concept lattice is constructed to produce the local ontology by constructing the variable precision concept lattice for each subsystem, and the distributed generation algorithm of variable precision concept lattice based on ontology heterogeneous database is proposed to draw support from the special relationship between concept lattice and ontology construction. Finally, based on the standard of main concept lattice of the existing heterogeneous database generated, a case study has been carried out in order to testify the feasibility and validity of this algorithm, and the differences between the main concept lattice and the standard concept lattice are compared. Analysis results show that this algorithm above-mentioned can automatically process the construction process of distributed concept lattice under the heterogeneous data sources.

LINEs, SINEs and other retroelements: do birds of a feather flock together?

PubMed

Roy-Engel, Astrid M

2012-01-01

Mobile elements account for almost half of the mass of the human genome. Only the retroelements from the non-LTR (long terminal repeat) retrotransposon family, which include the LINE-1 (L1) and its non-autonomous partners, are currently active and contributing to new insertions. Although these elements seem to share the same basic amplification mechanism, the activity and success of the different types of retroelements varies. For example, Alu-induced mutagenesis is responsible for the majority of the documented instances of human disease induced by insertion of retroelements. Using copy number in mammals as an indicator, some SINEs have been vastly more successful than other retroelements, such as the retropseudogenes and even L1, likely due to differences in post-insertion selection and ability to overcome cellular controls. SINE and LINE integration can be differentially influenced by cellular factors, indicating some differences between in their amplification mechanisms. We focus on the known aspects of this group of retroelements and highlight their similarities and differences that may significantly influence their biological impact.

LINEs, SINEs and other retroelements: do birds of a feather flock together?

PubMed Central

Roy-Engel, Astrid M.

2012-01-01

Mobile elements account for almost half of the mass of the human genome. Only the retroelements from the non-LTR (long terminal repeat) retrotransposon family, which include the LINE-1 (L1) and its non-autonomous partners, are currently active and contributing to new insertions. Although these elements seem to share the same basic amplification mechanism, the activity and success of the different types of retroelements varies. For example, Alu-induced mutagenesis is responsible for the majority of the documented instances of human disease induced by insertion of retroelements. Using copy number in mammals as an indicator, some SINEs have been vastly more successful than other retroelements, such as the retropseudogenes and even L1, likely due to differences in post-insertion selection and ability to overcome cellular controls. SINE and LINE integration can be differentially influenced by cellular factors, indicating some differences between in their amplification mechanisms. We focus on the known aspects of this group of retroelements and highlight their similarities and differences that may significantly influence their biological impact. PMID:22201808

Identification of an active ID-like group of SINEs in the mouse

PubMed Central

Kass, David H; Jamison, Nicole

2007-01-01

The mouse genome consists of five known families of SINEs: B1, B2, B4/RSINE, ID, and MIR. Using RT-PCR we identified a germ-line transcript that demonstrates 92.7% sequence identity to ID (excluding primer sequence), yet a BLAST search identified numerous matches of 100% sequence identity. We analyzed four of these elements for their presence in orthologous genes in strains and subspecies of M. musculus as well as other species of Mus using a PCR-based assay. All four analyzed elements were either identified only in M. musculus or exclusively in both M. musculus and M. domesticus indicative of recent integrations. In conjunction with the identification of transcripts, we present an active ID-like group of elements that is not derived from the proposed BC1 master gene of ID elements. A BLAST of the rat genome indicated that these elements were not in the rat. Therefore, this family of SINEs has recently evolved, and since thus far has mainly been observed in M. musculus, we then refer to this family as MMIDL. PMID:17572061

Identification of an active ID-like group of SINEs in the mouse.

PubMed

Kass, David H; Jamison, Nicole

2007-09-01

The mouse genome consists of five known families of SINEs: B1, B2, B4/RSINE, ID, and MIR. Using RT-PCR we identified a germ-line transcript that demonstrates 92.7% sequence identity to ID (excluding primer sequence), yet a BLAST search identified numerous matches of 100% sequence identity. We analyzed four of these elements for their presence in orthologous genes in strains and subspecies of Mus musculus as well as other species of Mus using a PCR-based assay. All four analyzed elements were identified either only in M. musculus or exclusively in both M. musculus and M. domesticus, indicative of recent integrations. In conjunction with the identification of transcripts, we present an active ID-like group of elements that is not derived from the proposed BC1 master gene of ID elements. A BLAST of the rat genome indicated that these elements were not in the rat. Therefore, this family of SINEs has recently evolved, and since it has thus far been observed mainly in M. musculus, we refer to this family as MMIDL.

Analysis of the mechanics and deformation characteristics of optical fiber acceleration sensor

NASA Astrophysics Data System (ADS)

Liu, Zong-kai; Bo, Yu-ming; Zhou, Ben-mou; Wang, Jun; Huang, Ya-dong

2016-10-01

The optical fiber sensor holds many advantages such as smaller volume, lighter weight, higher sensitivity, and stronger anti-interference ability, etc. It can be applied to oil exploration to improve the exploration efficiency, since the underground petroleum distribution can be obtained by detecting and analyzing the echo signals. In this paper, the cantilever beam optical fiber sensor was mainly investigated. Specifically, the finite element analysis method is applied to the numerical analysis of the changes and relations of the optical fiber rail slot elongation on the surface of the PC material fiber winding plate along with the changes of time and power under the action of sine force. The analysis results show that, when the upper and lower quality blocks are under the action of sine force, the cantilever beam optical fiber sensor structure can basically produce synchronized deformation along with the force. And the optical fiber elongation length basically has a linear relationship with the sine force within the time ranges of 0.2 0.4 and 0.6 0.8, which would be beneficial for the subsequent signal acquisition and data processing.

Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation

PubMed Central

Kozhuharova, Ana; Sharma, Harshita; Ohyama, Takako; Fasolo, Francesca; Yamazaki, Toshio; Cotella, Diego; Santoro, Claudio; Zucchelli, Silvia; Gustincich, Stefano; Carninci, Piero

2018-01-01

SINEUPs are antisense long noncoding RNAs, in which an embedded SINE B2 element UP-regulates translation of partially overlapping target sense mRNAs. SINEUPs contain two functional domains. First, the binding domain (BD) is located in the region antisense to the target, providing specific targeting to the overlapping mRNA. Second, the inverted SINE B2 represents the effector domain (ED) and enhances translation. To adapt SINEUP technology to a broader number of targets, we took advantage of a high-throughput, semi-automated imaging system to optimize synthetic SINEUP BD and ED design in HEK293T cell lines. Using SINEUP-GFP as a model SINEUP, we extensively screened variants of the BD to map features needed for optimal design. We found that most active SINEUPs overlap an AUG-Kozak sequence. Moreover, we report our screening of the inverted SINE B2 sequence to identify active sub-domains and map the length of the minimal active ED. Our synthetic SINEUP-GFP screening of both BDs and EDs constitutes a broad test with flexible applications to any target gene of interest. PMID:29414979

Optical Quantification of Harmonic Acoustic Radiation Force Excitation in a Tissue-Mimicking Phantom.

PubMed

Suomi, Visa; Edwards, David; Cleveland, Robin

2015-12-01

Optical tracking was used to characterize acoustic radiation force-induced displacements in a tissue-mimicking phantom. Amplitude-modulated 3.3-MHz ultrasound was used to induce acoustic radiation force in the phantom, which was embedded with 10-μm microspheres that were tracked using a microscope objective and high-speed camera. For sine and square amplitude modulation, the harmonic components of the fundamental and second and third harmonic frequencies were measured. The displacement amplitudes were found to increase linearly with acoustic radiation force up to 10 μm, with sine modulation having 19.5% lower peak-to-peak amplitude values than square modulation. Square modulation produced almost no second harmonic, but energy was present in the third harmonic. For the sine modulation, energy was present in the second harmonic and low energy in the third harmonic. A finite-element model was used to simulate the deformation and was both qualitatively and quantitatively in agreement with the measurements. Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Averaging peak-to-peak voltage detector for absolute mass determination of single particles with quadrupole ion traps

NASA Astrophysics Data System (ADS)

Peng, Wen-Ping; Lee, Yuan T.; Ting, Joseph W.; Chang, Huan-Cheng

2005-02-01

A sine wave that controls a quadrupole ion trap is generated from a low voltage source, boosted to high voltage through a transformer. Since not even the best transformers can keep a flat amplitude response with respect to frequency, knowing the accurate peak-to-peak value of the sine wave is paramount when the frequency is varied. We have developed an averaging peak-to-peak voltage detector for such measurements and demonstrated that the device is an essential tool to make possible high-precision mass determination of single charged microparticles with masses greater than 1×1011u. Tests of the detector with sine waves from a FLUKE 5720A standard source in the neighborhood of 1400Vpp and frequencies ranging from 100to700Hz showed a measurement accuracy better than 10ppm. The detector settled within 5s after each reset to 5 digits of DVM rock-steady reading, and the calibration against the same source after 3weeks of continuous use of the circuit produced a mere overall 1ppm difference.

Estimation of Contextual Effects through Nonlinear Multilevel Latent Variable Modeling with a Metropolis-Hastings Robbins-Monro Algorithm

ERIC Educational Resources Information Center

Yang, Ji Seung; Cai, Li

2014-01-01

The main purpose of this study is to improve estimation efficiency in obtaining maximum marginal likelihood estimates of contextual effects in the framework of nonlinear multilevel latent variable model by adopting the Metropolis-Hastings Robbins-Monro algorithm (MH-RM). Results indicate that the MH-RM algorithm can produce estimates and standard…

Automatic delineation of tumor volumes by co-segmentation of combined PET/MR data

NASA Astrophysics Data System (ADS)

Leibfarth, S.; Eckert, F.; Welz, S.; Siegel, C.; Schmidt, H.; Schwenzer, N.; Zips, D.; Thorwarth, D.

2015-07-01

Combined PET/MRI may be highly beneficial for radiotherapy treatment planning in terms of tumor delineation and characterization. To standardize tumor volume delineation, an automatic algorithm for the co-segmentation of head and neck (HN) tumors based on PET/MR data was developed. Ten HN patient datasets acquired in a combined PET/MR system were available for this study. The proposed algorithm uses both the anatomical T2-weighted MR and FDG-PET data. For both imaging modalities tumor probability maps were derived, assigning each voxel a probability of being cancerous based on its signal intensity. A combination of these maps was subsequently segmented using a threshold level set algorithm. To validate the method, tumor delineations from three radiation oncologists were available. Inter-observer variabilities and variabilities between the algorithm and each observer were quantified by means of the Dice similarity index and a distance measure. Inter-observer variabilities and variabilities between observers and algorithm were found to be comparable, suggesting that the proposed algorithm is adequate for PET/MR co-segmentation. Moreover, taking into account combined PET/MR data resulted in more consistent tumor delineations compared to MR information only.

Firefly algorithm versus genetic algorithm as powerful variable selection tools and their effect on different multivariate calibration models in spectroscopy: A comparative study

NASA Astrophysics Data System (ADS)

Attia, Khalid A. M.; Nassar, Mohammed W. I.; El-Zeiny, Mohamed B.; Serag, Ahmed

2017-01-01

For the first time, a new variable selection method based on swarm intelligence namely firefly algorithm is coupled with three different multivariate calibration models namely, concentration residual augmented classical least squares, artificial neural network and support vector regression in UV spectral data. A comparative study between the firefly algorithm and the well-known genetic algorithm was developed. The discussion revealed the superiority of using this new powerful algorithm over the well-known genetic algorithm. Moreover, different statistical tests were performed and no significant differences were found between all the models regarding their predictabilities. This ensures that simpler and faster models were obtained without any deterioration of the quality of the calibration.

Space shuttle propulsion parameter estimation using optimal estimation techniques

NASA Technical Reports Server (NTRS)

1983-01-01

The first twelve system state variables are presented with the necessary mathematical developments for incorporating them into the filter/smoother algorithm. Other state variables, i.e., aerodynamic coefficients can be easily incorporated into the estimation algorithm, representing uncertain parameters, but for initial checkout purposes are treated as known quantities. An approach for incorporating the NASA propulsion predictive model results into the optimal estimation algorithm was identified. This approach utilizes numerical derivatives and nominal predictions within the algorithm with global iterations of the algorithm. The iterative process is terminated when the quality of the estimates provided no longer significantly improves.

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome

PubMed Central

Konkel, Miriam K.; Batzer, Mark A.

2010-01-01

It is now commonly agreed that the human genome is not the stable entity originally presumed. Deletions, duplications, inversions, and insertions are common, and contribute significantly to genomic structural variations (SVs). Their collective impact generates much of the inter-individual genomic diversity observed among humans. Not only do these variations change the structure of the genome; they may also have functional implications, e.g. altered gene expression. Some SVs have been identified as the cause of genetic disorders, including cancer predisposition. Cancer cells are notorious for their genomic instability, and often show genomic rearrangements at the microscopic and submicroscopic level to which transposable elements (TEs) contribute. Here, we review the role of TEs in genome instability, with particular focus on non-LTR retrotransposons. Currently, three non-LTR retrotransposon families – long interspersed element 1 (L1), SVA (short interspersed element (SINE-R), variable number of tandem repeats (VNTR), and Alu), and Alu (a SINE) elements – mobilize in the human genome, and cause genomic instability through both insertion- and post-insertion-based mutagenesis. Due to the abundance and high sequence identity of TEs, they frequently mislead the homologous recombination repair pathway into non-allelic homologous recombination, causing deletions, duplications, and inversions. While less comprehensively studied, non-LTR retrotransposon insertions and TE-mediated rearrangements are probably more common in cancer cells than in healthy tissue. This may be at least partially attributed to the commonly seen global hypomethylation as well as general epigenetic dysfunction of cancer cells. Where possible, we provide examples that impact cancer predisposition and/or development. PMID:20307669

Assessment of economic status in trauma registries: A new algorithm for generating population-specific clustering-based models of economic status for time-constrained low-resource settings.

