Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication.

PubMed

Zhao, Meixia; Du, Jianchang; Lin, Feng; Tong, Chaobo; Yu, Jingyin; Huang, Shunmou; Wang, Xiaowu; Liu, Shengyi; Ma, Jianxin

2013-10-01

Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution. © 2013 Purdue University The Plant Journal © 2013 John Wiley & Sons Ltd.

Topological Constraints on Transvection between White Genes within the Transposing Element Te35b in Drosophila Melanogaster

PubMed Central

Gubb, D.; Roote, J.; Trenear, J.; Coulson, D.; Ashburner, M.

1997-01-01

The transposable element TE35B carries two copies of the white (w) gene at 35B1.2 on the second chromosome. These w genes are suppressed in a zeste-1 (z(1)) mutant background in a synapsis-dependent manner. Single-copy derivatives of the original TE35B stock give red eyes when heterozygous, but zeste eyes when homozygous. TE35B derivatives carrying single, double or triple copies of w were crossed to generate flies carrying from two to five ectopic w genes. Within this range, z(1)-mediated suppression is insensitive to copynumber and does not distinguish between w genes that are in cis or in trans. Suppression does not require the juxtaposition of even numbers of w genes, but is extremely sensitive to chromosomal topology. When arranged in a tight cluster, in triple-copy TE derivatives, w genes are nonsuppressible. Breakpoints falling within TE35B and separating two functional w genes act as partial suppressors of z(1). Similarly, breakpoints immediately proximal or distal to both w genes give partial suppression. This transvection-dependent downregulation of w genes may result from mis-activation of the X-chromosome dosage compensation mechanism. PMID:9215897

Bigfoot. a new family of MITE elements characterized from the Medicago genus.

PubMed

Charrier, B; Foucher, F; Kondorosi, E; d'Aubenton-Carafa, Y; Thermes, C; Kondorosi, A; Ratet, P

1999-05-01

We have characterized from the legume plant Medicago a new family of miniature inverted-repeat transposable elements (MITE), called the Bigfoot transposable elements. Two of these insertion elements are present only in a single allele of two different M. sativa genes. Using a PCR strategy we have isolated 19 other Bigfoot elements from the M. sativa and M. truncatula genomes. They differ from the previously characterized MITEs by their sequence, a target site of 9 bp and a partially clustered genomic distribution. In addition, we show that they exhibit a significantly stable secondary structure. These elements may represent up to 0.1% of the genome of the outcrossing Medicago sativa but are present at a reduced copy number in the genome of the autogamous M. truncatula plant, revealing major differences in the genome organization of these two plants.

The transposability of the Mediterranean-type diet in non-Mediterranean regions: application to the physician/allied health team.

PubMed

Speed, C

2004-12-01

Studies are consistently declaring that the Mediterranean-type diet is transposable to non-Mediterranean regions. The nutritional end points of Med-type eating appear to be achievable through foods from a variety of traditions and appear to support predetermined expectations surrounding food preparation, choice, taste and sensory appeal. The broad emphasis on minimally processed plants and their products (vegetables, fruit, legumes, wholegrains, nuts, seeds and oils); low fat dairy, fish, less emphasis on animal products and removal of partially hydrogenated fats has piqued the attention of health professionals who are interested in arresting the incidence of chronic disease. The theoretical underpinnings of Med-type eating have driven new understandings in dietary guidelines, which is especially timely as well-marketed fad diets loom large on the current health horizon.

Einstein-Podolsky-Rosen-like separability indicators for two-mode Gaussian states

NASA Astrophysics Data System (ADS)

Marian, Paulina; Marian, Tudor A.

2018-02-01

We investigate the separability of the two-mode Gaussian states (TMGSs) by using the variances of a pair of Einstein-Podolsky-Rosen (EPR)-like observables. Our starting point is inspired by the general necessary condition of separability introduced by Duan et al (2000 Phys. Rev. Lett. 84 2722). We evaluate the minima of the normalized forms of both the product and sum of such variances, as well as that of a regularized sum. Making use of Simon’s separability criterion, which is based on the condition of positivity of the partial transpose (PPT) of the density matrix (Simon 2000 Phys. Rev. Lett. 84 2726), we prove that these minima are separability indicators in their own right. They appear to quantify the greatest amount of EPR-like correlations that can be created in a TMGS by means of local operations. Furthermore, we reconsider the EPR-like approach to the separability of TMGSs which was developed by Duan et al with no reference to the PPT condition. By optimizing the regularized form of their EPR-like uncertainty sum, we derive a separability indicator for any TMGS. We prove that the corresponding EPR-like condition of separability is manifestly equivalent to Simon’s PPT one. The consistency of these two distinct approaches (EPR-like and PPT) affords a better understanding of the examined separability problem, whose explicit solution found long ago by Simon covers all situations of interest.

Evaluation of the best fit distribution for partial duration series of daily rainfall in Madinah, western Saudi Arabia

NASA Astrophysics Data System (ADS)

Alahmadi, F.; Rahman, N. A.; Abdulrazzak, M.

2014-09-01

Rainfall frequency analysis is an essential tool for the design of water related infrastructure. It can be used to predict future flood magnitudes for a given magnitude and frequency of extreme rainfall events. This study analyses the application of rainfall partial duration series (PDS) in the vast growing urban Madinah city located in the western part of Saudi Arabia. Different statistical distributions were applied (i.e. Normal, Log Normal, Extreme Value type I, Generalized Extreme Value, Pearson Type III, Log Pearson Type III) and their distribution parameters were estimated using L-moments methods. Also, different selection criteria models are applied, e.g. Akaike Information Criterion (AIC), Corrected Akaike Information Criterion (AICc), Bayesian Information Criterion (BIC) and Anderson-Darling Criterion (ADC). The analysis indicated the advantage of Generalized Extreme Value as the best fit statistical distribution for Madinah partial duration daily rainfall series. The outcome of such an evaluation can contribute toward better design criteria for flood management, especially flood protection measures.

Effects of task-irrelevant grouping on visual selection in partial report.

PubMed

Lunau, Rasmus; Habekost, Thomas

2017-07-01

Perceptual grouping modulates performance in attention tasks such as partial report and change detection. Specifically, grouping of search items according to a task-relevant feature improves the efficiency of visual selection. However, the role of task-irrelevant feature grouping is not clearly understood. In the present study, we investigated whether grouping of targets by a task-irrelevant feature influences performance in a partial-report task. In this task, participants must report as many target letters as possible from a briefly presented circular display. The crucial manipulation concerned the color of the elements in these trials. In the sorted-color condition, the color of the display elements was arranged according to the selection criterion, and in the unsorted-color condition, colors were randomly assigned. The distractor cost was inferred by subtracting performance in partial-report trials from performance in a control condition that had no distractors in the display. Across five experiments, we manipulated trial order, selection criterion, and exposure duration, and found that attentional selectivity was improved in sorted-color trials when the exposure duration was 200 ms and the selection criterion was luminance. This effect was accompanied by impaired selectivity in unsorted-color trials. Overall, the results suggest that the benefit of task-irrelevant color grouping of targets is contingent on the processing locus of the selection criterion.

Numerical estimation of the relative entropy of entanglement

NASA Astrophysics Data System (ADS)

Zinchenko, Yuriy; Friedland, Shmuel; Gour, Gilad

2010-11-01

We propose a practical algorithm for the calculation of the relative entropy of entanglement (REE), defined as the minimum relative entropy between a state and the set of states with positive partial transpose. Our algorithm is based on a practical semidefinite cutting plane approach. In low dimensions the implementation of the algorithm in matlab provides an estimation for the REE with an absolute error smaller than 10-3.

Validation of the peak bilirubin criterion for outcome after partial hepatectomy.

PubMed

van Mierlo, Kim M C; Lodewick, Toine M; Dhar, Dipok K; van Woerden, Victor; Kurstjens, Ralph; Schaap, Frank G; van Dam, Ronald M; Vyas, Soumil; Malagó, Massimo; Dejong, Cornelis H C; Olde Damink, Steven W M

2016-10-01

Postoperative liver failure (PLF) is a dreaded complication after partial hepatectomy. The peak bilirubin criterion (>7.0 mg/dL or ≥120 μmol/L) is used to define PLF. This study aimed to validate the peak bilirubin criterion as postoperative risk indicator for 90-day liver-related mortality. Characteristics of 956 consecutive patients who underwent partial hepatectomy at the Maastricht University Medical Centre or Royal Free London between 2005 and 2012 were analyzed by uni- and multivariable analyses with odds ratios (OR) and 95% confidence intervals (95%CI). Thirty-five patients (3.7%) met the postoperative peak bilirubin criterion at median day 19 with a median bilirubin level of 183 [121-588] μmol/L. Sensitivity and specificity for liver-related mortality after major hepatectomy were 41.2% and 94.6%, respectively. The positive predictive value was 22.6%. Predictors of liver-related mortality were the peak bilirubin criterion (p < 0.001, OR = 15.9 [95%CI 5.2-48.7]), moderate-severe steatosis and fibrosis (p = 0.013, OR = 8.5 [95%CI 1.6-46.6]), ASA 3-4 (p = 0.047, OR = 3.0 [95%CI 1.0-8.8]) and age (p = 0.044, OR = 1.1 [95%CI 1.0-1.1]). The peak bilirubin criterion has a low sensitivity and positive predictive value for 90-day liver-related mortality after major hepatectomy. Copyright © 2016 International Hepato-Pancreato-Biliary Association Inc. Published by Elsevier Ltd. All rights reserved.

Island palatal mucoperiosteal flap for repair of oronasal fistula in a dog.

PubMed

Smith, M M

2001-09-01

A two-year-old neutered/male mixed-breed dog had received partial maxillectomy for fibrosarcoma. An oronasal fistula occurred as a complication of the surgical procedure. An island palatal mucoperiosteal flap was developed and rotated to repair the oronasal fistula. Acute (1-month) and long-term (8-months) follow-up indicated appropriate healing of the transposed island palatal mucoperiosteal flap with resolution of clinical signs indicative of oronasal fistula.

Schmidt-number witnesses and bound entanglement

NASA Astrophysics Data System (ADS)

Sanpera, Anna; Bruß, Dagmar; Lewenstein, Maciej

2001-05-01

The Schmidt number of a mixed state characterizes the minimum Schmidt rank of the pure states needed to construct it. We investigate the Schmidt number of an arbitrary mixed state by studying Schmidt-number witnesses that detect it. We present a canonical form of such witnesses and provide constructive methods for their optimization. Finally, we present strong evidence that all bound entangled states with positive partial transpose in C3⊗C3 have Schmidt number 2.

Krylov Deferred Correction Accelerated Method of Lines Transpose for Parabolic Problems

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

Jia, Jun; Jingfang, Huang

2008-01-01

In this paper, a new class of numerical methods for the accurate and efficient solutions of parabolic partial differential equations is presented. Unlike traditional method of lines (MoL), the new {\\bf \\it Krylov deferred correction (KDC) accelerated method of lines transpose (MoL^T)} first discretizes the temporal direction using Gaussian type nodes and spectral integration, and symbolically applies low-order time marching schemes to form a preconditioned elliptic system, which is then solved iteratively using Newton-Krylov techniques such as Newton-GMRES or Newton-BiCGStab method. Each function evaluation in the Newton-Krylov method is simply one low-order time-stepping approximation of the error by solving amore » decoupled system using available fast elliptic equation solvers. Preliminary numerical experiments show that the KDC accelerated MoL^T technique is unconditionally stable, can be spectrally accurate in both temporal and spatial directions, and allows optimal time-step sizes in long-time simulations.« less

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

Albeverio, Sergio; Chen Kai; Fei Shaoming

A necessary separability criterion that relates the structures of the total density matrix and its reductions is given. The method used is based on the realignment method [K. Chen and L. A. Wu, Quant. Inf. Comput. 3, 193 (2003)]. The separability criterion naturally generalizes the reduction separability criterion introduced independently in the previous work [M. Horodecki and P. Horodecki, Phys. Rev. A 59, 4206 (1999) and N. J. Cerf, C. Adami, and R. M. Gingrich, Phys. Rev. A 60, 898 (1999)]. In special cases, it recovers the previous reduction criterion and the recent generalized partial transposition criterion [K. Chen andmore » L. A. Wu, Phys. Lett. A 306, 14 (2002)]. The criterion involves only simple matrix manipulations and can therefore be easily applied.« less

Entanglement transitions induced by large deviations

NASA Astrophysics Data System (ADS)

Bhosale, Udaysinh T.

2017-12-01

The probability of large deviations of the smallest Schmidt eigenvalue for random pure states of bipartite systems, denoted as A and B , is computed analytically using a Coulomb gas method. It is shown that this probability, for large N , goes as exp[-β N2Φ (ζ ) ] , where the parameter β is the Dyson index of the ensemble, ζ is the large deviation parameter, while the rate function Φ (ζ ) is calculated exactly. Corresponding equilibrium Coulomb charge density is derived for its large deviations. Effects of the large deviations of the extreme (largest and smallest) Schmidt eigenvalues on the bipartite entanglement are studied using the von Neumann entropy. Effect of these deviations is also studied on the entanglement between subsystems 1 and 2, obtained by further partitioning the subsystem A , using the properties of the density matrix's partial transpose ρ12Γ. The density of states of ρ12Γ is found to be close to the Wigner's semicircle law with these large deviations. The entanglement properties are captured very well by a simple random matrix model for the partial transpose. The model predicts the entanglement transition across a critical large deviation parameter ζ . Log negativity is used to quantify the entanglement between subsystems 1 and 2. Analytical formulas for it are derived using the simple model. Numerical simulations are in excellent agreement with the analytical results.

Entanglement transitions induced by large deviations.

PubMed

Bhosale, Udaysinh T

2017-12-01

The probability of large deviations of the smallest Schmidt eigenvalue for random pure states of bipartite systems, denoted as A and B, is computed analytically using a Coulomb gas method. It is shown that this probability, for large N, goes as exp[-βN^{2}Φ(ζ)], where the parameter β is the Dyson index of the ensemble, ζ is the large deviation parameter, while the rate function Φ(ζ) is calculated exactly. Corresponding equilibrium Coulomb charge density is derived for its large deviations. Effects of the large deviations of the extreme (largest and smallest) Schmidt eigenvalues on the bipartite entanglement are studied using the von Neumann entropy. Effect of these deviations is also studied on the entanglement between subsystems 1 and 2, obtained by further partitioning the subsystem A, using the properties of the density matrix's partial transpose ρ_{12}^{Γ}. The density of states of ρ_{12}^{Γ} is found to be close to the Wigner's semicircle law with these large deviations. The entanglement properties are captured very well by a simple random matrix model for the partial transpose. The model predicts the entanglement transition across a critical large deviation parameter ζ. Log negativity is used to quantify the entanglement between subsystems 1 and 2. Analytical formulas for it are derived using the simple model. Numerical simulations are in excellent agreement with the analytical results.

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

Demkowicz-Dobrzanski, Rafal; Lewenstein, Maciej; Institut fuer Theoretische Physik, Universitaet Hannover, D-30167 Hannover

We solve the problem of the optimal cloning of pure entangled two-qubit states with a fixed degree of entanglement using local operations and classical communication. We show that, amazingly, classical communication between the parties can improve the fidelity of local cloning if and only if the initial entanglement is higher than a certain critical value. It is completely useless for weakly entangled states. We also show that bound entangled states with positive partial transpose are not useful as a resource to improve the best local cloning fidelity.

Effect of atomic spontaneous decay on entanglement in the generalized Jaynes-Cummings model

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

Hessian, H.A.; Obada, A.-S.F.; Mohamed, A.-B.A.

2010-03-15

Some aspects of the irreversible dynamics of a generalized Jaynes-Cummings model are addressed. By working in the dressed-state representation, it is possible to split the dynamics of the entanglement and coherence. The exact solution of the master equation in the case of a high-Q cavity with atomic decay is found. Effects of the atomic spontaneous decay on the temporal evolution of partial entropies of the atom or the field and the total entropy as a quantitative measure entanglement are elucidated. The degree of entanglement, through the sum of the negative eigenvalues of the partially transposed density matrix and the negativemore » mutual information has been studied and compared with other measures.« less

Explanation-based generalization of partially ordered plans

NASA Technical Reports Server (NTRS)

Kambhampati, Subbarao; Kedar, Smadar

1991-01-01

Most previous work in analytic generalization of plans dealt with totally ordered plans. These methods cannot be directly applied to generalizing partially ordered plans, since they do not capture all interactions among plan operators for all total orders of such plans. We introduce a new method for generalizing partially ordered plans. This method is based on providing explanation-based generalization (EBG) with explanations which systematically capture the interactions among plan operators for all the total orders of a partially-ordered plan. The explanations are based on the Modal Truth Criterion which states the necessary and sufficient conditions for ensuring the truth of a proposition at any point in a plan, for a class of partially ordered plans. The generalizations obtained by this method guarantee successful and interaction-free execution of any total order of the generalized plan. In addition, the systematic derivation of the generalization algorithms from the Modal Truth Criterion obviates the need for carrying out a separate formal proof of correctness of the EBG algorithms.

Transposable genetic elements in Spirulina and potential applications for genetic engineering

NASA Astrophysics Data System (ADS)

Hiroyuki, Kojima; Qin, Song; Thankappan, Ajith Kumar; Yoshikazu, Kawata; Shin-Ichi, Yano

1998-03-01

Transposable elements in cyanobacteria are briefly reviewed. Evidence is presented to show that transposable elements in Spirulina platensis is actually reflected on the phenotype change, i e., helical to straight filaments. Transposition intermediates of DNA were isolated from the extrachromosome and the transposition was related to helical variations in Spirulina. Uses of transposable elements for microalgal recombination are discussed based on the transposition mechanism.

An Optimal Partial Differential Equations-based Stopping Criterion for Medical Image Denoising.

PubMed

Khanian, Maryam; Feizi, Awat; Davari, Ali

2014-01-01

Improving the quality of medical images at pre- and post-surgery operations are necessary for beginning and speeding up the recovery process. Partial differential equations-based models have become a powerful and well-known tool in different areas of image processing such as denoising, multiscale image analysis, edge detection and other fields of image processing and computer vision. In this paper, an algorithm for medical image denoising using anisotropic diffusion filter with a convenient stopping criterion is presented. In this regard, the current paper introduces two strategies: utilizing the efficient explicit method due to its advantages with presenting impressive software technique to effectively solve the anisotropic diffusion filter which is mathematically unstable, proposing an automatic stopping criterion, that takes into consideration just input image, as opposed to other stopping criteria, besides the quality of denoised image, easiness and time. Various medical images are examined to confirm the claim.

A stopping criterion for the iterative solution of partial differential equations

NASA Astrophysics Data System (ADS)

Rao, Kaustubh; Malan, Paul; Perot, J. Blair

2018-01-01

A stopping criterion for iterative solution methods is presented that accurately estimates the solution error using low computational overhead. The proposed criterion uses information from prior solution changes to estimate the error. When the solution changes are noisy or stagnating it reverts to a less accurate but more robust, low-cost singular value estimate to approximate the error given the residual. This estimator can also be applied to iterative linear matrix solvers such as Krylov subspace or multigrid methods. Examples of the stopping criterion's ability to accurately estimate the non-linear and linear solution error are provided for a number of different test cases in incompressible fluid dynamics.

Activating distillation with an infinitesimal amount of bound entanglement.

PubMed

Vollbrecht, Karl Gerd H; Wolf, Michael M

2002-06-17

We show that bipartite quantum states of any dimension, which do not have a positive partial transpose (NPPT), become 1-distillable when one adds an infinitesimal amount of bound entanglement. To this end we investigate the activation properties of a new class of symmetric bound entangled states of full rank. It is shown that in this set there exist universal activator states capable of activating the distillation of any NPPT state. The result shows that even a small amount of bound entanglement can be useful for quantum information purposes.

Generalized Choi states and 2-distillability of quantum states

NASA Astrophysics Data System (ADS)

Chen, Lin; Tang, Wai-Shing; Yang, Yu

2018-05-01

We investigate the distillability of bipartite quantum states in terms of positive and completely positive maps. We construct the so-called generalized Choi states and show that it is distillable when it has negative partial transpose. We convert the distillability problem of 2-copy n× n Werner states into the determination of the positivity of an Hermitian matrix. We obtain several sufficient conditions by which the positivity holds. Further, we investigate the case n=3 by the classification of 2× 3× 3 pure states.

Lateralization of high-frequency transposed stimuli under conditions of binaural interference

NASA Astrophysics Data System (ADS)

Bernstein, Leslie R.; Trahiotis, Constantine

2005-04-01

The purpose of this study was to determine whether binaural interference would occur if ITD-based extents of laterality were measured using high-frequency transposed stimuli as targets. The results of an earlier study [L. R. Bernstein and C. Trahiotis, J. Acoust. Soc. Am. 116, 3062-3069 (2004)], which focused on threshold-ITDs rather than extents of laterality, suggested that high-frequency transposed stimuli might be immune to binaural interference effects resulting from the addition of a spectrally-remote, low-frequency interferer. In contrast to the earlier findings, the data from this study indicate that high-frequency transposed targets can, indeed, be susceptible to binaural interference. High-frequency transposed targets, even when presented along with an interferer, yielded greater extents of ITD-based laterality than did Gaussian noise targets presented in isolation. That is, the enhanced potency of ITDs conveyed by transposed stimuli persisted even in the presence of a low-frequency interferer. Predictions made using an extension of the model of Heller and Trahiotis [L. M. Heller and C. Trahiotis, J. Acoust. Soc. Am. 99, 3632-3637 (1996)] accounted well for binaural interference obtained with conventional Gaussian noise targets but generally over-predicted the amounts of interference found with the transposed targets.

There is no clam with coats in the calm coast: delimiting the transposed-letter priming effect.

PubMed

Duñabeitia, Jon Andoni; Perea, Manuel; Carreiras, Manuel

2009-10-01

In this article, we explore the transposed-letter priming effect (e.g., jugde-JUDGE vs. jupte-JUDGE), a phenomenon that taps into some key issues on how the brain encodes letter positions and has favoured the creation of new input coding schemes. However, almost all the empirical evidence from transposed-letter priming experiments comes from nonword primes (e.g., jugde-JUDGE). Indeed, previous evidence when using word-word pairs (e.g., causal-CASUAL) is not conclusive. Here, we conducted five masked priming lexical decision experiments that examined the relationship between pairs of real words that differed only in the transposition of two of their letters (e.g., CASUAL vs. CAUSAL). Results showed that, unlike transposed-letter nonwords, transposed-letter words do not seem to affect the identification time of their transposed-letter mates. Thus, prime lexicality is a key factor that modulates the magnitude of transposed-letter priming effects. These results are interpreted under the assumption of the existence of lateral inhibition processes occurring within the lexical level-which cancels out any orthographic facilitation due to the overlapping letters. We examine the implications of these findings for models of visual-word recognition.

Orthographic Reading Deficits in Dyslexic Japanese Children: Examining the Transposed-Letter Effect in the Color-Word Stroop Paradigm

PubMed Central

Ogawa, Shino; Shibasaki, Masahiro; Isomura, Tomoko; Masataka, Nobuo

2016-01-01

In orthographic reading, the transposed-letter effect (TLE) is the perception of a transposed-letter position word such as “cholocate” as the correct word “chocolate.” Although previous studies on dyslexic children using alphabetic languages have reported such orthographic reading deficits, the extent of orthographic reading impairment in dyslexic Japanese children has remained unknown. This study examined the TLE in dyslexic Japanese children using the color-word Stroop paradigm comprising congruent and incongruent Japanese hiragana words with correct and transposed-letter positions. We found that typically developed children exhibited Stroop effects in Japanese hiragana words with both correct and transposed-letter positions, thus indicating the presence of TLE. In contrast, dyslexic children indicated Stroop effects in correct letter positions in Japanese words but not in transposed, which indicated an absence of the TLE. These results suggest that dyslexic Japanese children, similar to dyslexic children using alphabetic languages, may also have a problem with orthographic reading. PMID:27303331

Orthographic Reading Deficits in Dyslexic Japanese Children: Examining the Transposed-Letter Effect in the Color-Word Stroop Paradigm.

PubMed

Ogawa, Shino; Shibasaki, Masahiro; Isomura, Tomoko; Masataka, Nobuo

2016-01-01

In orthographic reading, the transposed-letter effect (TLE) is the perception of a transposed-letter position word such as "cholocate" as the correct word "chocolate." Although previous studies on dyslexic children using alphabetic languages have reported such orthographic reading deficits, the extent of orthographic reading impairment in dyslexic Japanese children has remained unknown. This study examined the TLE in dyslexic Japanese children using the color-word Stroop paradigm comprising congruent and incongruent Japanese hiragana words with correct and transposed-letter positions. We found that typically developed children exhibited Stroop effects in Japanese hiragana words with both correct and transposed-letter positions, thus indicating the presence of TLE. In contrast, dyslexic children indicated Stroop effects in correct letter positions in Japanese words but not in transposed, which indicated an absence of the TLE. These results suggest that dyslexic Japanese children, similar to dyslexic children using alphabetic languages, may also have a problem with orthographic reading.

Entanglement and nonclassicality for multimode radiation-field states

NASA Astrophysics Data System (ADS)

Ivan, J. Solomon; Chaturvedi, S.; Ercolessi, E.; Marmo, G.; Morandi, G.; Mukunda, N.; Simon, R.

2011-03-01

Nonclassicality in the sense of quantum optics is a prerequisite for entanglement in multimode radiation states. In this work we bring out the possibilities of passing from the former to the latter, via action of classicality preserving systems like beam splitters, in a transparent manner. For single-mode states, a complete description of nonclassicality is available via the classical theory of moments, as a set of necessary and sufficient conditions on the photon number distribution. We show that when the mode is coupled to an ancilla in any coherent state, and the system is then acted upon by a beam splitter, these conditions turn exactly into signatures of negativity under partial transpose (NPT) entanglement of the output state. Since the classical moment problem does not generalize to two or more modes, we turn in these cases to other familiar sufficient but not necessary conditions for nonclassicality, namely the Mandel parameter criterion and its extensions. We generalize the Mandel matrix from one-mode states to the two-mode situation, leading to a natural classification of states with varying levels of nonclassicality. For two-mode states we present a single test that can, if successful, simultaneously show nonclassicality as well as NPT entanglement. We also develop a test for NPT entanglement after beam-splitter action on a nonclassical state, tracing carefully the way in which it goes beyond the Mandel nonclassicality test. The result of three-mode beam-splitter action after coupling to an ancilla in the ground state is treated in the same spirit. The concept of genuine tripartite entanglement, and scalar measures of nonclassicality at the Mandel level for two-mode systems, are discussed. Numerous examples illustrating all these concepts are presented.

Transposed-Letter and Laterality Effects in Lexical Decision

ERIC Educational Resources Information Center

Perea, Manuel; Fraga, Isabel

2006-01-01

Two divided visual field lexical decision experiments were conducted to examine the role of the cerebral hemispheres in transposed-letter similarity effects. In Experiment 1, we created two types of nonwords: nonadjacent transposed-letter nonwords ("TRADEGIA"; the base word was "TRAGEDIA," the Spanish for "TRAGEDY") and two-letter different…

Measures of extents of laterality for high-frequency ``transposed'' stimuli under conditions of binaural interference

NASA Astrophysics Data System (ADS)

Bernstein, Leslie R.; Trahiotis, Constantine

2005-09-01

Our purpose in this study was to determine whether across-frequency binaural interference would occur if ITD-based extents of laterality were measured using high-frequency transposed stimuli as targets. The results of an earlier study [L. R. Bernstein and C. Trahiotis, J. Acoust. Soc. Am. 116, 3062-3069 (2004)], which focused on threshold-ITDs, rather than extents of laterality, suggested that high-frequency transposed stimuli might be ``immune'' to binaural interference effects resulting from the addition of a spectrally remote, low-frequency interferer. In contrast to the earlier findings, the data from this study indicate that high-frequency transposed targets are susceptible to binaural interference. Nevertheless, high-frequency transposed targets, even when presented along with an interferer, yielded greater extents of ITD-based laterality than did high-frequency Gaussian noise targets presented in isolation. That is, the ``enhanced potency'' of ITDs conveyed by transposed stimuli persisted, even in the presence of a low-frequency interferer. Predictions made using an extension of the model of Heller and Trahiotis [L. M. Heller and C. Trahiotis, J. Acoust. Soc. Am. 99, 3632-3637 (1996)] accounted well for across-frequency binaural interference obtained with conventional Gaussian noise targets but, in all but one case, overpredicted the amounts of interference found with the transposed targets.

Robust Criterion for the Existence of Nonhyperbolic Ergodic Measures

NASA Astrophysics Data System (ADS)

Bochi, Jairo; Bonatti, Christian; Díaz, Lorenzo J.

2016-06-01

We give explicit C 1-open conditions that ensure that a diffeomorphism possesses a nonhyperbolic ergodic measure with positive entropy. Actually, our criterion provides the existence of a partially hyperbolic compact set with one-dimensional center and positive topological entropy on which the center Lyapunov exponent vanishes uniformly. The conditions of the criterion are met on a C 1-dense and open subset of the set of diffeomorphisms having a robust cycle. As a corollary, there exists a C 1-open and dense subset of the set of non-Anosov robustly transitive diffeomorphisms consisting of systems with nonhyperbolic ergodic measures with positive entropy. The criterion is based on a notion of a blender defined dynamically in terms of strict invariance of a family of discs.

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

USDA-ARS?s Scientific Manuscript database

Small RNAs regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). Although miniature inverted-repeat transposable elements (MITEs) are closely associated with euchromatic genes, the br...

Can "CANISO" Activate "CASINO"? Transposed-Letter Similarity Effects with Nonadjacent Letter Positions

ERIC Educational Resources Information Center

Perea, Manuel; Lupker, Stephen J.

2004-01-01

Nonwords created by transposing two "adjacent" letters (i.e., transposed-letter (TL) nonwords like "jugde") are very effective at activating the lexical representation of their base words. This fact poses problems for most computational models of word recognition (e.g., the interactive-activation model and its extensions), which assume that exact…

TRANSPOSABLE REGULARIZED COVARIANCE MODELS WITH AN APPLICATION TO MISSING DATA IMPUTATION

PubMed Central

Allen, Genevera I.; Tibshirani, Robert

2015-01-01

Missing data estimation is an important challenge with high-dimensional data arranged in the form of a matrix. Typically this data matrix is transposable, meaning that either the rows, columns or both can be treated as features. To model transposable data, we present a modification of the matrix-variate normal, the mean-restricted matrix-variate normal, in which the rows and columns each have a separate mean vector and covariance matrix. By placing additive penalties on the inverse covariance matrices of the rows and columns, these so called transposable regularized covariance models allow for maximum likelihood estimation of the mean and non-singular covariance matrices. Using these models, we formulate EM-type algorithms for missing data imputation in both the multivariate and transposable frameworks. We present theoretical results exploiting the structure of our transposable models that allow these models and imputation methods to be applied to high-dimensional data. Simulations and results on microarray data and the Netflix data show that these imputation techniques often outperform existing methods and offer a greater degree of flexibility. PMID:26877823

TRANSPOSABLE REGULARIZED COVARIANCE MODELS WITH AN APPLICATION TO MISSING DATA IMPUTATION.

PubMed

Allen, Genevera I; Tibshirani, Robert

2010-06-01

Missing data estimation is an important challenge with high-dimensional data arranged in the form of a matrix. Typically this data matrix is transposable , meaning that either the rows, columns or both can be treated as features. To model transposable data, we present a modification of the matrix-variate normal, the mean-restricted matrix-variate normal , in which the rows and columns each have a separate mean vector and covariance matrix. By placing additive penalties on the inverse covariance matrices of the rows and columns, these so called transposable regularized covariance models allow for maximum likelihood estimation of the mean and non-singular covariance matrices. Using these models, we formulate EM-type algorithms for missing data imputation in both the multivariate and transposable frameworks. We present theoretical results exploiting the structure of our transposable models that allow these models and imputation methods to be applied to high-dimensional data. Simulations and results on microarray data and the Netflix data show that these imputation techniques often outperform existing methods and offer a greater degree of flexibility.

Non-Markovianity of Gaussian Channels.

PubMed

Torre, G; Roga, W; Illuminati, F

2015-08-14

We introduce a necessary and sufficient criterion for the non-Markovianity of Gaussian quantum dynamical maps based on the violation of divisibility. The criterion is derived by defining a general vectorial representation of the covariance matrix which is then exploited to determine the condition for the complete positivity of partial maps associated with arbitrary time intervals. Such construction does not rely on the Choi-Jamiolkowski representation and does not require optimization over states.

Enhancing interaural-delay-based extents of laterality at high frequencies by using ``transposed stimuli''

NASA Astrophysics Data System (ADS)

Bernstein, Leslie R.; Trahiotis, Constantine

2003-06-01

An acoustic pointing task was used to determine whether interaural temporal disparities (ITDs) conveyed by high-frequency ``transposed'' stimuli would produce larger extents of laterality than ITDs conveyed by bands of high-frequency Gaussian noise. The envelopes of transposed stimuli are designed to provide high-frequency channels with information similar to that conveyed by the waveforms of low-frequency stimuli. Lateralization was measured for low-frequency Gaussian noises, the same noises transposed to 4 kHz, and high-frequency Gaussian bands of noise centered at 4 kHz. Extents of laterality obtained with the transposed stimuli were greater than those obtained with bands of Gaussian noise centered at 4 kHz and, in some cases, were equivalent to those obtained with low-frequency stimuli. In a second experiment, the general effects on lateral position produced by imposed combinations of bandwidth, ITD, and interaural phase disparities (IPDs) on low-frequency stimuli remained when those stimuli were transposed to 4 kHz. Overall, the data were fairly well accounted for by a model that computes the cross-correlation subsequent to known stages of peripheral auditory processing augmented by low-pass filtering of the envelopes within the high-frequency channels of each ear.