PubMed

Eyler, Lauren; Hubbard, Alan; Juillard, Catherine

2016-10-01

Low and middle-income countries (LMICs) and the world's poor bear a disproportionate share of the global burden of injury. Data regarding disparities in injury are vital to inform injury prevention and trauma systems strengthening interventions targeted towards vulnerable populations, but are limited in LMICs. We aim to facilitate injury disparities research by generating a standardized methodology for assessing economic status in resource-limited country trauma registries where complex metrics such as income, expenditures, and wealth index are infeasible to assess. To address this need, we developed a cluster analysis-based algorithm for generating simple population-specific metrics of economic status using nationally representative Demographic and Health Surveys (DHS) household assets data. For a limited number of variables, g, our algorithm performs weighted k-medoids clustering of the population using all combinations of g asset variables and selects the combination of variables and number of clusters that maximize average silhouette width (ASW). In simulated datasets containing both randomly distributed variables and "true" population clusters defined by correlated categorical variables, the algorithm selected the correct variable combination and appropriate cluster numbers unless variable correlation was very weak. When used with 2011 Cameroonian DHS data, our algorithm identified twenty economic clusters with ASW 0.80, indicating well-defined population clusters. This economic model for assessing health disparities will be used in the new Cameroonian six-hospital centralized trauma registry. By describing our standardized methodology and algorithm for generating economic clustering models, we aim to facilitate measurement of health disparities in other trauma registries in resource-limited countries. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Doubling down on phosphorylation as a variable peptide modification.

PubMed

Cooper, Bret

2016-09-01

Some mass spectrometrists believe that searching for variable PTMs like phosphorylation of serine or threonine when using database-search algorithms to interpret peptide tandem mass spectra will increase false-positive matching. The basis for this is the premise that the algorithm compares a spectrum to both a nonphosphorylated peptide candidate and a phosphorylated candidate, which is double the number of candidates compared to a search with no possible phosphorylation. Hence, if the search space doubles, false-positive matching could increase accordingly as the algorithm considers more candidates to which false matches could be made. In this study, it is shown that the search for variable phosphoserine and phosphothreonine modifications does not always double the search space or unduly impinge upon the FDR. A breakdown of how one popular database-search algorithm deals with variable phosphorylation is presented. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Canonic FFT flow graphs for real-valued even/odd symmetric inputs

NASA Astrophysics Data System (ADS)

Lao, Yingjie; Parhi, Keshab K.

2017-12-01

Canonic real-valued fast Fourier transform (RFFT) has been proposed to reduce the arithmetic complexity by eliminating redundancies. In a canonic N-point RFFT, the number of signal values at each stage is canonic with respect to the number of signal values, i.e., N. The major advantage of the canonic RFFTs is that these require the least number of butterfly operations and only real datapaths when mapped to architectures. In this paper, we consider the FFT computation whose inputs are not only real but also even/odd symmetric, which indeed lead to the well-known discrete cosine and sine transforms (DCTs and DSTs). Novel algorithms for generating the flow graphs of canonic RFFTs with even/odd symmetric inputs are proposed. It is shown that the proposed algorithms lead to canonic structures with N/2 +1 signal values at each stage for an N-point real even symmetric FFT (REFFT) or N/2 -1 signal values at each stage for an N-point RFFT real odd symmetric FFT (ROFFT). In order to remove butterfly operations, several twiddle factor transformations are proposed in this paper. We also discuss the design of canonic REFFT for any composite length. Performances of the canonic REFFT/ROFFT are also discussed. It is shown that the flow graph of canonic REFFT/ROFFT has less number of interconnections, less butterfly operations, and less twiddle factor operations, compared to prior works.

Algorithms for Discovery of Multiple Markov Boundaries

PubMed Central

Statnikov, Alexander; Lytkin, Nikita I.; Lemeire, Jan; Aliferis, Constantin F.

2013-01-01

Algorithms for Markov boundary discovery from data constitute an important recent development in machine learning, primarily because they offer a principled solution to the variable/feature selection problem and give insight on local causal structure. Over the last decade many sound algorithms have been proposed to identify a single Markov boundary of the response variable. Even though faithful distributions and, more broadly, distributions that satisfy the intersection property always have a single Markov boundary, other distributions/data sets may have multiple Markov boundaries of the response variable. The latter distributions/data sets are common in practical data-analytic applications, and there are several reasons why it is important to induce multiple Markov boundaries from such data. However, there are currently no sound and efficient algorithms that can accomplish this task. This paper describes a family of algorithms TIE* that can discover all Markov boundaries in a distribution. The broad applicability as well as efficiency of the new algorithmic family is demonstrated in an extensive benchmarking study that involved comparison with 26 state-of-the-art algorithms/variants in 15 data sets from a diversity of application domains. PMID:25285052

Do bioclimate variables improve performance of climate envelope models?

USGS Publications Warehouse

Watling, James I.; Romañach, Stephanie S.; Bucklin, David N.; Speroterra, Carolina; Brandt, Laura A.; Pearlstine, Leonard G.; Mazzotti, Frank J.

2012-01-01

Climate envelope models are widely used to forecast potential effects of climate change on species distributions. A key issue in climate envelope modeling is the selection of predictor variables that most directly influence species. To determine whether model performance and spatial predictions were related to the selection of predictor variables, we compared models using bioclimate variables with models constructed from monthly climate data for twelve terrestrial vertebrate species in the southeastern USA using two different algorithms (random forests or generalized linear models), and two model selection techniques (using uncorrelated predictors or a subset of user-defined biologically relevant predictor variables). There were no differences in performance between models created with bioclimate or monthly variables, but one metric of model performance was significantly greater using the random forest algorithm compared with generalized linear models. Spatial predictions between maps using bioclimate and monthly variables were very consistent using the random forest algorithm with uncorrelated predictors, whereas we observed greater variability in predictions using generalized linear models.

Thrust stand evaluation of engine performance improvement algorithms in an F-15 airplane

NASA Technical Reports Server (NTRS)

Conners, Timothy R.

1992-01-01

Results are presented from the evaluation of the performance seeking control (PSC) optimization algorithm developed by Smith et al. (1990) for F-15 aircraft, which optimizes the quasi-steady-state performance of an F100 derivative turbofan engine for several modes of operation. The PSC algorithm uses onboard software engine model that calculates thrust, stall margin, and other unmeasured variables for use in the optimization. Comparisons are presented between the load cell measurements, PSC onboard model thrust calculations, and posttest state variable model computations. Actual performance improvements using the PSC algorithm are presented for its various modes. The results of using PSC algorithm are compared with similar test case results using the HIDEC algorithm.

Fast Solution in Sparse LDA for Binary Classification

NASA Technical Reports Server (NTRS)

Moghaddam, Baback

2010-01-01

An algorithm that performs sparse linear discriminant analysis (Sparse-LDA) finds near-optimal solutions in far less time than the prior art when specialized to binary classification (of 2 classes). Sparse-LDA is a type of feature- or variable- selection problem with numerous applications in statistics, machine learning, computer vision, computational finance, operations research, and bio-informatics. Because of its combinatorial nature, feature- or variable-selection problems are NP-hard or computationally intractable in cases involving more than 30 variables or features. Therefore, one typically seeks approximate solutions by means of greedy search algorithms. The prior Sparse-LDA algorithm was a greedy algorithm that considered the best variable or feature to add/ delete to/ from its subsets in order to maximally discriminate between multiple classes of data. The present algorithm is designed for the special but prevalent case of 2-class or binary classification (e.g. 1 vs. 0, functioning vs. malfunctioning, or change versus no change). The present algorithm provides near-optimal solutions on large real-world datasets having hundreds or even thousands of variables or features (e.g. selecting the fewest wavelength bands in a hyperspectral sensor to do terrain classification) and does so in typical computation times of minutes as compared to days or weeks as taken by the prior art. Sparse LDA requires solving generalized eigenvalue problems for a large number of variable subsets (represented by the submatrices of the input within-class and between-class covariance matrices). In the general (fullrank) case, the amount of computation scales at least cubically with the number of variables and thus the size of the problems that can be solved is limited accordingly. However, in binary classification, the principal eigenvalues can be found using a special analytic formula, without resorting to costly iterative techniques. The present algorithm exploits this analytic form along with the inherent sequential nature of greedy search itself. Together this enables the use of highly-efficient partitioned-matrix-inverse techniques that result in large speedups of computation in both the forward-selection and backward-elimination stages of greedy algorithms in general.

Criteria for representing circular arc and sine wave spar webs by non-curved elements

NASA Technical Reports Server (NTRS)

Jenkins, J. M.

1979-01-01

The basic problem of how to simply represent a curved web of a spar in a finite element structural model was addressed. The ratio of flat web to curved web axial deformations and longitudinal rotations were calculated using NASTRAN models. Multiplying factors were developed from these calculations for various web thicknesses. These multiplying factors can be applied directly to the area and moment of inertia inputs of the finite element model. This allows the thermal stress relieving configurations of sine wave and circular arc webs to be simply accounted for in finite element structural models.

A note on a boundary sine-Gordon model at the free-Fermion point

NASA Astrophysics Data System (ADS)

Murgan, Rajan

2018-02-01

We investigate the free-Fermion point of a boundary sine-Gordon model with nondiagonal boundary interactions for the ground state using auxiliary functions obtained from T  -  Q equations of a corresponding inhomogeneous open spin-\\frac{1}{2} XXZ chain with nondiagonal boundary terms. In particular, we obtain the Casimir energy. Our result for the Casimir energy is shown to agree with the result from the TBA approach. The analytical result for the effective central charge in the ultraviolet (UV) limit is also verified from the plots of effective central charge for intermediate values of volume.

Implementing the sine transform of fermionic modes as a tensor network

NASA Astrophysics Data System (ADS)

Epple, Hannes; Fries, Pascal; Hinrichsen, Haye

2017-09-01

Based on the algebraic theory of signal processing, we recursively decompose the discrete sine transform of the first kind (DST-I) into small orthogonal block operations. Using a diagrammatic language, we then second-quantize this decomposition to construct a tensor network implementing the DST-I for fermionic modes on a lattice. The complexity of the resulting network is shown to scale as 5/4 n logn (not considering swap gates), where n is the number of lattice sites. Our method provides a systematic approach of generalizing Ferris' spectral tensor network for nontrivial boundary conditions.

Multifluxon dynamics in driven Josephson junctions

NASA Astrophysics Data System (ADS)

Lawrence, Albert; Kim, Nung Soo; McDaniel, James; Jack, Michael

1985-06-01

The dynamics of fluxons in a long Josephson junction driven by time-varying nonuniform bias currents are described by a generalization of the sine-Gordon equation. This equation has solitary wave solutions which correspond to current vortices or quantized packets of magnetic flux in the junction. As with the sine-Gordon equation, multifluxon solutions may be demonstrated for the long Josephson junction. Our numerical calculations show that several fluxons may be launched or annihilated at the end of a junction. We also show multiple steady state conditions which correspond to one or more flux quanta trapped in the junction.

Retrobulbar optic neuritis and rhegmatogenous retinal detachment in a fourteen-year-old girl with retinitis pigmentosa sine pigmento.

PubMed

Hatta, M; Hayasaka, S; Kato, T; Kadoi, C

2000-01-01

A 14-year-old girl complained of a sudden decrease in right visual acuity. The patient had night blindness, a mottled retina but no pigments, extinguished scotopic electroretinographic response, central scotoma in the right eye and rhegmatogenous retinal detachment. She had initially received laser photocoagulation around the retinal tear and then corticosteroid therapy, cryoretinopexy and segmental buckling. Her right visual acuity increased to 1.0. The association of retinitis pigmentosa sine pigmento, retrobulbar optic neuritis and rhegmatogenous retinal detachment, as demonstrated in our patient, may be uncommon. Copyright 2000 S. Karger AG, Basel

High-Performance Psychometrics: The Parallel-E Parallel-M Algorithm for Generalized Latent Variable Models. Research Report. ETS RR-16-34

ERIC Educational Resources Information Center

von Davier, Matthias

2016-01-01

This report presents results on a parallel implementation of the expectation-maximization (EM) algorithm for multidimensional latent variable models. The developments presented here are based on code that parallelizes both the E step and the M step of the parallel-E parallel-M algorithm. Examples presented in this report include item response…

School Mathematics Study Group, Unit Number Two. Chapter 3 - Informal Algorithms and Flow Charts. Chapter 4 - Applications and Mathematics Models.

ERIC Educational Resources Information Center

Stanford Univ., CA. School Mathematics Study Group.

This is the second unit of a 15-unit School Mathematics Study Group (SMSG) mathematics text for high school students. Topics presented in the first chapter (Informal Algorithms and Flow Charts) include: changing a flat tire; algorithms, flow charts, and computers; assignment and variables; input and output; using a variable as a counter; decisions…

A parallel variable metric optimization algorithm

NASA Technical Reports Server (NTRS)

Straeter, T. A.

1973-01-01

An algorithm, designed to exploit the parallel computing or vector streaming (pipeline) capabilities of computers is presented. When p is the degree of parallelism, then one cycle of the parallel variable metric algorithm is defined as follows: first, the function and its gradient are computed in parallel at p different values of the independent variable; then the metric is modified by p rank-one corrections; and finally, a single univariant minimization is carried out in the Newton-like direction. Several properties of this algorithm are established. The convergence of the iterates to the solution is proved for a quadratic functional on a real separable Hilbert space. For a finite-dimensional space the convergence is in one cycle when p equals the dimension of the space. Results of numerical experiments indicate that the new algorithm will exploit parallel or pipeline computing capabilities to effect faster convergence than serial techniques.

Geostatistical uncertainty of assessing air quality using high-spatial-resolution lichen data: A health study in the urban area of Sines, Portugal.

PubMed

Ribeiro, Manuel C; Pinho, P; Branquinho, C; Llop, Esteve; Pereira, Maria J

2016-08-15

In most studies correlating health outcomes with air pollution, personal exposure assignments are based on measurements collected at air-quality monitoring stations not coinciding with health data locations. In such cases, interpolators are needed to predict air quality in unsampled locations and to assign personal exposures. Moreover, a measure of the spatial uncertainty of exposures should be incorporated, especially in urban areas where concentrations vary at short distances due to changes in land use and pollution intensity. These studies are limited by the lack of literature comparing exposure uncertainty derived from distinct spatial interpolators. Here, we addressed these issues with two interpolation methods: regression Kriging (RK) and ordinary Kriging (OK). These methods were used to generate air-quality simulations with a geostatistical algorithm. For each method, the geostatistical uncertainty was drawn from generalized linear model (GLM) analysis. We analyzed the association between air quality and birth weight. Personal health data (n=227) and exposure data were collected in Sines (Portugal) during 2007-2010. Because air-quality monitoring stations in the city do not offer high-spatial-resolution measurements (n=1), we used lichen data as an ecological indicator of air quality (n=83). We found no significant difference in the fit of GLMs with any of the geostatistical methods. With RK, however, the models tended to fit better more often and worse less often. Moreover, the geostatistical uncertainty results showed a marginally higher mean and precision with RK. Combined with lichen data and land-use data of high spatial resolution, RK is a more effective geostatistical method for relating health outcomes with air quality in urban areas. This is particularly important in small cities, which generally do not have expensive air-quality monitoring stations with high spatial resolution. Further, alternative ways of linking human activities with their environment are needed to improve human well-being. Copyright © 2016 Elsevier B.V. All rights reserved.

Firefly algorithm versus genetic algorithm as powerful variable selection tools and their effect on different multivariate calibration models in spectroscopy: A comparative study.

PubMed

Attia, Khalid A M; Nassar, Mohammed W I; El-Zeiny, Mohamed B; Serag, Ahmed

2017-01-05

For the first time, a new variable selection method based on swarm intelligence namely firefly algorithm is coupled with three different multivariate calibration models namely, concentration residual augmented classical least squares, artificial neural network and support vector regression in UV spectral data. A comparative study between the firefly algorithm and the well-known genetic algorithm was developed. The discussion revealed the superiority of using this new powerful algorithm over the well-known genetic algorithm. Moreover, different statistical tests were performed and no significant differences were found between all the models regarding their predictabilities. This ensures that simpler and faster models were obtained without any deterioration of the quality of the calibration. Copyright © 2016 Elsevier B.V. All rights reserved.

Technical Report Series on Global Modeling and Data Assimilation. Volume 12; Comparison of Satellite Global Rainfall Algorithms

NASA Technical Reports Server (NTRS)

Suarez, Max J. (Editor); Chang, Alfred T. C.; Chiu, Long S.

1997-01-01

Seventeen months of rainfall data (August 1987-December 1988) from nine satellite rainfall algorithms (Adler, Chang, Kummerow, Prabhakara, Huffman, Spencer, Susskind, and Wu) were analyzed to examine the uncertainty of satellite-derived rainfall estimates. The variability among algorithms, measured as the standard deviation computed from the ensemble of algorithms, shows regions of high algorithm variability tend to coincide with regions of high rain rates. Histograms of pattern correlation (PC) between algorithms suggest a bimodal distribution, with separation at a PC-value of about 0.85. Applying this threshold as a criteria for similarity, our analyses show that algorithms using the same sensor or satellite input tend to be similar, suggesting the dominance of sampling errors in these satellite estimates.

Aberrant methylation and associated transcriptional mobilization of Alu elements contributes to genomic instability in hypoxia.

PubMed

Pal, Arnab; Srivastava, Tapasya; Sharma, Manish K; Mehndiratta, Mohit; Das, Prerna; Sinha, Subrata; Chattopadhyay, Parthaprasad

2010-11-01

Hypoxia is an integral part of tumorigenesis and contributes extensively to the neoplastic phenotype including drug resistance and genomic instability. It has also been reported that hypoxia results in global demethylation. Because a majority of the cytosine-phosphate-guanine (CpG) islands are found within the repeat elements of DNA, and are usually methylated under normoxic conditions, we suggested that retrotransposable Alu or short interspersed nuclear elements (SINEs) which show altered methylation and associated changes of gene expression during hypoxia, could be associated with genomic instability. U87MG glioblastoma cells were cultured in 0.1% O₂ for 6 weeks and compared with cells cultured in 21% O₂ for the same duration. Real-time PCR analysis showed a significant increase in SINE and reverse transcriptase coding long interspersed nuclear element (LINE) transcripts during hypoxia. Sequencing of bisulphite treated DNA as well as the Combined Bisulfite Restriction Analysis (COBRA) assay showed that the SINE loci studied underwent significant hypomethylation though there was patchy hypermethylation at a few sites. The inter-alu PCR profile of DNA from cells cultured under 6-week hypoxia, its 4-week revert back to normoxia and 6-week normoxia showed several changes in the band pattern indicating increased alu mediated genomic alteration. Our results show that aberrant methylation leading to increased transcription of SINE and reverse transcriptase associated LINE elements could lead to increased genomic instability in hypoxia. This might be a cause of genetic heterogeneity in tumours especially in variegated hypoxic environment and lead to a development of foci of more aggressive tumour cells. © 2009 The Authors Journal compilation © 2010 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

Deterministic approach for multiple-source tsunami hazard assessment for Sines, Portugal

NASA Astrophysics Data System (ADS)

Wronna, M.; Omira, R.; Baptista, M. A.

2015-11-01

In this paper, we present a deterministic approach to tsunami hazard assessment for the city and harbour of Sines, Portugal, one of the test sites of project ASTARTE (Assessment, STrategy And Risk Reduction for Tsunamis in Europe). Sines has one of the most important deep-water ports, which has oil-bearing, petrochemical, liquid-bulk, coal, and container terminals. The port and its industrial infrastructures face 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, the tsunami hazard is described by maximum values of wave height, flow depth, drawback, maximum inundation area and run-up. Synthetic waveforms are computed at virtual tide gauges at specific locations outside and inside the harbour. The final results describe the impact at the 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 source of Horseshoe and Marques de Pombal faults as the worst-case scenario, with wave heights of over 10 m, which reach the coast approximately 22 min after the rupture. It dominates the aggregate scenario by about 60 % of the impact area at the test site, considering maximum wave height and maximum flow depth. The HSMPF scenario inundates a total area of 3.5 km2.

A Miniature Magnetic-Force-Based Three-Axis AC Magnetic Sensor with Piezoelectric/Vibrational Energy-Harvesting Functions.

PubMed

Hung, Chiao-Fang; Yeh, Po-Chen; Chung, Tien-Kan

2017-02-08

In this paper, we demonstrate a miniature magnetic-force-based, three-axis, AC magnetic sensor with piezoelectric/vibrational energy-harvesting functions. For magnetic sensing, the sensor employs a magnetic-mechanical-piezoelectric configuration (which uses magnetic force and torque, a compact, single, mechanical mechanism, and the piezoelectric effect) to convert x -axis and y -axis in-plane and z -axis magnetic fields into piezoelectric voltage outputs. Under the x -axis magnetic field (sine-wave, 100 Hz, 0.2-3.2 gauss) and the z -axis magnetic field (sine-wave, 142 Hz, 0.2-3.2 gauss), the voltage output with the sensitivity of the sensor are 1.13-26.15 mV with 8.79 mV/gauss and 1.31-8.92 mV with 2.63 mV/gauss, respectively. In addition, through this configuration, the sensor can harness ambient vibrational energy, i.e., possessing piezoelectric/vibrational energy-harvesting functions. Under x -axis vibration (sine-wave, 100 Hz, 3.5 g) and z -axis vibration (sine-wave, 142 Hz, 3.8 g), the root-mean-square voltage output with power output of the sensor is 439 mV with 0.333 μW and 138 mV with 0.051 μW, respectively. These results show that the sensor, using this configuration, successfully achieves three-axis magnetic field sensing and three-axis vibration energy-harvesting. Due to these features, the three-axis AC magnetic sensor could be an important design reference in order to develop future three-axis AC magnetic sensors, which possess energy-harvesting functions, for practical industrial applications, such as intelligent vehicle/traffic monitoring, processes monitoring, security systems, and so on.

A Miniature Magnetic-Force-Based Three-Axis AC Magnetic Sensor with Piezoelectric/Vibrational Energy-Harvesting Functions

PubMed Central

Hung, Chiao-Fang; Yeh, Po-Chen; Chung, Tien-Kan

2017-01-01

In this paper, we demonstrate a miniature magnetic-force-based, three-axis, AC magnetic sensor with piezoelectric/vibrational energy-harvesting functions. For magnetic sensing, the sensor employs a magnetic–mechanical–piezoelectric configuration (which uses magnetic force and torque, a compact, single, mechanical mechanism, and the piezoelectric effect) to convert x-axis and y-axis in-plane and z-axis magnetic fields into piezoelectric voltage outputs. Under the x-axis magnetic field (sine-wave, 100 Hz, 0.2–3.2 gauss) and the z-axis magnetic field (sine-wave, 142 Hz, 0.2–3.2 gauss), the voltage output with the sensitivity of the sensor are 1.13–26.15 mV with 8.79 mV/gauss and 1.31–8.92 mV with 2.63 mV/gauss, respectively. In addition, through this configuration, the sensor can harness ambient vibrational energy, i.e., possessing piezoelectric/vibrational energy-harvesting functions. Under x-axis vibration (sine-wave, 100 Hz, 3.5 g) and z-axis vibration (sine-wave, 142 Hz, 3.8 g), the root-mean-square voltage output with power output of the sensor is 439 mV with 0.333 μW and 138 mV with 0.051 μW, respectively. These results show that the sensor, using this configuration, successfully achieves three-axis magnetic field sensing and three-axis vibration energy-harvesting. Due to these features, the three-axis AC magnetic sensor could be an important design reference in order to develop future three-axis AC magnetic sensors, which possess energy-harvesting functions, for practical industrial applications, such as intelligent vehicle/traffic monitoring, processes monitoring, security systems, and so on. PMID:28208693

Large space structures control algorithm characterization

NASA Technical Reports Server (NTRS)

Fogel, E.

1983-01-01

Feedback control algorithms are developed for sensor/actuator pairs on large space systems. These algorithms have been sized in terms of (1) floating point operation (FLOP) demands; (2) storage for variables; and (3) input/output data flow. FLOP sizing (per control cycle) was done as a function of the number of control states and the number of sensor/actuator pairs. Storage for variables and I/O sizing was done for specific structure examples.

An efficient variable projection formulation for separable nonlinear least squares problems.

PubMed

Gan, Min; Li, Han-Xiong

2014-05-01

We consider in this paper a class of nonlinear least squares problems in which the model can be represented as a linear combination of nonlinear functions. The variable projection algorithm projects the linear parameters out of the problem, leaving the nonlinear least squares problems involving only the nonlinear parameters. To implement the variable projection algorithm more efficiently, we propose a new variable projection functional based on matrix decomposition. The advantage of the proposed formulation is that the size of the decomposed matrix may be much smaller than those of previous ones. The Levenberg-Marquardt algorithm using finite difference method is then applied to minimize the new criterion. Numerical results show that the proposed approach achieves significant reduction in computing time.

Assessing the Association Between Asthma and Air Quality in the Presence of Wildfires

NASA Technical Reports Server (NTRS)

Young, L. J.; Lopiano, K. K.; Xu, X.; Holt, N. M.; Leary, E.; Al-Hamdan, M. Z.; Crosson, W. L.; Estes, M. G.; Luvall, J. C.; Estes, S. M.;

Variable forgetting factor mechanisms for diffusion recursive least squares algorithm in sensor networks

NASA Astrophysics Data System (ADS)

Zhang, Ling; Cai, Yunlong; Li, Chunguang; de Lamare, Rodrigo C.

2017-12-01

In this work, we present low-complexity variable forgetting factor (VFF) techniques for diffusion recursive least squares (DRLS) algorithms. Particularly, we propose low-complexity VFF-DRLS algorithms for distributed parameter and spectrum estimation in sensor networks. For the proposed algorithms, they can adjust the forgetting factor automatically according to the posteriori error signal. We develop detailed analyses in terms of mean and mean square performance for the proposed algorithms and derive mathematical expressions for the mean square deviation (MSD) and the excess mean square error (EMSE). The simulation results show that the proposed low-complexity VFF-DRLS algorithms achieve superior performance to the existing DRLS algorithm with fixed forgetting factor when applied to scenarios of distributed parameter and spectrum estimation. Besides, the simulation results also demonstrate a good match for our proposed analytical expressions.

RB Particle Filter Time Synchronization Algorithm Based on the DPM Model.

PubMed

Guo, Chunsheng; Shen, Jia; Sun, Yao; Ying, Na

2015-09-03

Time synchronization is essential for node localization, target tracking, data fusion, and various other Wireless Sensor Network (WSN) applications. To improve the estimation accuracy of continuous clock offset and skew of mobile nodes in WSNs, we propose a novel time synchronization algorithm, the Rao-Blackwellised (RB) particle filter time synchronization algorithm based on the Dirichlet process mixture (DPM) model. In a state-space equation with a linear substructure, state variables are divided into linear and non-linear variables by the RB particle filter algorithm. These two variables can be estimated using Kalman filter and particle filter, respectively, which improves the computational efficiency more so than if only the particle filter was used. In addition, the DPM model is used to describe the distribution of non-deterministic delays and to automatically adjust the number of Gaussian mixture model components based on the observational data. This improves the estimation accuracy of clock offset and skew, which allows achieving the time synchronization. The time synchronization performance of this algorithm is also validated by computer simulations and experimental measurements. The results show that the proposed algorithm has a higher time synchronization precision than traditional time synchronization algorithms.

Chirp resonance spectroscopy of single lipid-coated microbubbles using an "acoustical camera".

PubMed

Renaud, G; Bosch, J G; van der Steen, A F W; de Jong, N

2012-12-01

An acoustical method was developed to study the resonance of single lipid-coated microbubbles. The response of 127 SonoVue microbubbles to a swept sine excitation between 0.5 and 5.5 MHz with a peak acoustic pressure amplitude of 70 kPa was measured by means of a 25 MHz probing wave. The relative amplitude modulation in the signal scattered in response to the probing wave is approximately equal to the radial strain induced by the swept sine excitation. An average damping coefficient of 0.33 and an average resonance frequency of 2.5 MHz were measured. Microbubbles experienced an average peak radial strain of 20%.

Sinusoidal transform coding

NASA Technical Reports Server (NTRS)

Mcaulay, Robert J.; Quatieri, Thomas F.

1988-01-01

It has been shown that an analysis/synthesis system based on a sinusoidal representation of speech leads to synthetic speech that is essentially perceptually indistinguishable from the original. Strategies for coding the amplitudes, frequencies and phases of the sine waves have been developed that have led to a multirate coder operating at rates from 2400 to 9600 bps. The encoded speech is highly intelligible at all rates with a uniformly improving quality as the data rate is increased. A real-time fixed-point implementation has been developed using two ADSP2100 DSP chips. The methods used for coding and quantizing the sine-wave parameters for operation at the various frame rates are described.