Surgical transposition of the ovaries: imaging findings in 14 patients.

PubMed

Kier, R; Chambers, S K

1989-11-01

Pelvic radiation therapy for cervical or vaginal cancer often leads to ovarian failure. To remove the ovaries from the radiation portal and preserve their function, they can be transposed to the lateral abdomen. Serial imaging studies in 14 patients who had undergone ovarian transposition (five bilateral, nine unilateral) were reviewed. Images obtained included 32 CT scans, 20 sonograms, and one MR image. Most transposed ovaries were located along the paracolic gutters near the iliac crests, creating an extrinsic mass effect on adjacent bowel. Detection of surgical clips on the ovary on CT scans allowed confident recognition of all 19 transposed ovaries. Cysts in the transposed ovaries, noted on most imaging studies, did not correlate with complications of pain or hormonal dysfunction. In one case, a large physiologic cyst in a transposed ovary distorted the cecum and was mistaken for a mucocele of the appendix. In another case, a large ovarian cyst was thought to be tumor recurrence or a lymphocele. These findings indicate that although the transposed ovaries can be recognized on CT scans by the surgical clips attached to the ovaries, the appearance of the ovary does not predict reliably the development of complications.

Tape casting and partial melting of Bi-2212 thick films

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

Buhl, D.; Lang, T.; Heeb, B.

1994-12-31

To produce Bi-2212 thick films with high critical current densities tape casting and partial melting is a promising fabrication method. Bi-2212 powder and organic additives were mixed into a slurry and tape casted onto glass by the doctor blade tape casting process. The films were cut from the green tape and partially molten on Ag foils during heat treatment. We obtained almost single-phase and well-textured films over the whole thickness of 20 {mu}m. The orientation of the (a,b)-plane of the grains were parallel to the substrate with a misalignment of less than 6{degrees}. At 77K/OT a critical current density ofmore » 15`000 A/cm{sup 2} was reached in films of the dimension 1cm x 2cm x 20{mu}m (1{mu}V/cm criterion, resistively measured). At 4K/OT the highest value was 350`000 A/cm{sup 2} (1nV/cm criterion, magnetically measured).« less

Tape casting and partial melting of Bi-2212 thick films

NASA Technical Reports Server (NTRS)

Buhl, D.; Lang, TH.; Heeb, B.; Gauckler, L. J.

1995-01-01

To produce Bi-2212 thick films with high critical current densities tape casting and partial melting is a promising fabrication method. Bi-2212 powder and organic additives were mixed into a slurry and tape casted onto glass by the doctor blade tape casting process. The films were cut from the green tape and partially molten on Ag foils during heat treatment. We obtained almost single-phase and well-textured films over the whole thickness of 20 microns. The orientation of the (a,b)-plane of the grains was parallel to the substrate with a misalignment of less than 6 deg. At 77 K/0T a critical current density of 15, 000 A/sq cm was reached in films of the dimension 1 cm x 2 cm x 20 microns (1 micron V/cm criterion, resistively measured). At 4 K/0T the highest value was 350,000 A/sq cm (1 nV/cm criterion, magnetically measured).

Complex symmetric matrices with strongly stable iterates

NASA Technical Reports Server (NTRS)

Tadmor, E.

1985-01-01

Complex-valued symmetric matrices are studied. A simple expression for the spectral norm of such matrices is obtained, by utilizing a unitarily congruent invariant form. A sharp criterion is provided for identifying those symmetric matrices whose spectral norm is not exceeding one: such strongly stable matrices are usually sought in connection with convergent difference approximations to partial differential equations. As an example, the derived criterion is applied to conclude the strong stability of a Lax-Wendroff scheme.

Orthodontic correction of a transposed maxillary canine and first premolar in the permanent dentition.

PubMed

Nishimura, Kazuaki; Nakao, Kimihisa; Aoki, Taijyu; Fuyamada, Mariko; Saito, Keisuke; Goto, Shigemi

2012-10-01

The patient was a 16-year-old Japanese girl whose chief complaints were crowding and transposition of the maxillary canine and first premolar. A setup model was used to preoperatively align the teeth in their transposed positions. The amount of postoperative reshaping was estimated for the occlusal surfaces of the teeth. However, the patient did not wish to have her teeth reduced by reshaping or to have composite materials for restorative camouflage. Because she strongly expected alignment of her teeth in the correct intra-arch position, her transposed teeth were corrected without extraction of the transposed teeth. Cone-beam computed tomography was used to obtain more detailed information about the transposition, and the direction of tooth movement was examined. Although the duration of the treatment was long, both the crowns and the roots of the transposed teeth were aligned correctly. Copyright © 2012 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

[The role of external letter positions in visual word recognition].

PubMed

Perea, Manuel; Lupker, Sthephen J

2007-11-01

A key issue for any computational model of visual word recognition is the choice of an input coding schema, which is responsible for assigning letter positions. Such a schema must reflect the fact that, according to recent research, nonwords created by transposing letters (e.g., caniso for CASINO ), typically, appear to be more similar to the word than nonwords created by replacing letters (e.g., caviro ). In the present research, we initially carried out a computational analysis examining the degree to which the position of the transposition influences transposed-letter similarity effects. We next conducted a masked priming experiment with the lexical decision task to determine whether a transposed-letter priming advantage occurs when the first letter position is involved. Primes were created by either transposing the first and third letters (démula-MEDULA ) or replacing the first and third letters (bérula-MEDULA). Results showed that there was no transposed-letter priming advantage in this situation. We discuss the implications of these results for models of visual word recognition.

Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells

PubMed Central

Dai, Qian; Shen, Yang; Wang, Yan; Wang, Xin; Francisco, Joel Celio; Luo, Zhuojuan

2017-01-01

Abstract Transposable elements (TEs) compose about 40% of the murine genome. Retrotransposition of active TEs such as LINE-1 (L1) tremendously impacts genetic diversification and genome stability. Therefore, transcription and transposition activities of retrotransposons are tightly controlled. Here, we show that the Krüppel-like zinc finger protein Zfp281 directly binds and suppresses a subset of retrotransposons, including the active young L1 repeat elements, in mouse embryonic stem (ES) cells. In addition, we find that Zfp281-regulated L1s are highly enriched for 5-hydroxymethylcytosine (5hmC) and H3K4me3. The COMPASS-like H3K4 methyltransferase Mll2 is the major H3K4me3 methylase at the Zfp281-regulated L1s and required for their proper expression. Our studies also reveal that Zfp281 functions partially through recruiting the L1 regulators DNA hydroxymethylase Tet1 and Sin3A, and restricting Mll2 at these active L1s, leading to their balanced expression. In summary, our data indicate an instrumental role of Zfp281 in suppressing the young active L1s in mouse ES cells. PMID:29036642

Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells.

PubMed

Dai, Qian; Shen, Yang; Wang, Yan; Wang, Xin; Francisco, Joel Celio; Luo, Zhuojuan; Lin, Chengqi

2017-12-01

Transposable elements (TEs) compose about 40% of the murine genome. Retrotransposition of active TEs such as LINE-1 (L1) tremendously impacts genetic diversification and genome stability. Therefore, transcription and transposition activities of retrotransposons are tightly controlled. Here, we show that the Krüppel-like zinc finger protein Zfp281 directly binds and suppresses a subset of retrotransposons, including the active young L1 repeat elements, in mouse embryonic stem (ES) cells. In addition, we find that Zfp281-regulated L1s are highly enriched for 5-hydroxymethylcytosine (5hmC) and H3K4me3. The COMPASS-like H3K4 methyltransferase Mll2 is the major H3K4me3 methylase at the Zfp281-regulated L1s and required for their proper expression. Our studies also reveal that Zfp281 functions partially through recruiting the L1 regulators DNA hydroxymethylase Tet1 and Sin3A, and restricting Mll2 at these active L1s, leading to their balanced expression. In summary, our data indicate an instrumental role of Zfp281 in suppressing the young active L1s in mouse ES cells. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The relative immunity of high-frequency transposed stimuli to low-frequency binaural interference

NASA Astrophysics Data System (ADS)

Bernstein, Leslie R.; Trahiotis, Constantine

2004-05-01

We have recently demonstrated that high-frequency transposed stimuli, having envelopes designed to provide high-frequency channels with information similar to that normally available in only low-frequency channels, yield threshold-ITDs and extents of laterality comparable to those obtained with conventional low-frequency stimuli. This enhanced potency of ITDs conveyed by high-frequency transposed stimuli, as compared to conventional high-frequency stimuli, suggested to us that ITDs conveyed by transposed stimuli might be relatively immune to the presence of low-frequency binaural interferers. To investigate this issue, threshold-ITDs and extents of laterality were measured with a variety of conventional and transposed targets centered at 4 kHz. The targets were presented either in the presence or absence of a simultaneously gated diotic noise centered at 500 Hz, the interferer. As expected, the presence of the low-frequency interferer resulted in substantially elevated threshold-ITDs and reduced extents of laterality for the conventional high-frequency stimuli. In contrast, these interference effects were either greatly attenuated or absent for ITDs conveyed by the high-frequency transposed targets. The results will be discussed in the context of current models of binaural interference. [Work supported by NIH DC 04147, NIH DC04073, NIH DC 002304.

Optimal moving grids for time-dependent partial differential equations

NASA Technical Reports Server (NTRS)

Wathen, A. J.

1989-01-01

Various adaptive moving grid techniques for the numerical solution of time-dependent partial differential equations were proposed. The precise criterion for grid motion varies, but most techniques will attempt to give grids on which the solution of the partial differential equation can be well represented. Moving grids are investigated on which the solutions of the linear heat conduction and viscous Burgers' equation in one space dimension are optimally approximated. Precisely, the results of numerical calculations of optimal moving grids for piecewise linear finite element approximation of partial differential equation solutions in the least squares norm.

Simple proof of the quantum benchmark fidelity for continuous-variable quantum devices

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

Namiki, Ryo

2011-04-15

An experimental success criterion for continuous-variable quantum teleportation and memory is to surpass the limit of the average fidelity achieved by classical measure-and-prepare schemes with respect to a Gaussian-distributed set of coherent states. We present an alternative proof of the classical limit based on the familiar notions of state-channel duality and partial transposition. The present method enables us to produce a quantum-domain criterion associated with a given set of measured fidelities.

Transposable elements in cancer.

PubMed

Burns, Kathleen H

2017-07-01

Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1). LINE-1 sequences are self-propagating, protein-coding retrotransposons, and their activity results in somatically acquired insertions in cancer genomes. Altered expression of transposable elements and animation of genomic LINE-1 sequences appear to be hallmarks of cancer, and can be responsible for driving mutations in tumorigenesis.

Avoidance symptoms and assessment of posttraumatic stress disorder in Arab immigrant women.

PubMed

Norris, Anne E; Aroian, Karen J

2008-10-01

This study investigates whether the avoidance symptom criterion required for a Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV; American Psychiatric Association, 1994) diagnosis of posttraumatic stress disorder (PTSD) is overly conservative. Arab immigrant women (N = 453), many of whom reported experiencing multiple traumatic events, completed the Posttraumatic Diagnostic Scale in Arabic as part of a face to face interview. Analyses indicated all but one avoidance symptom was reported less frequently than reexperiencing and arousal symptoms. However, those who fully met reexperiencing, avoidance, and arousal symptom criteria had worse symptom severity and functioning than those who fully met reexperiencing and arousal symptom criteria, but only partially met avoidance symptom criterion. Study findings support importance of the PTSD avoidance symptom criterion.

Nonlinear diffusion equations as asymptotic limits of Cahn-Hilliard systems on unbounded domains via Cauchy's criterion

NASA Astrophysics Data System (ADS)

Fukao, Takeshi; Kurima, Shunsuke; Yokota, Tomomi

2018-05-01

This paper develops an abstract theory for subdifferential operators to give existence and uniqueness of solutions to the initial-boundary problem (P) for the nonlinear diffusion equation in an unbounded domain $\\Omega\\subset\\mathbb{R}^N$ ($N\\in{\\mathbb N}$), written as \\[ \\frac{\\partial u}{\\partial t} + (-\\Delta+1)\\beta(u) = g \\quad \\mbox{in}\\ \\Omega\\times(0, T), \\] which represents the porous media, the fast diffusion equations, etc., where $\\beta$ is a single-valued maximal monotone function on $\\mathbb{R}$, and $T>0$. Existence and uniqueness for (P) were directly proved under a growth condition for $\\beta$ even though the Stefan problem was excluded from examples of (P). This paper completely removes the growth condition for $\\beta$ by confirming Cauchy's criterion for solutions of the following approximate problem (P)$_{\\varepsilon}$ with approximate parameter $\\varepsilon>0$: \\[ \\frac{\\partial u_{\\varepsilon}}{\\partial t} + (-\\Delta+1)(\\varepsilon(-\\Delta+1)u_{\\varepsilon} + \\beta(u_{\\varepsilon}) + \\pi_{\\varepsilon}(u_{\\varepsilon})) = g \\quad \\mbox{in}\\ \\Omega\\times(0, T), \\] which is called the Cahn--Hilliard system, even if $\\Omega \\subset \\mathbb{R}^N$ ($N \\in \\mathbb{N}$) is an unbounded domain. Moreover, it can be seen that the Stefan problem is covered in the framework of this paper.

Ovarian metastasis in a transposed ovary 10 years after primary cervical cancer: the importance of histologic examination and review of literature.

PubMed

Janse, Julienne A; Sie-Go, Daisy M D S; Schreuder, Henk W R

2011-06-17

Cases of cervical carcinoma metastasing to the transposed ovary are rarely reported in the literature. In this report, the authors present the case of a 53-year-old woman with a persisting, unsuspected cyst in the right transposed ovary, 10 years after treatment for adenosquamous carcinoma of the cervix. It is the first report describing a secondary ovarian malignancy originating from a cervical adenosquamous carcinoma in a transposed ovary. In addition, this is the first account of an ovarian metastasis 10 years after primary treatment for cervical cancer. Furthermore, pathologic examination with immunohistochemistry and human papillomavirus genotyping played a key role in the diagnostic process, as the case did not raise suspicion by ultrasound findings neither by cytological examination after cytological aspiration or by appearance during surgery.

The impact of dissociation on transposon-mediated disease control strategies.

PubMed

Marshall, John M

2008-03-01

Vector-borne diseases such as malaria and dengue fever continue to be a major health concern through much of the world. The emergence of chloroquine-resistant strains of malaria and insecticide-resistant mosquitoes emphasize the need for novel methods of disease control. Recently, there has been much interest in the use of transposable elements to drive resistance genes into vector populations as a means of disease control. One concern that must be addressed before a release is performed is the potential loss of linkage between a transposable element and a resistance gene. Transposable elements such as P and hobo have been shown to produce internal deletion derivatives at a significant rate, and there is concern that a similar process could lead to loss of the resistance gene from the drive system following a transgenic release. Additionally, transposable elements such as Himar1 have been shown to transpose significantly more frequently when free of exogenous DNA. Here, we show that any transposon-mediated gene drive strategy must have an exceptionally low rate of dissociation if it is to be effective. Additionally, the resistance gene must confer a large selective advantage to the vector to surmount the effects of a moderate dissociation rate and transpositional handicap.

Does letter position coding depend on consonant/vowel status? Evidence with the masked priming technique.

PubMed

Perea, Manuel; Acha, Joana

2009-02-01

Recently, a number of input coding schemes (e.g., SOLAR model, SERIOL model, open-bigram model, overlap model) have been proposed that capture the transposed-letter priming effect (i.e., faster response times for jugde-JUDGE than for jupte-JUDGE). In their current version, these coding schemes do not assume any processing differences between vowels and consonants. However, in a lexical decision task, Perea and Lupker (2004, JML; Lupker, Perea, & Davis, 2008, L&CP) reported that transposed-letter priming effects occurred for consonant transpositions but not for vowel transpositions. This finding poses a challenge for these recently proposed coding schemes. Here, we report four masked priming experiments that examine whether this consonant/vowel dissociation in transposed-letter priming is task-specific. In Experiment 1, we used a lexical decision task and found a transposed-letter priming effect only for consonant transpositions. In Experiments 2-4, we employed a same-different task - a task which taps early perceptual processes - and found a robust transposed-letter priming effect that did not interact with consonant/vowel status. We examine the implications of these findings for the front-end of the models of visual word recognition.

Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates.

PubMed

Warren, Ian A; Naville, Magali; Chalopin, Domitille; Levin, Perrine; Berger, Chloé Suzanne; Galiana, Delphine; Volff, Jean-Nicolas

2015-09-01

Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.

Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor.

PubMed

Labbé, Jessy; Murat, Claude; Morin, Emmanuelle; Tuskan, Gerald A; Le Tacon, François; Martin, Francis

2012-01-01

The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome. TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intact copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea. This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.

Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor

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

Labbe, Jessy L; Murat, Claude; Morin, Emmanuelle

2012-01-01

Background: The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TEspecific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome. Methodology/Principal Findings: TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copy elements distributed within 171 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs exhibits signs of ancient transposition except some intactmore » copies of terminal inverted repeats (TIRS), long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TE expansion in L. bicolor: the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 0.5 Mya ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea. Conclusions: This analysis 1) represents an initial characterization of TEs in the L. bicolor genome, 2) contributes to improve genome annotation and a greater understanding of the role TEs played in genome organization and evolution and 3) provides a valuable resource for future research on the genome evolution within the Laccaria genus.« less

Characterization of Transposable Elements in Laccaria bicolor

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

Labbe, Jessy L; Murat, Claude; Morin, Emmanuelle

2012-01-01

Background: The publicly available Laccaria bicolor genome sequence has provided a considerable genomic resource allowing systematic identification of transposable elements (TEs) in this symbiotic ectomycorrhizal fungus. Using a TE-specific annotation pipeline we have characterized and analyzed TEs in the L. bicolor S238N-H82 genome. Methodology/Principal Findings: TEs occupy 24% of the 60 Mb L. bicolor genome and represent 25,787 full-length and partial copies elements distributed within 172 families. The most abundant elements were the Copia-like. TEs are not randomly distributed across the genome, but are tightly nested or clustered. The majority of TEs are ancient except some terminal inverted repeats (TIRS),more » long terminal repeats (LTRs) and a large retrotransposon derivative (LARD) element. There were three main periods of TEs expansion in L. bicolor; the first from 57 to 10 Mya, the second from 5 to 1 Mya and the most recent from 500,000 years ago until now. LTR retrotransposons are closely related to retrotransposons found in another basidiomycete, Coprinopsis cinerea. Conclusions: This analysis represents an initial characterization of TEs in the L. bicolor genome, contributes to genome assembly and to a greater understanding of the role TEs played in genome organization and evolution, and provides a valuable resource for the ongoing Laccaria Pan-Genome project supported by the U.S.-DOE Joint Genome Institute.« less

Applying transpose matrix on advanced encryption standard (AES) for database content

NASA Astrophysics Data System (ADS)

Manurung, E. B. P.; Sitompul, O. S.; Suherman

2018-03-01

Advanced Encryption Standard (AES) is a specification for the encryption of electronic data established by the U.S. National Institute of Standards and Technology (NIST) and has been adopted by the U.S. government and is now used worldwide. This paper reports the impact of transpose matrix integration to AES. Transpose matrix implementation on AES is aimed at first stage of chypertext modifications for text based database security so that the confidentiality improves. The matrix is also able to increase the avalanche effect of the cryptography algorithm 4% in average.

Mucin gene expression in human urothelium and in intestinal segments transposed into the urinary tract.

PubMed

N'Dow, J; Pearson, J P; Bennett, M K; Neal, D E; Robson, C N

2000-10-01

The repertoire of mucin (MUC) gene expression in the normal human urothelium is poorly defined and the alterations in MUC gene expression following transposition of intestinal segments into the urinary tract has not previously been studied. The aims of this study were to define MUC gene expression in the normal human urothelium; and in transposed intestinal segments. Non-isotopic in-situ hybridization was carried out using eight digoxigenin labeled oligonucleotide mucin gene probes (MUC 1 - 7). Immunohistochemistry using NCL-MUC1 and NCL-MUC2 monoclonal antibodies was performed on sections of paraffin-embedded tissues. Twenty-seven patients were investigated (normal human urothelium, n = 6; transposed ileal segments, n = 14 and normal ileal controls, n = 7). MUC1 and MUC4 were the predominant mucin genes expressed in the normal urothelium with MUC3 being expressed in a third of cases studied; MUC2, 5AC, 5B, 6 and 7 were not expressed. Despite the morphological changes seen in transposed ileal segments, MUC2 and MUC3 continued to be expressed in these segments albeit in a disorganised fashion. Both MUC1 and MUC4 were up-regulated in transposed ileal segments, genes expressed by the normal human urothelium. All eight mucin genes were expressed in an area of pyloric-type metaplasia found in one transposed ileal segment. In patients with clam enterocystoplasty there was evidence of increasing up-regulation of MUC2, 3, 4 and 5AC expression in the urothelium toward the anastomotic site. Transposition of ileal segments into the urinary tract results in up-regulation of MUC1 and MUC4, the predominant MUC genes expressed in the human bladder. The clinical implication of the up-regulation of some MUC genes toward the anastomotic site in patients with an enteroplasty and the aberrant expression of MUC5AC - MUC7 by transposed segments is at present unclear.

Associative priming effects with visible, transposed-letter nonwords: JUGDE facilitates COURT.

PubMed

Perea, Manuel; Palti, Dafna; Gomez, Pablo

2012-04-01

Associative priming effects can be obtained with masked nonword primes or with masked pseudohomophone primes (e.g., judpe-COURT, tode-FROG), but not with visible primes. The usual explanation is that when the prime is visible, these stimuli no longer activate the semantic representations of their base words. Given the important role of transposed-letter stimuli (e.g., jugde) in visual word recognition, here we examined whether or not an associative priming effect could be obtained with visible transposed-letter nonword primes (e.g., jugde-COURT) in a series of lexical decision experiments. Results showed a sizable associative priming effect with visible transposed-letter nonword primes (i.e., jugde-COURT faster than neevr-COURT) in Experiments 1-3 that was close to that with word primes. In contrast, we failed to find a parallel effect with replacement-letter nonword primes (Experiment 2). These findings pose some constraints to models of visual word recognition.

Transposable Elements and Genetic Instabilities in Crop Plants

DOE R&D Accomplishments Database

Burr, B.; Burr, F.

1981-04-10

Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

Dissociation between judgments and outcome-expectancy measures in covariation learning: a signal detection theory approach.

PubMed

Perales, José C; Catena, Andrés; Shanks, David R; González, José A

2005-09-01

A number of studies using trial-by-trial learning tasks have shown that judgments of covariation between a cue c and an outcome o deviate from normative metrics. Parameters based on trial-by-trial predictions were estimated from signal detection theory (SDT) in a standard causal learning task. Results showed that manipulations of P(c) when contingency (deltaP) was held constant did not affect participants' ability to predict the appearance of the outcome (d') but had a significant effect on response criterion (c) and numerical causal judgments. The association between criterion c and judgment was further demonstrated in 2 experiments in which the criterion was directly manipulated by linking payoffs to the predictive responses made by learners. In all cases, the more liberal the criterion c was, the higher judgments were. The results imply that the mechanisms underlying the elaboration of judgments and those involved in the elaboration of predictive responses are partially dissociable.

Optimal moving grids for time-dependent partial differential equations

NASA Technical Reports Server (NTRS)

Wathen, A. J.

1992-01-01

Various adaptive moving grid techniques for the numerical solution of time-dependent partial differential equations were proposed. The precise criterion for grid motion varies, but most techniques will attempt to give grids on which the solution of the partial differential equation can be well represented. Moving grids are investigated on which the solutions of the linear heat conduction and viscous Burgers' equation in one space dimension are optimally approximated. Precisely, the results of numerical calculations of optimal moving grids for piecewise linear finite element approximation of PDE solutions in the least-squares norm are reported.

Jumping Genes: The Transposable DNAs of Bacteria.

ERIC Educational Resources Information Center

Berg, Claire M.; Berg, Douglas E.

1984-01-01

Transposons are transposable elements that carry genes for antibiotic resistance. Provides background information on the structure and organization of these "jumping genes" in bacteria. Also describes the use of transposons in tagging genes and lists pertinent references and resource materials. (DH)

Orthodontic Intervention to Impacted and Transposed Lower Canines

PubMed Central

Kılıç, Nihat

2017-01-01

Impacted and transposed teeth cause serious difficulties in tooth eruption and movement as well as esthetic and functional outcomes. Proper treatment planning including good biomechanical control is essential in order to avoid side effects during traction and aligning of the impacted and/or transposed teeth. The purpose of the present study was to present a successfully treated female patient having transposed and impacted lower canines by means of a modified lingual arch and fixed orthodontic appliance. A female patient aged 13 years and 9 months presented to the orthodontic department with a chief compliant of bilateral spacing and missing teeth in mandibular dentition. After leveling and creating sufficient space in the mandibular arch for the canines, a modified lingual arch was cemented to the mandibular first molars. The lingual arch had two hooks extending to the distobuccal areas of the canine spaces. Elastic chains were applied between the hooks on the lingual arch and the ligatures tied to the attachments on the canine crowns. The light forces generated by elastic materials caused impacted canines to erupt and tend towards their own spaces in the dental arch. As a result, impacted and transposed lower canines were properly positioned in their spaces, and the treatment results were stable during the retention period. PMID:28540090

Nongeneric positive partial transpose states of rank five in 3×3 dimensions

NASA Astrophysics Data System (ADS)

Hansen, Leif Ove; Myrheim, Jan

In 3×3 dimensions, entangled mixed states that are positive under partial transposition (PPT states) must have rank at least four. These rank four states are completely understood. We say that they have rank (4,4) since both a state ρ and its partial transpose ρP have rank four. The next problem is to understand the extremal PPT states of rank (5,5). We call two states SL⊗SL-equivalent if they are related by a product transformation. A generic rank (5,5) PPT state ρ is extremal, and both ρ and ρP have six product vectors in their ranges, and no product vectors in their kernels. The three numbers {6,6;0} are SL⊗SL-invariants that help us classify the state. There is no analytical understanding of such states. We have studied numerically a few types of nongeneric rank five PPT states, in particular, states with one or more product vectors in their kernels. We find an interesting new analytical construction of all rank four extremal PPT states, up to SL⊗SL-equivalence, where they appear as boundary states on one single five-dimensional face on the set of normalized PPT states. The interior of the face consists of rank (5,5) states with four common product vectors in their kernels, it is a simplex of separable states surrounded by entangled PPT states. We say that a state ρ is SL⊗SL-symmetric if ρ and ρP are SL⊗SL-equivalent, and is genuinely SL⊗SL-symmetric if it is SL⊗SL-equivalent to a state τ with τ=τP. Genuine SL⊗SL-symmetry implies a special form of SL⊗SL-symmetry. We have produced numerically, by a special method, a random sample of rank (5,5) SL⊗SL-symmetric states. About 50 of these are of type {6,6;0}, among those all are extremal and about half are genuinely SL⊗SL-symmetric. All these genuinely SL⊗SL-symmetric states can be transformed to have a circulant form. We find however that this is not a generic property of genuinely SL⊗SL-symmetric states. The remaining SL⊗SL-symmetric states found in the search have product vectors in their kernels, and they inspired us to study such states without regard to SL⊗SL-symmetry.

Correlation between location of transposed ovary and function in cervical cancer patients who underwent radical hysterectomy.

PubMed

Yoon, Aera; Lee, Yoo-Young; Park, Won; Huh, Seung Jae; Choi, Chel Hun; Kim, Tae-Joong; Lee, Jeong-Won; Kim, Byoung-Gie; Bae, Duk-Soo

2015-05-01

The study investigated the association between the location of transposed ovaries and posttreatment ovarian function in patients with early cervical cancer (IB1-IIA) who underwent radical hysterectomy and ovarian transposition with or without adjuvant therapies. Retrospective medical records were reviewed to enroll the patients with early cervical cancer who underwent ovarian transposition during radical hysterectomy at Samsung Medical Center between July 1995 and July 2012. Serum follicle-stimulating hormone (FSH) level was used as a surrogate marker for ovarian function. Twenty-one patients were enrolled. The median age and body mass index (BMI) were 31 years (range, 24-39 years) and 21.3 kg/m² (range, 17.7-31.2 kg/m²), respectively. The median serum FSH level after treatment was 7.9 mIU/mL (range, 2.4-143.4 mIU/mL). The median distance from the iliac crest to transposed ovaries on erect plain abdominal x-ray was 0.5 cm (range, -2.7 to 5.2 cm). In multivariate analysis, posttreatment serum FSH levels were significantly associated with the location of transposed ovaries (β = -8.1, P = 0.032), concurrent chemoradiation (CCRT) as an adjuvant therapy (β = 71.08, P = 0.006), and BMI before treatment (underweight: β = -59.93, P = 0.05; overweight: β = -40.62, P = 0.041). Location of transposed ovaries, adjuvant CCRT, and BMI before treatment may be associated with ovarian function after treatment. We suggest that ovaries should be transposed as highly as possible during radical hysterectomy to preserve ovarian function in young patients with early cervical cancer who might be a candidate for adjuvant CCRT and who have low BMI before treatment.

A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

PubMed Central

Biémont, Christian

2010-01-01

The idea that some genetic factors are able to move around chromosomes emerged more than 60 years ago when Barbara McClintock first suggested that such elements existed and had a major role in controlling gene expression and that they also have had a major influence in reshaping genomes in evolution. It was many years, however, before the accumulation of data and theories showed that this latter revolutionary idea was correct although, understandably, it fell far short of our present view of the significant influence of what are now known as “transposable elements” in evolution. In this article, I summarize the main events that influenced my thinking about transposable elements as a young scientist and the influence and role of these specific genomic elements in evolution over subsequent years. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. PMID:21156958

An efficient parallel-processing method for transposing large matrices in place.

PubMed

Portnoff, M R

1999-01-01

We have developed an efficient algorithm for transposing large matrices in place. The algorithm is efficient because data are accessed either sequentially in blocks or randomly within blocks small enough to fit in cache, and because the same indexing calculations are shared among identical procedures operating on independent subsets of the data. This inherent parallelism makes the method well suited for a multiprocessor computing environment. The algorithm is easy to implement because the same two procedures are applied to the data in various groupings to carry out the complete transpose operation. Using only a single processor, we have demonstrated nearly an order of magnitude increase in speed over the previously published algorithm by Gate and Twigg for transposing a large rectangular matrix in place. With multiple processors operating in parallel, the processing speed increases almost linearly with the number of processors. A simplified version of the algorithm for square matrices is presented as well as an extension for matrices large enough to require virtual memory.

Generalized Structured Component Analysis

ERIC Educational Resources Information Center

Hwang, Heungsun; Takane, Yoshio

2004-01-01

We propose an alternative method to partial least squares for path analysis with components, called generalized structured component analysis. The proposed method replaces factors by exact linear combinations of observed variables. It employs a well-defined least squares criterion to estimate model parameters. As a result, the proposed method…

The Role of the Pressure in the Partial Regularity Theory for Weak Solutions of the Navier-Stokes Equations

NASA Astrophysics Data System (ADS)

Chamorro, Diego; Lemarié-Rieusset, Pierre-Gilles; Mayoufi, Kawther

2018-04-01

We study the role of the pressure in the partial regularity theory for weak solutions of the Navier-Stokes equations. By introducing the notion of dissipative solutions, due to D uchon and R obert (Nonlinearity 13:249-255, 2000), we will provide a generalization of the Caffarelli, Kohn and Nirenberg theory. Our approach sheels new light on the role of the pressure in this theory in connection to Serrin's local regularity criterion.

Evolutionary trajectory of Pack-MULEs is determined by their epigenetic status

USDA-ARS?s Scientific Manuscript database

Acquisition and rearrangement of host genes by transposable elements is one mechanism to increase gene diversity. The rice genome is replete in such sequences and while ~3,000 Pack- Mutator-like transposable elements containing gene sequences (Pack-MULEs) have been identified, their function remains...

Detection and characterization of miniature inverted-repeat transposable elements in “Candidatus Liberibacter asiaticus”

USDA-ARS?s Scientific Manuscript database

Miniature inverted-repeat transposable elements (MITEs) are non-autonomous transposons (devoid a transposase gene, tps) involving insertion/deletion of genomic DNA in bacterial genomes influencing gene functions. No transposon has yet been reported in “Candidatus Liberibacter asiaticus”, an alpha-pr...

Transposed-Letter Priming across Inflectional Morpheme Boundaries

ERIC Educational Resources Information Center

Zargar, Ehsan Shafiee; Witzel, Naoko

2017-01-01

This study reports findings from two experiments testing whether a transposed-letter (TL) priming effect can be obtained when the transposition occurs across morphological boundaries. Previous studies have primarily tested derivationally complex words or compound words, but have not examined a more rule-based and productive morphological…

A data driven partial ambiguity resolution: Two step success rate criterion, and its simulation demonstration

NASA Astrophysics Data System (ADS)

Hou, Yanqing; Verhagen, Sandra; Wu, Jie

2016-12-01

Ambiguity Resolution (AR) is a key technique in GNSS precise positioning. In case of weak models (i.e., low precision of data), however, the success rate of AR may be low, which may consequently introduce large errors to the baseline solution in cases of wrong fixing. Partial Ambiguity Resolution (PAR) is therefore proposed such that the baseline precision can be improved by fixing only a subset of ambiguities with high success rate. This contribution proposes a new PAR strategy, allowing to select the subset such that the expected precision gain is maximized among a set of pre-selected subsets, while at the same time the failure rate is controlled. These pre-selected subsets are supposed to obtain the highest success rate among those with the same subset size. The strategy is called Two-step Success Rate Criterion (TSRC) as it will first try to fix a relatively large subset with the fixed failure rate ratio test (FFRT) to decide on acceptance or rejection. In case of rejection, a smaller subset will be fixed and validated by the ratio test so as to fulfill the overall failure rate criterion. It is shown how the method can be practically used, without introducing a large additional computation effort. And more importantly, how it can improve (or at least not deteriorate) the availability in terms of baseline precision comparing to classical Success Rate Criterion (SRC) PAR strategy, based on a simulation validation. In the simulation validation, significant improvements are obtained for single-GNSS on short baselines with dual-frequency observations. For dual-constellation GNSS, the improvement for single-frequency observations on short baselines is very significant, on average 68%. For the medium- to long baselines, with dual-constellation GNSS the average improvement is around 20-30%.

TEs or not TEs? That is the evolutionary question.

PubMed

Vaknin, Keren; Goren, Amir; Ast, Gil

2009-10-23

Transposable elements (TEs) have contributed a wide range of functional sequences to their host genomes. A recent paper in BMC Molecular Biology discusses the creation of new transcripts by transposable element insertion upstream of retrocopies and the involvement of such insertions in tissue-specific post-transcriptional regulation.

A non-autonomous insect piggyBac trasposable element is mobile in tobacco

USDA-ARS?s Scientific Manuscript database

The piggyBac transposable element, originally isolated from a virus in an insect cell line, is a valuable molecular tool for transgenesis and mutagenesis of invertebrates. For heterologous transgenesis in a variety of mammals, transfer of the piggyBac transposable element from an ectopic plasmid onl...

The hobo transposable element has transposase-dependent and -independent excision activity in drosophilid species

USDA-ARS?s Scientific Manuscript database

Mobility of the hobo transposable element was determined for several strains of Drosophila melanogaster and several Drosophila species. Mobility was assessed by use of an in vivo transient assay in the soma of developing embryos, which monitored hobo excision from injected indicator plasmids. Excisi...

In vitro fertilization surrogate pregnancy in a patient who underwent radical hysterectomy followed by ovarian transposition, lower abdominal wall radiotherapy, and chemotherapy.

PubMed

Steigrad, Stephen; Hacker, Neville F; Kolb, Bradford

2005-05-01

To describe an IVF surrogate pregnancy from a patient who had a radical hysterectomy followed by excision of a laparoscopic port site implantation with ovarian transposition followed by abdominal wall irradiation and chemotherapy, which resulted in premature ovarian failure from which there was partial recovery. Case report. Tertiary referral university women's hospital in Sydney, Australia and private reproductive medicine clinic in California. A 34-year-old woman who underwent laparoscopy for pelvic pain, shortly afterward followed by radical hysterectomy and pelvic lymph node dissection, who subsequently developed a laparoscopic port site recurrence, which was excised in association with ovarian transposition before abdominal wall irradiation and chemotherapy. Modified IVF treatment, transabdominal oocyte retrieval, embryo cryopreservation in Australia, and transfer to a surrogate mother in the United States. Pregnancy. Miscarriage in the second cycle and a twin pregnancy in the fourth cycle. This is the first case report of ovarian stimulation and oocyte retrieval performed on transposed ovaries after a patient developed premature ovarian failure after radiotherapy and chemotherapy with subsequent partial ovarian recovery.

The free growth criterion for grain initiation in TiB 2 inoculated γ-titanium aluminide based alloys

NASA Astrophysics Data System (ADS)

Gosslar, D.; Günther, R.

2014-02-01

γ-titanium aluminide (γ-TiAl) based alloys enable for the design of light-weight and high-temperature resistant engine components. This work centers on a numerical study of the condition for grain initiation during solidification of TiB2 inoculated γ-TiAl based alloys. Grain initiation is treated according to the so-called free growth criterion. This means that the free growth barrier for grain initiation is determined by the maximum interfacial mean curvature between a nucleus and the melt. The strategy presented in this paper relies on iteratively increasing the volume of a nucleus, which partially wets a hexagonal TiB2 crystal, minimizing the interfacial energy and calculating the corresponding interfacial curvature. The hereby obtained maximum curvature yields a scaling relation between the size of TiB2 crystals and the free growth barrier. Comparison to a prototypical TiB2 crystal in an as cast γ-TiAl based alloy allowed then to predict the free growth barrier prevailing under experimental conditions. The validity of the free growth criterion is discussed by an interfacial energy criterion.

Is comorbidity in the eating disorders related to perceptions of parenting? Criterion validity of the revised Young Parenting Inventory.

PubMed

Sheffield, Alexandra; Waller, Glenn; Emanuelli, Francesca; Murray, James

2006-01-01

Recent studies support the reliability and validity of the Young Parenting Inventory-Revised (YPI-R) and its use in investigating the role of parenting in the aetiology and maintenance of eating pathology. However, criterion validity has yet to be fully established. To investigate one aspect of criterion validity, this study examines the association between parenting and comorbid problems in the eating disorders (including general psychopathology and impulsivity). The participants were 124 women with eating disorders. They completed the YPI-R and the Brief Symptom Inventory (BSI; a measure of general psychopathology). They were also interviewed about their use of a number of impulsive behaviours. YPI-R scales were significant predictors of one of the nine BSI scales, and distinguished those patients who did or did not use specific impulsive behaviours. The criterion validity of the YPI-R is partially supported with regards to general psychopathology and impulsivity. The findings highlight the specificity of the parenting styles measured by the YPI-R, and the need for further research using this tool.

A mesh gradient technique for numerical optimization

NASA Technical Reports Server (NTRS)

Willis, E. A., Jr.

1973-01-01

A class of successive-improvement optimization methods in which directions of descent are defined in the state space along each trial trajectory are considered. The given problem is first decomposed into two discrete levels by imposing mesh points. Level 1 consists of running optimal subarcs between each successive pair of mesh points. For normal systems, these optimal two-point boundary value problems can be solved by following a routine prescription if the mesh spacing is sufficiently close. A spacing criterion is given. Under appropriate conditions, the criterion value depends only on the coordinates of the mesh points, and its gradient with respect to those coordinates may be defined by interpreting the adjoint variables as partial derivatives of the criterion value function. In level 2, the gradient data is used to generate improvement steps or search directions in the state space which satisfy the boundary values and constraints of the given problem.

Demonstration of analyzers for multimode photonic time-bin qubits

NASA Astrophysics Data System (ADS)

Jin, Jeongwan; Agne, Sascha; Bourgoin, Jean-Philippe; Zhang, Yanbao; Lütkenhaus, Norbert; Jennewein, Thomas

2018-04-01

We demonstrate two approaches for unbalanced interferometers as time-bin qubit analyzers for quantum communication, robust against mode distortions and polarization effects as expected from free-space quantum communication systems including wavefront deformations, path fluctuations, pointing errors, and optical elements. Despite strong spatial and temporal distortions of the optical mode of a time-bin qubit, entangled with a separate polarization qubit, we verify entanglement using the Negative Partial Transpose, with the measured visibility of up to 0.85 ±0.01 . The robustness of the analyzers is further demonstrated for various angles of incidence up to 0 .2∘ . The output of the interferometers is coupled into multimode fiber yielding a high system throughput of 0.74. Therefore, these analyzers are suitable and efficient for quantum communication over multimode optical channels.

Do Transposed-Letter Similarity Effects Occur at a Morpheme Level? Evidence for Morpho-Orthographic Decomposition

ERIC Educational Resources Information Center

Dunabeitia, Jon Andoni; Peream, Manuel; Carreiras, Manuel

2007-01-01

When does morphological decomposition occur in visual word recognition? An increasing body of evidence suggests the presence of early morphological processing. The present work investigates this issue via an orthographic similarity manipulation. Three masked priming lexical decision experiments were conducted to examine the transposed-letter…

A Stimulus Sampling Theory of Letter Identity and Order

ERIC Educational Resources Information Center

Norris, Dennis; Kinoshita, Sachiko; van Casteren, Maarten

2010-01-01

Early on during word recognition, letter positions are not accurately coded. Evidence for this comes from transposed-letter (TL) priming effects, in which letter strings generated by transposing two adjacent letters (e.g., "jugde") produce large priming effects, more than primes with the letters replaced in the corresponding position (e.g.,…

[Plant transposable elements and their application in genetics and biotechnology].

PubMed

Ovcharenko, O O; Rudas, V A; Kuchuk, M V

2006-01-01

Data concerning plant transposable elements and their contribution to plant genome evolution are reviewed. Much attention is focused on utilization of transgenic plants as heterologous hosts of transposons for investigation of transposition mechanisms and gene cloning. Probable ways of the use of plant transposons as genetic tools in biotechnology are discussed.

Does Kaniso activate CASINO?: input coding schemes and phonology in visual-word recognition.

PubMed

Acha, Joana; Perea, Manuel

2010-01-01

Most recent input coding schemes in visual-word recognition assume that letter position coding is orthographic rather than phonological in nature (e.g., SOLAR, open-bigram, SERIOL, and overlap). This assumption has been drawn - in part - by the fact that the transposed-letter effect (e.g., caniso activates CASINO) seems to be (mostly) insensitive to phonological manipulations (e.g., Perea & Carreiras, 2006, 2008; Perea & Pérez, 2009). However, one could argue that the lack of a phonological effect in prior research was due to the fact that the manipulation always occurred in internal letter positions - note that phonological effects tend to be stronger for the initial syllable (Carreiras, Ferrand, Grainger, & Perea, 2005). To reexamine this issue, we conducted a masked priming lexical decision experiment in which we compared the priming effect for transposed-letter pairs (e.g., caniso-CASINO vs. caviro-CASINO) and for pseudohomophone transposed-letter pairs (kaniso-CASINO vs. kaviro-CASINO). Results showed a transposed-letter priming effect for the correctly spelled pairs, but not for the pseudohomophone pairs. This is consistent with the view that letter position coding is (primarily) orthographic in nature.

The struggle for life of the genome's selfish architects

PubMed Central

2011-01-01

Transposable elements (TEs) were first discovered more than 50 years ago, but were totally ignored for a long time. Over the last few decades they have gradually attracted increasing interest from research scientists. Initially they were viewed as totally marginal and anecdotic, but TEs have been revealed as potentially harmful parasitic entities, ubiquitous in genomes, and finally as unavoidable actors in the diversity, structure, and evolution of the genome. Since Darwin's theory of evolution, and the progress of molecular biology, transposable elements may be the discovery that has most influenced our vision of (genome) evolution. In this review, we provide a synopsis of what is known about the complex interactions that exist between transposable elements and the host genome. Numerous examples of these interactions are provided, first from the standpoint of the genome, and then from that of the transposable elements. We also explore the evolutionary aspects of TEs in the light of post-Darwinian theories of evolution. Reviewers This article was reviewed by Jerzy Jurka, Jürgen Brosius and I. King Jordan. For complete reports, see the Reviewers' reports section. PMID:21414203

Letter position coding across modalities: the case of Braille readers.

PubMed

Perea, Manuel; García-Chamorro, Cristina; Martín-Suesta, Miguel; Gómez, Pablo

2012-01-01

The question of how the brain encodes letter position in written words has attracted increasing attention in recent years. A number of models have recently been proposed to accommodate the fact that transposed-letter stimuli like jugde or caniso are perceptually very close to their base words. Here we examined how letter position coding is attained in the tactile modality via Braille reading. The idea is that Braille word recognition may provide more serial processing than the visual modality, and this may produce differences in the input coding schemes employed to encode letters in written words. To that end, we conducted a lexical decision experiment with adult Braille readers in which the pseudowords were created by transposing/replacing two letters. We found a word-frequency effect for words. In addition, unlike parallel experiments in the visual modality, we failed to find any clear signs of transposed-letter confusability effects. This dissociation highlights the differences between modalities. The present data argue against models of letter position coding that assume that transposed-letter effects (in the visual modality) occur at a relatively late, abstract locus.

Rapid inactivation of the maize transposable element En/Spm in Medicago truncatula.

PubMed

d'Erfurth, I; Cosson, V; Eschstruth, A; Rippa, S; Messinese, E; Durand, P; Trinh, H; Kondorosi, A; Ratet, P

2003-09-01

Transposable elements have been widely used as mutagens in many organisms. Among them, the maize transposable element En/Spm has been shown to transpose efficiently in several plant species including the model plant Arabidopsis, where it has been used for large-scale mutagenesis. To determine whether we could use this transposon as a mutagen in the model legume plant Medicago truncatula, we tested the activity of the autonomous element, as well as two defective elements, in this plant, and in Arabidopsis as a positive control. In agreement with previous reports, we observed efficient excision of the autonomous En/Spm element in A. thaliana. This element was also active in M. truncatula, but the transposition activity was low and was apparently restricted to the tissue culture step necessary for the production of transgenic plants. The activity of one of the defective transposable elements, dSpm, was very low in A. thaliana and even lower in M. truncatula. The use of different sources of transposases suggested that this defect in transposition was associated with the dSpm element itself. Transposition of the other defective element, I6078, was also detected in M. truncatula, but, as observed with the autonomous element, transposition events were very rare and occurred during tissue culture. These results suggest that the En/Spm element is rapidly inactivated in the regenerated plants and their progeny, and therefore is not suitable for routine insertion mutagenesis in M. truncatula.

The Quiet Clam Is Quite Calm: Transposed-Letter Neighborhood Effects on Eye Movements during Reading

ERIC Educational Resources Information Center

Johnson, Rebecca L.

2009-01-01

In responses time tasks, inhibitory neighborhood effects have been found for word pairs that differ in a transposition of two adjacent letters (e.g., "clam/calm"). Here, the author describes two eye-tracking experiments conducted to explore transposed-letter (TL) neighborhood effects within the context of normal silent reading. In…

The diversity of sequence and chromosomal distribution of new transposable element-related segments in the rye genome revealed by FISH and lineage annotation

USDA-ARS?s Scientific Manuscript database

The rye genome features a high percentage of repetitive elements, especially transposable elements (TEs). However, studies about the constitution and organization of TEs on rye chromosomes are limited. In this study, 97 unique TE segments were isolated and characterized; 50 TE segmemts showed varyin...

Transposed Letter Priming with Horizontal and Vertical Text in Japanese and English Readers

ERIC Educational Resources Information Center

Witzel, Naoko; Qiao, Xiaomei; Forster, Kenneth

2011-01-01

It is well established that in masked priming, a target word (e.g., "JUDGE") is primed more effectively by a transposed letter (TL) prime (e.g., "jugde") than by an orthographic control prime (e.g., "junpe"). This is inconsistent with the slot coding schemes used in many models of visual word recognition. Several…

Genotype dependent burst of transposable element expression in crowns of hexaploid wheat (Triticum aestivum L.) during cold acclimation

USDA-ARS?s Scientific Manuscript database

The expression of 1,613 transposable elements (TEs) represented in the Affymetix Wheat Genome Chip was examined during cold treatment in crowns of 4 hexaploid wheat genotypes that vary in tolerance to cold and in flowering time. The TE expression profiles showed a constant level of expression throug...

Tn4556, a 6.8-kilobase-pair transposable element of Streptomyces fradiae.

PubMed Central

Chung, S T

1987-01-01

A 6.8-kilobase-pair (kbp) transposable element (Tn4556) was found in a neomycin-producing strain of Streptomyces fradiae. This element was first observed in two 30.3-kbp plasmids (pUC1123 and pUC1124) which arose when a thiostrepton resistance gene (1 kbp) was ligated with the BclI-2 fragment (22.5 kbp) that contains the origin of replication of phage SF1. The Tn4556 segment was deleted when these plasmids were transduced into another S. fradiae host with phage SF1. These deletion plasmids (pUC1210 and pUC1211) had copy numbers of less than 1 per chromosome and were unstable. In contrast, pUC1123 and pUC1124, with copy numbers of 12 to 15 per chromosome, respectively, were relatively stable. When pUC1210 and pUC1211 were reintroduced into S. fradiae by protoplast transformation, the Tn4556 element transposed again to the plasmids at numerous new locations in either of two orientations. A copy of Tn4556 was found in the S. fradiae chromosome by hybridization studies. It appears that Tn4556 originated from the chromosome, transposed into unstable pUC1210 and pUC1211, and made stable plasmids. A temperature-sensitive hybrid plasmid carrying a viomycin resistance derivative of Tn4556 (pMT660::Tn4556::vph) was constructed. When Streptomyces lividans UC8390 containing the hybrid plasmid was grown at 39 degrees C, Tn4556::vph (Tn4560) transposed to random positions in the host chromosome. Images PMID:2820925

Association between the location of transposed ovary and ovarian function in patients with uterine cervical cancer treated with (postoperative or primary) pelvic radiotherapy.

PubMed

Hwang, Jong Ha; Yoo, Heon Jong; Park, Sae Hyun; Lim, Myong Cheol; Seo, Sang-Soo; Kang, Sokbom; Kim, Joo-Young; Park, Sang-Yoon

2012-06-01

To evaluate the effectiveness of ovarian transposition procedures in preserving ovarian function in relation to the location of the transposed ovaries in patients who underwent surgery with or without pelvic radiotherapy. Retrospective. Uterine cancer center. A total of 53 patients with cervical cancer who underwent ovarian transposition between November 2002 and November 2010. Ovarian transposition to the paracolic gutters with or without radical hysterectomy and lymph node dissection. Preservation of ovarian function, which was assessed by patient's symptoms and serum FSH level. Lateral ovarian transposition was performed in 53 patients. Based on receiver operator characteristic curve analysis, optimum cutoff value of location more than 1.5 cm above the iliac crest was significantly associated with preservation of ovarian function after treatment (area under receiver operator characteristic curve: 0.757, 95% confidence interval [CI]: 0.572-0.943). In univariate analysis, higher location of transposed ovary more than 1.5 cm from the iliac crest was the only independent factor for intact ovarian function (odds ratio 9.91, 95% CI: 1.75-56.3). Multivariate analysis confirmed that the location of transposed ovary (odds ratio 11.72, 95% CI 1.64-83.39) was the most important factor for intact ovarian function. Location of transposed ovary higher than 1.5 cm above the iliac crest is recommended to avoid ovarian failure after lateral ovarian transposition after primary or adjuvant pelvic radiotherapy in cervical cancer. Copyright © 2012 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Identification and characterization of the first active endogenous transposable element in soybean

USDA-ARS?s Scientific Manuscript database

In soybean [Glycine max (L.) Merr.], W4 is one of the loci that control anthocyanin biosynthesis in flowers and hypocotyls. A putative transposable element was suggested to reside within or adjacent to this locus in the mutable T322 line resulting in the w4-m allele. We have shown that the W4 locu...

Moving from Science to Service: Transposing and Sustaining the Early Risers Prevention Program in a Community Service System

ERIC Educational Resources Information Center

Bloomquist, Michael L.; August, Gerald J.; Horowitz, Jason L.; Lee, Susanne S.; Jensen, Cheryl

2008-01-01

This paper summarizes an effort to transpose and sustain the evidence-based Early Risers "Skills for Success" conduct problems prevention program in a real world community service system. The Early Risers program had previously been implemented by a local agency within the context of research-based operations. In the current initiative,…

A Helitron-like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

USDA-ARS?s Scientific Manuscript database

Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A+T content (62.3%),...

Distributional Analysis of the Transposed-Letter Neighborhood Effect on Naming Latency

ERIC Educational Resources Information Center

Johnson, Rebecca L.; Staub, Adrian; Fleri, Amanda M.

2012-01-01

Printed words that have a transposed-letter (TL) neighbor (e.g., angel has the TL neighbor angle) have been shown to be more difficult to process, in a range of paradigms, than words that do not have a TL neighbor. However, eye movement evidence suggests that this processing difficulty may occur on only a subset of trials. To investigate this…

Albinism due to transposable element insertion in fish.

PubMed

Koga, A; Hori, H

1997-12-01

The i locus of the medaka fish, Oryzias latipes, is responsible for tyrosinase expression, and several mutant alleles have been identified. The genotype i1/i1 exhibits a complete albino phenotype, having pale orange-red skin and red eyes. This mutant lacks in vivo tyrosinase activity. The genotype i4/i4, on the other hand, shows a quasi-albino phenotype with skin as bright as that of i1/i1 but with red-wine-colored eyes. At the light microscope level, reduced pigmentation is observed both in the skin and eyes of this mutant. The tyrosinase genes for the i1 and the i4 alleles were cloned and sequenced, and compared with that of the wild-type tyrosinase gene. The i1 allele was found to contain a 1.9-kb transposable element in the 1st exon, and the i4 allele was found to contain a 4.7-kb transposable element in the 5th exon. Both i1 and i4 are alleles that were found in a commercial breeding population. The insertion of a transposable element thus appears to constitute a natural cause of mutations that cause albinism in this organism.

Letter Position Coding Across Modalities: The Case of Braille Readers

PubMed Central

Perea, Manuel; García-Chamorro, Cristina; Martín-Suesta, Miguel; Gómez, Pablo

2012-01-01

Background The question of how the brain encodes letter position in written words has attracted increasing attention in recent years. A number of models have recently been proposed to accommodate the fact that transposed-letter stimuli like jugde or caniso are perceptually very close to their base words. Methodology Here we examined how letter position coding is attained in the tactile modality via Braille reading. The idea is that Braille word recognition may provide more serial processing than the visual modality, and this may produce differences in the input coding schemes employed to encode letters in written words. To that end, we conducted a lexical decision experiment with adult Braille readers in which the pseudowords were created by transposing/replacing two letters. Principal Findings We found a word-frequency effect for words. In addition, unlike parallel experiments in the visual modality, we failed to find any clear signs of transposed-letter confusability effects. This dissociation highlights the differences between modalities. Conclusions The present data argue against models of letter position coding that assume that transposed-letter effects (in the visual modality) occur at a relatively late, abstract locus. PMID:23071522

Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids

PubMed Central

Romero-Soriano, Valèria; Modolo, Laurent; Lopez-Maestre, Hélène; Mugat, Bruno; Pessia, Eugénie; Chambeyron, Séverine; Vieira, Cristina

2017-01-01

Abstract Interspecific hybridization is a genomic stress condition that leads to the activation of transposable elements (TEs) in both animals and plants. In hybrids between Drosophila buzzatii and Drosophila koepferae, mobilization of at least 28 TEs has been described. However, the molecular mechanisms underlying this TE release remain poorly understood. To give insight on the causes of this TE activation, we performed a TE transcriptomic analysis in ovaries (notorious for playing a major role in TE silencing) of parental species and their F1 and backcrossed (BC) hybrids. We find that 15.2% and 10.6% of the expressed TEs are deregulated in F1 and BC1 ovaries, respectively, with a bias toward overexpression in both cases. Although differences between parental piRNA (Piwi-interacting RNA) populations explain only partially these results, we demonstrate that piRNA pathway proteins have divergent sequences and are differentially expressed between parental species. Thus, a functional divergence of the piRNA pathway between parental species, together with some differences between their piRNA pools, might be at the origin of hybrid instabilities and ultimately cause TE misregulation in ovaries. These analyses were complemented with the study of F1 testes, where TEs tend to be less expressed than in D. buzzatii. This can be explained by an increase in piRNA production, which probably acts as a defence mechanism against TE instability in the male germline. Hence, we describe a differential impact of interspecific hybridization in testes and ovaries, which reveals that TE expression and regulation are sex-biased. PMID:28854624

LINE-1 Elements in Structural Variation and Disease

PubMed Central

Beck, Christine R.; Garcia-Perez, José Luis; Badge, Richard M.; Moran, John V.

2014-01-01

The completion of the human genome reference sequence ushered in a new era for the study and discovery of human transposable elements. It now is undeniable that transposable elements, historically dismissed as junk DNA, have had an instrumental role in sculpting the structure and function of our genomes. In particular, long interspersed element-1 (LINE-1 or L1) and short interspersed elements (SINEs) continue to affect our genome, and their movement can lead to sporadic cases of disease. Here, we briefly review the types of transposable elements present in the human genome and their mechanisms of mobility. We next highlight how advances in DNA sequencing and genomic technologies have enabled the discovery of novel retrotransposons in individual genomes. Finally, we discuss how L1-mediated retrotransposition events impact human genomes. PMID:21801021

A Navier-Strokes Chimera Code on the Connection Machine CM-5: Design and Performance

NASA Technical Reports Server (NTRS)

Jespersen, Dennis C.; Levit, Creon; Kwak, Dochan (Technical Monitor)

1994-01-01

We have implemented a three-dimensional compressible Navier-Stokes code on the Connection Machine CM-5. The code is set up for implicit time-stepping on single or multiple structured grids. For multiple grids and geometrically complex problems, we follow the 'chimera' approach, where flow data on one zone is interpolated onto another in the region of overlap. We will describe our design philosophy and give some timing results for the current code. A parallel machine like the CM-5 is well-suited for finite-difference methods on structured grids. The regular pattern of connections of a structured mesh maps well onto the architecture of the machine. So the first design choice, finite differences on a structured mesh, is natural. We use centered differences in space, with added artificial dissipation terms. When numerically solving the Navier-Stokes equations, there are liable to be some mesh cells near a solid body that are small in at least one direction. This mesh cell geometry can impose a very severe CFL (Courant-Friedrichs-Lewy) condition on the time step for explicit time-stepping methods. Thus, though explicit time-stepping is well-suited to the architecture of the machine, we have adopted implicit time-stepping. We have further taken the approximate factorization approach. This creates the need to solve large banded linear systems and creates the first possible barrier to an efficient algorithm. To overcome this first possible barrier we have considered two options. The first is just to solve the banded linear systems with data spread over the whole machine, using whatever fast method is available. This option is adequate for solving scalar tridiagonal systems, but for scalar pentadiagonal or block tridiagonal systems it is somewhat slower than desired. The second option is to 'transpose' the flow and geometry variables as part of the time-stepping process: Start with x-lines of data in-processor. Form explicit terms in x, then transpose so y-lines of data are in-processor. Form explicit terms in y, then transpose so z-lines are in processor. Form explicit terms in z, then solve linear systems in the z-direction. Transpose to the y-direction, then solve linear systems in the y-direction. Finally transpose to the x direction and solve linear systems in the x-direction. This strategy avoids inter-processor communication when differencing and solving linear systems, but requires a large amount of communication when doing the transposes. The transpose method is more efficient than the non-transpose strategy when dealing with scalar pentadiagonal or block tridiagonal systems. For handling geometrically complex problems the chimera strategy was adopted. For multiple zone cases we compute on each zone sequentially (using the whole parallel machine), then send the chimera interpolation data to a distributed data structure (array) laid out over the whole machine. This information transfer implies an irregular communication pattern, and is the second possible barrier to an efficient algorithm. We have implemented these ideas on the CM-5 using CMF (Connection Machine Fortran), a data parallel language which combines elements of Fortran 90 and certain extensions, and which bears a strong similarity to High Performance Fortran. We make use of the Connection Machine Scientific Software Library (CMSSL) for the linear solver and array transpose operations.

Technical Note: Approximate solution of transient drawdown for constant-flux pumping at a partially penetrating well in a radial two-zone confined aquifer

NASA Astrophysics Data System (ADS)

Huang, C.-S.; Yang, S.-Y.; Yeh, H.-D.

2015-03-01

An aquifer consisting of a skin zone and a formation zone is considered as a two-zone aquifer. Existing solutions for the problem of constant-flux pumping (CFP) in a two-zone confined aquifer involve laborious calculation. This study develops a new approximate solution for the problem based on a mathematical model including two steady-state flow equations with different hydraulic parameters for the skin and formation zones. A partially penetrating well may be treated as the Neumann condition with a known flux along the screened part and zero flux along the unscreened part. The aquifer domain is finite with an outer circle boundary treated as the Dirichlet condition. The steady-state drawdown solution of the model is derived by the finite Fourier cosine transform. Then, an approximate transient solution is developed by replacing the radius of the boundary in the steady-state solution with an analytical expression for a dimensionless time-dependent radius of influence. The approximate solution is capable of predicting good temporal drawdown distributions over the whole pumping period except at the early stage. A quantitative criterion for the validity of neglecting the vertical flow component due to a partially penetrating well is also provided. Conventional models considering radial flow without the vertical component for the CFP have good accuracy if satisfying the criterion.

Knowledge of removable partial denture wearers on denture hygiene.

PubMed

Milward, P; Katechia, D; Morgan, M Z

2013-11-01

Regular good denture hygiene by individuals with removable partial dentures (RPDs) is an important component of oral health and in the prevention of further dental problems. These individuals should be provided with advice on the importance of denture care and be aware of this information. To establish deficiencies in patient knowledge surrounding denture hygiene by RPD wearers. The study was undertaken as an audit. Data was collected from April 2012 to October 2012 via a questionnaire completed by 196 RPD wearers attending as patients at the University Dental Hospital Wales and the dental units at St David's Hospital and Cynon Valley Hospital. The audit criterion was patients with RPDs should have knowledge of denture hygiene, with the standard set at 100%. While 91.8% of participants stated they were provided with instructions on denture hygiene when provided with their current prosthesis, 60.2% were shown to have less than an appropriate level of denture cleanliness, with 9.2% reporting that they slept wearing their prosthesis. The audit criterion and standard set were not achieved. A lack of knowledge surrounding denture hygiene was demonstrated among participants. As a part of the audit process the health education of RPD wearers' hygiene needs to be improved and awareness levels of the whole dental team needs to be raised. All partial dentures should receive information and regular reinforcement of key dental hygiene messages.

Entanglement spectrum degeneracy and the Cardy formula in 1+1 dimensional conformal field theories

NASA Astrophysics Data System (ADS)

Alba, Vincenzo; Calabrese, Pasquale; Tonni, Erik

2018-01-01

We investigate the effect of a global degeneracy in the distribution of the entanglement spectrum in conformal field theories in one spatial dimension. We relate the recently found universal expression for the entanglement Hamiltonian to the distribution of the entanglement spectrum. The main tool to establish this connection is the Cardy formula. It turns out that the Affleck-Ludwig non-integer degeneracy, appearing because of the boundary conditions induced at the entangling surface, can be directly read from the entanglement spectrum distribution. We also clarify the effect of the non-integer degeneracy on the spectrum of the partial transpose, which is the central object for quantifying the entanglement in mixed states. We show that the exact knowledge of the entanglement spectrum in some integrable spin-chains provides strong analytical evidences corroborating our results.

Transposition of Francis turbine cavitation compliance at partial load to different operating conditions

NASA Astrophysics Data System (ADS)

Gomes, J.; Favrel, A.; Landry, C.; Nicolet, C.; Avellan, F.

2017-04-01

Francis turbines operating in part load conditions experience a swirling flow at the runner outlet leading to the development of a precessing cavitation vortex rope in the draft tube. This cavitation vortex rope changes drastically the velocity of pressure waves traveling in the draft tube and may lead to resonance conditions in the hydraulic circuit. The wave speed being strongly related to the cavitation compliance, this research work presents a simple model to explain how it is affected by variations of operating conditions and proposes a method to transpose its values. Even though the focus of this paper is on transpositions within the same turbine scale, the methodology is also expected to be tested for the model to prototype transposition in the future. Comparisons between measurements and calculations are in good agreement.

Renormalization of the global quantum correlation and monogamy relation in the anisotropic Heisenberg XXZ model

NASA Astrophysics Data System (ADS)

Qin, Meng; Ren, Zhong-Zhou; Zhang, Xin

2016-01-01

In this study, the global quantum correlation, monogamy relation and quantum phase transition of the Heisenberg XXZ model are investigated by the method of quantum renormalization group. We obtain, analytically, the expressions of the global negativity, the global measurement-induced disturbance and the monogamy relation for the system. The result shows that for a three-site block state, the partial transpose of an asymmetric block can get stronger entanglement than that of the symmetric one. The residual entanglement and the difference of the monogamy relation of measurement-induced disturbance show a scaling behavior with the size of the system becoming large. Moreover, the monogamy nature of entanglement measured by negativity exists in the model, while the nonclassical correlation quantified by measurement-induced disturbance violates the monogamy relation and demonstrates polygamy.

Measurement-Device-Independent Approach to Entanglement Measures

NASA Astrophysics Data System (ADS)

Shahandeh, Farid; Hall, Michael J. W.; Ralph, Timothy C.

2017-04-01

Within the context of semiquantum nonlocal games, the trust can be removed from the measurement devices in an entanglement-detection procedure. Here, we show that a similar approach can be taken to quantify the amount of entanglement. To be specific, first, we show that in this context, a small subset of semiquantum nonlocal games is necessary and sufficient for entanglement detection in the local operations and classical communication paradigm. Second, we prove that the maximum payoff for these games is a universal measure of entanglement which is convex and continuous. Third, we show that for the quantification of negative-partial-transpose entanglement, this subset can be further reduced down to a single arbitrary element. Importantly, our measure is measurement device independent by construction and operationally accessible. Finally, our approach straightforwardly extends to quantify the entanglement within any partitioning of multipartite quantum states.