New optical solitons of space-time conformable fractional perturbed Gerdjikov-Ivanov equation by sine-Gordon equation method

NASA Astrophysics Data System (ADS)

Yaşar, Elif; Yıldırım, Yakup; Yaşar, Emrullah

2018-06-01

This paper devotes to conformable fractional space-time perturbed Gerdjikov-Ivanov (GI) equation which appears in nonlinear fiber optics and photonic crystal fibers (PCF). We consider the model with full nonlinearity in order to give a generalized flavor. The sine-Gordon equation approach is carried out to model equation for retrieving the dark, bright, dark-bright, singular and combined singular optical solitons. The constraint conditions are also reported for guaranteeing the existence of these solitons. We also present some graphical simulations of the solutions for better understanding the physical phenomena of the behind the considered model.

Fast measurement of proton exchange membrane fuel cell impedance based on pseudo-random binary sequence perturbation signals and continuous wavelet transform

NASA Astrophysics Data System (ADS)

Debenjak, Andrej; Boškoski, Pavle; Musizza, Bojan; Petrovčič, Janko; Juričić, Đani

2014-05-01

This paper proposes an approach to the estimation of PEM fuel cell impedance by utilizing pseudo-random binary sequence as a perturbation signal and continuous wavelet transform with Morlet mother wavelet. With the approach, the impedance characteristic in the frequency band from 0.1 Hz to 500 Hz is identified in 60 seconds, approximately five times faster compared to the conventional single-sine approach. The proposed approach was experimentally evaluated on a single PEM fuel cell of a larger fuel cell stack. The quality of the results remains at the same level compared to the single-sine approach.

Sine-Gordon solitonic scalar stars and black holes

NASA Astrophysics Data System (ADS)

Franzin, Edgardo; Cadoni, Mariano; Tuveri, Matteo

2018-06-01

We study exact, analytic, static, spherically symmetric, four-dimensional solutions of minimally coupled Einstein-scalar gravity, sourced by a scalar field whose profile has the form of the sine-Gordon soliton. We present a horizonless, everywhere regular and positive-mass solution—a solitonic star—and a black hole. The scalar potential behaves as a constant near the origin and vanishes at infinity. In particular, the solitonic scalar star interpolates between an anti-de Sitter and an asympototically flat spacetime. The black-hole spacetime is unstable against linear perturbations, while due to numerical issues, we were not able to determine with confidence whether or not the starlike background solution is stable.

Fast Boundary Element Method for acoustics with the Sparse Cardinal Sine Decomposition

NASA Astrophysics Data System (ADS)

Alouges, François; Aussal, Matthieu; Parolin, Emile

2017-07-01

This paper presents the newly proposed method Sparse Cardinal Sine Decomposition that allows fast convolution on unstructured grids. We focus on its use when coupled with finite element techniques to solve acoustic problems with the (compressed) Boundary Element Method. In addition, we also compare the computational performances of two equivalent Matlab® and Python implementations of the method. We show validation test cases in order to assess the precision of the approach. Eventually, the performance of the method is illustrated by the computation of the acoustic target strength of a realistic submarine from the Benchmark Target Strength Simulation international workshop.

Retinitis pigmentosa sine pigmenti. Debut with macular oedema.

PubMed

de la Mata Pérez, G; Ruiz-Moreno, O; Fernández-Pérez, S; Torrón Fernández-Blanco, C; Pablo-Júlvez, L

2014-09-01

A 25-year-old woman, with metamorphopsia in her left eye of one year onset. The examination revealed a bilateral cystoid macular oedema (CME) and vascular attenuation. We describe the diagnostic tests, as well as differential diagnosis and treatment response with carbonic anhydrase inhibitors. The retinitis pigmentosa sine pigment is a subtype of atypical retinitis pigmentosa characterised by the absence of pigment deposits. The night blindness is milder, and perimetric and electroretinographic impairment is lower. CME is an important cause of central vision loss, and responds to anhydrase carbonic inhibitors. Copyright © 2012 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

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.

A smoothing algorithm using cubic spline functions

NASA Technical Reports Server (NTRS)

Smith, R. E., Jr.; Price, J. M.; Howser, L. M.

1974-01-01

Two algorithms are presented for smoothing arbitrary sets of data. They are the explicit variable algorithm and the parametric variable algorithm. The former would be used where large gradients are not encountered because of the smaller amount of calculation required. The latter would be used if the data being smoothed were double valued or experienced large gradients. Both algorithms use a least-squares technique to obtain a cubic spline fit to the data. The advantage of the spline fit is that the first and second derivatives are continuous. This method is best used in an interactive graphics environment so that the junction values for the spline curve can be manipulated to improve the fit.

AUTOCLASSIFICATION OF THE VARIABLE 3XMM SOURCES USING THE RANDOM FOREST MACHINE LEARNING ALGORITHM

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

Farrell, Sean A.; Murphy, Tara; Lo, Kitty K., E-mail: s.farrell@physics.usyd.edu.au

In the current era of large surveys and massive data sets, autoclassification of astrophysical sources using intelligent algorithms is becoming increasingly important. In this paper we present the catalog of variable sources in the Third XMM-Newton Serendipitous Source catalog (3XMM) autoclassified using the Random Forest machine learning algorithm. We used a sample of manually classified variable sources from the second data release of the XMM-Newton catalogs (2XMMi-DR2) to train the classifier, obtaining an accuracy of ∼92%. We also evaluated the effectiveness of identifying spurious detections using a sample of spurious sources, achieving an accuracy of ∼95%. Manual investigation of amore » random sample of classified sources confirmed these accuracy levels and showed that the Random Forest machine learning algorithm is highly effective at automatically classifying 3XMM sources. Here we present the catalog of classified 3XMM variable sources. We also present three previously unidentified unusual sources that were flagged as outlier sources by the algorithm: a new candidate supergiant fast X-ray transient, a 400 s X-ray pulsar, and an eclipsing 5 hr binary system coincident with a known Cepheid.« less

ALGORITHM TO REDUCE APPROXIMATION ERROR FROM THE COMPLEX-VARIABLE BOUNDARY-ELEMENT METHOD APPLIED TO SOIL FREEZING.

USGS Publications Warehouse

Hromadka, T.V.; Guymon, G.L.

1985-01-01

An algorithm is presented for the numerical solution of the Laplace equation boundary-value problem, which is assumed to apply to soil freezing or thawing. The Laplace equation is numerically approximated by the complex-variable boundary-element method. The algorithm aids in reducing integrated relative error by providing a true measure of modeling error along the solution domain boundary. This measure of error can be used to select locations for adding, removing, or relocating nodal points on the boundary or to provide bounds for the integrated relative error of unknown nodal variable values along the boundary.

Heavy metals in Parmelia sulcata collected in the neighborhood of a coal-fired power station.

PubMed

Freitas, M C

1994-01-01

The epiphytic lichen Parmelia sulcata was collected in the neighborhood of a Portuguese coal-fired power station (Sines coal power station) as monitor for heavy metal air pollution. A study of the metal contents variability along 1991 and 1992 was performed. The heavy metals Ag, As, Br, Co, Cr, Fe, Hg, Sb, Se, and Zn were determined by k0-based instrumental neutron activation analysis. The concentrations found in 1991 and 1992 show an accumulating process of Co and Fe (approximately 5%/mo) and of Cr and Sb (approximately 7%/mo). Low accumulation is observed for Ag, Se, and Zn (approximately 2%/mo), and no concentration variation is observed for As, Br, and Hg. It is concluded that the metal accumulation observed is the result of the nearby ash and coal deposits.

A family of variable step-size affine projection adaptive filter algorithms using statistics of channel impulse response

NASA Astrophysics Data System (ADS)

Shams Esfand Abadi, Mohammad; AbbasZadeh Arani, Seyed Ali Asghar

2011-12-01

This paper extends the recently introduced variable step-size (VSS) approach to the family of adaptive filter algorithms. This method uses prior knowledge of the channel impulse response statistic. Accordingly, optimal step-size vector is obtained by minimizing the mean-square deviation (MSD). The presented algorithms are the VSS affine projection algorithm (VSS-APA), the VSS selective partial update NLMS (VSS-SPU-NLMS), the VSS-SPU-APA, and the VSS selective regressor APA (VSS-SR-APA). In VSS-SPU adaptive algorithms the filter coefficients are partially updated which reduce the computational complexity. In VSS-SR-APA, the optimal selection of input regressors is performed during the adaptation. The presented algorithms have good convergence speed, low steady state mean square error (MSE), and low computational complexity features. We demonstrate the good performance of the proposed algorithms through several simulations in system identification scenario.

Learning Instance-Specific Predictive Models

PubMed Central

Visweswaran, Shyam; Cooper, Gregory F.

2013-01-01

This paper introduces a Bayesian algorithm for constructing predictive models from data that are optimized to predict a target variable well for a particular instance. This algorithm learns Markov blanket models, carries out Bayesian model averaging over a set of models to predict a target variable of the instance at hand, and employs an instance-specific heuristic to locate a set of suitable models to average over. We call this method the instance-specific Markov blanket (ISMB) algorithm. The ISMB algorithm was evaluated on 21 UCI data sets using five different performance measures and its performance was compared to that of several commonly used predictive algorithms, including nave Bayes, C4.5 decision tree, logistic regression, neural networks, k-Nearest Neighbor, Lazy Bayesian Rules, and AdaBoost. Over all the data sets, the ISMB algorithm performed better on average on all performance measures against all the comparison algorithms. PMID:25045325

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome.

PubMed

Konkel, Miriam K; Batzer, Mark A

2010-08-01

It is now commonly agreed that the human genome is not the stable entity originally presumed. Deletions, duplications, inversions, and insertions are common, and contribute significantly to genomic structural variations (SVs). Their collective impact generates much of the inter-individual genomic diversity observed among humans. Not only do these variations change the structure of the genome; they may also have functional implications, e.g. altered gene expression. Some SVs have been identified as the cause of genetic disorders, including cancer predisposition. Cancer cells are notorious for their genomic instability, and often show genomic rearrangements at the microscopic and submicroscopic level to which transposable elements (TEs) contribute. Here, we review the role of TEs in genome instability, with particular focus on non-LTR retrotransposons. Currently, three non-LTR retrotransposon families - long interspersed element 1 (L1), SVA (short interspersed element (SINE-R), variable number of tandem repeats (VNTR), and Alu), and Alu (a SINE) elements - mobilize in the human genome, and cause genomic instability through both insertion- and post-insertion-based mutagenesis. Due to the abundance and high sequence identity of TEs, they frequently mislead the homologous recombination repair pathway into non-allelic homologous recombination, causing deletions, duplications, and inversions. While less comprehensively studied, non-LTR retrotransposon insertions and TE-mediated rearrangements are probably more common in cancer cells than in healthy tissue. This may be at least partially attributed to the commonly seen global hypomethylation as well as general epigenetic dysfunction of cancer cells. Where possible, we provide examples that impact cancer predisposition and/or development. Copyright © 2010 Elsevier Ltd. All rights reserved.

Determination of colonoscopy indication from administrative claims data.

PubMed

Ko, Cynthia W; Dominitz, Jason A; Neradilek, Moni; Polissar, Nayak; Green, Pam; Kreuter, William; Baldwin, Laura-Mae

2014-04-01

Colonoscopy outcomes, such as polyp detection or complication rates, may differ by procedure indication. To develop methods to classify colonoscopy indications from administrative data, facilitating study of colonoscopy quality and outcomes. We linked 14,844 colonoscopy reports from the Clinical Outcomes Research Initiative, a national repository of endoscopic reports, to the corresponding Medicare Carrier and Outpatient File claims. Colonoscopy indication was determined from the procedure reports. We developed algorithms using classification and regression trees and linear discriminant analysis (LDA) to classify colonoscopy indication. Predictor variables included ICD-9CM and CPT/HCPCS codes present on the colonoscopy claim or in the 12 months prior, patient demographics, and site of colonoscopy service. Algorithms were developed on a training set of 7515 procedures, then validated using a test set of 7329 procedures. Sensitivity was lowest for identifying average-risk screening colonoscopies, varying between 55% and 86% for the different algorithms, but specificity for this indication was consistently over 95%. Sensitivity for diagnostic colonoscopy varied between 77% and 89%, with specificity between 55% and 87%. Algorithms with classification and regression trees with 7 variables or LDA with 10 variables had similar overall accuracy, and generally lower accuracy than the algorithm using LDA with 30 variables. Algorithms using Medicare claims data have moderate sensitivity and specificity for colonoscopy indication, and will be useful for studying colonoscopy quality in this population. Further validation may be needed before use in alternative populations.

PCA-LBG-based algorithms for VQ codebook generation

NASA Astrophysics Data System (ADS)

Tsai, Jinn-Tsong; Yang, Po-Yuan

2015-04-01

Vector quantisation (VQ) codebooks are generated by combining principal component analysis (PCA) algorithms with Linde-Buzo-Gray (LBG) algorithms. All training vectors are grouped according to the projected values of the principal components. The PCA-LBG-based algorithms include (1) PCA-LBG-Median, which selects the median vector of each group, (2) PCA-LBG-Centroid, which adopts the centroid vector of each group, and (3) PCA-LBG-Random, which randomly selects a vector of each group. The LBG algorithm finds a codebook based on the better vectors sent to an initial codebook by the PCA. The PCA performs an orthogonal transformation to convert a set of potentially correlated variables into a set of variables that are not linearly correlated. Because the orthogonal transformation efficiently distinguishes test image vectors, the proposed PCA-LBG-based algorithm is expected to outperform conventional algorithms in designing VQ codebooks. The experimental results confirm that the proposed PCA-LBG-based algorithms indeed obtain better results compared to existing methods reported in the literature.

A new hybrid meta-heuristic algorithm for optimal design of large-scale dome structures

NASA Astrophysics Data System (ADS)

Kaveh, A.; Ilchi Ghazaan, M.

2018-02-01

In this article a hybrid algorithm based on a vibrating particles system (VPS) algorithm, multi-design variable configuration (Multi-DVC) cascade optimization, and an upper bound strategy (UBS) is presented for global optimization of large-scale dome truss structures. The new algorithm is called MDVC-UVPS in which the VPS algorithm acts as the main engine of the algorithm. The VPS algorithm is one of the most recent multi-agent meta-heuristic algorithms mimicking the mechanisms of damped free vibration of single degree of freedom systems. In order to handle a large number of variables, cascade sizing optimization utilizing a series of DVCs is used. Moreover, the UBS is utilized to reduce the computational time. Various dome truss examples are studied to demonstrate the effectiveness and robustness of the proposed method, as compared to some existing structural optimization techniques. The results indicate that the MDVC-UVPS technique is a powerful search and optimization method for optimizing structural engineering problems.

Frequency-domain-independent vector analysis for mode-division multiplexed transmission

NASA Astrophysics Data System (ADS)

Liu, Yunhe; Hu, Guijun; Li, Jiao

2018-04-01

In this paper, we propose a demultiplexing method based on frequency-domain independent vector analysis (FD-IVA) algorithm for mode-division multiplexing (MDM) system. FD-IVA extends frequency-domain independent component analysis (FD-ICA) from unitary variable to multivariate variables, and provides an efficient method to eliminate the permutation ambiguity. In order to verify the performance of FD-IVA algorithm, a 6 ×6 MDM system is simulated. The simulation results show that the FD-IVA algorithm has basically the same bit-error-rate(BER) performance with the FD-ICA algorithm and frequency-domain least mean squares (FD-LMS) algorithm. Meanwhile, the convergence speed of FD-IVA algorithm is the same as that of FD-ICA. However, compared with the FD-ICA and the FD-LMS, the FD-IVA has an obviously lower computational complexity.

The use of the multi-cumulant tensor analysis for the algorithmic optimisation of investment portfolios

NASA Astrophysics Data System (ADS)

Domino, Krzysztof

2017-02-01

The cumulant analysis plays an important role in non Gaussian distributed data analysis. The shares' prices returns are good example of such data. The purpose of this research is to develop the cumulant based algorithm and use it to determine eigenvectors that represent investment portfolios with low variability. Such algorithm is based on the Alternating Least Square method and involves the simultaneous minimisation 2'nd- 6'th cumulants of the multidimensional random variable (percentage shares' returns of many companies). Then the algorithm was tested during the recent crash on the Warsaw Stock Exchange. To determine incoming crash and provide enter and exit signal for the investment strategy the Hurst exponent was calculated using the local DFA. It was shown that introduced algorithm is on average better that benchmark and other portfolio determination methods, but only within examination window determined by low values of the Hurst exponent. Remark that the algorithm is based on cumulant tensors up to the 6'th order calculated for a multidimensional random variable, what is the novel idea. It can be expected that the algorithm would be useful in the financial data analysis on the world wide scale as well as in the analysis of other types of non Gaussian distributed data.

MLP based models to predict PM10, O3 concentrations, in Sines industrial area

NASA Astrophysics Data System (ADS)

Durao, R.; Pereira, M. J.

2012-04-01

Sines is an important Portuguese industrial area located southwest cost of Portugal with important nearby protected natural areas. The main economical activities are related with this industrial area, the deep-water port, petrochemical and thermo-electric industry. Nevertheless, tourism is also an important economic activity especially in summer time with potential to grow. The aim of this study is to develop prediction models of pollutant concentration categories (e.g. low concentration and high concentration) in order to provide early warnings to the competent authorities who are responsible for the air quality management. The knowledge in advanced of pollutant high concentrations occurrence will allow the implementation of mitigation actions and the release of precautionary alerts to population. The regional air quality monitoring network consists in three monitoring stations where a set of pollutants' concentrations are registered on a continuous basis. From this set stands out the tropospheric ozone (O3) and particulate matter (PM10) due to the high concentrations occurring in the region and their adverse effects on human health. Moreover, the major industrial plants of the region monitor SO2, NO2 and particles emitted flows at the principal chimneys (point sources), also on a continuous basis,. Therefore Artificial neuronal networks (ANN) were the applied methodology to predict next day pollutant concentrations; due to the ANNs structure they have the ability to capture the non-linear relationships between predictor variables. Hence the first step of this study was to apply multivariate exploratory techniques to select the best predictor variables. The classification trees methodology (CART) was revealed to be the most appropriate in this case.. Results shown that pollutants atmospheric concentrations are mainly dependent on industrial emissions and a complex combination of meteorological factors and the time of the year. In the second step, the Multi-layer perceptron (MLP) have shown to be able to learn the existent complex relationships using different combination of meteorological and emissions variables. Furthermore, MLP models identified what are the meteorological conditions that most affect O3 and PM10 concentrations in the region, namely wind speed and direction, boundary layer height, temperature, sunshine duration, relative humidity and the weather type. The developed MLP models showed good predictive success with model performances between 0.66 and 0.87, indicating a reasonable accuracy for models development and generalization capability. These performance values are obtained using cross entropy error functions. This error functions are only available for classification problems and ensure that the network outputs are true class membership probabilities, which is known to enhance the performance of classification neural networks.

Bio-inspired online variable recruitment control of fluidic artificial muscles

NASA Astrophysics Data System (ADS)

Jenkins, Tyler E.; Chapman, Edward M.; Bryant, Matthew

2016-12-01

This paper details the creation of a hybrid variable recruitment control scheme for fluidic artificial muscle (FAM) actuators with an emphasis on maximizing system efficiency and switching control performance. Variable recruitment is the process of altering a system’s active number of actuators, allowing operation in distinct force regimes. Previously, FAM variable recruitment was only quantified with offline, manual valve switching; this study addresses the creation and characterization of novel, on-line FAM switching control algorithms. The bio-inspired algorithms are implemented in conjunction with a PID and model-based controller, and applied to a simulated plant model. Variable recruitment transition effects and chatter rejection are explored via a sensitivity analysis, allowing a system designer to weigh tradeoffs in actuator modeling, algorithm choice, and necessary hardware. Variable recruitment is further developed through simulation of a robotic arm tracking a variety of spline position inputs, requiring several levels of actuator recruitment. Switching controller performance is quantified and compared with baseline systems lacking variable recruitment. The work extends current variable recruitment knowledge by creating novel online variable recruitment control schemes, and exploring how online actuator recruitment affects system efficiency and control performance. Key topics associated with implementing a variable recruitment scheme, including the effects of modeling inaccuracies, hardware considerations, and switching transition concerns are also addressed.

Ventricular repolarization variability for hypoglycemia detection.

PubMed

Ling, Steve; Nguyen, H T

2011-01-01

Hypoglycemia is the most acute and common complication of Type 1 diabetes and is a limiting factor in a glycemic management of diabetes. In this paper, two main contributions are presented; firstly, ventricular repolarization variabilities are introduced for hypoglycemia detection, and secondly, a swarm-based support vector machine (SVM) algorithm with the inputs of the repolarization variabilities is developed to detect hypoglycemia. By using the algorithm and including several repolarization variabilities as inputs, the best hypoglycemia detection performance is found with sensitivity and specificity of 82.14% and 60.19%, respectively.

Parameterization of typhoon-induced ocean cooling using temperature equation and machine learning algorithms: an example of typhoon Soulik (2013)

NASA Astrophysics Data System (ADS)

Wei, Jun; Jiang, Guo-Qing; Liu, Xin

2017-09-01

This study proposed three algorithms that can potentially be used to provide sea surface temperature (SST) conditions for typhoon prediction models. Different from traditional data assimilation approaches, which provide prescribed initial/boundary conditions, our proposed algorithms aim to resolve a flow-dependent SST feedback between growing typhoons and oceans in the future time. Two of these algorithms are based on linear temperature equations (TE-based), and the other is based on an innovative technique involving machine learning (ML-based). The algorithms are then implemented into a Weather Research and Forecasting model for the simulation of typhoon to assess their effectiveness, and the results show significant improvement in simulated storm intensities by including ocean cooling feedback. The TE-based algorithm I considers wind-induced ocean vertical mixing and upwelling processes only, and thus obtained a synoptic and relatively smooth sea surface temperature cooling. The TE-based algorithm II incorporates not only typhoon winds but also ocean information, and thus resolves more cooling features. The ML-based algorithm is based on a neural network, consisting of multiple layers of input variables and neurons, and produces the best estimate of the cooling structure, in terms of its amplitude and position. Sensitivity analysis indicated that the typhoon-induced ocean cooling is a nonlinear process involving interactions of multiple atmospheric and oceanic variables. Therefore, with an appropriate selection of input variables and neuron sizes, the ML-based algorithm appears to be more efficient in prognosing the typhoon-induced ocean cooling and in predicting typhoon intensity than those algorithms based on linear regression methods.

A non-linear data mining parameter selection algorithm for continuous variables

PubMed Central

Razavi, Marianne; Brady, Sean

2017-01-01

In this article, we propose a new data mining algorithm, by which one can both capture the non-linearity in data and also find the best subset model. To produce an enhanced subset of the original variables, a preferred selection method should have the potential of adding a supplementary level of regression analysis that would capture complex relationships in the data via mathematical transformation of the predictors and exploration of synergistic effects of combined variables. The method that we present here has the potential to produce an optimal subset of variables, rendering the overall process of model selection more efficient. This algorithm introduces interpretable parameters by transforming the original inputs and also a faithful fit to the data. The core objective of this paper is to introduce a new estimation technique for the classical least square regression framework. This new automatic variable transformation and model selection method could offer an optimal and stable model that minimizes the mean square error and variability, while combining all possible subset selection methodology with the inclusion variable transformations and interactions. Moreover, this method controls multicollinearity, leading to an optimal set of explanatory variables. PMID:29131829

An enhanced sine dwell method as applied to the Galileo core structure modal survey

NASA Technical Reports Server (NTRS)

Smith, Kenneth S.; Trubert, Marc

1990-01-01

An incremental modal survey performed in 1988 on the core structure of the Galileo spacecraft with its adapters with the purpose of assessing the dynamics of the new portions of the structure is considered. Emphasis is placed on the enhancements of the sine dwell method employed in the test. For each mode, response data is acquired at 32 frequencies in a narrow band enclosing the resonance, utilizing the SWIFT technique. It is pointed out that due to the simplicity of the data processing involved, the diagnostic and modal-parameter data is available within several minutes after data acquisition; however, compared with straight curve-fitting approaches, the method requires more time for data acquisition.

Experimental study of isolas in nonlinear systems featuring modal interactions

PubMed Central

Noël, Jean-Philippe; Virgin, Lawrence N.; Kerschen, Gaëtan

2018-01-01

The objective of the present paper is to provide experimental evidence of isolated resonances in the frequency response of nonlinear mechanical systems. More specifically, this work explores the presence of isolas, which are periodic solutions detached from the main frequency response, in the case of a nonlinear set-up consisting of two masses sliding on a horizontal guide. A careful experimental investigation of isolas is carried out using responses to swept-sine and stepped-sine excitations. The experimental findings are validated with advanced numerical simulations combining nonlinear modal analysis and bifurcation monitoring. In particular, the interactions between two nonlinear normal modes are shown to be responsible for the creation of the isolas. PMID:29584758

Data-driven process decomposition and robust online distributed modelling for large-scale processes

NASA Astrophysics Data System (ADS)

Shu, Zhang; Lijuan, Li; Lijuan, Yao; Shipin, Yang; Tao, Zou

2018-02-01

With the increasing attention of networked control, system decomposition and distributed models show significant importance in the implementation of model-based control strategy. In this paper, a data-driven system decomposition and online distributed subsystem modelling algorithm was proposed for large-scale chemical processes. The key controlled variables are first partitioned by affinity propagation clustering algorithm into several clusters. Each cluster can be regarded as a subsystem. Then the inputs of each subsystem are selected by offline canonical correlation analysis between all process variables and its controlled variables. Process decomposition is then realised after the screening of input and output variables. When the system decomposition is finished, the online subsystem modelling can be carried out by recursively block-wise renewing the samples. The proposed algorithm was applied in the Tennessee Eastman process and the validity was verified.

Variable screening via quantile partial correlation

PubMed Central

Ma, Shujie; Tsai, Chih-Ling

2016-01-01

In quantile linear regression with ultra-high dimensional data, we propose an algorithm for screening all candidate variables and subsequently selecting relevant predictors. Specifically, we first employ quantile partial correlation for screening, and then we apply the extended Bayesian information criterion (EBIC) for best subset selection. Our proposed method can successfully select predictors when the variables are highly correlated, and it can also identify variables that make a contribution to the conditional quantiles but are marginally uncorrelated or weakly correlated with the response. Theoretical results show that the proposed algorithm can yield the sure screening set. By controlling the false selection rate, model selection consistency can be achieved theoretically. In practice, we proposed using EBIC for best subset selection so that the resulting model is screening consistent. Simulation studies demonstrate that the proposed algorithm performs well, and an empirical example is presented. PMID:28943683

Fast parallel MR image reconstruction via B1-based, adaptive restart, iterative soft thresholding algorithms (BARISTA).

PubMed

Muckley, Matthew J; Noll, Douglas C; Fessler, Jeffrey A

2015-02-01

Sparsity-promoting regularization is useful for combining compressed sensing assumptions with parallel MRI for reducing scan time while preserving image quality. Variable splitting algorithms are the current state-of-the-art algorithms for SENSE-type MR image reconstruction with sparsity-promoting regularization. These methods are very general and have been observed to work with almost any regularizer; however, the tuning of associated convergence parameters is a commonly-cited hindrance in their adoption. Conversely, majorize-minimize algorithms based on a single Lipschitz constant have been observed to be slow in shift-variant applications such as SENSE-type MR image reconstruction since the associated Lipschitz constants are loose bounds for the shift-variant behavior. This paper bridges the gap between the Lipschitz constant and the shift-variant aspects of SENSE-type MR imaging by introducing majorizing matrices in the range of the regularizer matrix. The proposed majorize-minimize methods (called BARISTA) converge faster than state-of-the-art variable splitting algorithms when combined with momentum acceleration and adaptive momentum restarting. Furthermore, the tuning parameters associated with the proposed methods are unitless convergence tolerances that are easier to choose than the constraint penalty parameters required by variable splitting algorithms.

Fast Parallel MR Image Reconstruction via B1-based, Adaptive Restart, Iterative Soft Thresholding Algorithms (BARISTA)

PubMed Central

Noll, Douglas C.; Fessler, Jeffrey A.