Entanglement criteria via the uncertainty relations in su(2) and su(1,1) algebras: Detection of non-Gaussian entangled states

NASA Astrophysics Data System (ADS)

Nha, Hyunchul; Kim, Jaewan

2006-07-01

We derive a class of inequalities, from the uncertainty relations of the su(1,1) and the su(2) algebra in conjunction with partial transposition, that must be satisfied by any separable two-mode states. These inequalities are presented in terms of the su(2) operators Jx=(a†b+ab†)/2 , Jy=(a†b-ab†)/2i , and the total photon number ⟨Na+Nb⟩ . They include as special cases the inequality derived by Hillery and Zubairy [Phys. Rev. Lett. 96, 050503 (2006)], and the one by Agarwal and Biswas [New J. Phys. 7, 211 (2005)]. In particular, optimization over the whole inequalities leads to the criterion obtained by Agarwal and Biswas. We show that this optimal criterion can detect entanglement for a broad class of non-Gaussian entangled states, i.e., the su(2) minimum-uncertainty states. Experimental schemes to test the optimal criterion are also discussed, especially the one using linear optical devices and photodetectors.

Preview Effects of Plausibility and Character Order in Reading Chinese Transposed Words: Evidence from Eye Movements

ERIC Educational Resources Information Center

Yang, Jinmian

2013-01-01

The current paper examined the role of plausibility information in the parafovea for Chinese readers by using two-character transposed words (in which the order of the component characters is reversed but are still words). In two eye-tracking experiments, readers received a preview of a target word that was (1) identical to the target word, (2) a…

The endogenous transposable element Tgm9 is suitable for functional analyses of soybean genes and generating novel mutants for genetic improvement of soybean

USDA-ARS?s Scientific Manuscript database

In soybean, variegated flowers can be caused by somatic excision of the CACTA-type transposable element Tgm9 from intron 2 of the DFR2 gene encoding dihydroflavonol-4-reductase in the anthocyanin pigment biosynthetic pathway. DFR2 has been mapped to the W4 locus where the allele containing the elem...

Unextendible product bases and extremal density matrices with positive partial transpose

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

Oyvind Sollid, Per; Magne Leinaas, Jon; Myrheim, Jan

2011-10-15

In bipartite quantum systems of dimension 3x3, entangled states that are positive under partial transposition (PPT) can be constructed with the use of unextendible product bases (UPBs). As discussed in a previous publication, all the lowest rank entangled PPT states of this system seem to be equivalent, under SL x SL transformations, to states that are constructed in this way. Here we consider a possible generalization of the UPB constuction to low-rank entangled PPT states in higher dimensions. The idea is to give up the condition of orthogonality of the product vectors, while keeping the relation between the density matrixmore » and the projection on the subspace defined by the UPB. We examine first this generalization for the 3x3 system where numerical studies indicate that one-parameter families of such generalized states can be found. Similar numerical searches in higher dimensional systems show the presence of extremal PPT states of similar form. Based on these results we suggest that the UPB construction of the lowest rank entangled states in the 3x3 system can be generalized to higher dimensions, with the use of nonorthogonal UPBs.« less

Factor Retention in Exploratory Factor Analysis: A Comparison of Alternative Methods.

ERIC Educational Resources Information Center

Mumford, Karen R.; Ferron, John M.; Hines, Constance V.; Hogarty, Kristine Y.; Kromrey, Jeffery D.

This study compared the effectiveness of 10 methods of determining the number of factors to retain in exploratory common factor analysis. The 10 methods included the Kaiser rule and a modified Kaiser criterion, 3 variations of parallel analysis, 4 regression-based variations of the scree procedure, and the minimum average partial procedure. The…

The infinum principle

NASA Technical Reports Server (NTRS)

Geering, H. P.; Athans, M.

1973-01-01

A complete theory of necessary and sufficient conditions is discussed for a control to be superior with respect to a nonscalar-valued performance criterion. The latter maps into a finite dimensional, integrally closed directed, partially ordered linear space. The applicability of the theory to the analysis of dynamic vector estimation problems and to a class of uncertain optimal control problems is demonstrated.

Acquisition, Maintenance and Generalization of Vending Machine Purchasing Skills by Moderately Handicapped Students.

ERIC Educational Resources Information Center

Nietupski, John; And Others

1984-01-01

Four elementary age moderately disabled students were taught to use a picture-prompt prosthetic to make vending machine purchases. All students reached criterion on the vending machine use task, demonstrated partial generalization to untrained machines, and three Ss exhibited maintenance as much as six weeks beyond the termination of instruction.…

Development of Bone-Conducted Ultrasonic Hearing Aid for the Profoundly Deaf: Assessments of the Modulation Type with Regard to Intelligibility and Sound Quality

NASA Astrophysics Data System (ADS)

Nakagawa, Seiji; Fujiyuki, Chika; Kagomiya, Takayuki

2012-07-01

Bone-conducted ultrasound (BCU) is perceived even by the profoundly sensorineural deaf. A novel hearing aid using the perception of amplitude-modulated BCU (BCU hearing aid: BCUHA) has been developed; however, further improvements are needed, especially in terms of articulation and sound quality. In this study, the intelligibility and sound quality of BCU speech with several types of amplitude modulation [double-sideband with transmitted carrier (DSB-TC), double-sideband with suppressed carrier (DSB-SC), and transposed modulation] were evaluated. The results showed that DSB-TC and transposed speech were more intelligible than DSB-SC speech, and transposed speech was closer than the other types of BCU speech to air-conducted speech in terms of sound quality. These results provide useful information for further development of the BCUHA.

Analysis of metal tolerance in Rhizobium leguminosarum strains isolated from an ultramafic soil.

PubMed

Rubio-Sanz, Laura; Brito, Belén; Palacios, Jose

2018-02-01

Natural habitats containing high amounts of heavy metals provide a valuable source of bacteria adapted to deal with metal toxicity. A functional analysis of the population of legume endosymbiotic bacteria in an ultramafic soil was undertaken by studying a collection of Rhizobium leguminosarum bv viciae (Rlv) isolates obtained using pea as trap plant. One of the isolates, Rlv UPM1137, was selected on the basis of its higher tolerance to nickel and cobalt and presence of inducible mechanisms for such tolerance. A random transposon mutagenesis of Rlv UPM1137 allowed the generation of 14 transposant derivatives with increased nickel sensitivity; five of these transposants were also more sensitive to cobalt. Sequencing of the insertion sites revealed that one of the transposants (D2250) was affected in a gene homologous to the cation diffusion facilitator gene dmeF first identified in the metal-resistant bacterium Cupriavidus metallidurans CH34. The symbiotic performance of D2250 and two other transposants bearing single transposon insertions was unaffected under high-metal conditions, suggesting that, in contrast to previous observations in other Rlv strain, metal tolerance in UPM1137 under symbiotic conditions might be supported by functional redundancy between several mechanisms. © FEMS 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes

PubMed Central

Puterova, Janka; Razumova, Olga; Martinek, Tomas; Alexandrov, Oleg; Divashuk, Mikhail; Kubat, Zdenek; Hobza, Roman; Karlov, Gennady

2017-01-01

Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites but most satellites were found on autosomes. Transposable elements were located mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes. PMID:28057732

Substituted-letter and transposed-letter effects in a masked priming paradigm with French developing readers and dyslexics.

PubMed

Lété, Bernard; Fayol, Michel

2013-01-01

The aim of the study was to undertake a behavioral investigation of the development of automatic orthographic processing during reading acquisition in French. Following Castles and colleagues' 2007 study (Journal of Experimental Child Psychology, 97, 165-182) and their lexical tuning hypothesis framework, substituted-letter and transposed-letter primes were used in a masked priming paradigm with third graders, fifth graders, adults, and phonological dyslexics matched on reading level with the third graders. No priming effect was found in third graders. In adults, only a transposed-letter priming effect was found; there was no substituted-letter priming effect. Finally, fifth graders and dyslexics showed both substituted-letter and transposed-letter priming effects. Priming effects between the two groups were of the same magnitude after response time (RT) z-score transformation. Taken together, our results show that the pattern of priming effects found by Castles and colleagues in English normal readers emerges later in French normal readers. In other words, language orthographies seem to constrain the tuning of the orthographic system, with an opaque orthography producing faster tuning of orthographic processing than more transparent orthographies because of the high level of reliance on phonological decoding while learning to read. Copyright © 2012 Elsevier Inc. All rights reserved.

Letter-transposition effects are not universal: The impact of transposing letters in Hebrew

PubMed Central

Velan, Hadas; Frost, Ram

2009-01-01

We examined the effects of letter transposition in Hebrew in three masked-priming experiments. Hebrew, like English has an alphabetic orthography where sequential and contiguous letter strings represent phonemes. However, being a Semitic language it has a non-concatenated morphology that is based on root derivations. Experiment 1 showed that transposed-letter (TL) root primes inhibited responses to targets derived from the non-transposed root letters, and that this inhibition was unrelated to relative root frequency. Experiment 2 replicated this result and showed that if the transposed letters of the root created a nonsense-root that had no lexical representation, then no inhibition and no facilitation were obtained. Finally, Experiment 3 demonstrated that in contrast to English, French, or Spanish, TL nonword primes did not facilitate recognition of targets, and when the root letters embedded in them consisted of a legal root morpheme, they produced inhibition. These results suggest that lexical space in alphabetic orthographies may be structured very differently in different languages if their morphological structure diverges qualitatively. In Hebrew, lexical space is organized according to root families rather than simple orthographic structure, so that all words derived from the same root are interconnected or clustered together, independent of overall orthographic similarity. PMID:20161017

Shape selection criterion for cellular array during constrained growth of binary alloys - Need for low gravity experiment

NASA Technical Reports Server (NTRS)

Tewari, Surendra N.; Trivedi, Rohit

1991-01-01

Development of steady-state periodic cellular array is one of the critical problems in the study of nonlinear pattern formation during directional solidification of binary alloys. The criterion which establishes the values of cell tip radius and spacing under given growth condition is not known. Theoretical models, such as marginal stability and microscopic solvability, have been developed for purely diffusive regime. However, the experimental conditions where cellular structures are stable are precisely the ones where the convection effects are predominant. Thus, the critical data for meaningful evaluation of cellular array growth models can only be obtained by partial directional solidification and quenching experiments carried out in the low gravity environment of space.

Spec Rekindled-A Simple Torque Correction Mechanics for Transposed Teeth in Conjunction with Pre-adjusted Edgewise Appliance System.

PubMed

Singh, Harpreet; Maurya, Raj Kumar; Thakkar, Surbhi

2016-12-01

Complete transposition of teeth is a rather rare phenomenon. After correction of transposed and malaligned lateral incisor and canine, attainment of appropriate individual antagonistic tooth torque is indispensable, which many orthodontists consider to be a herculean task. Here, a novel method is proposed which demonstrates the use of Spec reverse torquing auxillary as an effective adjunctive aid in conjunction with pre-adjusted edgewise brackets.

Colonization of heterochromatic genes by transposable elements in Drosophila.

PubMed

Dimitri, Patrizio; Junakovic, Nikolaj; Arcà, Bruno

2003-04-01

As a further step toward understanding transposable element-host genome interactions, we investigated the molecular anatomy of introns from five heterochromatic and 22 euchromatic protein-coding genes of Drosophila melanogaster. A total of 79 kb of intronic sequences from heterochromatic genes and 355 kb of intronic sequences from euchromatic genes have been used in Blast searches against Drosophila transposable elements (TEs). The results show that TE-homologous sequences belonging to 19 different families represent about 50% of intronic DNA from heterochromatic genes. In contrast, only 0.1% of the euchromatic intron DNA exhibits homology to known TEs. Intraspecific and interspecific size polymorphisms of introns were found, which are likely to be associated with changes in TE-related sequences. Together, the enrichment in TEs and the apparent dynamic state of heterochromatic introns suggest that TEs contribute significantly to the evolution of genes located in heterochromatin.

[Active miniature inverted-repeat transposable elements transposon in plants: a review].

PubMed

Hu, Bingjie; Zhou, Mingbing

2018-02-25

Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family. Moreover, we summarize the structure (terminal inverse repeats and target site duplications), copy number, evolution pattern and transposition characteristics of these active MITEs, to provide the foundation for the identification of other active MITEs and subsequent research on MITE transposition and amplification mechanism.

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.

PubMed

Kuhn, Alexandre; Ong, Yao Min; Quake, Stephen R; Burkholder, William F

2015-07-08

Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed. We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds of optimization), cost-effective and highly accurate. This method can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.

Transposition of the maize transposable element Ac in barley (Hordeum vulgare L.).

PubMed

Scholz, S; Lörz, H; Lütticke, S

2001-01-01

Transposition of the maize autonomous element Ac (Activator) was investigated in barley (Hordeum vulgare L.) with the aim of developing a transposon tagging system for the latter. The Ac element was introduced into meristematic tissue of barley by microprojectile bombardment. Transposon activity was then examined in the resulting transgenic plants. Multiple excision events were detected in leaf tissue of all plant lines. The mobile elements generated empty donor sites with small DNA sequence alterations, similar to those found in maize. Reintegration of Ac at independent genomic loci in somatic tissue was demonstrated by isolation of new element-flanking regions by AIMS-PCR (amplification of insertion-mutagenized sites). In addition, transmission of transposed Ac elements to progeny plants was confirmed. The results indicate that the introduced Ac element is able to transpose in barley. This is a first step towards the establishment of a transposon tagging system in this economically important crop.

Predicting Job Performance for the Visually Impaired: Validity of the Fine Finger Dexterity Work Task.

ERIC Educational Resources Information Center

Giesen, J. Martin; And Others

The study was designed to determine the reliability and criterion validity of a psychomotor performance test (the Fine Finger Dexterity Work Task Unit) with 40 partially or totally blind adults. Reliability was established by using the test-retest method. A supervisory rating was developed and the reliability established by using the split-half…

Entanglement negativity bounds for fermionic Gaussian states

NASA Astrophysics Data System (ADS)

Eisert, Jens; Eisler, Viktor; Zimborás, Zoltán

2018-04-01

The entanglement negativity is a versatile measure of entanglement that has numerous applications in quantum information and in condensed matter theory. It can not only efficiently be computed in the Hilbert space dimension, but for noninteracting bosonic systems, one can compute the negativity efficiently in the number of modes. However, such an efficient computation does not carry over to the fermionic realm, the ultimate reason for this being that the partial transpose of a fermionic Gaussian state is no longer Gaussian. To provide a remedy for this state of affairs, in this work, we introduce efficiently computable and rigorous upper and lower bounds to the negativity, making use of techniques of semidefinite programming, building upon the Lagrangian formulation of fermionic linear optics, and exploiting suitable products of Gaussian operators. We discuss examples in quantum many-body theory and hint at applications in the study of topological properties at finite temperature.

Technical Note: Approximate solution of transient drawdown for constant-flux pumping at a partially penetrating well in a radial two-zone confined aquifer

NASA Astrophysics Data System (ADS)

Huang, C.-S.; Yang, S.-Y.; Yeh, H.-D.

2015-06-01

An aquifer consisting of a skin zone and a formation zone is considered as a two-zone aquifer. Existing solutions for the problem of constant-flux pumping in a two-zone confined aquifer involve laborious calculation. This study develops a new approximate solution for the problem based on a mathematical model describing steady-state radial and vertical flows in a two-zone aquifer. Hydraulic parameters in these two zones can be different but are assumed homogeneous in each zone. A partially penetrating well may be treated as the Neumann condition with a known flux along the screened part and zero flux along the unscreened part. The aquifer domain is finite with an outer circle boundary treated as the Dirichlet condition. The steady-state drawdown solution of the model is derived by the finite Fourier cosine transform. Then, an approximate transient solution is developed by replacing the radius of the aquifer domain in the steady-state solution with an analytical expression for a dimensionless time-dependent radius of influence. The approximate solution is capable of predicting good temporal drawdown distributions over the whole pumping period except at the early stage. A quantitative criterion for the validity of neglecting the vertical flow due to a partially penetrating well is also provided. Conventional models considering radial flow without the vertical component for the constant-flux pumping have good accuracy if satisfying the criterion.

A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response.

PubMed

Bousios, Alexandros; Diez, Concepcion M; Takuno, Shohei; Bystry, Vojtech; Darzentas, Nikos; Gaut, Brandon S

2016-02-01

Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length of TEs, yet this information may provide crucial insights into the dynamics between hosts and TEs. By focusing on 6456 carefully annotated, full-length Sirevirus LTR retrotransposons in maize, we show that their silencing associates with underlying characteristics of the TE sequence and also uncover three features of the host-TE interaction. First, siRNA mapping varies among families and among elements, but particularly along the length of elements. Within the cis-regulatory portion of the LTRs, a complex palindrome-rich region acts as a hotspot of both siRNA matching and sequence evolution. These patterns are consistent across leaf, tassel, and immature ear libraries, but particularly emphasized for floral tissues and 21- to 22-nt siRNAs. Second, this region has the ability to form hairpins, making it a potential template for the production of miRNA-like, hairpin-derived small RNAs. Third, Sireviruses are targeted by siRNAs as a decreasing function of their age, but the oldest elements remain highly targeted, partially by siRNAs that cross-map to the youngest elements. We show that the targeting of older Sireviruses reflects their conserved palindromes. Altogether, we hypothesize that the palindromes aid the silencing of active elements and influence transposition potential, siRNA targeting levels, and ultimately the fate of an element within the genome. © 2016 Bousios et al.; Published by Cold Spring Harbor Laboratory Press.

Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids.

PubMed

Romero-Soriano, Valèria; Modolo, Laurent; Lopez-Maestre, Hélène; Mugat, Bruno; Pessia, Eugénie; Chambeyron, Séverine; Vieira, Cristina; Garcia Guerreiro, Maria Pilar

2017-06-01

Interspecific hybridization is a genomic stress condition that leads to the activation of transposable elements (TEs) in both animals and plants. In hybrids between Drosophila buzzatii and Drosophila koepferae, mobilization of at least 28 TEs has been described. However, the molecular mechanisms underlying this TE release remain poorly understood. To give insight on the causes of this TE activation, we performed a TE transcriptomic analysis in ovaries (notorious for playing a major role in TE silencing) of parental species and their F1 and backcrossed (BC) hybrids. We find that 15.2% and 10.6% of the expressed TEs are deregulated in F1 and BC1 ovaries, respectively, with a bias toward overexpression in both cases. Although differences between parental piRNA (Piwi-interacting RNA) populations explain only partially these results, we demonstrate that piRNA pathway proteins have divergent sequences and are differentially expressed between parental species. Thus, a functional divergence of the piRNA pathway between parental species, together with some differences between their piRNA pools, might be at the origin of hybrid instabilities and ultimately cause TE misregulation in ovaries. These analyses were complemented with the study of F1 testes, where TEs tend to be less expressed than in D. buzzatii. This can be explained by an increase in piRNA production, which probably acts as a defence mechanism against TE instability in the male germline. Hence, we describe a differential impact of interspecific hybridization in testes and ovaries, which reveals that TE expression and regulation are sex-biased. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Estimation from incomplete multinomial data. Ph.D. Thesis - Harvard Univ.

NASA Technical Reports Server (NTRS)

Credeur, K. R.

1978-01-01

The vector of multinomial cell probabilities was estimated from incomplete data, incomplete in that it contains partially classified observations. Each such partially classified observation was observed to fall in one of two or more selected categories but was not classified further into a single category. The data were assumed to be incomplete at random. The estimation criterion was minimization of risk for quadratic loss. The estimators were the classical maximum likelihood estimate, the Bayesian posterior mode, and the posterior mean. An approximation was developed for the posterior mean. The Dirichlet, the conjugate prior for the multinomial distribution, was assumed for the prior distribution.

Spec Rekindled-A Simple Torque Correction Mechanics for Transposed Teeth in Conjunction with Pre-adjusted Edgewise Appliance System

PubMed Central

Singh, Harpreet; Thakkar, Surbhi

2016-01-01

Complete transposition of teeth is a rather rare phenomenon. After correction of transposed and malaligned lateral incisor and canine, attainment of appropriate individual antagonistic tooth torque is indispensable, which many orthodontists consider to be a herculean task. Here, a novel method is proposed which demonstrates the use of Spec reverse torquing auxillary as an effective adjunctive aid in conjunction with pre-adjusted edgewise brackets. PMID:28209017

Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes.

PubMed

Puterova, Janka; Razumova, Olga; Martinek, Tomas; Alexandrov, Oleg; Divashuk, Mikhail; Kubat, Zdenek; Hobza, Roman; Karlov, Gennady; Kejnovsky, Eduard

2017-01-01

Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites but most satellites were found on autosomes. Transposable elements were located mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

DNA methylation dynamics during early plant life.

PubMed

Bouyer, Daniel; Kramdi, Amira; Kassam, Mohamed; Heese, Maren; Schnittger, Arp; Roudier, François; Colot, Vincent

2017-09-25

Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mammals, the extent to which DNA methylation is reset between generations in plants remains largely unknown. Using Arabidopsis as a model, we uncovered distinct DNA methylation dynamics over transposable element sequences during the early stages of plant development. Specifically, transposable elements and their relics show invariably high methylation at CG sites but increasing methylation at CHG and CHH sites. This non-CG methylation culminates in mature embryos, where it reaches saturation for a large fraction of methylated CHH sites, compared to the typical 10-20% methylation level observed in seedlings or adult plants. Moreover, the increase in CHH methylation during embryogenesis matches the hypomethylated state in the early endosperm. Finally, we show that interfering with the embryo-to-seedling transition results in the persistence of high CHH methylation levels after germination, specifically over sequences that are targeted by the RNA-directed DNA methylation (RdDM) machinery. Our findings indicate the absence of extensive resetting of DNA methylation patterns during early plant life and point instead to an important role of RdDM in reinforcing DNA methylation of transposable element sequences in every cell of the mature embryo. Furthermore, we provide evidence that this elevated RdDM activity is a specific property of embryogenesis.

Genetic and DNA sequence analysis of the kanamycin resistance transposon Tn903.

PubMed Central

Grindley, N D; Joyce, C M

1980-01-01

The kanamycin resistance transposon Tn903 consists of a unique region of about 1000 base pairs bounded by a pair of 1050-base-pair inverted repeat sequences. Each repeat contains two Pvu II endonuclease cleavage sites separated by 520 base pairs. We have constructed derivatives of Tn903 in which this 520-base-pair fragment is deleted from one or both repeats. Those derivatives that lack both 520-base-pair fragments cannot transpose, whereas those that lack just one remain transposition proficient. One such transposable derivative, Tn903 delta I, has been selected for further study. We have determined the sequence of the intact inverted repeat. The 18 base pairs at each end are identical and inverted relative to one another, a structure characteristic of insertion sequences. Additional experiments indicate that a single inverted repeat from Tn903 can, in fact, transpose; we propose that this element be called IS903. To correlate the DNA sequence with genetic activities, we have created mutations by inserting a 10-base-pair DNA fragment at several sites within the intact repeat of Tn903 delta 1, and we have examined the effect of such insertions on transposability. The results suggest that IS903 encodes a 307-amino-acid polypeptide (a "transposase") that is absolutely required for transposition of IS903 or Tn903. Images PMID:6261245

Atomistic potentials based energy flux integral criterion for dynamic adiabatic shear banding

NASA Astrophysics Data System (ADS)

Xu, Yun; Chen, Jun

2015-02-01

The energy flux integral criterion based on atomistic potentials within the framework of hyperelasticity-plasticity is proposed for dynamic adiabatic shear banding (ASB). System Helmholtz energy decomposition reveals that the dynamic influence on the integral path dependence is originated from the volumetric strain energy and partial deviatoric strain energy, and the plastic influence only from the rest part of deviatoric strain energy. The concept of critical shear banding energy is suggested for describing the initiation of ASB, which consists of the dynamic recrystallization (DRX) threshold energy and the thermal softening energy. The criterion directly relates energy flux to the basic physical processes that induce shear instability such as dislocation nucleations and multiplications, without introducing ad-hoc parameters in empirical constitutive models. It reduces to the classical path independent J-integral for quasi-static loading and elastic solids. The atomistic-to-continuum multiscale coupling method is used to simulate the initiation of ASB. Atomic configurations indicate that DRX induced microstructural softening may be essential to the dynamic shear localization and hence the initiation of ASB.

Cache and energy efficient algorithms for Nussinov's RNA Folding.

PubMed

Zhao, Chunchun; Sahni, Sartaj

2017-12-06

An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implementations of Nussinov's classical RNA folding algorithm have been proposed. Our focus is to obtain run time and energy efficiency by reducing the number of cache misses. Three cache-efficient algorithms, ByRow, ByRowSegment and ByBox, for Nussinov's RNA folding are developed. Using a simple LRU cache model, we show that the Classical algorithm of Nussinov has the highest number of cache misses followed by the algorithms Transpose (Li et al.), ByRow, ByRowSegment, and ByBox (in this order). Extensive experiments conducted on four computational platforms-Xeon E5, AMD Athlon 64 X2, Intel I7 and PowerPC A2-using two programming languages-C and Java-show that our cache efficient algorithms are also efficient in terms of run time and energy. Our benchmarking shows that, depending on the computational platform and programming language, either ByRow or ByBox give best run time and energy performance. The C version of these algorithms reduce run time by as much as 97.2% and energy consumption by as much as 88.8% relative to Classical and by as much as 56.3% and 57.8% relative to Transpose. The Java versions reduce run time by as much as 98.3% relative to Classical and by as much as 75.2% relative to Transpose. Transpose achieves run time and energy efficiency at the expense of memory as it takes twice the memory required by Classical. The memory required by ByRow, ByRowSegment, and ByBox is the same as that of Classical. As a result, using the same amount of memory, the algorithms proposed by us can solve problems up to 40% larger than those solvable by Transpose.

A specific insertion of a solo-LTR characterizes the Y-chromosome of Bryonia dioica (Cucurbitaceae).

PubMed

Oyama, Ryan K; Silber, Martina V; Renner, Susanne S

2010-06-14

Relatively few species of flowering plants are dioecious and even fewer are known to have sex chromosomes. Current theory posits that homomorphic sex chromosomes, such as found in Bryonia dioica (Cucurbitaceae), offer insight into the early stages in the evolution of sex chromosomes from autosomes. Little is known about these early steps, but an accumulation of transposable element sequences has been observed on the Y-chromosomes of some species with heteromorphic sex chromosomes. Recombination, by which transposable elements are removed, is suppressed on at least part of the emerging Y-chromosome, and this may explain the correlation between the emergence of sex chromosomes and transposable element enrichment. We sequenced 2321 bp of the Y-chromosome in Bryonia dioica that flank a male-linked marker, BdY1, reported previously. Within this region, which should be suppressed for recombination, we observed a solo-LTR nested in a Copia-like transposable element. We also found other, presumably paralogous, solo-LTRs in a consensus sequence of the underlying Copia-like transposable element. Given that solo-LTRs arise via recombination events, it is noteworthy that we find one in a genomic region where recombination should be suppressed. Although the solo-LTR could have arisen before recombination was suppressed, creating the male-linked marker BdY1, our previous study on B. dioica suggested that BdY1 may not lie in the recombination-suppressed region of the Y-chromosome in all populations. Presence of a solo-LTR near BdY1 therefore fits with the observed correlation between retrotransposon accumulation and the suppression of recombination early in the evolution of sex chromosomes. These findings further suggest that the homomorphic sex chromosomes of B. dioica, the first organism for which genetic XY sex-determination was inferred, are evolutionarily young and offer reference information for comparative studies of other plant sex chromosomes.

Measurement of the lowest dosage of phenobarbital that can produce drug discrimination in rats

PubMed Central

Overton, Donald A.; Stanwood, Gregg D.; Patel, Bhavesh N.; Pragada, Sreenivasa R.; Gordon, M. Kathleen

2009-01-01

Rationale Accurate measurement of the threshold dosage of phenobarbital that can produce drug discrimination (DD) may improve our understanding of the mechanisms and properties of such discrimination. Objectives Compare three methods for determining the threshold dosage for phenobarbital (D) versus no drug (N) DD. Methods Rats learned a D versus N DD in 2-lever operant training chambers. A titration scheme was employed to increase or decrease dosage at the end of each 18-day block of sessions depending on whether the rat had achieved criterion accuracy during the sessions just completed. Three criterion rules were employed, all based on average percent drug lever responses during initial links of the last 6 D and 6 N sessions of a block. The criteria were: D%>66 and N%<33; D%>50 and N%<50; (D%-N%)>33. Two squads of rats were trained, one immediately after the other. Results All rats discriminated drug versus no drug. In most rats, dosage decreased to low levels and then oscillated near the minimum level required to maintain criterion performance. The lowest discriminated dosage significantly differed under the three criterion rules. The squad that was trained 2nd may have benefited by partially duplicating the lever choices of the previous squad. Conclusions The lowest discriminated dosage is influenced by the criterion of discriminative control that is employed, and is higher than the absolute threshold at which discrimination entirely disappears. Threshold estimations closer to absolute threshold can be obtained when criteria are employed that are permissive, and that allow rats to maintain lever preferences. PMID:19082992

Feminist theorizing as 'transposed autobiography'.

PubMed

Hoogland, Renée C

2007-01-01

This piece considers personal investments endemic in academic writing, more specifically, in Lesbian Studies. Taking Elizabeth Bowen's phrase, "transposed autobiography," as a starting-point, the author briefly discusses the development of lesbian/straight feminist debates, and continues to explore the relative absence of lesbianism in current feminist and queer theorizing. Three 'moments' serve to explain the casting aside of lesbian desire: the subsidence of lesbian/straight feminist debates, the prevalence of 'race'/ethnicity in critical theorizing and the emergence of post-theoretical trends of thought.

Transposable elements as a molecular evolutionary force

NASA Technical Reports Server (NTRS)

Fedoroff, N. V.

1999-01-01

This essay addresses the paradoxes of the complex and highly redundant genomes. The central theses developed are that: (1) the distinctive feature of complex genomes is the existence of epigenetic mechanisms that permit extremely high levels of both tandem and dispersed redundancy; (2) the special contribution of transposable elements is to modularize the genome; and (3) the labilizing forces of recombination and transposition are just barely contained, giving a dynamic genetic system of ever increasing complexity that verges on the chaotic.

Marangoni-flow-induced partial coalescence of a droplet on a liquid/air interface

NASA Astrophysics Data System (ADS)

Sun, Kai; Zhang, Peng; Che, Zhizhao; Wang, Tianyou

2018-02-01

The coalescence of a droplet and a liquid/air interface of lower surface tension was numerically studied by using the lattice Boltzmann phase-field method. The experimental phenomenon of droplet ejection observed by Blanchette et al. [Phys. Fluids 21, 072107 (2009), 10.1063/1.3177339] at sufficiently large surface tension differences was successfully reproduced for the first time. Furthermore, the emergence, disappearance, and re-emergence of "partial coalescence" with increasing surface tension difference was observed and explained. The re-emergence of partial coalescence under large surface tension differences is caused by the remarkable lifting motion of the Marangoni flow, which significantly retards the vertical collapse. Two different modes of partial coalescence were identified by the simulation, namely peak injection occurs at lower Ohnesorge numbers and bottom pinch-off at higher Ohnesorge numbers. By comparing the characteristic timescales of the upward Marangoni flow with that of the downward flow driven by capillary pressure, a criterion for the transition from partial to total coalescence was derived based on scaling analysis and numerically validated.

Damage in Monolithic Thin-Film Photovoltaic Modules Due to Partial Shade

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

Silverman, Timothy J.; Mansfield, Lorelle; Repins, Ingrid

2016-09-01

The typical configuration of monolithic thin-film photovoltaic modules makes it possible for partial shade to place one or more cells in such a module in reverse bias. Reverse bias operation leads to high voltage, current density, and power density conditions, which can act as driving forces for failure. We showed that a brief outdoor shadow event can cause a 7% permanent loss in power. We applied an indoor partial shade durability test that moves beyond the standard hot spot endurance test by using more realistic mask and bias conditions and by carefully quantifying the permanent change in performance due tomore » the stress. With the addition of a pass criterion based on change in maximum power, this procedure will soon be proposed as a part of the module-type qualification test. All six commercial copper indium gallium diselenide and cadmium telluride modules we tested experienced permanent damage due to the indoor partial shade test, ranging from 4% to 14% loss in maximum power. We conclude by summarizing ways to mitigate partial shade stress at the cell, module, and system levels.« less

Male Germline Control of Transposable Elements1

PubMed Central

Bao, Jianqiang; Yan, Wei

2012-01-01

ABSTRACT Repetitive sequences, especially transposon-derived interspersed repetitive elements, account for a large fraction of the genome in most eukaryotes. Despite the repetitive nature, these transposable elements display quantitative and qualitative differences even among species of the same lineage. Although transposable elements contribute greatly as a driving force to the biological diversity during evolution, they can induce embryonic lethality and genetic disorders as a result of insertional mutagenesis and genomic rearrangement. Temporary relaxation of the epigenetic control of retrotransposons during early germline development opens a risky window that can allow retrotransposons to escape from host constraints and to propagate abundantly in the host genome. Because germline mutations caused by retrotransposon activation are heritable and thus can be deleterious to the offspring, an adaptive strategy has evolved in host cells, especially in the germline. In this review, we will attempt to summarize general defense mechanisms deployed by the eukaryotic genome, with an emphasis on pathways utilized by the male germline to confer retrotransposon silencing. PMID:22357546

Does letter rotation slow down orthographic processing in word recognition?