2014-01-01

Sparsity-promoting regularization is useful for combining compressed sensing assumptions with parallel MRI for reducing scan time while preserving image quality. Variable splitting algorithms are the current state-of-the-art algorithms for SENSE-type MR image reconstruction with sparsity-promoting regularization. These methods are very general and have been observed to work with almost any regularizer; however, the tuning of associated convergence parameters is a commonly-cited hindrance in their adoption. Conversely, majorize-minimize algorithms based on a single Lipschitz constant have been observed to be slow in shift-variant applications such as SENSE-type MR image reconstruction since the associated Lipschitz constants are loose bounds for the shift-variant behavior. This paper bridges the gap between the Lipschitz constant and the shift-variant aspects of SENSE-type MR imaging by introducing majorizing matrices in the range of the regularizer matrix. The proposed majorize-minimize methods (called BARISTA) converge faster than state-of-the-art variable splitting algorithms when combined with momentum acceleration and adaptive momentum restarting. Furthermore, the tuning parameters associated with the proposed methods are unitless convergence tolerances that are easier to choose than the constraint penalty parameters required by variable splitting algorithms. PMID:25330484

Electronic Thermometer Readings

NASA Technical Reports Server (NTRS)

2001-01-01

NASA Stennis' adaptive predictive algorithm for electronic thermometers uses sample readings during the initial rise in temperature and applies an algorithm that accurately and rapidly predicts the steady state temperature. The final steady state temperature of an object can be calculated based on the second-order logarithm of the temperature signals acquired by the sensor and predetermined variables from the sensor characteristics. These variables are calculated during tests of the sensor. Once the variables are determined, relatively little data acquisition and data processing time by the algorithm is required to provide a near-accurate approximation of the final temperature. This reduces the delay in the steady state response time of a temperature sensor. This advanced algorithm can be implemented in existing software or hardware with an erasable programmable read-only memory (EPROM). The capability for easy integration eliminates the expense of developing a whole new system that offers the benefits provided by NASA Stennis' technology.

Identification of Genes Involved in Breast Cancer Metastasis by Integrating Protein-Protein Interaction Information with Expression Data.

PubMed

Tian, Xin; Xin, Mingyuan; Luo, Jian; Liu, Mingyao; Jiang, Zhenran

2017-02-01

The selection of relevant genes for breast cancer metastasis is critical for the treatment and prognosis of cancer patients. Although much effort has been devoted to the gene selection procedures by use of different statistical analysis methods or computational techniques, the interpretation of the variables in the resulting survival models has been limited so far. This article proposes a new Random Forest (RF)-based algorithm to identify important variables highly related with breast cancer metastasis, which is based on the important scores of two variable selection algorithms, including the mean decrease Gini (MDG) criteria of Random Forest and the GeneRank algorithm with protein-protein interaction (PPI) information. The new gene selection algorithm can be called PPIRF. The improved prediction accuracy fully illustrated the reliability and high interpretability of gene list selected by the PPIRF approach.

On Some Separated Algorithms for Separable Nonlinear Least Squares Problems.

PubMed

Gan, Min; Chen, C L Philip; Chen, Guang-Yong; Chen, Long

2017-10-03

For a class of nonlinear least squares problems, it is usually very beneficial to separate the variables into a linear and a nonlinear part and take full advantage of reliable linear least squares techniques. Consequently, the original problem is turned into a reduced problem which involves only nonlinear parameters. We consider in this paper four separated algorithms for such problems. The first one is the variable projection (VP) algorithm with full Jacobian matrix of Golub and Pereyra. The second and third ones are VP algorithms with simplified Jacobian matrices proposed by Kaufman and Ruano et al. respectively. The fourth one only uses the gradient of the reduced problem. Monte Carlo experiments are conducted to compare the performance of these four algorithms. From the results of the experiments, we find that: 1) the simplified Jacobian proposed by Ruano et al. is not a good choice for the VP algorithm; moreover, it may render the algorithm hard to converge; 2) the fourth algorithm perform moderately among these four algorithms; 3) the VP algorithm with the full Jacobian matrix perform more stable than that of the VP algorithm with Kuafman's simplified one; and 4) the combination of VP algorithm and Levenberg-Marquardt method is more effective than the combination of VP algorithm and Gauss-Newton method.

Empirical study of seven data mining algorithms on different characteristics of datasets for biomedical classification applications.

PubMed

Zhang, Yiyan; Xin, Yi; Li, Qin; Ma, Jianshe; Li, Shuai; Lv, Xiaodan; Lv, Weiqi

2017-11-02

Various kinds of data mining algorithms are continuously raised with the development of related disciplines. The applicable scopes and their performances of these algorithms are different. Hence, finding a suitable algorithm for a dataset is becoming an important emphasis for biomedical researchers to solve practical problems promptly. In this paper, seven kinds of sophisticated active algorithms, namely, C4.5, support vector machine, AdaBoost, k-nearest neighbor, naïve Bayes, random forest, and logistic regression, were selected as the research objects. The seven algorithms were applied to the 12 top-click UCI public datasets with the task of classification, and their performances were compared through induction and analysis. The sample size, number of attributes, number of missing values, and the sample size of each class, correlation coefficients between variables, class entropy of task variable, and the ratio of the sample size of the largest class to the least class were calculated to character the 12 research datasets. The two ensemble algorithms reach high accuracy of classification on most datasets. Moreover, random forest performs better than AdaBoost on the unbalanced dataset of the multi-class task. Simple algorithms, such as the naïve Bayes and logistic regression model are suitable for a small dataset with high correlation between the task and other non-task attribute variables. K-nearest neighbor and C4.5 decision tree algorithms perform well on binary- and multi-class task datasets. Support vector machine is more adept on the balanced small dataset of the binary-class task. No algorithm can maintain the best performance in all datasets. The applicability of the seven data mining algorithms on the datasets with different characteristics was summarized to provide a reference for biomedical researchers or beginners in different fields.

Edge Pushing is Equivalent to Vertex Elimination for Computing Hessians

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

Wang, Mu; Pothen, Alex; Hovland, Paul

We prove the equivalence of two different Hessian evaluation algorithms in AD. The first is the Edge Pushing algorithm of Gower and Mello, which may be viewed as a second order Reverse mode algorithm for computing the Hessian. In earlier work, we have derived the Edge Pushing algorithm by exploiting a Reverse mode invariant based on the concept of live variables in compiler theory. The second algorithm is based on eliminating vertices in a computational graph of the gradient, in which intermediate variables are successively eliminated from the graph, and the weights of the edges are updated suitably. We provemore » that if the vertices are eliminated in a reverse topological order while preserving symmetry in the computational graph of the gradient, then the Vertex Elimination algorithm and the Edge Pushing algorithm perform identical computations. In this sense, the two algorithms are equivalent. This insight that unifies two seemingly disparate approaches to Hessian computations could lead to improved algorithms and implementations for computing Hessians. Read More: http://epubs.siam.org/doi/10.1137/1.9781611974690.ch11« less

Bearing Fault Diagnosis under Variable Speed Using Convolutional Neural Networks and the Stochastic Diagonal Levenberg-Marquardt Algorithm

PubMed Central

Tra, Viet; Kim, Jaeyoung; Kim, Jong-Myon

2017-01-01

This paper presents a novel method for diagnosing incipient bearing defects under variable operating speeds using convolutional neural networks (CNNs) trained via the stochastic diagonal Levenberg-Marquardt (S-DLM) algorithm. The CNNs utilize the spectral energy maps (SEMs) of the acoustic emission (AE) signals as inputs and automatically learn the optimal features, which yield the best discriminative models for diagnosing incipient bearing defects under variable operating speeds. The SEMs are two-dimensional maps that show the distribution of energy across different bands of the AE spectrum. It is hypothesized that the variation of a bearing’s speed would not alter the overall shape of the AE spectrum rather, it may only scale and translate it. Thus, at different speeds, the same defect would yield SEMs that are scaled and shifted versions of each other. This hypothesis is confirmed by the experimental results, where CNNs trained using the S-DLM algorithm yield significantly better diagnostic performance under variable operating speeds compared to existing methods. In this work, the performance of different training algorithms is also evaluated to select the best training algorithm for the CNNs. The proposed method is used to diagnose both single and compound defects at six different operating speeds. PMID:29211025

Variable selection for zero-inflated and overdispersed data with application to health care demand in Germany

PubMed Central

Wang, Zhu; Shuangge, Ma; Wang, Ching-Yun

2017-01-01

In health services and outcome research, count outcomes are frequently encountered and often have a large proportion of zeros. The zero-inflated negative binomial (ZINB) regression model has important applications for this type of data. With many possible candidate risk factors, this paper proposes new variable selection methods for the ZINB model. We consider maximum likelihood function plus a penalty including the least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP). An EM (expectation-maximization) algorithm is proposed for estimating the model parameters and conducting variable selection simultaneously. This algorithm consists of estimating penalized weighted negative binomial models and penalized logistic models via the coordinated descent algorithm. Furthermore, statistical properties including the standard error formulae are provided. A simulation study shows that the new algorithm not only has more accurate or at least comparable estimation, also is more robust than the traditional stepwise variable selection. The proposed methods are applied to analyze the health care demand in Germany using an open-source R package mpath. PMID:26059498

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.

Three-Dimensional Inverse Transport Solver Based on Compressive Sensing Technique

NASA Astrophysics Data System (ADS)

Cheng, Yuxiong; Wu, Hongchun; Cao, Liangzhi; Zheng, Youqi

2013-09-01

According to the direct exposure measurements from flash radiographic image, a compressive sensing-based method for three-dimensional inverse transport problem is presented. The linear absorption coefficients and interface locations of objects are reconstructed directly at the same time. It is always very expensive to obtain enough measurements. With limited measurements, compressive sensing sparse reconstruction technique orthogonal matching pursuit is applied to obtain the sparse coefficients by solving an optimization problem. A three-dimensional inverse transport solver is developed based on a compressive sensing-based technique. There are three features in this solver: (1) AutoCAD is employed as a geometry preprocessor due to its powerful capacity in graphic. (2) The forward projection matrix rather than Gauss matrix is constructed by the visualization tool generator. (3) Fourier transform and Daubechies wavelet transform are adopted to convert an underdetermined system to a well-posed system in the algorithm. Simulations are performed and numerical results in pseudo-sine absorption problem, two-cube problem and two-cylinder problem when using compressive sensing-based solver agree well with the reference value.

Multivariate quantile mapping bias correction: an N-dimensional probability density function transform for climate model simulations of multiple variables

NASA Astrophysics Data System (ADS)

Cannon, Alex J.

2018-01-01

Most bias correction algorithms used in climatology, for example quantile mapping, are applied to univariate time series. They neglect the dependence between different variables. Those that are multivariate often correct only limited measures of joint dependence, such as Pearson or Spearman rank correlation. Here, an image processing technique designed to transfer colour information from one image to another—the N-dimensional probability density function transform—is adapted for use as a multivariate bias correction algorithm (MBCn) for climate model projections/predictions of multiple climate variables. MBCn is a multivariate generalization of quantile mapping that transfers all aspects of an observed continuous multivariate distribution to the corresponding multivariate distribution of variables from a climate model. When applied to climate model projections, changes in quantiles of each variable between the historical and projection period are also preserved. The MBCn algorithm is demonstrated on three case studies. First, the method is applied to an image processing example with characteristics that mimic a climate projection problem. Second, MBCn is used to correct a suite of 3-hourly surface meteorological variables from the Canadian Centre for Climate Modelling and Analysis Regional Climate Model (CanRCM4) across a North American domain. Components of the Canadian Forest Fire Weather Index (FWI) System, a complicated set of multivariate indices that characterizes the risk of wildfire, are then calculated and verified against observed values. Third, MBCn is used to correct biases in the spatial dependence structure of CanRCM4 precipitation fields. Results are compared against a univariate quantile mapping algorithm, which neglects the dependence between variables, and two multivariate bias correction algorithms, each of which corrects a different form of inter-variable correlation structure. MBCn outperforms these alternatives, often by a large margin, particularly for annual maxima of the FWI distribution and spatiotemporal autocorrelation of precipitation fields.

Newton Algorithms for Analytic Rotation: An Implicit Function Approach

ERIC Educational Resources Information Center

Boik, Robert J.

2008-01-01

In this paper implicit function-based parameterizations for orthogonal and oblique rotation matrices are proposed. The parameterizations are used to construct Newton algorithms for minimizing differentiable rotation criteria applied to "m" factors and "p" variables. The speed of the new algorithms is compared to that of existing algorithms and to…

Design and Implementation of an Electronic Front-End Based on Square Wave Excitation for Ultrasonic Torsional Guided Wave Viscosity Sensor

PubMed Central

Rabani, Amir

2016-01-01

The market for process instruments generally requires low cost devices that are robust, small in size, portable, and usable in-plant. Ultrasonic torsional guided wave sensors have received much attention by researchers for measurement of viscosity and/or density of fluids in recent years. The supporting electronic systems for these sensors providing many different settings of sine-wave signals are bulky and expensive. In contrast, a system based on bursts of square waves instead of sine waves would have a considerable advantage in that respect and could be built using simple integrated circuits at a cost that is orders of magnitude lower than for a windowed sine wave device. This paper explores the possibility of using square wave bursts as the driving signal source for the ultrasonic torsional guided wave viscosity sensor. A simple design of a compact and fully automatic analogue square wave front-end for the sensor is also proposed. The successful operation of the system is demonstrated by using the sensor for measuring the viscosity in a representative fluid. This work provides the basis for design and manufacture of low cost compact standalone ultrasonic guided wave sensors and enlightens the possibility of using coded excitation techniques utilising square wave sequences in such applications. PMID:27754324

Binding of TFIIIC to sine elements controls the relocation of activity-dependent neuronal genes to transcription factories.

PubMed

Crepaldi, Luca; Policarpi, Cristina; Coatti, Alessandro; Sherlock, William T; Jongbloets, Bart C; Down, Thomas A; Riccio, Antonella

2013-01-01

In neurons, the timely and accurate expression of genes in response to synaptic activity relies on the interplay between epigenetic modifications of histones, recruitment of regulatory proteins to chromatin and changes to nuclear structure. To identify genes and regulatory elements responsive to synaptic activation in vivo, we performed a genome-wide ChIPseq analysis of acetylated histone H3 using somatosensory cortex of mice exposed to novel enriched environmental (NEE) conditions. We discovered that Short Interspersed Elements (SINEs) located distal to promoters of activity-dependent genes became acetylated following exposure to NEE and were bound by the general transcription factor TFIIIC. Importantly, under depolarizing conditions, inducible genes relocated to transcription factories (TFs), and this event was controlled by TFIIIC. Silencing of the TFIIIC subunit Gtf3c5 in non-stimulated neurons induced uncontrolled relocation to TFs and transcription of activity-dependent genes. Remarkably, in cortical neurons, silencing of Gtf3c5 mimicked the effects of chronic depolarization, inducing a dramatic increase of both dendritic length and branching. These findings reveal a novel and essential regulatory function of both SINEs and TFIIIC in mediating gene relocation and transcription. They also suggest that TFIIIC may regulate the rearrangement of nuclear architecture, allowing the coordinated expression of activity-dependent neuronal genes.