PubMed

Perea, Manuel; Marcet, Ana; Fernández-López, María

2018-02-01

Leading neural models of visual word recognition assume that letter rotation slows down the conversion of the visual input to a stable orthographic representation (e.g., local detectors combination model; Dehaene, Cohen, Sigman, & Vinckier, 2005, Trends in Cognitive Sciences, 9, 335-341). If this premise is true, briefly presented rotated primes should be less effective at activating word representations than those primes with upright letters. To test this question, we conducted a masked priming lexical decision experiment with vertically presented words either rotated 90° or in marquee format (i.e., vertically but with upright letters). We examined the impact of the format on both letter identity (masked identity priming: identity vs. unrelated) and letter position (masked transposed-letter priming: transposed-letter prime vs. replacement-letter prime). Results revealed sizeable masked identity and transposed-letter priming effects that were similar in magnitude for rotated and marquee words. Therefore, the reading cost from letter rotation does not arise in the initial access to orthographic/lexical representations.

Evolutionary interaction between W/Y chromosome and transposable elements.

PubMed

Śliwińska, Ewa B; Martyka, Rafał; Tryjanowski, Piotr

2016-06-01

The W/Y chromosome is unique among chromosomes as it does not recombine in its mature form. The main side effect of cessation of recombination is evolutionary instability and degeneration of the W/Y chromosome, or frequent W/Y chromosome turnovers. Another important feature of W/Y chromosome degeneration is transposable element (TEs) accumulation. Transposon accumulation has been confirmed for all W/Y chromosomes that have been sequenced so far. Models of W/Y chromosome instability include the assemblage of deleterious mutations in protein coding genes, but do not include the influence of transposable elements that are accumulated gradually in the non-recombining genome. The multiple roles of genomic TEs, and the interactions between retrotransposons and genome defense proteins are currently being studied intensively. Small RNAs originating from retrotransposon transcripts appear to be, in some cases, the only mediators of W/Y chromosome function. Based on the review of the most recent publications, we present knowledge on W/Y evolution in relation to retrotransposable element accumulation.

The application of the high throughput sequencing technology in the transposable elements.

PubMed

Liu, Zhen; Xu, Jian-hong

2015-09-01

High throughput sequencing technology has dramatically improved the efficiency of DNA sequencing, and decreased the costs to a great extent. Meanwhile, this technology usually has advantages of better specificity, higher sensitivity and accuracy. Therefore, it has been applied to the research on genetic variations, transcriptomics and epigenomics. Recently, this technology has been widely employed in the studies of transposable elements and has achieved fruitful results. In this review, we summarize the application of high throughput sequencing technology in the fields of transposable elements, including the estimation of transposon content, preference of target sites and distribution, insertion polymorphism and population frequency, identification of rare copies, transposon horizontal transfers as well as transposon tagging. We also briefly introduce the major common sequencing strategies and algorithms, their advantages and disadvantages, and the corresponding solutions. Finally, we envision the developing trends of high throughput sequencing technology, especially the third generation sequencing technology, and its application in transposon studies in the future, hopefully providing a comprehensive understanding and reference for related scientific researchers.

Transposed-letter priming effects in reading aloud words and nonwords.

PubMed

Mousikou, Petroula; Kinoshita, Sachiko; Wu, Simon; Norris, Dennis

2015-10-01

A masked nonword prime generated by transposing adjacent inner letters in a word (e.g., jugde) facilitates the recognition of the target word (JUDGE) more than a prime in which the relevant letters are replaced by different letters (e.g., junpe). This transposed-letter (TL) priming effect has been widely interpreted as evidence that the coding of letter position is flexible, rather than precise. Although the TL priming effect has been extensively investigated in the domain of visual word recognition using the lexical decision task, very few studies have investigated this empirical phenomenon in reading aloud. In the present study, we investigated TL priming effects in reading aloud words and nonwords and found that these effects are of equal magnitude for the two types of items. We take this result as support for the view that the TL priming effect arises from noisy perception of letter order within the prime prior to the mapping of orthography to phonology.

Recent Amplification of the Kangaroo Endogenous Retrovirus, KERV, Limited to the Centromere▿

PubMed Central

Ferreri, Gianni C.; Brown, Judith D.; Obergfell, Craig; Jue, Nathaniel; Finn, Caitlin E.; O'Neill, Michael J.; O'Neill, Rachel J.

2011-01-01

Mammalian retrotransposons, transposable elements that are processed through an RNA intermediate, are categorized as short interspersed elements (SINEs), long interspersed elements (LINEs), and long terminal repeat (LTR) retroelements, which include endogenous retroviruses. The ability of transposable elements to autonomously amplify led to their initial characterization as selfish or junk DNA; however, it is now known that they may acquire specific cellular functions in a genome and are implicated in host defense mechanisms as well as in genome evolution. Interactions between classes of transposable elements may exert a markedly different and potentially more significant effect on a genome than interactions between members of a single class of transposable elements. We examined the genomic structure and evolution of the kangaroo endogenous retrovirus (KERV) in the marsupial genus Macropus. The complete proviral structure of the kangaroo endogenous retrovirus, phylogenetic relationship among relative retroviruses, and expression of this virus in both Macropus rufogriseus and M. eugenii are presented for the first time. In addition, we show the relative copy number and distribution of the kangaroo endogenous retrovirus in the Macropus genus. Our data indicate that amplification of the kangaroo endogenous retrovirus occurred in a lineage-specific fashion, is restricted to the centromeres, and is not correlated with LINE depletion. Finally, analysis of KERV long terminal repeat sequences using massively parallel sequencing indicates that the recent amplification in M. rufogriseus is likely due to duplications and concerted evolution rather than a high number of independent insertion events. PMID:21389136

Isolation and molecular characterization of dTnp1, a mobile and defective transposable element of Nicotiana plumbaginifolia.

PubMed

Meyer, C; Pouteau, S; Rouzé, P; Caboche, M

1994-01-01

By Northern blot analysis of nitrate reductase-deficient mutants of Nicotiana plumbaginifolia, we identified a mutant (mutant D65), obtained after gamma-ray irradiation of protoplasts, which contained an insertion sequence in the nitrate reductase (NR) mRNA. This insertion sequence was localized by polymerase chain reaction (PCR) in the first exon of NR and was also shown to be present in the NR gene. The mutant gene contained a 565 bp insertion sequence that exhibits the sequence characteristics of a transposable element, which was thus named dTnp1. The dTnp1 element has 14 bp terminal inverted repeats and is flanked by an 8-bp target site duplication generated upon transposition. These inverted repeats have significant sequence homology with those of other transposable elements. Judging by its size and the absence of a long open reading frame, dTnp1 appears to represent a defective, although mobile, transposable element. The octamer motif TTTAGGCC was found several times in direct orientation near the 5' and 3' ends of dTnp1 together with a perfect palindrome located after the 5' inverted repeat. Southern blot analysis using an internal probe of dTnp1 suggested that this element occurs as a single copy in the genome of N. plumbaginifolia. It is also present in N. tabacum, but absent in tomato or petunia. The dTnp1 element is therefore of potential use for gene tagging in Nicotiana species.

Identification and applications of the Petunia class II Act1/dTph1 transposable element system.

PubMed

Gerats, Tom; Zethof, Jan; Vandenbussche, Michiel

2013-01-01

Transposable genetic elements are considered to be ubiquitous. Despite this, their mutagenic capacity has been exploited in only a few species. The main plant species are maize, Antirrhinum, and Petunia. Representatives of all three major groups of class II elements, viz., hAT-, CACTA- and Mutator-like elements, have been identified in Petunia. Here we focus on the research "history" of the Petunia two-element Act1-dTph1 system and the development of its application in forward- and reverse-genetics studies.

Sequence of retrovirus provirus resembles that of bacterial transposable elements

NASA Astrophysics Data System (ADS)

Shimotohno, Kunitada; Mizutani, Satoshi; Temin, Howard M.

1980-06-01

The nucleotide sequences of the terminal regions of an infectious integrated retrovirus cloned in the modified λ phage cloning vector Charon 4A have been elucidated. There is a 569-base pair direct repeat at both ends of the viral DNA. The cell-virus junctions at each end consist of a 5-base pair direct repeat of cell DNA next to a 3-base pair inverted repeat of viral DNA. This structure resembles that of a transposable element and is consistent with the protovirus hypothesis that retroviruses evolved from the cell genome.

Multi-tissue partial volume quantification in multi-contrast MRI using an optimised spectral unmixing approach.

PubMed

Collewet, Guylaine; Moussaoui, Saïd; Deligny, Cécile; Lucas, Tiphaine; Idier, Jérôme

2018-06-01

Multi-tissue partial volume estimation in MRI images is investigated with a viewpoint related to spectral unmixing as used in hyperspectral imaging. The main contribution of this paper is twofold. It firstly proposes a theoretical analysis of the statistical optimality conditions of the proportion estimation problem, which in the context of multi-contrast MRI data acquisition allows to appropriately set the imaging sequence parameters. Secondly, an efficient proportion quantification algorithm based on the minimisation of a penalised least-square criterion incorporating a regularity constraint on the spatial distribution of the proportions is proposed. Furthermore, the resulting developments are discussed using empirical simulations. The practical usefulness of the spectral unmixing approach for partial volume quantification in MRI is illustrated through an application to food analysis on the proving of a Danish pastry. Copyright © 2018 Elsevier Inc. All rights reserved.

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

DNA transposons have colonized the genome of the giant virus Pandoravirus salinus.

PubMed

Sun, Cheng; Feschotte, Cédric; Wu, Zhiqiang; Mueller, Rachel Lockridge

2015-06-12

Transposable elements are mobile DNA sequences that are widely distributed in prokaryotic and eukaryotic genomes, where they represent a major force in genome evolution. However, transposable elements have rarely been documented in viruses, and their contribution to viral genome evolution remains largely unexplored. Pandoraviruses are recently described DNA viruses with genome sizes that exceed those of some prokaryotes, rivaling parasitic eukaryotes. These large genomes appear to include substantial noncoding intergenic spaces, which provide potential locations for transposable element insertions. However, no mobile genetic elements have yet been reported in pandoravirus genomes. Here, we report a family of miniature inverted-repeat transposable elements (MITEs) in the Pandoravirus salinus genome, representing the first description of a virus populated with a canonical transposable element family that proliferated by transposition within the viral genome. The MITE family, which we name Submariner, includes 30 copies with all the hallmarks of MITEs: short length, terminal inverted repeats, TA target site duplication, and no coding capacity. Submariner elements show signs of transposition and are undetectable in the genome of Pandoravirus dulcis, the closest known relative Pandoravirus salinus. We identified a DNA transposon related to Submariner in the genome of Acanthamoeba castellanii, a species thought to host pandoraviruses, which contains remnants of coding sequence for a Tc1/mariner transposase. These observations suggest that the Submariner MITEs of P. salinus belong to the widespread Tc1/mariner superfamily and may have been mobilized by an amoebozoan host. Ten of the 30 MITEs in the P. salinus genome are located within coding regions of predicted genes, while others are close to genes, suggesting that these transposons may have contributed to viral genetic novelty. Our discovery highlights the remarkable ability of DNA transposons to colonize and shape genomes from all domains of life, as well as giant viruses. Our findings continue to blur the division between viral and cellular genomes, adhering to the emerging view that the content, dynamics, and evolution of the genomes of giant viruses do not substantially differ from those of cellular organisms.

Identification of a high frequency transposon induced by tissue culture, nDaiZ, a member of the hAT family in rice.

PubMed

Huang, Jian; Zhang, Kewei; Shen, Yi; Huang, Zejun; Li, Ming; Tang, Ding; Gu, Minghong; Cheng, Zhukuan

2009-03-01

Recent completion of rice genome sequencing has revealed that more than 40% of its genome consists of repetitive sequences, and most of them are related to inactive transposable elements. In the present study, a transposable element, nDaiZ0, which is induced by tissue culture with high frequency, was identified by sequence analysis of an allelic line of the golden hull and internode 2 (gh2) mutant, which was integrated into the forth exon of GH2. The 528-bp nDaiZ0 has 14-bp terminal inverted repeats (TIRs), and generates an 8-bp duplication of its target sites (TSD) during its mobilization. nDaiZs are non-autonomous transposons and have no coding capacity. Bioinformatics analysis and southern blot hybridization showed that at least 16 copies of nDaiZ elements exist in the japonica cultivar Nipponbare genome and 11 copies in the indica cultivar 93-11 genome. During tissue culture, only one copy, nDaiZ9, located on chromosome 5 in the genome of Nipponbare can be activated with its transposable frequency reaching 30%. However, nDaiZ9 was not present in the 93-11 genome. The larger elements, DaiZs, were further identified by database searching using nDaiZ0 as a query because they share similar TIRs and subterminal sequences. DaiZ can also generate an 8-bp TSD. DaiZ elements contain a conserved region with a high similarity to the hAT dimerization motif, suggesting that the nDaiZ-DaiZ transposon system probably belongs to the hAT superfamily of class II transposons. Phylogenetic analysis indicated that it is a new type of plant hAT-like transposon. Although nDaiZ is activated by tissue culture, the high transposable frequency indicates that it could become a useful gene tagging system for rice functional genomic studies. In addition, the mechanism of the high transposable ability of nDaiZ9 is discussed.

The Transposable Element Mariner Mediates Germline Transformation in Drosophila Melanogaster

PubMed Central

Lidholm, D. A.; Lohe, A. R.; Hartl, D. L.

1993-01-01

A vector for germline transformation in Drosophila melanogaster was constructed using the transposable element mariner. The vector, denoted pMlwB, contains a mariner element disrupted by an insertion containing the wild-type white gene from D. melanogaster, the β-galactosidase gene from Escherichia coli and sequences that enable plasmid replication and selection in E. coli. The white gene is controlled by the promoter of the D. melanogaster gene for heat-shock protein 70, and the β-galactosidase gene is flanked upstream by the promoter of the transposable element P as well as that of mariner. The MlwB element was introduced into the germline of D. melanogaster by co-injection into embryos with an active mariner element, Mos1, which codes for a functional transposase and serves as a helper. Two independent germline insertions were isolated and characterized. The results show that the MlwB element inserted into the genome in a mariner-dependent manner with the termini of the inverted repeats inserted at a TA dinucleotide. Both insertions exhibit an unexpected degree of germline and somatic stability, even in the presence of an active mariner element in the genetic background. These results demonstrate that the mariner transposable element, which is small (1286 bp) and relatively homogeneous in size among different copies, is nevertheless capable of promoting the insertion of the large (13.2 kb) MlwB element. Because of the widespread phylogenetic distribution of mariner among insects, these results suggest that mariner might provide a wide hostrange transformation vector for insects. PMID:8394264

The industrial melanism mutation in British peppered moths is a transposable element.

PubMed

Van't Hof, Arjen E; Campagne, Pascal; Rigden, Daniel J; Yung, Carl J; Lingley, Jessica; Quail, Michael A; Hall, Neil; Darby, Alistair C; Saccheri, Ilik J

2016-06-02

Discovering the mutational events that fuel adaptation to environmental change remains an important challenge for evolutionary biology. The classroom example of a visible evolutionary response is industrial melanism in the peppered moth (Biston betularia): the replacement, during the Industrial Revolution, of the common pale typica form by a previously unknown black (carbonaria) form, driven by the interaction between bird predation and coal pollution. The carbonaria locus has been coarsely localized to a 200-kilobase region, but the specific identity and nature of the sequence difference controlling the carbonaria-typica polymorphism, and the gene it influences, are unknown. Here we show that the mutation event giving rise to industrial melanism in Britain was the insertion of a large, tandemly repeated, transposable element into the first intron of the gene cortex. Statistical inference based on the distribution of recombined carbonaria haplotypes indicates that this transposition event occurred around 1819, consistent with the historical record. We have begun to dissect the mode of action of the carbonaria transposable element by showing that it increases the abundance of a cortex transcript, the protein product of which plays an important role in cell-cycle regulation, during early wing disc development. Our findings fill a substantial knowledge gap in the iconic example of microevolutionary change, adding a further layer of insight into the mechanism of adaptation in response to natural selection. The discovery that the mutation itself is a transposable element will stimulate further debate about the importance of 'jumping genes' as a source of major phenotypic novelty.

Correlation of LNCR rasiRNAs Expression with Heterochromatin Formation during Development of the Holocentric Insect Spodoptera frugiperda

PubMed Central

Stanojcic, Slavica; Gimenez, Sylvie; Permal, Emmanuelle; Cousserans, François; Quesneville, Hadi; Fournier, Philippe; d'Alençon, Emmanuelle

2011-01-01

Repeat-associated small interfering RNAs (rasiRNAs) are derived from various genomic repetitive elements and ensure genomic stability by silencing endogenous transposable elements. Here we describe a novel subset of 46 rasiRNAs named LNCR rasiRNAs due to their homology with one long non-coding RNA (LNCR) of Spodoptera frugiperda. LNCR operates as the intermediate of an unclassified transposable element (TE-LNCR). TE-LNCR is a very invasive transposable element, present in high copy numbers in the S. frugiperda genome. LNCR rasiRNAs are single-stranded RNAs without a prominent nucleotide motif, which are organized in two distinct, strand-specific clusters. The expression of LNCR and LNCR rasiRNAs is developmentally regulated. Formation of heterochromatin in the genomic region where three copies of the TE-LNCR are embedded was followed by chromatin immunoprecipitation (ChIP) and we observed this chromatin undergo dynamic changes during development. In summary, increased LNCR expression in certain developmental stages is followed by the appearance of a variety of LNCR rasiRNAs which appears to correlate with subsequent accumulation of a heterochromatic histone mark and silencing of the genomic region with TE-LNCR. These results support the notion that a repeat-associated small interfering RNA pathway is linked to heterochromatin formation and/or maintenance during development to establish repression of the TE-LNCR transposable element. This study provides insights into the rasiRNA silencing pathway and its role in the formation of fluctuating heterochromatin during the development of one holocentric organism. PMID:21980354

Coherent Radiative Control of Chemical Reactions

DTIC Science & Technology

1992-01-01

calculation. The criterion used i Cm to resrict the number of states to be included was that the overlaps Figure 10. Case i: Stimulated emission spectrum...is reflected in the fluorescence emission as quantum beats. It is well known that both the state created by photon excitation and any subsequent...Combining eqs. (4) and (5) gives the general expression for the fluo- rescence emission spectrum associated with a state created by a partially coherent

Small RNAs, big impact: small RNA pathways in transposon control and their effect on the host stress response.

PubMed

Wheeler, Bayly S

2013-12-01

Transposons are mobile genetic elements that are a major constituent of most genomes. Organisms regulate transposable element expression, transposition, and insertion site preference, mitigating the genome instability caused by uncontrolled transposition. A recent burst of research has demonstrated the critical role of small non-coding RNAs in regulating transposition in fungi, plants, and animals. While mechanistically distinct, these pathways work through a conserved paradigm. The presence of a transposon is communicated by the presence of its RNA or by its integration into specific genomic loci. These signals are then translated into small non-coding RNAs that guide epigenetic modifications and gene silencing back to the transposon. In addition to being regulated by the host, transposable elements are themselves capable of influencing host gene expression. Transposon expression is responsive to environmental signals, and many transposons are activated by various cellular stresses. TEs can confer local gene regulation by acting as enhancers and can also confer global gene regulation through their non-coding RNAs. Thus, transposable elements can act as stress-responsive regulators that control host gene expression in cis and trans.

Expressing genes do not forget their LINEs: transposable elements and gene expression

PubMed Central

Kines, Kristine J.; Belancio, Victoria P.

2012-01-01

1. ABSTRACT Historically the accumulated mass of mammalian transposable elements (TEs), particularly those located within gene boundaries, was viewed as a genetic burden potentially detrimental to the genomic landscape. This notion has been strengthened by the discovery that transposable sequences can alter the architecture of the transcriptome, not only through insertion, but also long after the integration process is completed. Insertions previously considered harmless are now known to impact the expression of host genes via modification of the transcript quality or quantity, transcriptional interference, or by the control of pathways that affect the mRNA life-cycle. Conversely, several examples of the evolutionary advantageous impact of TEs on the host gene structure that diversified the cellular transcriptome are reported. TE-induced changes in gene expression can be tissue-or disease-specific, raising the possibility that the impact of TE sequences may vary during development, among normal cell types, and between normal and disease-affected tissues. The understanding of the rules and abundance of TE-interference with gene expression is in its infancy, and its contribution to human disease and/or evolution remains largely unexplored. PMID:22201807

Loss-of-function of a ubiquitin-related modifier promotes the mobilization of the active MITE mPing.

PubMed

Tsukiyama, Takuji; Teramoto, Shota; Yasuda, Kanako; Horibata, Akira; Mori, Nanako; Okumoto, Yutaka; Teraishi, Masayoshi; Saito, Hiroki; Onishi, Akiko; Tamura, Kanako; Tanisaka, Takatoshi

2013-05-01

Miniature inverted-repeat transposable elements (MITEs) are widespread in both prokaryotic and eukaryotic genomes, where their copy numbers can attain several thousands. Little is known, however, about the genetic factor(s) affecting their transpositions. Here, we show that disruption of a gene encoding ubiquitin-like protein markedly enhances the transposition activity of a MITE mPing in intact rice plants without any exogenous stresses. We found that the transposition activity of mPing is far higher in the lines harboring a non-functional allele at the Rurm1 (Rice ubiquitin-related modifier-1) locus than in the wild-type line. Although the alteration of cytosine methylation pattern triggers the activation of transposable elements under exogenous stress conditions, the methylation degrees in the whole genome, the mPing-body region, and the mPing-flanking regions of the non-functional Rurm1 line were unchanged. This study provides experimental evidence for one of the models of genome shock theory that genetic accidents within cells enhance the transposition activities of transposable elements.

HTT-DB: horizontally transferred transposable elements database.

PubMed

Dotto, Bruno Reis; Carvalho, Evelise Leis; Silva, Alexandre Freitas; Duarte Silva, Luiz Fernando; Pinto, Paulo Marcos; Ortiz, Mauro Freitas; Wallau, Gabriel Luz

2015-09-01

Horizontal transfer of transposable (HTT) elements among eukaryotes was discovered in the mid-1980s. As then, >300 new cases have been described. New findings about HTT are revealing the evolutionary impact of this phenomenon on host genomes. In order to provide an up to date, interactive and expandable database for such events, we developed the HTT-DB database. HTT-DB allows easy access to most of HTT cases reported along with rich information about each case. Moreover, it allows the user to generate tables and graphs based on searches using Transposable elements and/or host species classification and export them in several formats. This database is freely available on the web at http://lpa.saogabriel.unipampa.edu.br:8080/httdatabase. HTT-DB was developed based on Java and MySQL with all major browsers supported. Tools and software packages used are free for personal or non-profit projects. bdotto82@gmail.com or gabriel.wallau@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription.

PubMed

Akay, Alper; Di Domenico, Tomas; Suen, Kin M; Nabih, Amena; Parada, Guillermo E; Larance, Mark; Medhi, Ragini; Berkyurek, Ahmet C; Zhang, Xinlian; Wedeles, Christopher J; Rudolph, Konrad L M; Engelhardt, Jan; Hemberg, Martin; Ma, Ping; Lamond, Angus I; Claycomb, Julie M; Miska, Eric A

2017-08-07

Small RNAs play a crucial role in genome defense against transposable elements and guide Argonaute proteins to nascent RNA transcripts to induce co-transcriptional gene silencing. However, the molecular basis of this process remains unknown. Here, we identify the conserved RNA helicase Aquarius/EMB-4 as a direct and essential link between small RNA pathways and the transcriptional machinery in Caenorhabditis elegans. Aquarius physically interacts with the germline Argonaute HRDE-1. Aquarius is required to initiate small-RNA-induced heritable gene silencing. HRDE-1 and Aquarius silence overlapping sets of genes and transposable elements. Surprisingly, removal of introns from a target gene abolishes the requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene silencing. We conclude that Aquarius allows small RNA pathways to compete for access to nascent transcripts undergoing co-transcriptional splicing in order to detect and silence transposable elements. Thus, Aquarius and HRDE-1 act as gatekeepers coordinating gene expression and genome defense. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Transposed-letter priming of prelexical orthographic representations.

PubMed

Kinoshita, Sachiko; Norris, Dennis

2009-01-01

A prime generated by transposing two internal letters (e.g., jugde) produces strong priming of the original word (judge). In lexical decision, this transposed-letter (TL) priming effect is generally weak or absent for nonword targets; thus, it is unclear whether the origin of this effect is lexical or prelexical. The authors describe the Bayesian Reader theory of masked priming (D. Norris & S. Kinoshita, 2008), which explains why nonwords do not show priming in lexical decision but why they do in the cross-case same-different task. This analysis is followed by 3 experiments that show that priming in this task is not based on low-level perceptual similarity between the prime and target, or on phonology, to make the case that priming is based on prelexical orthographic representation. The authors then use this task to demonstrate equivalent TL priming effects for nonwords and words. The results are interpreted as the first reliable evidence based on the masked priming procedure that letter position is not coded absolutely within the prelexical, orthographic representation. The implications of the results for current letter position coding schemes are discussed.

Physiological impact of transposable elements encoding DDE transposases in the environmental adaptation of Streptococcus agalactiae.

PubMed

Fléchard, Maud; Gilot, Philippe

2014-07-01

We have referenced and described Streptococcus agalactiae transposable elements encoding DDE transposases. These elements belonged to nine families of insertion sequences (ISs) and to a family of conjugative transposons (TnGBSs). An overview of the physiological impact of the insertion of all these elements is provided. DDE-transposable elements affect S. agalactiae in a number of aspects of its capability to adapt to various environments and modulate the expression of several virulence genes, the scpB-lmB genomic region and the genes involved in capsule expression and haemolysin transport being the targets of several different mobile elements. The referenced mobile elements modify S. agalactiae behaviour by transferring new gene(s) to its genome, by modifying the expression of neighbouring genes at the integration site or by promoting genomic rearrangements. Transposition of some of these elements occurs in vivo, suggesting that by dynamically regulating some adaptation and/or virulence genes, they improve the ability of S. agalactiae to reach different niches within its host and ensure the 'success' of the infectious process. © 2014 The Authors.

Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

PubMed

Kijima, T E; Innan, Hideki

2013-11-01

A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

Character Decomposition and Transposition Processes of Chinese Compound Words in Rapid Serial Visual Presentation.

PubMed

Cao, Hong-Wen; Yang, Ke-Yu; Yan, Hong-Mei

2017-01-01

Character order information is encoded at the initial stage of Chinese word processing, however, its time course remains underspecified. In this study, we assess the exact time course of the character decomposition and transposition processes of two-character Chinese compound words (canonical, transposed, or reversible words) compared with pseudowords using dual-target rapid serial visual presentation (RSVP) of stimuli appearing at 30 ms per character with no inter-stimulus interval. The results indicate that Chinese readers can identify words with character transpositions in rapid succession; however, a transposition cost is involved in identifying transposed words compared to canonical words. In RSVP reading, character order of words is more likely to be reversed during the period from 30 to 180 ms for canonical and reversible words, but the period from 30 to 240 ms for transposed words. Taken together, the findings demonstrate that the holistic representation of the base word is activated, however, the order of the two constituent characters is not strictly processed during the very early stage of visual word processing.

Searching for non-transposable targets of planarian nuclear PIWI in pluripotent stem cells and differentiated cells.

PubMed

Kashima, Makoto; Agata, Kiyokazu; Shibata, Norito

2018-06-01

Nuclear PIWIs together with their guide RNAs (piRNAs) epigenetically silence various genes including transposons in many organisms. In planarians, the nuclear piwi family gene, DjpiwiB is specifically transcribed in adult pluripotent stem cells (adult PSC, neoblast), but not in differentiated cells. However, the protein accumulates in the nuclei of both neoblasts and their descendant differentiated cells. Interestingly, PIWI(DjPiwiB)-piRNA complexes are indispensable for the repression of transposable genes at the onset of differentiation from neoblasts. Here, we conducted a comparative transcriptome analysis between control and DjpiwiB(RNAi) animals to identify non-transposable target genes of the DjPiwiB-piRNA complexes. Using bioinformatic analyses and RNAi we demonstrate that DjPiwiB-piRNA complexes are required for the proper expression of Djmcm2 and Djhistone h4 in neoblasts and that DjPiwiB-piRNA complexes regulate the transient expression of Djcalu during neoblast differentiation. Thus, DjPiwiB-piRNA complexes regulate the correct expression patterns during neoblast self-renewal and differentiation. © 2018 Japanese Society of Developmental Biologists.

An efficient tensor transpose algorithm for multicore CPU, Intel Xeon Phi, and NVidia Tesla GPU

NASA Astrophysics Data System (ADS)

Lyakh, Dmitry I.

2015-04-01

An efficient parallel tensor transpose algorithm is suggested for shared-memory computing units, namely, multicore CPU, Intel Xeon Phi, and NVidia GPU. The algorithm operates on dense tensors (multidimensional arrays) and is based on the optimization of cache utilization on x86 CPU and the use of shared memory on NVidia GPU. From the applied side, the ultimate goal is to minimize the overhead encountered in the transformation of tensor contractions into matrix multiplications in computer implementations of advanced methods of quantum many-body theory (e.g., in electronic structure theory and nuclear physics). A particular accent is made on higher-dimensional tensors that typically appear in the so-called multireference correlated methods of electronic structure theory. Depending on tensor dimensionality, the presented optimized algorithms can achieve an order of magnitude speedup on x86 CPUs and 2-3 times speedup on NVidia Tesla K20X GPU with respect to the naïve scattering algorithm (no memory access optimization). The tensor transpose routines developed in this work have been incorporated into a general-purpose tensor algebra library (TAL-SH).

When Genomics Is Not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials

PubMed Central

Gallus, Susanne; Lammers, Fritjof

2016-01-01

The autonomous transposable element LINE-1 is a highly abundant element that makes up between 15% and 20% of therian mammal genomes. Since their origin before the divergence of marsupials and placental mammals, LINE-1 elements have contributed actively to the genome landscape. A previous in silico screen of the Tasmanian devil genome revealed a lack of functional coding LINE-1 sequences. In this study we present the results of an in vitro analysis from a partial LINE-1 reverse transcriptase coding sequence in five marsupial species. Our experimental screen supports the in silico findings of the genome-wide degradation of LINE-1 sequences in the Tasmanian devil, and identifies a high frequency of degraded LINE-1 sequences in other Australian marsupials. The comparison between the experimentally obtained LINE-1 sequences and reference genome assemblies suggests that conclusions from in silico analyses of retrotransposition activity can be influenced by incomplete genome assemblies from short reads. PMID:27389686

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.

PubMed

Secco, David; Wang, Chuang; Shou, Huixia; Schultz, Matthew D; Chiarenza, Serge; Nussaume, Laurent; Ecker, Joseph R; Whelan, James; Lister, Ryan

2015-07-21

Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.

Efficient Transition Probability Computation for Continuous-Time Branching Processes via Compressed Sensing.

PubMed

Xu, Jason; Minin, Vladimir N

2015-07-01

Branching processes are a class of continuous-time Markov chains (CTMCs) with ubiquitous applications. A general difficulty in statistical inference under partially observed CTMC models arises in computing transition probabilities when the discrete state space is large or uncountable. Classical methods such as matrix exponentiation are infeasible for large or countably infinite state spaces, and sampling-based alternatives are computationally intensive, requiring integration over all possible hidden events. Recent work has successfully applied generating function techniques to computing transition probabilities for linear multi-type branching processes. While these techniques often require significantly fewer computations than matrix exponentiation, they also become prohibitive in applications with large populations. We propose a compressed sensing framework that significantly accelerates the generating function method, decreasing computational cost up to a logarithmic factor by only assuming the probability mass of transitions is sparse. We demonstrate accurate and efficient transition probability computations in branching process models for blood cell formation and evolution of self-replicating transposable elements in bacterial genomes.

Unitarily localizable entanglement of Gaussian states

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

Serafini, Alessio; Adesso, Gerardo; Illuminati, Fabrizio

2005-03-01

We consider generic (mxn)-mode bipartitions of continuous-variable systems, and study the associated bisymmetric multimode Gaussian states. They are defined as (m+n)-mode Gaussian states invariant under local mode permutations on the m-mode and n-mode subsystems. We prove that such states are equivalent, under local unitary transformations, to the tensor product of a two-mode state and of m+n-2 uncorrelated single-mode states. The entanglement between the m-mode and the n-mode blocks can then be completely concentrated on a single pair of modes by means of local unitary operations alone. This result allows us to prove that the PPT (positivity of the partial transpose)more » condition is necessary and sufficient for the separability of (m+n)-mode bisymmetric Gaussian states. We determine exactly their negativity and identify a subset of bisymmetric states whose multimode entanglement of formation can be computed analytically. We consider explicit examples of pure and mixed bisymmetric states and study their entanglement scaling with the number of modes.« less

Efficient Transition Probability Computation for Continuous-Time Branching Processes via Compressed Sensing

PubMed Central

Xu, Jason; Minin, Vladimir N.

2016-01-01

Branching processes are a class of continuous-time Markov chains (CTMCs) with ubiquitous applications. A general difficulty in statistical inference under partially observed CTMC models arises in computing transition probabilities when the discrete state space is large or uncountable. Classical methods such as matrix exponentiation are infeasible for large or countably infinite state spaces, and sampling-based alternatives are computationally intensive, requiring integration over all possible hidden events. Recent work has successfully applied generating function techniques to computing transition probabilities for linear multi-type branching processes. While these techniques often require significantly fewer computations than matrix exponentiation, they also become prohibitive in applications with large populations. We propose a compressed sensing framework that significantly accelerates the generating function method, decreasing computational cost up to a logarithmic factor by only assuming the probability mass of transitions is sparse. We demonstrate accurate and efficient transition probability computations in branching process models for blood cell formation and evolution of self-replicating transposable elements in bacterial genomes. PMID:26949377

Computing row and column counts for sparse QR and LU factorization

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

Gilbert, John R.; Li, Xiaoye S.; Ng, Esmond G.

2001-01-01

We present algorithms to determine the number of nonzeros in each row and column of the factors of a sparse matrix, for both the QR factorization and the LU factorization with partial pivoting. The algorithms use only the nonzero structure of the input matrix, and run in time nearly linear in the number of nonzeros in that matrix. They may be used to set up data structures or schedule parallel operations in advance of the numerical factorization. The row and column counts we compute are upper bounds on the actual counts. If the input matrix is strong Hall and theremore » is no coincidental numerical cancellation, the counts are exact for QR factorization and are the tightest bounds possible for LU factorization. These algorithms are based on our earlier work on computing row and column counts for sparse Cholesky factorization, plus an efficient method to compute the column elimination tree of a sparse matrix without explicitly forming the product of the matrix and its transpose.« less

A reliability and mass perspective of SP-100 Stirling cycle lunar-base powerplant designs

NASA Technical Reports Server (NTRS)

Bloomfield, Harvey S.

1991-01-01

The purpose was to obtain reliability and mass perspectives on selection of space power system conceptual designs based on SP-100 reactor and Stirling cycle power-generation subsystems. The approach taken was to: (1) develop a criterion for an acceptable overall reliability risk as a function of the expected range of emerging technology subsystem unit reliabilities; (2) conduct reliability and mass analyses for a diverse matrix of 800-kWe lunar-base design configurations employing single and multiple powerplants with both full and partial subsystem redundancy combinations; and (3) derive reliability and mass perspectives on selection of conceptual design configurations that meet an acceptable reliability criterion with the minimum system mass increase relative to reference powerplant design. The developed perspectives provided valuable insight into the considerations required to identify and characterize high-reliability and low-mass lunar-base powerplant conceptual design.

Germline Transformation of Drosophila Virilis Mediated by the Transposable Element Hobo

PubMed Central

Lozovskaya, E. R.; Nurminsky, D. I.; Hartl, D. L.; Sullivan, D. T.

1996-01-01

A laboratory strain of Drosophila virilis was genetically transformed with a hobo vector carrying the miniwhite cassette using a helper plasmid with an hsp70-driven hobo transposase-coding sequence. The rate of transformation was 0.5% per fertile G0 animal. Three transgenic insertions were cloned and characterized and found to be authentic hobo insertions. These results, together with the known wide-spread distribution of hobo in diverse insect species, suggest that hobo and related transposable elements may be of considerable utility in the germline transformation of insects other than D. melanogaster. PMID:8770594

Global Solutions to Repulsive Hookean Elastodynamics

NASA Astrophysics Data System (ADS)

Hu, Xianpeng; Masmoudi, Nader

2017-01-01

The global existence of classical solutions to the three dimensional repulsive Hookean elastodynamics around an equilibrium is considered. By linearization and Hodge's decomposition, the compressible part of the velocity, the density, and the compressible part of the transpose of the deformation gradient satisfy Klein-Gordon equations with speed {√{2}}, while the incompressible parts of the velocity and of the transpose of the deformation gradient satisfy wave equations with speed one. The space-time resonance method combined with the vector field method is used in a novel way to obtain the decay of the solution and hence global existence.

Transposable elements re-wire and fine-tune the transcriptome.

PubMed

Cowley, Michael; Oakey, Rebecca J

2013-01-01

What good are transposable elements (TEs)? Although their activity can be harmful to host genomes and can cause disease, they nevertheless represent an important source of genetic variation that has helped shape genomes. In this review, we examine the impact of TEs, collectively referred to as the mobilome, on the transcriptome. We explore how TEs-particularly retrotransposons-contribute to transcript diversity and consider their potential significance as a source of small RNAs that regulate host gene transcription. We also discuss a critical role for the mobilome in engineering transcriptional networks, permitting coordinated gene expression, and facilitating the evolution of novel physiological processes.

Operational Testing of Satellite based Hydrological Model (SHM)

NASA Astrophysics Data System (ADS)

Gaur, Srishti; Paul, Pranesh Kumar; Singh, Rajendra; Mishra, Ashok; Gupta, Praveen Kumar; Singh, Raghavendra P.

2017-04-01

Incorporation of the concept of transposability in model testing is one of the prominent ways to check the credibility of a hydrological model. Successful testing ensures ability of hydrological models to deal with changing conditions, along with its extrapolation capacity. For a newly developed model, a number of contradictions arises regarding its applicability, therefore testing of credibility of model is essential to proficiently assess its strength and limitations. This concept emphasizes to perform 'Hierarchical Operational Testing' of Satellite based Hydrological Model (SHM), a newly developed surface water-groundwater coupled model, under PRACRITI-2 program initiated by Space Application Centre (SAC), Ahmedabad. SHM aims at sustainable water resources management using remote sensing data from Indian satellites. It consists of grid cells of 5km x 5km resolution and comprises of five modules namely: Surface Water (SW), Forest (F), Snow (S), Groundwater (GW) and Routing (ROU). SW module (functions in the grid cells with land cover other than forest and snow) deals with estimation of surface runoff, soil moisture and evapotranspiration by using NRCS-CN method, water balance and Hragreaves method, respectively. The hydrology of F module is dependent entirely on sub-surface processes and water balance is calculated based on it. GW module generates baseflow (depending on water table variation with the level of water in streams) using Boussinesq equation. ROU module is grounded on a cell-to-cell routing technique based on the principle of Time Variant Spatially Distributed Direct Runoff Hydrograph (SDDH) to route the generated runoff and baseflow by different modules up to the outlet. For this study Subarnarekha river basin, flood prone zone of eastern India, has been chosen for hierarchical operational testing scheme which includes tests under stationary as well as transitory conditions. For this the basin has been divided into three sub-basins using three flow gauging sites as reference, viz., Muri, Jamshedpur and Ghatshila. Individual model set-up has been prepared for these sub-basins and calibration and validation using Split-sample test, first level of operational testing scheme is in progress. Subsequently for geographic transposability, Proxy-basin test will be done using Muri and Jamshedpur as proxy basins. Climatic transposability will be tested for dry and wet years using Differential split-sample test. For incorporating both geographic and climatic transposability Proxy-basin differential split sample test will be used. For quantitative evaluation of SHM, during Split-sample test Nash-Sutcliffe efficiency (NSE), Coefficient of Determination (R R^2)) and Percent BIAS (PBIAS) are being used. However, for transposability, a productive approach involving these performance measures, i.e. NSE*R R^2)*PBIAS will be used to decide the best value of parameters. Keywords: SHM, credibility, operational testing, transposability.

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

PubMed Central

Kapusta, Aurélie; Zhuo, Xiaoyu; Ramsay, LeeAnn; Bourque, Guillaume; Yandell, Mark; Feschotte, Cédric

2013-01-01

Advances in vertebrate genomics have uncovered thousands of loci encoding long noncoding RNAs (lncRNAs). While progress has been made in elucidating the regulatory functions of lncRNAs, little is known about their origins and evolution. Here we explore the contribution of transposable elements (TEs) to the makeup and regulation of lncRNAs in human, mouse, and zebrafish. Surprisingly, TEs occur in more than two thirds of mature lncRNA transcripts and account for a substantial portion of total lncRNA sequence (∼30% in human), whereas they seldom occur in protein-coding transcripts. While TEs contribute less to lncRNA exons than expected, several TE families are strongly enriched in lncRNAs. There is also substantial interspecific variation in the coverage and types of TEs embedded in lncRNAs, partially reflecting differences in the TE landscapes of the genomes surveyed. In human, TE sequences in lncRNAs evolve under greater evolutionary constraint than their non–TE sequences, than their intronic TEs, or than random DNA. Consistent with functional constraint, we found that TEs contribute signals essential for the biogenesis of many lncRNAs, including ∼30,000 unique sites for transcription initiation, splicing, or polyadenylation in human. In addition, we identified ∼35,000 TEs marked as open chromatin located within 10 kb upstream of lncRNA genes. The density of these marks in one cell type correlate with elevated expression of the downstream lncRNA in the same cell type, suggesting that these TEs contribute to cis-regulation. These global trends are recapitulated in several lncRNAs with established functions. Finally a subset of TEs embedded in lncRNAs are subject to RNA editing and predicted to form secondary structures likely important for function. In conclusion, TEs are nearly ubiquitous in lncRNAs and have played an important role in the lineage-specific diversification of vertebrate lncRNA repertoires. PMID:23637635

Tnt1 Retrotransposon Mutagenesis: A Tool for Soybean Functional Genomics1[W][OA

PubMed Central

Cui, Yaya; Barampuram, Shyam; Stacey, Minviluz G.; Hancock, C. Nathan; Findley, Seth; Mathieu, Melanie; Zhang, Zhanyuan; Parrott, Wayne A.; Stacey, Gary

2013-01-01

Insertional mutagenesis is a powerful tool for determining gene function in both model and crop plant species. Tnt1, the transposable element of tobacco (Nicotiana tabacum) cell type 1, is a retrotransposon that replicates via an RNA copy that is reverse transcribed and integrated elsewhere in the plant genome. Based on studies in a variety of plants, Tnt1 appears to be inactive in normal plant tissue but can be reactivated by tissue culture. Our goal was to evaluate the utility of the Tnt1 retrotransposon as a mutagenesis strategy in soybean (Glycine max). Experiments showed that the Tnt1 element was stably transformed into soybean plants by Agrobacterium tumefaciens-mediated transformation. Twenty-seven independent transgenic lines carrying Tnt1 insertions were generated. Southern-blot analysis revealed that the copy number of transposed Tnt1 elements ranged from four to 19 insertions, with an average of approximately eight copies per line. These insertions showed Mendelian segregation and did not transpose under normal growth conditions. Analysis of 99 Tnt1 flanking sequences revealed insertions into 62 (62%) annotated genes, indicating that the element preferentially inserts into protein-coding regions. Tnt1 insertions were found in all 20 soybean chromosomes, indicating that Tnt1 transposed throughout the soybean genome. Furthermore, fluorescence in situ hybridization experiments validated that Tnt1 inserted into multiple chromosomes. Passage of transgenic lines through two different tissue culture treatments resulted in Tnt1 transposition, significantly increasing the number of insertions per line. Thus, our data demonstrate the Tnt1 retrotransposon to be a powerful system that can be used for effective large-scale insertional mutagenesis in soybean. PMID:23124322

Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene.

PubMed

Amit, Maayan; Sela, Noa; Keren, Hadas; Melamed, Ze'ev; Muler, Inna; Shomron, Noam; Izraeli, Shai; Ast, Gil

2007-11-29

Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization of transposed elements in duplicated genes than in single-copy genes. Genome-wide analysis of exonization of transposed elements revealed a higher rate of exonization within duplicated genes relative to single-copy genes. The gene for TIF-IA, an RNA polymerase I transcription initiation factor, underwent a humanoid-specific triplication, all three copies of the gene are active transcriptionally, although only one copy retains the ability to generate the TIF-IA protein. Prior to TIF-IA triplication, an Alu element was inserted into the first intron. In one of the non-protein coding copies, this Alu is exonized. We identified a single point mutation leading to exonization in one of the gene duplicates. When this mutation was introduced into the TIF-IA coding copy, exonization was activated and the level of the protein-coding mRNA was reduced substantially. A very low level of exonization was detected in normal human cells. However, this exonization was abundant in most leukemia cell lines evaluated, although the genomic sequence is unchanged in these cancerous cells compared to normal cells. The definition of the Alu element within the TIF-IA gene as an exon is restricted to certain types of cancers; the element is not exonized in normal human cells. These results further our understanding of the delicate interplay between gene duplication and alternative splicing and of the molecular evolutionary mechanisms leading to genetic innovations. This implies the existence of purifying selection against exonization in single copy genes, with duplicate genes free from such constrains.

Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene

PubMed Central

Amit, Maayan; Sela, Noa; Keren, Hadas; Melamed, Ze'ev; Muler, Inna; Shomron, Noam; Izraeli, Shai; Ast, Gil

2007-01-01

Background Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization of transposed elements in duplicated genes than in single-copy genes. Results Genome-wide analysis of exonization of transposed elements revealed a higher rate of exonization within duplicated genes relative to single-copy genes. The gene for TIF-IA, an RNA polymerase I transcription initiation factor, underwent a humanoid-specific triplication, all three copies of the gene are active transcriptionally, although only one copy retains the ability to generate the TIF-IA protein. Prior to TIF-IA triplication, an Alu element was inserted into the first intron. In one of the non-protein coding copies, this Alu is exonized. We identified a single point mutation leading to exonization in one of the gene duplicates. When this mutation was introduced into the TIF-IA coding copy, exonization was activated and the level of the protein-coding mRNA was reduced substantially. A very low level of exonization was detected in normal human cells. However, this exonization was abundant in most leukemia cell lines evaluated, although the genomic sequence is unchanged in these cancerous cells compared to normal cells. Conclusion The definition of the Alu element within the TIF-IA gene as an exon is restricted to certain types of cancers; the element is not exonized in normal human cells. These results further our understanding of the delicate interplay between gene duplication and alternative splicing and of the molecular evolutionary mechanisms leading to genetic innovations. This implies the existence of purifying selection against exonization in single copy genes, with duplicate genes free from such constrains. PMID:18047649

Intimate relationships and changing patterns of money management at the beginning of the twenty-first century.

PubMed

Vogler, Carolyn; Brockmann, Michaela; Wiggins, Richard D

2006-09-01

Drawing on British data from two annual sweeps of the ISSP eight years apart in 1994 and 2002, for modules focusing on 'Family and Changing Gender Roles', this paper examines the extent to which changes in women's labour market participation, changing ideologies/discourses of gender and changing forms of intimate relationships are affecting the ways in which couples organize household money, and the implications of such changes for recent theories of intimate relationships. The analysis indicates that by 2002, the type of relationship respondents had established, together with their social class position, were both independently related to the ways in which they managed money, after controlling for socio-economic and cultural or discursive factors. Our findings also provide a degree of support for the thesis of a partial decline in the male breadwinner model of gender, as indicated by small declines in the use of the relatively inegalitarian female whole wage and housekeeping allowance systems which were most likely to be used by married couples and cohabiting fathers, expressing relatively traditional ideologies/discourses of breadwinning - and a slight increase in the use of the partial pool, which was most likely to be used by childless cohabiting couples in which male partners expressed less traditional ideologies of breadwinning and women were in middle-class jobs with incomes high enough to facilitate partially separate finances. We also suggest, however, that in so far as cohabiting couples earning different amounts define equality as contributing equally to household expenditure, it is possible that rather than being associated with shifts to greater equality in access to money for personal spending and saving, the partial pool may be associated with marked inequalities, because it may enable gender inequalities generated in the labour market to be more directly transposed into inequalities within households, despite the decline of traditional discourses of male breadwinning and the increasing importance of egalitarian ideologies of co-provisioning.

Criterion-Related Validity of Sit-and-Reach Tests for Estimating Hamstring and Lumbar Extensibility: a Meta-Analysis

PubMed Central

Mayorga-Vega, Daniel; Merino-Marban, Rafael; Viciana, Jesús

2014-01-01

The main purpose of the present meta-analysis was to examine the scientific literature on the criterion-related validity of sit-and-reach tests for estimating hamstring and lumbar extensibility. For this purpose relevant studies were searched from seven electronic databases dated up through December 2012. Primary outcomes of criterion-related validity were Pearson´s zero-order correlation coefficients (r) between sit-and-reach tests and hamstrings and/or lumbar extensibility criterion measures. Then, from the included studies, the Hunter- Schmidt´s psychometric meta-analysis approach was conducted to estimate population criterion- related validity of sit-and-reach tests. Firstly, the corrected correlation mean (rp), unaffected by statistical artefacts (i.e., sampling error and measurement error), was calculated separately for each sit-and-reach test. Subsequently, the three potential moderator variables (sex of participants, age of participants, and level of hamstring extensibility) were examined by a partially hierarchical analysis. Of the 34 studies included in the present meta-analysis, 99 correlations values across eight sit-and-reach tests and 51 across seven sit-and-reach tests were retrieved for hamstring and lumbar extensibility, respectively. The overall results showed that all sit-and-reach tests had a moderate mean criterion-related validity for estimating hamstring extensibility (rp = 0.46-0.67), but they had a low mean for estimating lumbar extensibility (rp = 0. 16-0.35). Generally, females, adults and participants with high levels of hamstring extensibility tended to have greater mean values of criterion-related validity for estimating hamstring extensibility. When the use of angular tests is limited such as in a school setting or in large scale studies, scientists and practitioners could use the sit-and-reach tests as a useful alternative for hamstring extensibility estimation, but not for estimating lumbar extensibility. Key Points Overall sit-and-reach tests have a moderate mean criterion-related validity for estimating hamstring extensibility, but they have a low mean validity for estimating lumbar extensibility. Among all the sit-and-reach test protocols, the Classic sit-and-reach test seems to be the best option to estimate hamstring extensibility. End scores (e.g., the Classic sit-and-reach test) are a better indicator of hamstring extensibility than the modifications that incorporate fingers-to-box distance (e.g., the Modified sit-and-reach test). When angular tests such as straight leg raise or knee extension tests cannot be used, sit-and-reach tests seem to be a useful field test alternative to estimate hamstring extensibility, but not to estimate lumbar extensibility. PMID:24570599

Reviewing employee turnover: focusing on proximal withdrawal states and an expanded criterion.

PubMed

Hom, Peter W; Mitchell, Terence R; Lee, Thomas W; Griffeth, Rodger W

2012-09-01

We reconceptualize employee turnover to promote researchers' understanding and prediction of why employees quit or stay in employing institutions. A literature review identifies shortcomings with prevailing turnover dimensions. In response, we expand the conceptual domain of the turnover criterion to include multiple types of turnover (notably, involuntary quits) and multiple types of staying. Guided by the premise that "everyone eventually leaves; no one stays with an organization forever," we also suggest considering where leavers end up-or post-exit destinations, such as another job, full-time parenting, or educational pursuits. We propose "proximal withdrawal states" that motivate members to participate or withdraw from organizations as an expanded criterion. These motivational states precede turnover and are derived from 2 overarching dimensions: desired employment status (whether employees want to stay or leave) and perceived volitional control (whether quit or stay decisions are completely up to them or at least partially under external regulation). Crossing these dimensions yields 4 prime states: enthusiastic leavers and stayers and reluctant leavers and stayers. We further subdivide these mind-sets into subtypes by differentiating employer from other forms of external control (e.g., family). Focusing on more common subtypes, we explain how they arise from particular motivational forces and profile how they differ by attitudes, behaviors, and turnover speed and destinations. We further discuss ways to measure this expanded criterion and proximal states (and subtypes) and investigate the latter's profiled differences. Finally, we discuss scientific and practical implications and future research directions. (PsycINFO Database Record (c) 2012 APA, all rights reserved).

The biology and evolution of transposable elements in parasites.

PubMed

Thomas, M Carmen; Macias, Francisco; Alonso, Carlos; López, Manuel C

2010-07-01

Transposable elements (TEs) are dynamic elements that can reshape host genomes by generating rearrangements with the potential to create or disrupt genes, to shuffle existing genes, and to modulate their patterns of expression. In the genomes of parasites that infect mammals several TEs have been identified that probably have been maintained throughout evolution due to their contribution to gene function and regulation of gene expression. This review addresses how TEs are organized, how they colonize the genomes of mammalian parasites, the functional role these elements play in parasite biology, and the interactions between these elements and the parasite genome. Copyright 2010 Elsevier Ltd. All rights reserved.

Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response.

PubMed

Horváth, Vivien; Merenciano, Miriam; González, Josefa

2017-11-01

A relationship between transposable elements (TEs) and the eukaryotic stress response was suggested in the first publications describing TEs. Since then, it has often been assumed that TEs are activated by stress, and that this activation is often beneficial for the organism. In recent years, the availability of new high-throughput experimental techniques has allowed further interrogation of the relationship between TEs and stress. By reviewing the recent literature, we conclude that although there is evidence for a beneficial effect of TE activation under stress conditions, the relationship between TEs and the eukaryotic stress response is quite complex. Copyright © 2017 Elsevier Ltd. All rights reserved.

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

PubMed Central

Cowley, Michael; Oakey, Rebecca J.

2013-01-01

What good are transposable elements (TEs)? Although their activity can be harmful to host genomes and can cause disease, they nevertheless represent an important source of genetic variation that has helped shape genomes. In this review, we examine the impact of TEs, collectively referred to as the mobilome, on the transcriptome. We explore how TEs—particularly retrotransposons—contribute to transcript diversity and consider their potential significance as a source of small RNAs that regulate host gene transcription. We also discuss a critical role for the mobilome in engineering transcriptional networks, permitting coordinated gene expression, and facilitating the evolution of novel physiological processes. PMID:23358118

Transcriptional activity of transposable elements in coelacanth.

PubMed

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

2014-09-01

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

LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences.

PubMed

Disdero, Eric; Filée, Jonathan

2017-01-01

Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when Illumina or 454 technologies are used. Fortunately, long read sequencing technologies generating read length that may span the entire length of full transposons are now available. However, existing TE population genomic softwares were not designed to handle long reads and the development of new dedicated tools is needed. LoRTE is the first tool able to use PacBio long read sequences to identify transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against simulated and genuine Drosophila melanogaster PacBio datasets, LoRTE appears to be a reliable and broadly applicable tool to study the dynamic and evolutionary impact of transposable elements using low coverage, long read sequences. LoRTE is an efficient and accurate tool to identify structural genomic variants caused by TE insertion or deletion. LoRTE is available for download at http://www.egce.cnrs-gif.fr/?p=6422.

The processing of consonants and vowels during letter identity and letter position assignment in visual-word recognition: an ERP study.

PubMed

Vergara-Martínez, Marta; Perea, Manuel; Marín, Alejandro; Carreiras, Manuel

2011-09-01

Recent research suggests that there is a processing distinction between consonants and vowels in visual-word recognition. Here we conjointly examine the time course of consonants and vowels in processes of letter identity and letter position assignment. Event related potentials (ERPs) were recorded while participants read words and pseudowords in a lexical decision task. The stimuli were displayed under different conditions in a masked priming paradigm with a 50-ms SOA: (i) identity/baseline condition e.g., chocolate-CHOCOLATE); (ii) vowels-delayed condition (e.g., choc_l_te-CHOCOLATE); (iii) consonants-delayed condition (cho_o_ate-CHOCOLATE); (iv) consonants-transposed condition (cholocate-CHOCOLATE); (v) vowels-transposed condition (chocalote-CHOCOLATE), and (vi) unrelated condition (editorial-CHOCOLATE). Results showed earlier ERP effects and longer reaction times for the delayed-letter compared to the transposed-letter conditions. Furthermore, at early stages of processing, consonants may play a greater role during letter identity processing. Differences between vowels and consonants regarding letter position assignment are discussed in terms of a later phonological level involved in lexical retrieval. Copyright © 2010 Elsevier Inc. All rights reserved.

The role of transposable elements in health and diseases of the central nervous system.

PubMed

Reilly, Matthew T; Faulkner, Geoffrey J; Dubnau, Joshua; Ponomarev, Igor; Gage, Fred H

2013-11-06

First discovered in maize by Barbara McClintock in the 1940s, transposable elements (TEs) are DNA sequences that in some cases have the ability to move along chromosomes or "transpose" in the genome. This revolutionary finding was initially met with resistance by the scientific community and viewed by some as heretical. A large body of knowledge has accumulated over the last 60 years on the biology of TEs. Indeed, it is now known that TEs can generate genomic instability and reconfigure gene expression networks both in the germline and somatic cells. This review highlights recent findings on the role of TEs in health and diseases of the CNS, which were presented at the 2013 Society for Neuroscience meeting. The work of the speakers in this symposium shows that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings on TE expression and function in the CNS have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in shaping individual behavior and contribute to vulnerability to disease.

Does location uncertainty in letter position coding emerge because of literacy training?

PubMed

Perea, Manuel; Jiménez, María; Gomez, Pablo

2016-06-01

In the quest to unveil the nature of the orthographic code, a useful strategy is to examine the transposed-letter effect (e.g., JUGDE is more confusable with its base word, JUDGE, than the replacement-letter nonword JUPTE). A leading explanation of this phenomenon, which is line with models of visual attention, is that there is perceptual uncertainty at assigning letters ("objects") to positions. This mechanism would be at work not only with skilled readers but also with preliterate children. An alternative explanation is that the transposed-letter effect emerges at an orthographic level of processing as a direct consequence of literacy training. To test these accounts, we conducted a same-different matching experiment with preliterate 4-year-old children using same versus different trials (created by letter transposition or replacement). Results showed a significantly larger number of false positives (i.e., "same" responses) to transposed-letter strings than to 1/2 replacement-letter strings. Therefore, the present data favor the view that the visual processing of location information is inherently noisy and rule out an interpretation of confusability in letter position coding as emerging from literacy training. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Polymorphism and methylation patterns in Agave tequilana Weber var. 'Azul' plants propagated asexually by three different methods.

PubMed

Díaz-Martínez, Miriam; Nava-Cedillo, Alejandro; Guzmán-López, José Alfredo; Escobar-Guzmán, Rocío; Simpson, June

2012-04-01

Genetic variation in three forms of asexually propagated Agave tequilana Weber var. 'Azul' plants namely offsets, bulbils and in vitro cultured individuals was studied by AFLP analysis. Low levels of variation were observed between mother plants and offsets and a higher level between mother plant and bulbils. Families obtained from commercial plantations showed lower levels of variation in comparison to families grown as ornamentals. No variation was observed between the original explant and four generations of in vitro cultured plants. Epigenetic variation was also studied by analyzing changes in methylation patterns between mother plants and offspring in each form of asexual reproduction. Offsets and bulbils showed an overall decrease in methylation whereas in vitro cultured plants showed patterns specific to each generation: Generations 1 and 4 showed overall demethylation whereas Generations 2 and 3 showed increased methylation. Analysis of ESTs associated with transposable elements revealed higher proportions of ESTs from Ty1-copia-like, Gypsy and CACTA transposable elements in cDNA libraries obtained from pluripotent tissue suggesting a possible correlation between methylation patterns, expression of transposable element associated genes and somaclonal variation. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula.

PubMed

d'Erfurth, Isabelle; Cosson, Viviane; Eschstruth, Alexis; Lucas, Helene; Kondorosi, Adam; Ratet, P

2003-04-01

The tobacco element, Tnt1, is one of the few active retrotransposons in plants. Its transposition is activated during protoplast culture in tobacco and tissue culture in the heterologous host Arabidopsis thaliana. Here, we report its transposition in the R108 line of Medicago truncatula during the early steps of the in vitro transformation-regeneration process. Two hundred and twenty-five primary transformants containing Tnt1 were obtained. Among them, 11.2% contained only transposed copies of the element, indicating that Tnt1 transposed very early and efficiently during the in vitro transformation process, possibly even before the T-DNA integration. The average number of insertions per transgenic line was estimated to be about 15. These insertions were stable in the progeny and could be separated by segregation. Inspection of the sequences flanking the insertion sites revealed that Tnt1 had no insertion site specificity and often inserted in genes (one out of three insertions). Thus, our work demonstrates the functioning of an efficient transposable element in leguminous plants. These results indicate that Tnt1 can be used as a powerful tool for insertion mutagenesis in M. truncatula.

Formation and loss of large, unstable tandem arrays of the piggyBac transposable element in the yellow fever mosquito, Aedes aegypti.

PubMed

Adelman, Zach N; Jasinskiene, Nijole; Vally, K J M; Peek, Corrie; Travanty, Emily A; Olson, Ken E; Brown, Susan E; Stephens, Janice L; Knudson, Dennis L; Coates, Craig J; James, Anthony A

2004-10-01

The Class II transposable element, piggyBac, was used to transform the yellow fever mosquito, Aedes aegypti. In two transformed lines only 15-30% of progeny inherited the transgene, with these individuals displaying mosaic expression of the EGFP marker gene. Southern analyses, gene amplification of genomic DNA, and plasmid rescue experiments provided evidence that these lines contained a high copy number of piggyBac transformation constructs and that much of this DNA consisted of both donor and helper plasmids. A detailed analysis of one line showed that the majority of piggyBac sequences were unit-length donor or helper plasmids arranged in a large tandem array that could be lost en masse in a single generation. Despite the presence of a transposase source and many intact donor elements, no conservative (cut and paste) transposition of piggyBac was observed in these lines. These results reveal one possible outcome of uncontrolled and/or unexpected recombination in this mosquito, and support the conclusion that further investigation is necessary before transposable elements such as piggyBac can be used as genetic drive mechanisms to move pathogen-resistance genes into mosquito populations.

An efficient tensor transpose algorithm for multicore CPU, Intel Xeon Phi, and NVidia Tesla GPU

DOE PAGES

Lyakh, Dmitry I.

2015-01-05

An efficient parallel tensor transpose algorithm is suggested for shared-memory computing units, namely, multicore CPU, Intel Xeon Phi, and NVidia GPU. The algorithm operates on dense tensors (multidimensional arrays) and is based on the optimization of cache utilization on x86 CPU and the use of shared memory on NVidia GPU. From the applied side, the ultimate goal is to minimize the overhead encountered in the transformation of tensor contractions into matrix multiplications in computer implementations of advanced methods of quantum many-body theory (e.g., in electronic structure theory and nuclear physics). A particular accent is made on higher-dimensional tensors that typicallymore » appear in the so-called multireference correlated methods of electronic structure theory. Depending on tensor dimensionality, the presented optimized algorithms can achieve an order of magnitude speedup on x86 CPUs and 2-3 times speedup on NVidia Tesla K20X GPU with respect to the na ve scattering algorithm (no memory access optimization). Furthermore, the tensor transpose routines developed in this work have been incorporated into a general-purpose tensor algebra library (TAL-SH).« less

SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.

PubMed

Do, Dang Vinh; Strauss, Bernhard; Cukuroglu, Engin; Macaulay, Iain; Wee, Keng Boon; Hu, Tim Xiaoming; Igor, Ruiz De Los Mozos; Lee, Caroline; Harrison, Andrew; Butler, Richard; Dietmann, Sabine; Jernej, Ule; Marioni, John; Smith, Christopher W J; Göke, Jonathan; Surani, M Azim

2018-01-01

The RNA-binding protein SRSF3 (also known as SRp20) has critical roles in the regulation of pre-mRNA splicing. Zygotic knockout of Srsf3 results in embryo arrest at the blastocyst stage. However, SRSF3 is also present in oocytes, suggesting that it might be critical as a maternally inherited factor. Here we identify SRSF3 as an essential regulator of alternative splicing and of transposable elements to maintain transcriptome integrity in mouse oocyte. Using 3D time-lapse confocal live imaging, we show that conditional deletion of Srsf3 in fully grown germinal vesicle oocytes substantially compromises the capacity of germinal vesicle breakdown (GVBD), and consequently entry into meiosis. By combining single cell RNA-seq, and oocyte micromanipulation with steric blocking antisense oligonucleotides and RNAse-H inducing gapmers, we found that the GVBD defect in mutant oocytes is due to both aberrant alternative splicing and derepression of B2 SINE transposable elements. Together, our study highlights how control of transcriptional identity of the maternal transcriptome by the RNA-binding protein SRSF3 is essential to the development of fertilized-competent oocytes.

Making things difficult in lexical decision: the impact of pseudohomophones and transposed-letter nonwords on frequency and semantic priming effects.

PubMed

Lupker, Stephen J; Pexman, Penny M

2010-09-01

Performance in a lexical decision task is crucially dependent on the difficulty of the word-nonword discrimination. More wordlike nonwords cause not only a latency increase for words but also, as reported by Stone and Van Orden (1993), larger word frequency effects. Several current models of lexical decision making can explain these types of results in terms of a single mechanism, a mechanism driven by the nature of the interactions within the lexicon. In 2 experiments, we replicated Stone and Van Orden's increased frequency effect using both pseudohomophones (e.g., BEEST) and transposed-letter nonwords (e.g., JUGDE) as the more wordlike nonwords. In a 3rd experiment, we demonstrated that simply increasing word latencies without changing the difficulty of the word-nonword discrimination does not produce larger frequency effects. These results are reasonably consistent with many current models. In contrast, neither pseudohomophones nor transposed-letter nonwords altered the size of semantic priming effects across 4 additional experiments, posing a challenge to models that would attempt to explain both nonword difficulty effects and semantic priming effects in lexical decision tasks in terms of a single, lexically driven mechanism. (c) 2010 APA, all rights reserved).

Development of a Bone-Conducted Ultrasonic Hearing Aid for the Profoundly Deaf: Evaluation of Sound Quality Using a Semantic Differential Method

NASA Astrophysics Data System (ADS)

Nakagawa, Seiji; Fujiyuki, Chika; Kagomiya, Takayuki

2013-07-01

Bone-conducted ultrasound (BCU) is perceived even by the profoundly sensorineural deaf. A novel hearing aid using the perception of amplitude-modulated BCU (BCU hearing aid: BCUHA) has been developed. However, there is room for improvement particularly in terms of sound quality. BCU speech is accompanied by a strong high-pitched tone and contain some distortion. In this study, the sound quality of BCU speech with several types of amplitude modulation [double-sideband with transmitted carrier (DSB-TC), double-sideband with suppressed carrier (DSB-SC), and transposed modulations] and air-conducted (AC) speech was quantitatively evaluated using semantic differential and factor analysis. The results showed that all the types of BCU speech had higher metallic and lower esthetic factor scores than AC speech. On the other hand, transposed speech was closer than the other types of BCU speech to AC speech generally; the transposed speech showed a higher powerfulness factor score than the other types of BCU speech and a higher esthetic factor score than DSB-SC speech. These results provide useful information for further development of the BCUHA.