Dynamic Spectral Structure Specifies Vowels for Adults and Children

PubMed Central

Nittrouer, Susan; Lowenstein, Joanna H.

2014-01-01

The dynamic specification account of vowel recognition suggests that formant movement between vowel targets and consonant margins is used by listeners to recognize vowels. This study tested that account by measuring contributions to vowel recognition of dynamic (i.e., time-varying) spectral structure and coarticulatory effects on stationary structure. Adults and children (four-and seven-year-olds) were tested with three kinds of consonant-vowel-consonant syllables: (1) unprocessed; (2) sine waves that preserved both stationary coarticulated and dynamic spectral structure; and (3) vocoded signals that primarily preserved that stationary, but not dynamic structure. Sections of two lengths were removed from syllable middles: (1) half the vocalic portion; and (2) all but the first and last three pitch periods. Adults performed accurately with unprocessed and sine-wave signals, as long as half the syllable remained; their recognition was poorer for vocoded signals, but above chance. Seven-year-olds performed more poorly than adults with both sorts of processed signals, but disproportionately worse with vocoded than sine-wave signals. Most four-year-olds were unable to recognize vowels at all with vocoded signals. Conclusions were that both dynamic and stationary coarticulated structures support vowel recognition for adults, but children attend to dynamic spectral structure more strongly because early phonological organization favors whole words. PMID:25536845

125 GHz sine wave gating InGaAs/InP single-photon detector with a monolithically integrated readout circuit

NASA Astrophysics Data System (ADS)

Jiang, Wen-Hao; Liu, Jian-Hong; Liu, Yin; Jin, Ge; Zhang, Jun; Pan, Jian-Wei

2017-12-01

InGaAs/InP single-photon detectors (SPDs) are the key devices for applications requiring near-infrared single-photon detection. Gating mode is an effective approach to synchronous single-photon detection. Increasing gating frequency and reducing module size are important challenges for the design of such detector system. Here we present for the first time an InGaAs/InP SPD with 1.25 GHz sine wave gating using a monolithically integrated readout circuit (MIRC). The MIRC has a size of 15 mm * 15 mm and implements the miniaturization of avalanche extraction for high-frequency sine wave gating. In the MIRC, low-pass filters and a low-noise radio frequency amplifier are integrated based on the technique of low temperature co-fired ceramic, which can effectively reduce the parasitic capacitance and extract weak avalanche signals. We then characterize the InGaAs/InP SPD to verify the functionality and reliability of MIRC, and the SPD exhibits excellent performance with 27.5 % photon detection efficiency, 1.2 kcps dark count rate, and 9.1 % afterpulse probability at 223 K and 100 ns hold-off time. With this MIRC, one can further design miniaturized high-frequency SPD modules that are highly required for practical applications.

How sensitivity to ongoing interaural temporal disparities is affected by manipulations of temporal features of the envelopes of high-frequency stimuli

PubMed Central

Bernstein, Leslie R.; Trahiotis, Constantine

2009-01-01

This study addressed how manipulating certain aspects of the envelopes of high-frequency stimuli affects sensitivity to envelope-based interaural temporal disparities (ITDs). Listener’s threshold ITDs were measured using an adaptive two-alternative paradigm employing “raised-sine” stimuli [John, M. S., et al. (2002). Ear Hear. 23, 106–117] which permit independent variation in their modulation frequency, modulation depth, and modulation exponent. Threshold ITDs were measured while manipulating modulation exponent for stimuli having modulation frequencies between 32 and 256 Hz. The results indicated that graded increases in the exponent led to graded decreases in envelope-based threshold ITDs. Threshold ITDs were also measured while parametrically varying modulation exponent and modulation depth. Overall, threshold ITDs decreased with increases in the modulation depth. Unexpectedly, increases in the exponent of the raised-sine led to especially large decreases in threshold ITD when the modulation depth was low. An interaural correlation-based model was generally able to capture changes in threshold ITD stemming from changes in the exponent, depth of modulation, and frequency of modulation of the raised-sine stimuli. The model (and several variations of it), however, could not account for the unexpected interaction between the value of raised-sine exponent and its modulation depth. PMID:19425666

Stringy horizons and generalized FZZ duality in perturbation theory

NASA Astrophysics Data System (ADS)

Giribet, Gaston

2017-02-01

We study scattering amplitudes in two-dimensional string theory on a black hole bakground. We start with a simple derivation of the Fateev-Zamolodchikov-Zamolodchikov (FZZ) duality, which associates correlation functions of the sine-Liouville integrable model on the Riemann sphere to tree-level string amplitudes on the Euclidean two-dimensional black hole. This derivation of FZZ duality is based on perturbation theory, and it relies on a trick originally due to Fateev, which involves duality relations between different Selberg type integrals. This enables us to rewrite the correlation functions of sine-Liouville theory in terms of a special set of correlators in the gauged Wess-Zumino-Witten (WZW) theory, and use this to perform further consistency checks of the recently conjectured Generalized FZZ (GFZZ) duality. In particular, we prove that n-point correlation functions in sine-Liouville theory involving n - 2 winding modes actually coincide with the correlation functions in the SL(2,R)/U(1) gauged WZW model that include n - 2 oscillator operators of the type described by Giveon, Itzhaki and Kutasov in reference [1]. This proves the GFZZ duality for the case of tree level maximally winding violating n-point amplitudes with arbitrary n. We also comment on the connection between GFZZ and other marginal deformations previously considered in the literature.

Binding of TFIIIC to SINE Elements Controls the Relocation of Activity-Dependent Neuronal Genes to Transcription Factories

PubMed Central

Crepaldi, Luca; Policarpi, Cristina; Coatti, Alessandro; Sherlock, William T.; Jongbloets, Bart C.; Down, Thomas A.; Riccio, Antonella

2013-01-01

In neurons, the timely and accurate expression of genes in response to synaptic activity relies on the interplay between epigenetic modifications of histones, recruitment of regulatory proteins to chromatin and changes to nuclear structure. To identify genes and regulatory elements responsive to synaptic activation in vivo, we performed a genome-wide ChIPseq analysis of acetylated histone H3 using somatosensory cortex of mice exposed to novel enriched environmental (NEE) conditions. We discovered that Short Interspersed Elements (SINEs) located distal to promoters of activity-dependent genes became acetylated following exposure to NEE and were bound by the general transcription factor TFIIIC. Importantly, under depolarizing conditions, inducible genes relocated to transcription factories (TFs), and this event was controlled by TFIIIC. Silencing of the TFIIIC subunit Gtf3c5 in non-stimulated neurons induced uncontrolled relocation to TFs and transcription of activity-dependent genes. Remarkably, in cortical neurons, silencing of Gtf3c5 mimicked the effects of chronic depolarization, inducing a dramatic increase of both dendritic length and branching. These findings reveal a novel and essential regulatory function of both SINEs and TFIIIC in mediating gene relocation and transcription. They also suggest that TFIIIC may regulate the rearrangement of nuclear architecture, allowing the coordinated expression of activity-dependent neuronal genes. PMID:23966877

Design and Implementation of an Electronic Front-End Based on Square Wave Excitation for Ultrasonic Torsional Guided Wave Viscosity Sensor.

PubMed

Rabani, Amir

2016-10-12

The market for process instruments generally requires low cost devices that are robust, small in size, portable, and usable in-plant. Ultrasonic torsional guided wave sensors have received much attention by researchers for measurement of viscosity and/or density of fluids in recent years. The supporting electronic systems for these sensors providing many different settings of sine-wave signals are bulky and expensive. In contrast, a system based on bursts of square waves instead of sine waves would have a considerable advantage in that respect and could be built using simple integrated circuits at a cost that is orders of magnitude lower than for a windowed sine wave device. This paper explores the possibility of using square wave bursts as the driving signal source for the ultrasonic torsional guided wave viscosity sensor. A simple design of a compact and fully automatic analogue square wave front-end for the sensor is also proposed. The successful operation of the system is demonstrated by using the sensor for measuring the viscosity in a representative fluid. This work provides the basis for design and manufacture of low cost compact standalone ultrasonic guided wave sensors and enlightens the possibility of using coded excitation techniques utilising square wave sequences in such applications.

Speech perception of sine-wave signals by children with cochlear implants

PubMed Central

Nittrouer, Susan; Kuess, Jamie; Lowenstein, Joanna H.

2015-01-01

Children need to discover linguistically meaningful structures in the acoustic speech signal. Being attentive to recurring, time-varying formant patterns helps in that process. However, that kind of acoustic structure may not be available to children with cochlear implants (CIs), thus hindering development. The major goal of this study was to examine whether children with CIs are as sensitive to time-varying formant structure as children with normal hearing (NH) by asking them to recognize sine-wave speech. The same materials were presented as speech in noise, as well, to evaluate whether any group differences might simply reflect general perceptual deficits on the part of children with CIs. Vocabulary knowledge, phonemic awareness, and “top-down” language effects were all also assessed. Finally, treatment factors were examined as possible predictors of outcomes. Results showed that children with CIs were as accurate as children with NH at recognizing sine-wave speech, but poorer at recognizing speech in noise. Phonemic awareness was related to that recognition. Top-down effects were similar across groups. Having had a period of bimodal stimulation near the time of receiving a first CI facilitated these effects. Results suggest that children with CIs have access to the important time-varying structure of vocal-tract formants. PMID:25994709

Mapping and Assessing Variability in the Antarctic Marginal Ice Zone, the Pack Ice and Coastal Polynyas

NASA Astrophysics Data System (ADS)

Stroeve, Julienne; Jenouvrier, Stephanie

2016-04-01

Sea ice variability within the marginal ice zone (MIZ) and polynyas plays an important role for phytoplankton productivity and krill abundance. Therefore mapping their spatial extent, seasonal and interannual variability is essential for understanding how current and future changes in these biological active regions may impact the Antarctic marine ecosystem. Knowledge of the distribution of different ice types to the total Antarctic sea ice cover may also help to shed light on the factors contributing towards recent expansion of the Antarctic ice cover in some regions and contraction in others. The long-term passive microwave satellite data record provides the longest and most consistent data record for assessing different ice types. However, estimates of the amount of MIZ, consolidated pack ice and polynyas depends strongly on what sea ice algorithm is used. This study uses two popular passive microwave sea ice algorithms, the NASA Team and Bootstrap to evaluate the distribution and variability in the MIZ, the consolidated pack ice and coastal polynyas. Results reveal the NASA Team algorithm has on average twice the MIZ and half the consolidated pack ice area as the Bootstrap algorithm. Polynya area is also larger in the NASA Team algorithm, and the timing of maximum polynya area may differ by as much as 5 months between algorithms. These differences lead to different relationships between sea ice characteristics and biological processes, as illustrated here with the breeding success of an Antarctic seabird.

Improving permafrost distribution modelling using feature selection algorithms

NASA Astrophysics Data System (ADS)

Deluigi, Nicola; Lambiel, Christophe; Kanevski, Mikhail

2016-04-01

The availability of an increasing number of spatial data on the occurrence of mountain permafrost allows the employment of machine learning (ML) classification algorithms for modelling the distribution of the phenomenon. One of the major problems when dealing with high-dimensional dataset is the number of input features (variables) involved. Application of ML classification algorithms to this large number of variables leads to the risk of overfitting, with the consequence of a poor generalization/prediction. For this reason, applying feature selection (FS) techniques helps simplifying the amount of factors required and improves the knowledge on adopted features and their relation with the studied phenomenon. Moreover, taking away irrelevant or redundant variables from the dataset effectively improves the quality of the ML prediction. This research deals with a comparative analysis of permafrost distribution models supported by FS variable importance assessment. The input dataset (dimension = 20-25, 10 m spatial resolution) was constructed using landcover maps, climate data and DEM derived variables (altitude, aspect, slope, terrain curvature, solar radiation, etc.). It was completed with permafrost evidences (geophysical and thermal data and rock glacier inventories) that serve as training permafrost data. Used FS algorithms informed about variables that appeared less statistically important for permafrost presence/absence. Three different algorithms were compared: Information Gain (IG), Correlation-based Feature Selection (CFS) and Random Forest (RF). IG is a filter technique that evaluates the worth of a predictor by measuring the information gain with respect to the permafrost presence/absence. Conversely, CFS is a wrapper technique that evaluates the worth of a subset of predictors by considering the individual predictive ability of each variable along with the degree of redundancy between them. Finally, RF is a ML algorithm that performs FS as part of its overall operation. It operates by constructing a large collection of decorrelated classification trees, and then predicts the permafrost occurrence through a majority vote. With the so-called out-of-bag (OOB) error estimate, the classification of permafrost data can be validated as well as the contribution of each predictor can be assessed. The performances of compared permafrost distribution models (computed on independent testing sets) increased with the application of FS algorithms on the original dataset and irrelevant or redundant variables were removed. As a consequence, the process provided faster and more cost-effective predictors and a better understanding of the underlying structures residing in permafrost data. Our work demonstrates the usefulness of a feature selection step prior to applying a machine learning algorithm. In fact, permafrost predictors could be ranked not only based on their heuristic and subjective importance (expert knowledge), but also based on their statistical relevance in relation of the permafrost distribution.

Simulation and experimental design of a new advanced variable step size Incremental Conductance MPPT algorithm for PV systems.

PubMed

Loukriz, Abdelhamid; Haddadi, Mourad; Messalti, Sabir

2016-05-01

Improvement of the efficiency of photovoltaic system based on new maximum power point tracking (MPPT) algorithms is the most promising solution due to its low cost and its easy implementation without equipment updating. Many MPPT methods with fixed step size have been developed. However, when atmospheric conditions change rapidly , the performance of conventional algorithms is reduced. In this paper, a new variable step size Incremental Conductance IC MPPT algorithm has been proposed. Modeling and simulation of different operational conditions of conventional Incremental Conductance IC and proposed methods are presented. The proposed method was developed and tested successfully on a photovoltaic system based on Flyback converter and control circuit using dsPIC30F4011. Both, simulation and experimental design are provided in several aspects. A comparative study between the proposed variable step size and fixed step size IC MPPT method under similar operating conditions is presented. The obtained results demonstrate the efficiency of the proposed MPPT algorithm in terms of speed in MPP tracking and accuracy. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

An algorithm for the design and tuning of RF accelerating structures with variable cell lengths

NASA Astrophysics Data System (ADS)

Lal, Shankar; Pant, K. K.