How does interhemispheric communication in visual word recognition work? Deciding between early and late integration accounts of the split fovea theory.

PubMed

Van der Haegen, Lise; Brysbaert, Marc; Davis, Colin J

2009-02-01

It has recently been shown that interhemispheric communication is needed for the processing of foveally presented words. In this study, we examine whether the integration of information happens at an early stage, before word recognition proper starts, or whether the integration is part of the recognition process itself. Two lexical decision experiments are reported in which words were presented at different fixation positions. In Experiment 1, a masked form priming task was used with primes that had two adjacent letters transposed. The results showed that although the fixation position had a substantial influence on the transposed letter priming effect, the priming was not smaller when the transposed letters were sent to different hemispheres than when they were projected to the same hemisphere. In Experiment 2, stimuli were presented that either had high frequency hemifield competitors or could be identified unambiguously on the basis of the information in one hemifield. Again, the lexical decision times did not vary as a function of hemifield competitors. These results are consistent with the early integration account, as presented in the SERIOL model of visual word recognition.

Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion.

PubMed

Vaschetto, Luis María

2018-04-01

In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular type of transposons referred to as miniature inverted-repeat transposable elements (MITEs) has shown a series of interesting characteristics for designing functional drivers. Here, recent insights into MITE elements and versatile RNA-guided CRISPR/Cas9 genome engineering system are given to understand how to deploy the potential of TEs for control of the host transcriptional activity.

Determination analaysis of the power losses of transformers with continuously transpored conductors (CTC) based fuzzy logic

NASA Astrophysics Data System (ADS)

Kaloko, Bambang Sri; Atsari, Erinna Dyah

2017-03-01

Electric motive force which flows into the iron core continuously on a plate - plate iron isolated may cause heat posed by current eddy (eddy current). No water loss occurs due to detainees on the circuit at the the flow of current load because this loss happened on the entanglement of the transformer is made of copper. Continuously Transposed Conductors (CTC) consist of a number of enameled rectangular wires (5-84 strands) made into an assembly. Each strand is transposed in turn to each position in the cable and is then covered with layers of insulation paper. Continuously Transposed Conductors are used in winding wires for medium and ultra high power transformers. CTC is manufactured by OFHC copper and indeed, is able to supply polyester roped. CTC which has been designed to reduce production cost, oil pocket and improve cooling efficiency. Hardened type CTC (CPR1, CPR2, and CPR3: BS1432) and Self-bonding CTC which can be used to improve mechanical and electrical strength are also available. This analysis is performed using the methods of fuzzy logic in taking account of the resources.

Hybrid theory and calculation of e-N2 scattering. [quantum mechanics - nuclei (nuclear physics)

NASA Technical Reports Server (NTRS)

Chandra, N.; Temkin, A.

1975-01-01

A theory of electron-molecule scattering was developed which was a synthesis of close coupling and adiabatic-nuclei theories. The theory is shown to be a close coupling theory with respect to vibrational degrees of freedom but is a adiabatic-nuclei theory with respect to rotation. It can be applied to any number of partial waves required, and the remaining ones can be calculated purely in one or the other approximation. A theoretical criterion based on fixed-nuclei calculations and not on experiment can be given as to which partial waves and energy domains require the various approximations. The theory allows all cross sections (i.e., pure rotational, vibrational, simultaneous vibration-rotation, differential and total) to be calculated. Explicit formulae for all the cross sections are presented.

Application of Tactical Data Systems for Training. Volume IV. Development of Courseware and Analysis of Results for GED Math

DTIC Science & Technology

1974-01-02

Disjointed..,little continuity - Omission of the "why" of training, which leaves it up to the individual student to determine the importance of the...the student when a response was required. A "roll- up " function caused old information on the screen to be completely or partially removed, depending on...each game inter- action, the student is asked questions which build up to a generalized statement of the rounding rules. Finally, the criterion items

Visual judgements of steadiness in one-legged stance: reliability and validity.

PubMed

Haupstein, T; Goldie, P

2000-01-01

There is a paucity of information about the validity and reliability of clinicians' visual judgements of steadiness in one-legged stance. Such judgements are used frequently in clinical practice to support decisions about treatment in the fields of neurology, sports medicine, paediatrics and orthopaedics. The aim of the present study was to address the validity and reliability of visual judgements of steadiness in one-legged stance in a group of physiotherapists. A videotape of 20 five-second performances was shown to 14 physiotherapists with median clinical experience of 6.75 years. Validity of visual judgement was established by correlating scores obtained from an 11-point rating scale with criterion scores obtained from a force platform. In addition, partial correlations were used to control for the potential influence of body weight on the relationship between the visual judgements and criterion scores. Inter-observer reliability was quantified between the physiotherapists; intra-observer reliability was quantified between two tests four weeks apart. Mean criterion-related validity was high, regardless of whether body weight was controlled for statistically (Pearson's r = 0.84, 0.83, respectively). The standard error of estimating the criterion score was 3.3 newtons. Inter-observer reliability was high (ICC (2,1) = 0.81 at Test 1 and 0.82 at Test 2). Intra-observer reliability was high (on average ICC (2,1) = 0.88; Pearson's r = 0.90). The standard error of measurement for the 11-point scale was one unit. The finding of higher accuracy of making visual judgements than previously reported may be due to several aspects of design: use of a criterion score derived from the variability of the force signal which is more discriminating than variability of centre of pressure; use of a discriminating visual rating scale; specificity and clear definition of the phenomenon to be rated.

Theoretical and Numerical Investigations on Shallow Tunnelling in Unsaturated Soils

NASA Astrophysics Data System (ADS)

Soranzo, Enrico; Wu, Wei

2013-04-01

Excavation of shallow tunnels with the New Austrian Tunnelling Method (NATM) requires proper assessing of the tunnel face stability, to enable an open-face excavation, and the estimation of the correspondent surface settlements. Soils in a partially saturated condition exhibit a higher cohesion than in a fully saturated state, which can be taken into account when assessing the stability of the tunnel face. For the assessment of the face support pressure, different methods are used in engineering practice, varying from simple empirical and analytical formulations to advanced finite element analysis. Such procedures can be modified to account for the unsaturated state of soils. In this study a method is presented to incorporate the effect of partial saturation in the numerical analysis. The results are then compared with a simple analytical formulation derived from parametric studies. As to the numerical analysis, the variation of cohesion and of Young's modulus with saturation can be considered when the water table lies below the tunnel in a soil exhibiting a certain capillary rise, so that the tunnel is driven in a partially saturated layer. The linear elastic model with Mohr-Coulomb failure criterion can be extended to partially saturated states and calibrated with triaxial tests on unsaturated. In order to model both positive and negative pore water pressure (suction), Bishop's effective stress is incorporated into Mohr-Coulomb's failure criterion. The effective stress parameter in Bishop's formulation is related to the degree of saturation as suggested by Fredlund. If a linear suction distribution is assumed, the degree of saturation can be calculated from the Soil Water Characteristic Curve (SWCC). Expressions exist that relate the Young's modulus of unsaturated soils to the net mean stress and the matric suction. The results of the numerical computation can be compared to Vermeer & Ruse's closed-form formula that expresses the limit support pressure of the tunnel face. The expression is derived from parametric studies and predicts stability of the tunnel face when negative values are returned, suggesting that open-face tunnelling can be performed. The formula can be modified to account for the variation of cohesion along the tunnel face. The results obtained from both the numerical analysis and the analytical formulation are well in agreement and show that the stability of the tunnel face can greatly benefit from the enhanced cohesion of partially saturated soils.

Altering Genomic Integrity: Heavy Metal Exposure Promotes Transposable Element-Mediated Damage.

PubMed

Morales, Maria E; Servant, Geraldine; Ade, Catherine; Roy-Engel, Astrid M

2015-07-01

Maintenance of genomic integrity is critical for cellular homeostasis and survival. The active transposable elements (TEs) composed primarily of three mobile element lineages LINE-1, Alu, and SVA comprise approximately 30% of the mass of the human genome. For the past 2 decades, studies have shown that TEs significantly contribute to genetic instability and that TE-caused damages are associated with genetic diseases and cancer. Different environmental exposures, including several heavy metals, influence how TEs interact with its host genome increasing their negative impact. This mini-review provides some basic knowledge on TEs, their contribution to disease, and an overview of the current knowledge on how heavy metals influence TE-mediated damage.

Rational rates of uniform decay for strong solutions to a fluid-structure PDE system

NASA Astrophysics Data System (ADS)

Avalos, George; Bucci, Francesca

2015-06-01

In this work we investigate the uniform stability properties of solutions to a well-established partial differential equation (PDE) model for a fluid-structure interaction. The PDE system under consideration comprises a Stokes flow which evolves within a three-dimensional cavity; moreover, a Kirchhoff plate equation is invoked to describe the displacements along a (fixed) portion - say, Ω - of the cavity wall. Contact between the respective fluid and structure dynamics occurs on the boundary interface Ω. The main result in the paper is as follows: the solutions to the composite PDE system, corresponding to smooth initial data, decay at the rate of O (1 / t). Our method of proof hinges upon the appropriate invocation of a relatively recent resolvent criterion for polynomial decays of C0-semigroups. While the characterization provided by said criterion originates in the context of operator theory and functional analysis, the work entailed here is wholly within the realm of PDE.

Geometric convex cone volume analysis

NASA Astrophysics Data System (ADS)

Li, Hsiao-Chi; Chang, Chein-I.

2016-05-01

Convexity is a major concept used to design and develop endmember finding algorithms (EFAs). For abundance unconstrained techniques, Pixel Purity Index (PPI) and Automatic Target Generation Process (ATGP) which use Orthogonal Projection (OP) as a criterion, are commonly used method. For abundance partially constrained techniques, Convex Cone Analysis is generally preferred which makes use of convex cones to impose Abundance Non-negativity Constraint (ANC). For abundance fully constrained N-FINDR and Simplex Growing Algorithm (SGA) are most popular methods which use simplex volume as a criterion to impose ANC and Abundance Sum-to-one Constraint (ASC). This paper analyze an issue encountered in volume calculation with a hyperplane introduced to illustrate an idea of bounded convex cone. Geometric Convex Cone Volume Analysis (GCCVA) projects the boundary vectors of a convex cone orthogonally on a hyperplane to reduce the effect of background signatures and a geometric volume approach is applied to address the issue arose from calculating volume and further improve the performance of convex cone-based EFAs.

Axisymmetric micromechanics of elastic-perfectly plastic fibrous composites under uniaxial tension loading

NASA Technical Reports Server (NTRS)

Lee, Jong-Won; Allen, David H.

1993-01-01

The uniaxial response of a continuous fiber elastic-perfectly plastic composite is modeled herein as a two-element composite cylinder. An axisymmetric analytical micromechanics solution is obtained for the rate-independent elastic-plastic response of the two-element composite cylinder subjected to tensile loading in the fiber direction for the case wherein the core fiber is assumed to be a transversely isotropic elastic-plastic material obeying the Tsai-Hill yield criterion, with yielding simulating fiber failure. The matrix is assumed to be an isotropic elastic-plastic material obeying the Tresca yield criterion. It is found that there are three different circumstances that depend on the fiber and matrix properties: fiber yield, followed by matrix yielding; complete matrix yield, followed by fiber yielding; and partial matrix yield, followed by fiber yielding, followed by complete matrix yield. The order in which these phenomena occur is shown to have a pronounced effect on the predicted uniaxial effective composite response.

Introduction.

ERIC Educational Resources Information Center

Voneche, Jacques

1984-01-01

Discusses ontogeny and phylogeny in Piaget's work, differences between Piagetian (constructivist) and Darwinian (selectionist) approaches, and problems associated with transposing conceptual systems from one field to another. (RH)

Bombyx mori histone methyltransferase BmAsh2 is essential for silkworm piRNA-mediated sex determination.

PubMed

Li, Zhiqian; You, Lang; Yan, Dong; James, Anthony A; Huang, Yongping; Tan, Anjiang

2018-02-01

Sex determination is a hierarchically-regulated process with high diversity in different organisms including insects. The W chromosome-derived Fem piRNA has been identified as the primary sex determination factor in the lepidopteran insect, Bombyx mori, revealing a distinctive piRNA-mediated sex determination pathway. However, the comprehensive mechanism of silkworm sex determination is still poorly understood. We show here that the silkworm PIWI protein BmSiwi, but not BmAgo3, is essential for silkworm sex determination. CRISPR/Cas9-mediated depletion of BmSiwi results in developmental arrest in oogenesis and partial female sexual reversal, while BmAgo3 depletion only affects oogenesis. We identify three histone methyltransferases (HMTs) that are significantly down-regulated in BmSiwi mutant moths. Disruption one of these, BmAsh2, causes dysregulation of piRNAs and transposable elements (TEs), supporting a role for it in the piRNA signaling pathway. More importantly, we find that BmAsh2 mutagenesis results in oogenesis arrest and partial female-to-male sexual reversal as well as dysregulation of the sex determination genes, Bmdsx and BmMasc. Mutagenesis of other two HMTs, BmSETD2 and BmEggless, does not affect piRNA-mediated sex determination. Histological analysis and immunoprecipitation results support a functional interaction between the BmAsh2 and BmSiwi proteins. Our data provide the first evidence that the HMT, BmAsh2, plays key roles in silkworm piRNA-mediated sex determination.

Forecasting mortality of road traffic injuries in China using seasonal autoregressive integrated moving average model.

PubMed

Zhang, Xujun; Pang, Yuanyuan; Cui, Mengjing; Stallones, Lorann; Xiang, Huiyun

2015-02-01

Road traffic injuries have become a major public health problem in China. This study aimed to develop statistical models for predicting road traffic deaths and to analyze seasonality of deaths in China. A seasonal autoregressive integrated moving average (SARIMA) model was used to fit the data from 2000 to 2011. Akaike Information Criterion, Bayesian Information Criterion, and mean absolute percentage error were used to evaluate the constructed models. Autocorrelation function and partial autocorrelation function of residuals and Ljung-Box test were used to compare the goodness-of-fit between the different models. The SARIMA model was used to forecast monthly road traffic deaths in 2012. The seasonal pattern of road traffic mortality data was statistically significant in China. SARIMA (1, 1, 1) (0, 1, 1)12 model was the best fitting model among various candidate models; the Akaike Information Criterion, Bayesian Information Criterion, and mean absolute percentage error were -483.679, -475.053, and 4.937, respectively. Goodness-of-fit testing showed nonautocorrelations in the residuals of the model (Ljung-Box test, Q = 4.86, P = .993). The fitted deaths using the SARIMA (1, 1, 1) (0, 1, 1)12 model for years 2000 to 2011 closely followed the observed number of road traffic deaths for the same years. The predicted and observed deaths were also very close for 2012. This study suggests that accurate forecasting of road traffic death incidence is possible using SARIMA model. The SARIMA model applied to historical road traffic deaths data could provide important evidence of burden of road traffic injuries in China. Copyright © 2015 Elsevier Inc. All rights reserved.

Proposals or findings for a new approach about how to define and diagnose premature ejaculation.

PubMed

Wang, Weifu; Kumar, Pardeep; Minhas, Suks; Ralph, David

2005-09-01

To review and present the proposals or findings for a new approach about how to define and diagnose premature ejaculation (PE). Using Medline to search for international peer reviewed manuscripts published from 1996 to 2004 about the definition and diagnosis of PE. PE, to date, has not a universally agreed definition and diagnostic criterion. Many definitions are partial, subjective and nonspecific. An ideal definition or diagnostic criterion should consist of intravaginal ejaculatory latency time (IELT), the ability to control over ejaculation, the extent of male sexual satisfaction, the extent of female sexual satisfaction, the frequency of female sexual partner reaching orgasm and the extent of psychological and pathological factors. Therefore, the Chinese Index of Premature Ejaculation (CIPE) seems an ideal tool and criterion used to diagnose PE due to including all the elements above. In the majority of cases, PE is the result of a mix of psychogenic, physiological and organic factors. So, besides some routine tests such as urine routine test, endocrine hormone assay, psychosexual counseling, couple evaluation and physical examination, prostate examination, serum leptin assay, semen magnesium assessment and glans hypersensitivity measurement, are suggested to be performed in the diagnosis of PE. Although elucidated by two clinical trials and further confirmed, serum leptin assay seems a promising and objective marker to diagnose PE because it is related to the serotonergic system whose disorder has been confirmed to contribute to the etiology of PE. None of these definitions and diagnoses has been accepted as a universal agreement of PE. CIPE seems an ideal tool and criterion used to diagnose PE and leptin maybe become a promising and objective marker for PE.

Optimal control theory for non-scalar-valued performance criteria. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Gerring, H. P.

1971-01-01

The theory of optimal control for nonscalar-valued performance criteria is discussed. In the space, where the performance criterion attains its value, the relations better than, worse than, not better than, and not worse than are defined by a partial order relation. The notion of optimality splits up into superiority and non-inferiority, because worse than is not the complement of better than, in general. A superior solution is better than every other solution. A noninferior solution is not worse than any other solution. Noninferior solutions have been investigated particularly for vector-valued performance criteria. Superior solutions for non-scalar-valued performance criteria attaining their values in abstract partially ordered spaces are emphasized. The main result is the infimum principle which constitutes necessary conditions for a control to be a superior solution to an optimal control problem.

Joint pricing, inventory, and preservation decisions for deteriorating items with stochastic demand and promotional efforts

NASA Astrophysics Data System (ADS)

Soni, Hardik N.; Chauhan, Ashaba D.

2018-03-01

This study models a joint pricing, inventory, and preservation decision-making problem for deteriorating items subject to stochastic demand and promotional effort. The generalized price-dependent stochastic demand, time proportional deterioration, and partial backlogging rates are used to model the inventory system. The objective is to find the optimal pricing, replenishment, and preservation technology investment strategies while maximizing the total profit per unit time. Based on the partial backlogging and lost sale cases, we first deduce the criterion for optimal replenishment schedules for any given price and technology investment cost. Second, we show that, respectively, total profit per time unit is concave function of price and preservation technology cost. At the end, some numerical examples and the results of a sensitivity analysis are used to illustrate the features of the proposed model.

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

Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera

PubMed Central

2013-01-01

Background Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. Results We determined that TEs comprise ~25% of the genome. The predominant class of TEs (~12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. Conclusions Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group. PMID:24088337

On the nature of consonant/vowel differences in letter position coding: Evidence from developing and adult readers.

PubMed

Comesaña, Montserrat; Soares, Ana P; Marcet, Ana; Perea, Manuel

2016-11-01

In skilled adult readers, transposed-letter effects (jugde-JUDGE) are greater for consonant than for vowel transpositions. These differences are often attributed to phonological rather than orthographic processing. To examine this issue, we employed a scenario in which phonological involvement varies as a function of reading experience: A masked priming lexical decision task with 50-ms primes in adult and developing readers. Indeed, masked phonological priming at this prime duration has been consistently reported in adults, but not in developing readers (Davis, Castles, & Iakovidis, 1998). Thus, if consonant/vowel asymmetries in letter position coding with adults are due to phonological influences, transposed-letter priming should occur for both consonant and vowel transpositions in developing readers. Results with adults (Experiment 1) replicated the usual consonant/vowel asymmetry in transposed-letter priming. In contrast, no signs of an asymmetry were found with developing readers (Experiments 2-3). However, Experiments 1-3 did not directly test the existence of phonological involvement. To study this question, Experiment 4 manipulated the phonological prime-target relationship in developing readers. As expected, we found no signs of masked phonological priming. Thus, the present data favour an interpretation of the consonant/vowel dissociation in letter position coding as due to phonological rather than orthographic processing. © 2016 The British Psychological Society.

Pictorial relief for equiluminant images

NASA Astrophysics Data System (ADS)

van Doorn, Andrea J.; de Ridder, Huib; Koenderink, Jan J.

2005-03-01

Pictorial relief depends strongly on "cues" in the image. For isoluminant renderings some cues are missing, namely all information that is related to luminance contrast (e.g., shading, atmospheric perspective). It has been suggested that spatial discrimination and especially pictorial space suffer badly in isoluminant conditions. We have investigated the issue through quantitative measurement of pictorial depth-structure under normal and isoluminant conditions. As stimuli we used monochrome halftone photographs, either as such, or "transposed" to Red/Green or Green/Red hue modulations. We used two distinct methods, one to probe pictorial pose (by way of correspondences settings between pictures of an object in different poses), the other to probe pictorial depth (by way of attitude settings of a gauge figure to a perceptual "fit"). In both experiments the depth reconstructions for Red/Green, Green/Red and monochrome conditions were very similar. Moreover, observers performed equally well in Red/Green, Green/Red and monochrome conditions. Thus, the general conclusion is that observers did not do markedly worse with the isoluminant Red/Green and Green/Red transposed images. Whereas the transposed images certainly looked weird, they were easily interpreted. Much of the structure of pictorial space was apparently preserved. Thus the notion that spatial representations are not sustained under isoluminant conditions should be applied with caution.

Distribution of Unlinked Transpositions of a Ds Element from a T-DNA Locus on Tomato Chromosome 4

PubMed Central

Briza, J.; Carroll, B. J.; Klimyuk, V. I.; Thomas, C. M.; Jones, D. A.; Jones, JDG.

1995-01-01

In maize, receptor sites for unlinked transpositions of Activator (Ac) elements are not distributed randomly. To test whether the same is true in tomato, the receptor sites for a Dissociation (Ds) element derived from Ac, were mapped for 26 transpositions unlinked to a donor T-DNA locus on chromosome 4. Four independent transposed Dss mapped to sites on chromosome 4 genetically unlinked to the donor T-DNA, consistent with a preference for transposition to unlinked sites on the same chromosome as opposed to sites on other chromosomes. There was little preference among the nondonor chromosomes, except perhaps for chromosome 2, which carried seven transposed Dss, but these could not be proven to be independent. However, these data, when combined with those from other studies in tomato examining the distribution of transposed Acs or Dss among nondonor chromosomes, suggest there may be absolute preferences for transposition irrespective of the chromosomal location of the donor site. If true, transposition to nondonor chromosomes in tomato would differ from that in maize, where the preference seems to be determined by the spatial arrangement of chromosomes in the interphase nucleus. The tomato lines carrying Ds elements at known locations are available for targeted transposon tagging experiments. PMID:8536985

From Embryo to Adult: piRNA-Mediated Silencing throughout Germline Development in Drosophila

PubMed Central

Marie, Pauline P.; Ronsseray, Stéphane; Boivin, Antoine

2016-01-01

In metazoan germ cells, transposable element activity is repressed by small noncoding PIWI-associated RNAs (piRNAs). Numerous studies in Drosophila have elucidated the mechanism of this repression in the adult germline. However, when and how transposable element repression is established during germline development has not been addressed. Here, we show that homology-dependent trans silencing is active in female primordial germ cells from late embryogenesis through pupal stages, and that genes related to the adult piRNA pathway are required for silencing during development. In larval gonads, we detect rhino-dependent piRNAs indicating de novo biogenesis of functional piRNAs during development. Those piRNAs exhibit the molecular signature of the “ping-pong” amplification step. Moreover, we show that Heterochromatin Protein 1a is required for the production of piRNAs coming from telomeric transposable elements. Furthermore, as in adult ovaries, incomplete, bimodal, and stochastic repression resembling variegation can occur at all developmental stages. Clonal analysis indicates that the repression status established in embryonic germ cells is maintained until the adult stage, suggesting the implication of a cellular memory mechanism. Taken together, data presented here show that piRNAs and their associated proteins are epigenetic components of a continuous repression system throughout germ cell development. PMID:27932388

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

PubMed

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

2014-12-12

To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. Copyright © 2014, American Association for the Advancement of Science.

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

PubMed Central

Secco, David; Wang, Chuang; Shou, Huixia; Schultz, Matthew D; Chiarenza, Serge; Nussaume, Laurent; Ecker, Joseph R; Whelan, James; Lister, Ryan

2015-01-01

Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, and could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress. DOI: http://dx.doi.org/10.7554/eLife.09343.001 PMID:26196146

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

PubMed Central

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

2015-01-01

To provide context for the diversifications of archosaurs, the group that includes crocodilians, dinosaurs and birds, we generated draft genomes of three crocodilians, Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the relatively rapid evolution of bird genomes represents an autapomorphy within that clade. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these new data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. PMID:25504731

Genomic patterns associated with paternal/maternal distribution of transposable elements

NASA Astrophysics Data System (ADS)

Jurka, Jerzy

2003-03-01

Transposable elements (TEs) are specialized DNA or RNA fragments capable of surviving in intragenomic niches. They are commonly, perhaps unjustifiably referred to as "selfish" or "parasitic" elements. TEs can be divided in two major classes: retroelements and DNA transposons. The former include non-LTR retrotransposons and retrovirus-like elements, using reverse transriptase for their reproduction prior to integration into host DNA. The latter depend mostly on host DNA replication, with possible exception of rolling-circle transposons recently discovered by our team. I will review basic information on TEs, with emphasis on human Alu and L1 retroelements discussed in the context of genomic organization. TEs are non-randomly distributed in chromosomal DNA. In particular, human Alu elements tend to prefer GC-rich regions, whereas L1 accumulate in AT-rich regions. Current explanations of this phenomenon focus on the so called "target effects" and post-insertional selection. However, the proposed models appear to be unsatisfactory and alternative explanations invoking "channeling" to different chromosomal regions will be a major focus of my presentation. Transposable elements (TEs) can be expressed and integrated into host DNA in the male or female germlines, or both. Different models of expression and integration imply different proportions of TEs on sex chromosomes and autosomes. The density of recently retroposed human Alu elements is around three times higher on chromosome Y than on chromosome X, and over two times higher than the average density for all human autosomes. This implies Alu activity in paternal germlines. Analogous inter-chromosomal proportions for other repeat families should determine their compatibility with one of the three basic models describing the inheritance of TEs. Published evidence indicates that maternally and paternally imprinted genes roughly correspond to GC-rich and AT-rich DNA. This may explain the observed chromosomal distribution of Alu and L1 elements. Finally, paternal models of inheritance predict rapid accumulation of active TEs on chromosome Y. I will discuss potential implications of this phenomenon for evolution of chromosome Y and transposable elements.

Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry for peptide de novo amino acid sequencing for a seven-protein mixture by paired single-residue transposed Lys-N and Lys-C digestion.

PubMed

Guan, Xiaoyan; Brownstein, Naomi C; Young, Nicolas L; Marshall, Alan G

2017-01-30

Bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics to identify proteins from a sequence database. De novo sequencing is also available for sequencing peptides with relatively short sequence lengths. We recently showed that paired Lys-C and Lys-N proteases produce peptides of identical mass and similar retention time, but different tandem mass spectra. Such parallel experiments provide complementary information, and allow for up to 100% MS/MS sequence coverage. Here, we report digestion by paired Lys-C and Lys-N proteases of a seven-protein mixture: human hemoglobin alpha, bovine carbonic anhydrase 2, horse skeletal muscle myoglobin, hen egg white lysozyme, bovine pancreatic ribonuclease, bovine rhodanese, and bovine serum albumin, followed by reversed-phase nanoflow liquid chromatography, collision-induced dissociation, and 14.5 T Fourier transform ion cyclotron resonance mass spectrometry. Matched pairs of product peptide ions of equal precursor mass and similar retention times from each digestion are compared, leveraging single-residue transposed information with independent interferences to confidently identify fragment ion types, residues, and peptides. Selected pairs of product ion mass spectra for de novo sequenced protein segments from each member of the mixture are presented. Pairs of the transposed product ions as well as complementary information from the parallel experiments allow for both high MS/MS coverage for long peptide sequences and high confidence in the amino acid identification. Moreover, the parallel experiments in the de novo sequencing reduce false-positive matches of product ions from the single-residue transposed peptides from the same segment, and thereby further improve the confidence in protein identification. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Proteomic analysis of urine in patients with intestinal segments transposed into the urinary tract.

PubMed

Nabi, Ghulam; N'Dow, James; Hasan, Tahseen S; Booth, Ian R; Cash, Phil

2005-04-01

Intestinal segments are used to replace or reconstruct the urinary bladder when it has become dysfunctional or develops life-threatening disease such as cancer. The quality of life in patients with intestinal segments used to either enlarge or completely replace the native bladder is adversely affected by recurrent urinary tract infections, excessive mucus production and the occasional development of malignancy. At present, there is no reliable method of predicting or noninvasively monitoring these patients for the development of these complications. The characterisation of proteins secreted into urine from the transposed intestinal segments could serve as important indicators of these clinical complications. Urine is an ideal source of material in which to search for biomarkers, since it bathes the affected tissues and can be obtained relatively easily by noninvasive methods. The urinary proteome of patients with intestinal segments transposed into the urinary tract is unknown and we present the first global description of the urinary protein profile in these patients. Sample preparation is a critical step in achieving accurate and reliable data. We describe a method to prepare urinary proteins that was compatible with their subsequent analysis using two-dimensional polyacrylamide gel electrophoresis. This method helped to overcome some of the technical problems encountered in analysing urine from this patient cohort. The method was used to analyse urinary proteins recovered from five healthy controls and ten patients with intestinal segments transposed into the urinary tract. Four low molecular weight proteins were found to be present in nine out of ten for the patient group but for none of the healthy controls. The four proteins were identified as lithostathine-1 alpha precursor, pancreatitis associated protein-1 precursor, liver fatty acid binding protein and testis expressed protein-12. The role of these proteins as potential biomarkers of intestinal cell activity within the reconstructed bladder is discussed.

Biofeedback in Partial Weight Bearing: Validity of 3 Different Devices.

PubMed

van Lieshout, Remko; Stukstette, Mirelle J; de Bie, Rob A; Vanwanseele, Benedicte; Pisters, Martijn F

2016-11-01

Study Design Controlled laboratory study to assess criterion-related validity, with a cross-sectional within-subject design. Background Patients with orthopaedic conditions have difficulties complying with partial weight-bearing instructions. Technological advances have resulted in biofeedback devices that offer real-time feedback. However, the accuracy of these devices is mostly unknown. Inaccurate feedback can result in incorrect lower-limb loading and may lead to delayed healing. Objectives To investigate validity of peak force measurements obtained using 3 different biofeedback devices under varying levels of partial weight-bearing categories. Methods Validity of 3 biofeedback devices (OpenGo science, SmartStep, and SensiStep) was assessed. Healthy participants were instructed to walk at a self-selected speed with crutches under 3 different weight-bearing conditions, categorized as a percentage range of body weight: 1% to 20%, greater than 20% to 50%, and greater than 50% to 75%. Peak force data from the biofeedback devices were compared with the peak vertical ground reaction force measured with a force plate. Criterion validity was estimated using simple and regression-based Bland-Altman 95% limits of agreement and weighted kappas. Results Fifty-five healthy adults (58% male) participated. Agreement with the gold standard was substantial for the SmartStep, moderate for OpenGo science, and slight for SensiStep (weighted ± = 0.76, 0.58, and 0.19, respectively). For the 1% to 20% and greater than 20% to 50% weight-bearing categories, both the OpenGo science and SmartStep had acceptable limits of agreement. For the weight-bearing category greater than 50% to 75%, none of the devices had acceptable agreement. Conclusion The OpenGo science and SmartStep provided valid feedback in the lower weight-bearing categories, and the SensiStep showed poor validity of feedback in all weight-bearing categories. J Orthop Sports Phys Ther 2016;46(11):-1. Epub 12 Oct 2016. doi:10.2519/jospt.2016.6625.

Correlation between hepatobiliary scintigraphy and surgery or postmortem examination findings in dogs and cats with extrahepatic biliary obstruction, partial obstruction, or patency of the biliary system: 18 cases (1995-2004).

PubMed

Head, Laurie L; Daniel, Gregory B

2005-11-15

To evaluate the usefulness of serum biochemical variables and scintigraphic study results for differentiating between dogs and cats with complete extrahepatic biliary obstruction (EHO) and those with partial EHO or patent bile ducts. Retrospective case series. 17 dogs and 1 cat. Animals that underwent hepatobiliary scintigraphy and had either surgical or postmortem confirmation of the degree of bile duct patency were included. Scintigraphic images were evaluated and biliary tracts were classified as patent, partially obstructed but patent, or obstructed. Surgery or postmortem examination was considered the gold standard for diagnosis, and compared with those findings, sensitivity and specificity of scintigraphy were calculated. With absence of radioactivity in the intestinal tract as the diagnostic criterion for EHO, the sensitivity and specificity of scintigraphic diagnosis were both 83% when final images were acquired at 19 to 24 hours, compared with 100% and 33%, respectively, when 180 minutes was used as the cutoff time. Animals with partial biliary obstruction had less intestinal radioactivity that arrived later than that observed in animals with patent biliary tracts. Animals in which intestinal radioactivity has not been observed after the standard 3 to 4 hours should undergo additional scintigraphic imaging. Findings in animals with partial biliary obstruction include delayed arrival of radioactivity and less radioactivity in the intestine. Distinguishing between complete and partial biliary tract obstruction is important because animals with partial obstruction may respond favorably to medical management and should not be given an erroneous diagnosis of complete obstruction.