2018-05-01

An algorithm is proposed for the design of a π mode standing wave buncher structure with variable cell lengths. It employs a two-parameter, multi-step approach for the design of the structure with desired resonant frequency and field flatness. The algorithm, along with analytical scaling laws for the design of the RF power coupling slot, makes it possible to accurately design the structure employing a freely available electromagnetic code like SUPERFISH. To compensate for machining errors, a tuning method has been devised to achieve desired RF parameters for the structure, which has been qualified by the successful tuning of a 7-cell buncher to π mode frequency of 2856 MHz with field flatness <3% and RF coupling coefficient close to unity. The proposed design algorithm and tuning method have demonstrated the feasibility of developing an S-band accelerating structure for desired RF parameters with a relatively relaxed machining tolerance of ∼ 25 μm. This paper discusses the algorithm for the design and tuning of an RF accelerating structure with variable cell lengths.

Detection of Nitrogen Content in Rubber Leaves Using Near-Infrared (NIR) Spectroscopy with Correlation-Based Successive Projections Algorithm (SPA).

PubMed

Tang, Rongnian; Chen, Xupeng; Li, Chuang

2018-05-01

Near-infrared spectroscopy is an efficient, low-cost technology that has potential as an accurate method in detecting the nitrogen content of natural rubber leaves. Successive projections algorithm (SPA) is a widely used variable selection method for multivariate calibration, which uses projection operations to select a variable subset with minimum multi-collinearity. However, due to the fluctuation of correlation between variables, high collinearity may still exist in non-adjacent variables of subset obtained by basic SPA. Based on analysis to the correlation matrix of the spectra data, this paper proposed a correlation-based SPA (CB-SPA) to apply the successive projections algorithm in regions with consistent correlation. The result shows that CB-SPA can select variable subsets with more valuable variables and less multi-collinearity. Meanwhile, models established by the CB-SPA subset outperform basic SPA subsets in predicting nitrogen content in terms of both cross-validation and external prediction. Moreover, CB-SPA is assured to be more efficient, for the time cost in its selection procedure is one-twelfth that of the basic SPA.

Maximum wind energy extraction strategies using power electronic converters

NASA Astrophysics Data System (ADS)

Wang, Quincy Qing

2003-10-01

This thesis focuses on maximum wind energy extraction strategies for achieving the highest energy output of variable speed wind turbine power generation systems. Power electronic converters and controls provide the basic platform to accomplish the research of this thesis in both hardware and software aspects. In order to send wind energy to a utility grid, a variable speed wind turbine requires a power electronic converter to convert a variable voltage variable frequency source into a fixed voltage fixed frequency supply. Generic single-phase and three-phase converter topologies, converter control methods for wind power generation, as well as the developed direct drive generator, are introduced in the thesis for establishing variable-speed wind energy conversion systems. Variable speed wind power generation system modeling and simulation are essential methods both for understanding the system behavior and for developing advanced system control strategies. Wind generation system components, including wind turbine, 1-phase IGBT inverter, 3-phase IGBT inverter, synchronous generator, and rectifier, are modeled in this thesis using MATLAB/SIMULINK. The simulation results have been verified by a commercial simulation software package, PSIM, and confirmed by field test results. Since the dynamic time constants for these individual models are much different, a creative approach has also been developed in this thesis to combine these models for entire wind power generation system simulation. An advanced maximum wind energy extraction strategy relies not only on proper system hardware design, but also on sophisticated software control algorithms. Based on literature review and computer simulation on wind turbine control algorithms, an intelligent maximum wind energy extraction control algorithm is proposed in this thesis. This algorithm has a unique on-line adaptation and optimization capability, which is able to achieve maximum wind energy conversion efficiency through continuously improving the performance of wind power generation systems. This algorithm is independent of wind power generation system characteristics, and does not need wind speed and turbine speed measurements. Therefore, it can be easily implemented into various wind energy generation systems with different turbine inertia and diverse system hardware environments. In addition to the detailed description of the proposed algorithm, computer simulation results are presented in the thesis to demonstrate the advantage of this algorithm. As a final confirmation of the algorithm feasibility, the algorithm has been implemented inside a single-phase IGBT inverter, and tested with a wind simulator system in research laboratory. Test results were found consistent with the simulation results. (Abstract shortened by UMI.)

Energy efficient wireless sensor network for structural health monitoring using distributed embedded piezoelectric transducers

NASA Astrophysics Data System (ADS)

Li, Peng; Olmi, Claudio; Song, Gangbing

2010-04-01

Piezoceramic based transducers are widely researched and used for structural health monitoring (SHM) systems due to the piezoceramic material's inherent advantage of dual sensing and actuation. Wireless sensor network (WSN) technology benefits from advances made in piezoceramic based structural health monitoring systems, allowing easy and flexible installation, low system cost, and increased robustness over wired system. However, piezoceramic wireless SHM systems still faces some drawbacks, one of these is that the piezoceramic based SHM systems require relatively high computational capabilities to calculate damage information, however, battery powered WSN sensor nodes have strict power consumption limitation and hence limited computational power. On the other hand, commonly used centralized processing networks require wireless sensors to transmit all data back to the network coordinator for analysis. This signal processing procedure can be problematic for piezoceramic based SHM applications as it is neither energy efficient nor robust. In this paper, we aim to solve these problems with a distributed wireless sensor network for piezoceramic base structural health monitoring systems. Three important issues: power system, waking up from sleep impact detection, and local data processing, are addressed to reach optimized energy efficiency. Instead of sweep sine excitation that was used in the early research, several sine frequencies were used in sequence to excite the concrete structure. The wireless sensors record the sine excitations and compute the time domain energy for each sine frequency locally to detect the energy change. By comparing the data of the damaged concrete frame with the healthy data, we are able to find out the damage information of the concrete frame. A relative powerful wireless microcontroller was used to carry out the sampling and distributed data processing in real-time. The distributed wireless network dramatically reduced the data transmission between wireless sensor and the wireless coordinator, which in turn reduced the power consumption of the overall system.

Liquid Motion in a Rotating Tank Experiment (LME)

NASA Technical Reports Server (NTRS)

Deffenbaugh, D. M.; Dodge, F. T.; Green, S. T.

1998-01-01

The Liquid Motion Experiment (LME), which flew on STS 84 in May 1997, was an investigation of liquid motions in spinning, nutating tanks. LME was designed to quantify the effects of such liquid motions on the stability of spinning spacecraft, which are known to be adversely affected by the energy dissipated by the liquid motions. The LME hardware was essentially a spin table which could be forced to nutate at specified frequencies at a constant cone angle, independently of the spin rate. Cylindrical and spherical test tanks, partially filled with liquids of different viscosities, were located at the periphery of the spin table to simulate a spacecraft with off-axis propellant tanks; one set of tanks contained generic propellant management devices (PMDs). The primary quantitative data from the flight tests were the liquid-induced torques exerted on the tanks about radial and tangential axes through the center of the tank. Visual recordings of the liquid oscillations also provided qualitative information. The flight program incorporated two types of tests: sine sweep tests, in which the spin rate was held constant and the nutation frequency varied over a wide range; and sine dwell test, in which both the spin rate and the nutation frequency were held constant. The sine sweep tests were meant to investigate all the prominent liquid resonant oscillations and the damping of the resonances, and the sine dwell tests were meant to quantify the viscous energy dissipation rate of the liquid oscillations for steady state conditions. The LME flight data were compared to analytical results obtained from two companion IR&D programs at Southwest Research Institute. The comparisons indicated that the models predicted the observed liquid resonances, damping, and energy dissipation rates for many test conditions but not for all. It was concluded that improved models and CFD simulations are needed to resolve the differences. This work is ongoing under a current IR&D program.

Unsupervised Unmixing of Hyperspectral Images Accounting for Endmember Variability.

PubMed

Halimi, Abderrahim; Dobigeon, Nicolas; Tourneret, Jean-Yves

2015-12-01

This paper presents an unsupervised Bayesian algorithm for hyperspectral image unmixing, accounting for endmember variability. The pixels are modeled by a linear combination of endmembers weighted by their corresponding abundances. However, the endmembers are assumed random to consider their variability in the image. An additive noise is also considered in the proposed model, generalizing the normal compositional model. The proposed algorithm exploits the whole image to benefit from both spectral and spatial information. It estimates both the mean and the covariance matrix of each endmember in the image. This allows the behavior of each material to be analyzed and its variability to be quantified in the scene. A spatial segmentation is also obtained based on the estimated abundances. In order to estimate the parameters associated with the proposed Bayesian model, we propose to use a Hamiltonian Monte Carlo algorithm. The performance of the resulting unmixing strategy is evaluated through simulations conducted on both synthetic and real data.

A finite element solution algorithm for the Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Baker, A. J.

1974-01-01

A finite element solution algorithm is established for the two-dimensional Navier-Stokes equations governing the steady-state kinematics and thermodynamics of a variable viscosity, compressible multiple-species fluid. For an incompressible fluid, the motion may be transient as well. The primitive dependent variables are replaced by a vorticity-streamfunction description valid in domains spanned by rectangular, cylindrical and spherical coordinate systems. Use of derived variables provides a uniformly elliptic partial differential equation description for the Navier-Stokes system, and for which the finite element algorithm is established. Explicit non-linearity is accepted by the theory, since no psuedo-variational principles are employed, and there is no requirement for either computational mesh or solution domain closure regularity. Boundary condition constraints on the normal flux and tangential distribution of all computational variables, as well as velocity, are routinely piecewise enforceable on domain closure segments arbitrarily oriented with respect to a global reference frame.

Continuous-variable quantum Gaussian process regression and quantum singular value decomposition of nonsparse low-rank matrices

NASA Astrophysics Data System (ADS)

Das, Siddhartha; Siopsis, George; Weedbrook, Christian

2018-02-01

With the significant advancement in quantum computation during the past couple of decades, the exploration of machine-learning subroutines using quantum strategies has become increasingly popular. Gaussian process regression is a widely used technique in supervised classical machine learning. Here we introduce an algorithm for Gaussian process regression using continuous-variable quantum systems that can be realized with technology based on photonic quantum computers under certain assumptions regarding distribution of data and availability of efficient quantum access. Our algorithm shows that by using a continuous-variable quantum computer a dramatic speedup in computing Gaussian process regression can be achieved, i.e., the possibility of exponentially reducing the time to compute. Furthermore, our results also include a continuous-variable quantum-assisted singular value decomposition method of nonsparse low rank matrices and forms an important subroutine in our Gaussian process regression algorithm.

Environmental Fluctuations and Acoustic Data Communications

DTIC Science & Technology

2015-09-30

July 2011 along with subsequent analysis of the experiment data. KAM11 Experiment (2011) A shallow water acoustic communications experiment...packet and packet-to-packet variability. Algorithm Design and Experiment Data Analysis Communication receiver algorithm design for shallow water is...exhibited substantial daily oceanographic variability. Analysis of the KAM11 experiment data this past year has focused on fixed source transmissions

Clustering Binary Data in the Presence of Masking Variables

ERIC Educational Resources Information Center

Brusco, Michael J.

2004-01-01

A number of important applications require the clustering of binary data sets. Traditional nonhierarchical cluster analysis techniques, such as the popular K-means algorithm, can often be successfully applied to these data sets. However, the presence of masking variables in a data set can impede the ability of the K-means algorithm to recover the…

Modelling and control algorithms of the cross conveyors line with multiengine variable speed drives

NASA Astrophysics Data System (ADS)

Cheremushkina, M. S.; Baburin, S. V.

2017-02-01

The paper deals with the actual problem of developing the control algorithm that meets the technical requirements of the mine belt conveyors, and enables energy and resource savings taking into account a random sort of traffic. The most effective method of solution of these tasks is the construction of control systems with the use of variable speed drives for asynchronous motors. The authors designed the mathematical model of the system ‘variable speed multiengine drive - conveyor - control system of conveyors’ that takes into account the dynamic processes occurring in the elements of the transport system, provides an assessment of the energy efficiency of application the developed algorithms, which allows one to reduce the dynamic overload in the belt to 15-20%.

Comparison of the effects of model-based iterative reconstruction and filtered back projection algorithms on software measurements in pulmonary subsolid nodules.

PubMed

Cohen, Julien G; Kim, Hyungjin; Park, Su Bin; van Ginneken, Bram; Ferretti, Gilbert R; Lee, Chang Hyun; Goo, Jin Mo; Park, Chang Min

2017-08-01

To evaluate the differences between filtered back projection (FBP) and model-based iterative reconstruction (MBIR) algorithms on semi-automatic measurements in subsolid nodules (SSNs). Unenhanced CT scans of 73 SSNs obtained using the same protocol and reconstructed with both FBP and MBIR algorithms were evaluated by two radiologists. Diameter, mean attenuation, mass and volume of whole nodules and their solid components were measured. Intra- and interobserver variability and differences between FBP and MBIR were then evaluated using Bland-Altman method and Wilcoxon tests. Longest diameter, volume and mass of nodules and those of their solid components were significantly higher using MBIR (p < 0.05) with mean differences of 1.1% (limits of agreement, -6.4 to 8.5%), 3.2% (-20.9 to 27.3%) and 2.9% (-16.9 to 22.7%) and 3.2% (-20.5 to 27%), 6.3% (-51.9 to 64.6%), 6.6% (-50.1 to 63.3%), respectively. The limits of agreement between FBP and MBIR were within the range of intra- and interobserver variability for both algorithms with respect to the diameter, volume and mass of nodules and their solid components. There were no significant differences in intra- or interobserver variability between FBP and MBIR (p > 0.05). Semi-automatic measurements of SSNs significantly differed between FBP and MBIR; however, the differences were within the range of measurement variability. • Intra- and interobserver reproducibility of measurements did not differ between FBP and MBIR. • Differences in SSNs' semi-automatic measurement induced by reconstruction algorithms were not clinically significant. • Semi-automatic measurement may be conducted regardless of reconstruction algorithm. • SSNs' semi-automated classification agreement (pure vs. part-solid) did not significantly differ between algorithms.

Using collective variables to drive molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme

2013-12-01

A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.