The effect of moonlight on observation of cloud cover at night, and application to cloud climatology

NASA Technical Reports Server (NTRS)

Hahn, Carole J.; Warren, Stephen G.; London, Julius

1995-01-01

Ten years of nighttime weather observations from the Northern Hemisphere in December were classified according to the illuminance of moonlight or twilight on the cloud tops, and a threshold level of illuminance was determined, above which the clouds are apparently detected adequately. This threshold corresponds to light from a full moon at an elevation angle of 6 deg, light from a partial moon at higher elevation, or twilight from the sun less than 9 deg bvelow the horizon. It permits the use of about 38% of the observations made with the sun below the horizon. The computed diurnal cycles of total cloud cover are altered considerably when this moonlight criterion is imposed. Maximum cloud cover over much of the ocean is now found to be at night or in the morning, whereas computations obtained without benefit of the moonlight criterion, as in our published atlases, showed the time of maximum to be noon or early afternoon in many regions. The diurnal cycles of total cloud cover we obtain are compared with those of the International Satellite Cloud Climatology Project (ISCCP) for a few regions; they are generally in better agreement if the moonlight criterion is imposed on the surface observations. Using the moonlight criterion, we have analyzed 10 years (1982-91) of surface weather observations over land and ocean, worldwide, for total cloud cover and for the frequency of occurrence of clear sky, fog, and precipitation. The global average cloud cover (average of day and night) is about 2% higher if the moonlight criterion is imposed than if all observations are used. The difference is greater in winter than in summer, because of the fewer hours of darkness in summer. The amplitude of the annual cycle of total cloud cover over the Arctic Ocean and at the South Pole is diminished by a few percent when the moonlight criterion is imposed. The average cloud cover for 1982-91 is found to be 55% for Northern Hemisphere land, 53% for Southern Hemisphere land, 66% for Northern Hemisphere ocean, and 70% for Southern Hemisphere ocean, giving a global average of 64%. The global average for daytime is 64.6%; for nighttime 63.3%.

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

Transposable elements as genetic regulatory substrates in early development.

PubMed

Gifford, Wesley D; Pfaff, Samuel L; Macfarlan, Todd S

2013-05-01

The abundance and ancient origins of transposable elements (TEs) in eukaryotic genomes has spawned research into the potential symbiotic relationship between these elements and their hosts. In this review, we introduce the diversity of TEs, discuss how distinct classes are uniquely regulated in development, and describe how they appear to have been coopted for the purposes of gene regulation and the orchestration of a number of processes during early embryonic development. Although young, active TEs play an important role in somatic tissues and evolution, we focus mostly on the contributions of the older, fixed elements in mammalian genomes. We also discuss major challenges inherent in the study of TEs and contemplate future experimental approaches to further investigate how they coordinate developmental processes. Published by Elsevier Ltd.

Transposable elements as genetic regulatory substrates in early development

PubMed Central

Gifford, Wesley D.; Pfaff, Samuel L.; Macfarlan, Todd S.

2014-01-01

The abundance and ancient origins of transposable elements (TEs) in eukaryotic genomes has spawned research into the potential symbiotic relationship between these elements and their hosts. In this review, we introduce the diversity of TEs, discuss how distinct classes are uniquely regulated in development, and describe how they appear to have been coopted for the purposes of gene regulation and the orchestration of a number of processes during early embryonic development. Although young, active TEs play an important role in somatic tissues and evolution, we focus mostly on the contributions of the older, fixed elements in mammalian genomes. We also discuss major challenges inherent in the study of TEs and contemplate future experimental approaches to further investigate how they coordinate developmental processes. PMID:23411159

Potential roles for transposable elements in creating imprinted expression.

PubMed

Anderson, Sarah N; Springer, Nathan M

2018-04-01

Changes in gene expression can have profound effects on phenotype. Nature has provided many complex patterns of gene regulation such as imprinting. Imprinted genes exhibit differences in the expression of the maternal and paternal alleles, even though they reside in the same nucleus with access to the same trans-acting factors. Significant attention has been focused on the potential reasons that imprinted expression could be beneficial and stabilized by selection. However, less attention has focused on understanding how imprinted expression might arise or decay. We discuss the evidence for frequent turnover of imprinted expression based on evolutionary analyses in plants and the potential role for transposable elements (TEs) in creating imprinted expression patterns. Copyright © 2018 Elsevier Ltd. All rights reserved.

Transposable elements in TDP-43-mediated neurodegenerative disorders.

PubMed

Li, Wanhe; Jin, Ying; Prazak, Lisa; Hammell, Molly; Dubnau, Josh

2012-01-01

Elevated expression of specific transposable elements (TEs) has been observed in several neurodegenerative disorders. TEs also can be active during normal neurogenesis. By mining a series of deep sequencing datasets of protein-RNA interactions and of gene expression profiles, we uncovered extensive binding of TE transcripts to TDP-43, an RNA-binding protein central to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Second, we find that association between TDP-43 and many of its TE targets is reduced in FTLD patients. Third, we discovered that a large fraction of the TEs to which TDP-43 binds become de-repressed in mouse TDP-43 disease models. We propose the hypothesis that TE mis-regulation contributes to TDP-43 related neurodegenerative diseases.

Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genera Drosophila and Zaprionus

PubMed Central

2011-01-01

We have recently reported numerous cases of horizontal transfers of transposable elements between species of drosophilids. These studies revealed a substantial number of horizontal transfers between species of the subgroup melanogaster of the genus Drosophila and between these species and species of the genus Zaprionus. In this review, these transfers and similar, previously reported events are discussed and reanalysed to portray the interrelationships between the species that allowed the occurrence of so many horizontal transfers. The paper also addresses problems that may arise in drawing inferences about the time period during which the horizontal transfers occurred and the factors that may be associated with these transfers are discussed. PMID:22312591

Regulatory activities of transposable elements: from conflicts to benefits

PubMed Central

Chuong, Edward B.; Elde, Nels C.; Feschotte, Cédric

2017-01-01

Transposable elements (TEs) are a prolific source of tightly regulated, biochemically active non-coding elements, such as transcription factor binding sites and non-coding RNAs. A wealth of recent studies reinvigorates the idea that these elements are pervasively co-opted for the regulation of host genes. We argue that the inherent genetic properties of TEs and conflicting relationships with their hosts facilitate their recruitment for regulatory functions in diverse genomes. We review recent findings supporting the long-standing hypothesis that the waves of TE invasions endured by organisms for eons have catalyzed the evolution of gene regulatory networks. We also discuss the challenges of dissecting and interpreting the phenotypic impact of regulatory activities encoded by TEs in health and disease. PMID:27867194

Performance enhancement of optical code-division multiple-access systems using transposed modified Walsh code

NASA Astrophysics Data System (ADS)

Sikder, Somali; Ghosh, Shila

2018-02-01

This paper presents the construction of unipolar transposed modified Walsh code (TMWC) and analysis of its performance in optical code-division multiple-access (OCDMA) systems. Specifically, the signal-to-noise ratio, bit error rate (BER), cardinality, and spectral efficiency were investigated. The theoretical analysis demonstrated that the wavelength-hopping time-spreading system using TMWC was robust against multiple-access interference and more spectrally efficient than systems using other existing OCDMA codes. In particular, the spectral efficiency was calculated to be 1.0370 when TMWC of weight 3 was employed. The BER and eye pattern for the designed TMWC were also successfully obtained using OptiSystem simulation software. The results indicate that the proposed code design is promising for enhancing network capacity.

Sickling of red blood cells through rapid oxygen exchange in microfluidic drops.

PubMed

Abbyad, Paul; Tharaux, Pierre-Louis; Martin, Jean-Louis; Baroud, Charles N; Alexandrou, Antigoni

2010-10-07

We have developed a microfluidic approach to study the sickling of red blood cells associated with sickle cell anemia by rapidly varying the oxygen partial pressure within flowing microdroplets. By using the perfluorinated carrier oil as a sink or source of oxygen, the oxygen level within the water droplets quickly equilibrates through exchange with the surrounding oil. This provides control over the oxygen partial pressure within an aqueous drop ranging from 1 kPa to ambient partial pressure, i.e. 21 kPa. The dynamics of the oxygen exchange is characterized through fluorescence lifetime measurements of a ruthenium compound dissolved in the aqueous phase. The gas exchange is shown to occur primarily during and directly after droplet formation, in 0.1 to 0.5 s depending on the droplet diameter and speed. The controlled deoxygenation is used to trigger the polymerization of hemoglobin within sickle red blood cells, encapsulated in drops. This process is observed using polarization microscopy, which yields a robust criterion to detect polymerization based on transmitted light intensity through crossed polarizers.

Partial least squares density modeling (PLS-DM) - a new class-modeling strategy applied to the authentication of olives in brine by near-infrared spectroscopy.

PubMed

Oliveri, Paolo; López, M Isabel; Casolino, M Chiara; Ruisánchez, Itziar; Callao, M Pilar; Medini, Luca; Lanteri, Silvia

2014-12-03

A new class-modeling method, referred to as partial least squares density modeling (PLS-DM), is presented. The method is based on partial least squares (PLS), using a distance-based sample density measurement as the response variable. Potential function probability density is subsequently calculated on PLS scores and used, jointly with residual Q statistics, to develop efficient class models. The influence of adjustable model parameters on the resulting performances has been critically studied by means of cross-validation and application of the Pareto optimality criterion. The method has been applied to verify the authenticity of olives in brine from cultivar Taggiasca, based on near-infrared (NIR) spectra recorded on homogenized solid samples. Two independent test sets were used for model validation. The final optimal model was characterized by high efficiency and equilibrate balance between sensitivity and specificity values, if compared with those obtained by application of well-established class-modeling methods, such as soft independent modeling of class analogy (SIMCA) and unequal dispersed classes (UNEQ). Copyright © 2014 Elsevier B.V. All rights reserved.

Linear spreading speeds from nonlinear resonant interaction

NASA Astrophysics Data System (ADS)

Faye, Grégory; Holzer, Matt; Scheel, Arnd

2017-06-01

We identify a new mechanism for propagation into unstable states in spatially extended systems, that is based on resonant interaction in the leading edge of invasion fronts. Such resonant invasion speeds can be determined solely based on the complex linear dispersion relation at the unstable equilibrium, but rely on the presence of a nonlinear term that facilitates the resonant coupling. We prove that these resonant speeds give the correct invasion speed in a simple example, we show that fronts with speeds slower than the resonant speed are unstable, and corroborate our speed criterion numerically in a variety of model equations, including a nonlocal scalar neural field model. GF received support from the project NONLOCAL (ANR-14-CE25-0013) funded by the French National Research Agency. MH was partially supported by the National Science Foundation through grant NSF-DMS-1516155. AS was partially supported by the National Science Foundation through grant NSF-DMS-1311740 and through a DAAD Fellowship.

An improved partial least-squares regression method for Raman spectroscopy

NASA Astrophysics Data System (ADS)

Momenpour Tehran Monfared, Ali; Anis, Hanan

2017-10-01

It is known that the performance of partial least-squares (PLS) regression analysis can be improved using the backward variable selection method (BVSPLS). In this paper, we further improve the BVSPLS based on a novel selection mechanism. The proposed method is based on sorting the weighted regression coefficients, and then the importance of each variable of the sorted list is evaluated using root mean square errors of prediction (RMSEP) criterion in each iteration step. Our Improved BVSPLS (IBVSPLS) method has been applied to leukemia and heparin data sets and led to an improvement in limit of detection of Raman biosensing ranged from 10% to 43% compared to PLS. Our IBVSPLS was also compared to the jack-knifing (simpler) and Genetic Algorithm (more complex) methods. Our method was consistently better than the jack-knifing method and showed either a similar or a better performance compared to the genetic algorithm.

Identification of confounders in the assessment of the relationship between lead exposure and child development.

PubMed

Tong, I S; Lu, Y

2001-01-01

To explore the best approach to identify and adjust for confounders in epidemiologic practice. In the Port Pirie cohort study, the selection of covariates was based on both a priori and an empirical consideration. In an assessment of the relationship between exposure to environmental lead and child development, change-in-estimate (CE) and significance testing (ST) criteria were compared in identifying potential confounders. The Pearson correlation coefficients were used to evaluate the potential for collinearity between pairs of major quantitative covariates. In multivariate analyses, the effects of confounding factors were assessed with multiple linear regression models. The nature and number of covariates selected varied with different confounder selection criteria and different cutoffs. Four covariates (i.e., quality of home environment, socioeconomic status (SES), maternal intelligence, and parental smoking behaviour) met the conventional CE criterion (> or =10%), whereas 14 variables met the ST criterion (p < or = 0.25). However, the magnitude of the relationship between blood lead concentration and children's IQ differed slightly after adjustment for confounding, using either the CE (partial regression coefficient: -4.4; 95% confidence interval (CI): -0.5 to -8.3) or ST criterion (-4.3; 95% CI: -0.2 to -8.4). Identification and selection of confounding factors need to be viewed cautiously in epidemiologic studies. Either the CE (e.g., > or = 10%) or ST (e.g., p < or = 0.25) criterion may be implemented in identification of a potential confounder if a study sample is sufficiently large, and both the methods are subject to arbitrariness of selecting a cut-off point. In this study, the CE criterion (i.e., > or = 10%) appears to be more stringent than the ST method (i.e., p < or = 0.25) in the identification of confounders. However, the ST rule cannot be used to determine the trueness of confounding because it cannot reflect the causal relationship between the confounder and outcome. This study shows the complexities one can expect to encounter in the identification of and adjustment for confounders.

SU-E-T-769: T-Test Based Prior Error Estimate and Stopping Criterion for Monte Carlo Dose Calculation in Proton Therapy

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

Hong, X; Gao, H; Schuemann, J

2015-06-15

Purpose: The Monte Carlo (MC) method is a gold standard for dose calculation in radiotherapy. However, it is not a priori clear how many particles need to be simulated to achieve a given dose accuracy. Prior error estimate and stopping criterion are not well established for MC. This work aims to fill this gap. Methods: Due to the statistical nature of MC, our approach is based on one-sample t-test. We design the prior error estimate method based on the t-test, and then use this t-test based error estimate for developing a simulation stopping criterion. The three major components are asmore » follows.First, the source particles are randomized in energy, space and angle, so that the dose deposition from a particle to the voxel is independent and identically distributed (i.i.d.).Second, a sample under consideration in the t-test is the mean value of dose deposition to the voxel by sufficiently large number of source particles. Then according to central limit theorem, the sample as the mean value of i.i.d. variables is normally distributed with the expectation equal to the true deposited dose.Third, the t-test is performed with the null hypothesis that the difference between sample expectation (the same as true deposited dose) and on-the-fly calculated mean sample dose from MC is larger than a given error threshold, in addition to which users have the freedom to specify confidence probability and region of interest in the t-test based stopping criterion. Results: The method is validated for proton dose calculation. The difference between the MC Result based on the t-test prior error estimate and the statistical Result by repeating numerous MC simulations is within 1%. Conclusion: The t-test based prior error estimate and stopping criterion are developed for MC and validated for proton dose calculation. Xiang Hong and Hao Gao were partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000) and the Shanghai Pujiang Talent Program (#14PJ1404500)« less

piRNAs and their diverse roles: a transposable element-driven tactic for gene regulation?

PubMed

Sarkar, Arpita; Volff, Jean-Nicolas; Vaury, Chantal

2017-02-01

P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are small, noncoding RNAs known for silencing transposable elements (TEs) in the germline of animals. Most genomes host TEs, which are notorious for mobilizing themselves and endangering survival of the host if not controlled. By silencing TEs in the germline, piRNAs prevent harmful mutations from being passed on to the next generation. How piRNAs are generated and how they silence TEs were the focus of researchers ever since their discovery. Now a spate of recent papers are beginning to tell us that piRNAs can play roles beyond TE silencing and are involved in diverse cellular processes from mRNA regulation to development or genome rearrangement. In this review, we discuss some of these recently reported roles. Data on these new roles are often rudimentary, and the involvement of piRNAs in these processes is yet to be definitely established. What is interesting is that the reports are on animals widely separated on the phylogenetic tree of life and that piRNAs were also found outside the gonadal tissues. Some of these piRNAs map to TE sequences, prompting us to hypothesize that genomes may have co-opted the TE-derived piRNA system for their own regulation.-Sarkar, A., Volff, J.-N., Vaury, C. piRNAs and their diverse roles: a transposable element-driven tactic for gene regulation? © FASEB.

LINE dancing in the human genome: transposable elements and disease.

PubMed

Belancio, Victoria P; Deininger, Prescott L; Roy-Engel, Astrid M

2009-10-27

Transposable elements (TEs) have been consistently underestimated in their contribution to genetic instability and human disease. TEs can cause human disease by creating insertional mutations in genes, and also contributing to genetic instability through non-allelic homologous recombination and introduction of sequences that evolve into various cis-acting signals that alter gene expression. Other outcomes of TE activity, such as their potential to cause DNA double-strand breaks or to modulate the epigenetic state of chromosomes, are less fully characterized. The currently active human transposable elements are members of the non-LTR retroelement families, LINE-1, Alu (SINE), and SVA. The impact of germline insertional mutagenesis by TEs is well established, whereas the rate of post-insertional TE-mediated germline mutations and all forms of somatic mutations remain less well quantified. The number of human diseases discovered to be associated with non-allelic homologous recombination between TEs, and particularly between Alu elements, is growing at an unprecedented rate. Improvement in the technology for detection of such events, as well as the mounting interest in the research and medical communities in resolving the underlying causes of the human diseases with unknown etiology, explain this increase. Here, we focus on the most recent advances in understanding of the impact of the active human TEs on the stability of the human genome and its relevance to human disease.

GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii).

PubMed

Xu, Zhenzhen; Liu, Jing; Ni, Wanchao; Peng, Zhen; Guo, Yue; Ye, Wuwei; Huang, Fang; Zhang, Xianggui; Xu, Peng; Guo, Qi; Shen, Xinlian; Du, Jianchang

2017-01-01

Although several diploid and tetroploid Gossypium species genomes have been sequenced, the well annotated web-based transposable elements (TEs) database is lacking. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the cotton genome, a comprehensive, specific, and user-friendly web-based database, Gossypium raimondii transposable elements database (GrTEdb), was constructed. A total of 14 332 TEs were structurally annotated and clearly categorized in G. raimondii genome, and these elements have been classified into seven distinct superfamilies based on the order of protein-coding domains, structures and/or sequence similarity, including 2929 Copia-like elements, 10 368 Gypsy-like elements, 299 L1 , 12 Mutators , 435 PIF-Harbingers , 275 CACTAs and 14 Helitrons . Meanwhile, the web-based sequence browsing, searching, downloading and blast tool were implemented to help users easily and effectively to annotate the TEs or TE fragments in genomic sequences from G. raimondii and other closely related Gossypium species. GrTEdb provides resources and information related with TEs in G. raimondii , and will facilitate gene and genome analyses within or across Gossypium species, evaluating the impact of TEs on their host genomes, and investigating the potential interaction between TEs and protein-coding genes in Gossypium species. http://www.grtedb.org/. © The Author(s) 2017. Published by Oxford University Press.

Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species.

PubMed

Stapley, Jessica; Santure, Anna W; Dennis, Stuart R

2015-05-01

Rapid adaptation of invasive species to novel habitats has puzzled evolutionary biologists for decades, especially as this often occurs in the face of limited genetic variability. Although some ecological traits common to invasive species have been identified, little is known about the possible genomic/genetic mechanisms that may underlie their success. A common scenario in many introductions is that small founder population sizes will often lead to reduced genetic diversity, but that invading populations experience large environmental perturbations, such as changes in habitat and environmental stress. Although sudden and intense stress is usually considered in a negative context, these perturbations may actually facilitate rapid adaptation by affecting genome structure, organization and function via interactions with transposable elements (TEs), especially in populations with low genetic diversity. Stress-induced changes in TE activity can alter gene action and can promote structural variation that may facilitate the rapid adaptation observed in new environments. We focus here on the adaptive potential of TEs in relation to invasive species and highlight their role as powerful mutational forces that can rapidly create genetic diversity. We hypothesize that activity of transposable elements can explain rapid adaptation despite low genetic variation (the genetic paradox of invasive species), and provide a framework under which this hypothesis can be tested using recently developed and emerging genomic technologies. © 2015 John Wiley & Sons Ltd.

Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes.

PubMed

Lau, Billy T; Ji, Hanlee P

2017-09-21

RNA-Seq measures gene expression by counting sequence reads belonging to unique cDNA fragments. Molecular barcodes commonly in the form of random nucleotides were recently introduced to improve gene expression measures by detecting amplification duplicates, but are susceptible to errors generated during PCR and sequencing. This results in false positive counts, leading to inaccurate transcriptome quantification especially at low input and single-cell RNA amounts where the total number of molecules present is minuscule. To address this issue, we demonstrated the systematic identification of molecular species using transposable error-correcting barcodes that are exponentially expanded to tens of billions of unique labels. We experimentally showed random-mer molecular barcodes suffer from substantial and persistent errors that are difficult to resolve. To assess our method's performance, we applied it to the analysis of known reference RNA standards. By including an inline random-mer molecular barcode, we systematically characterized the presence of sequence errors in random-mer molecular barcodes. We observed that such errors are extensive and become more dominant at low input amounts. We described the first study to use transposable molecular barcodes and its use for studying random-mer molecular barcode errors. Extensive errors found in random-mer molecular barcodes may warrant the use of error correcting barcodes for transcriptome analysis as input amounts decrease.

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.

A reconfigurable continuous-flow fluidic routing fabric using a modular, scalable primitive.

PubMed

Silva, Ryan; Bhatia, Swapnil; Densmore, Douglas

2016-07-05

Microfluidic devices, by definition, are required to move liquids from one physical location to another. Given a finite and frequently fixed set of physical channels to route fluids, a primitive design element that allows reconfigurable routing of that fluid from any of n input ports to any n output ports will dramatically change the paradigms by which these chips are designed and applied. Furthermore, if these elements are "regular" regarding their design, the programming and fabrication of these elements becomes scalable. This paper presents such a design element called a transposer. We illustrate the design, fabrication and operation of a single transposer. We then scale this design to create a programmable fabric towards a general-purpose, reconfigurable microfluidic platform analogous to the Field Programmable Gate Array (FPGA) found in digital electronics.

Initial investigations into preschoolers' mirror-style versus transposed bodily imitation.

PubMed

Dunphy-Lelii, Sarah

2014-03-01

In typical development, imitation plays a key role in sociocognitive competence. The current study investigated a hypothesised developmental trajectory in face-to-face full body imitation style in 91 preschoolers, as well as a relation between imitation style and theory of mind (ToM). Children's response style to 8 lateralized action prompts was recorded as either "mirror" or "transposed." Overall, mirror-style response increased with age, and was predominant for children and an adult comparison group. Imitation style varied depending on the prompt given, with certain actions showing a side bias regardless of prompt viewed. Mirror-style response was correlated with ToM performance after controlling for language ability, but not after controlling for age. Findings are discussed regarding the hypothesised relation between postural synchrony and larger perspective-taking competence.

Evaluation of expert criteria for preoperative magnetic resonance imaging of newly diagnosed breast cancer.

PubMed

Behrendt, Carolyn E; Tumyan, Lusine; Gonser, Laura; Shaw, Sara L; Vora, Lalit; Paz, I Benjamin; Ellenhorn, Joshua D I; Yim, John H

2014-08-01

Despite 2 randomized trials reporting no reduction in operations or local recurrence at 1 year, preoperative magnetic resonance imaging (MRI) is increasingly used in diagnostic workup of breast cancer. We evaluated 5 utilization criteria recently proposed by experts. Of women (n = 340) newly diagnosed with unilateral breast cancer who underwent bilateral MRI, most (69.4%) met at least 1 criterion before MRI: mammographic density (44.4%), under consideration for partial breast irradiation (PBI) (19.7%), genetic-familial risk (12.9%), invasive lobular carcinoma (11.8%), and multifocal/multicentric disease (10.6%). MRI detected occult malignant lesion or extension of index lesion in 21.2% of index, 3.3% of contralateral, breasts. No expert criterion was associated with MRI-detected malignant lesion, which associated instead with pre-MRI plan of lumpectomy without PBI (48.2% of subjects): Odds Ratio 3.05, 95% CI 1.57-5.91 (p adjusted for multiple hypothesis testing = 0.007, adjusted for index-vs-contralateral breast and covariates). The expert guidelines were not confirmed by clinical evidence. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

Khan, Salman, E-mail: sksafi@comsats.edu.pk

The dynamics of tripartite entanglement of fermionic system in noninertial frames through linear contraction criterion when one or two observers are accelerated is investigated. In one observer accelerated case the entanglement measurement is not invariant with respect to the partial realignment of different subsystems and for two observers accelerated case it is invariant. It is shown that the acceleration of the frame does not generate entanglement in any bipartite subsystems. Unlike the bipartite states, the genuine tripartite entanglement does not completely vanish in both one observer accelerated and two observers accelerated cases even in the limit of infinite acceleration. Themore » degradation of tripartite entanglement is fast when two observers are accelerated than when one observer is accelerated. It is shown that tripartite entanglement is a better resource for quantum information processing than the bipartite entanglement in noninertial frames. - Highlights: • Tripartite entanglement of fermionic system in noninertial frames is studied. • Linear contraction criterion for quantifying tripartite entanglement is used. • Acceleration does not produce any bipartite entanglement. • The invariance of entanglement quantifier depends on accelerated observers. • The tripartite entanglement degrades against the acceleration, it never vanishes.« less

Jeans instability in collisional strongly coupled dusty plasma with radiative condensation and polarization force

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

Prajapati, R. P., E-mail: prajapati-iter@yahoo.co.in; Bhakta, S.; Chhajlani, R. K.

2016-05-15

The influence of dust-neutral collisions, polarization force, and electron radiative condensation is analysed on the Jeans (gravitational) instability of partially ionized strongly coupled dusty plasma (SCDP) using linear perturbation (normal mode) analysis. The Boltzmann distributed ions, dynamics of inertialess electrons, charged dust and neutral particles are considered. Using the plane wave solutions, a general dispersion relation is derived which is modified due to the presence of dust-neutral collisions, strong coupling effect, polarization force, electron radiative condensation, and Jeans dust/neutral frequencies. In the long wavelength perturbations, the Jeans instability criterion depends upon strong coupling effect, polarization interaction parameter, and thermal loss,more » but it is independent of dust-neutral collision frequency. The stability of the considered configuration is analysed using the Routh–Hurwitz criterion. The growth rates of Jeans instability are illustrated, and stabilizing influence of viscoelasticity and dust-neutral collision frequency while destabilizing effect of electron radiative condensation, polarization force, and Jeans dust-neutral frequency ratio is observed. This work is applied to understand the gravitational collapse of SCDP with dust-neutral collisions.« less

Partially coherent polarized atmospheric transmission characteristics and application technology research

NASA Astrophysics Data System (ADS)

Fu, Qiang; Gao, Duorui; Liu, Zhi; Chen, Chunyi; Lou, Yan; Jiang, Huilin

2014-11-01

Based on partially coherent polarized light transmission characteristics of the atmosphere, an intensity expression of completely coherent flashing light is derived from Andrews scale modulation method. According to the generalized Huygens-Fresnel principle and Rytov theory, the phase fluctuation structure function is obtained on condition that the refractive index profile in the atmosphere meet Von Karman spectrum, then get the arrival Angle fluctuation variance. Through the RMS beam width of gaussian beams in turbulent atmosphere, deviation angle formula of fully coherent gaussian beams in turbulence atmosphere is attained, then get the RMS beam width of partially coherent and derivation angle expression of GSM beam in turbulent atmosphere. Combined with transmission properties of radial polarized laser beam, cross spectral density matrix of partially coherent radially polarized light can be gained by using generalized huygens-fresnel principle. And light intensity and polarization after transmission can be known according to the unity of coherence and polarization theory. On the basis of the analysis model and numerical simulation, the simulation results show that: the light spot caused by atmospheric turbulence of partially coherent polarization will be superior to completely polarized light.Taking advantage of this feature, designed a new wireless suppression technology of atmospheric turbulence, that is the optimization criterion of initial degree of coherent light beam. The optimal initial degree of coherent light beam will change along with the change of atmospheric turbulence conditions,make control the beam's initial degree of coherence to realize the initial degree of coherence of light beam in real time and dynamic control. A spatial phase screen before emission aperture of fully coherent light is to generate the partially coherent light, liquid crystal spatial light modulator is is a preferable way to realize the dynamic random phase. Finally look future of the application research of partially coherent light.

Arabidopsis homologs of retinoblastoma-associated protein 46/48 associate with a histone deacetylase to act redundantly in chromatin silencing.

PubMed

Gu, Xiaofeng; Jiang, Danhua; Yang, Wannian; Jacob, Yannick; Michaels, Scott D; He, Yuehui

2011-11-01

RNA molecules such as small-interfering RNAs (siRNAs) and antisense RNAs (asRNAs) trigger chromatin silencing of target loci. In the model plant Arabidopsis, RNA-triggered chromatin silencing involves repressive histone modifications such as histone deacetylation, histone H3 lysine-9 methylation, and H3 lysine-27 monomethylation. Here, we report that two Arabidopsis homologs of the human histone-binding proteins Retinoblastoma-Associated Protein 46/48 (RbAp46/48), known as MSI4 (or FVE) and MSI5, function in partial redundancy in chromatin silencing of various loci targeted by siRNAs or asRNAs. We show that MSI5 acts in partial redundancy with FVE to silence FLOWERING LOCUS C (FLC), which is a crucial floral repressor subject to asRNA-mediated silencing, FLC homologs, and other loci including transposable and repetitive elements which are targets of siRNA-directed DNA Methylation (RdDM). Both FVE and MSI5 associate with HISTONE DEACETYLASE 6 (HDA6) to form complexes and directly interact with the target loci, leading to histone deacetylation and transcriptional silencing. In addition, these two genes function in de novo CHH (H = A, T, or C) methylation and maintenance of symmetric cytosine methylation (mainly CHG methylation) at endogenous RdDM target loci, and they are also required for establishment of cytosine methylation in the previously unmethylated sequences directed by the RdDM pathway. This reveals an important functional divergence of the plant RbAp46/48 relatives from animal counterparts.

A numerical calculation of outward propagation of solar disturbances. [solar atmospheric model with shock wave propagation

NASA Technical Reports Server (NTRS)

Wu, S. T.

1974-01-01

The responses of the solar atmosphere due to an outward propagation shock are examined by employing the Lax-Wendroff method to solve the set of nonlinear partial differential equations in the model of the solar atmosphere. It is found that this theoretical model can be used to explain the solar phenomena of surge and spray. A criterion to discriminate the surge and spray is established and detailed information concerning the density, velocity, and temperature distribution with respect to the height and time is presented. The complete computer program is also included.

Transposition of the great arteries

MedlinePlus

... that carry blood away from the heart -- the aorta and the pulmonary artery -- are switched (transposed). ... side of the heart and travels out the aorta to the body. In TGA, venous blood returns ...

Mariner transposons are sailing in the genome of the blood-sucking bug Rhodnius prolixus.

PubMed

Filée, Jonathan; Rouault, Jacques-Deric; Harry, Myriam; Hua-Van, Aurélie

2015-12-15

The Triatomine bug Rhodnius prolixus is a vector of Trypanosoma cruzi, which causes the Chagas disease in Latin America. R. prolixus can also transfer transposable elements horizontally across a wide range of species. We have taken advantage of the availability of the 700 Mbp complete genome sequence of R. prolixus to study the dynamics of invasion and persistence of transposable elements in this species. Using both library-based and de novo methods of transposon detection, we found less than 6 % of transposable elements in the R. prolixus genome, a relatively low percentage compared to other insect genomes with a similar genome size. DNA transposons are surprisingly abundant and elements belonging to the mariner family are by far the most preponderant components of the mobile part of this genome with 11,015 mariner transposons that could be clustered in 89 groups (75 % of the mobilome). Our analysis allowed the detection of a new mariner clade in the R. prolixus genome, that we called nosferatis. We demonstrated that a large diversity of mariner elements invaded the genome and expanded successfully over time via three main processes. (i) several families experienced recent and massive expansion, for example an explosive burst of a single mariner family led to the generation of more than 8000 copies. These recent expansion events explain the unusual prevalence of mariner transposons in the R. prolixus genome. Other families expanded via older bursts of transposition demonstrating the long lasting permissibility of mariner transposons in the R. prolixus genome. (ii) Many non-autonomous families generated by internal deletions were also identified. Interestingly, two non autonomous families were generated by atypical recombinations (5' part replacement with 3' part). (iii) at least 10 cases of horizontal transfers were found, supporting the idea that host/vector relationships played a pivotal role in the transmission and subsequent persistence of transposable elements in this genome. These data provide a new insight into the evolution of transposons in the genomes of hematophagous insects and bring additional evidences that lateral exchanges of mobile genetics elements occur frequently in the R. prolixus genome.

The impact of transposable elements on mammalian development

PubMed Central

Garcia-Perez, Jose L.; Widmann, Thomas J.; Adams, Ian R.

2018-01-01

Summary Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that significantly impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and how the somatic activity of TEs can influence gene regulatory networks. PMID:27875251

Evolution and genome architecture in fungal plant pathogens.

PubMed

Möller, Mareike; Stukenbrock, Eva H

2017-12-01

The fungal kingdom comprises some of the most devastating plant pathogens. Sequencing the genomes of fungal pathogens has shown a remarkable variability in genome size and architecture. Population genomic data enable us to understand the mechanisms and the history of changes in genome size and adaptive evolution in plant pathogens. Although transposable elements predominantly have negative effects on their host, fungal pathogens provide prominent examples of advantageous associations between rapidly evolving transposable elements and virulence genes that cause variation in virulence phenotypes. By providing homogeneous environments at large regional scales, managed ecosystems, such as modern agriculture, can be conducive for the rapid evolution and dispersal of pathogens. In this Review, we summarize key examples from fungal plant pathogen genomics and discuss evolutionary processes in pathogenic fungi in the context of molecular evolution, population genomics and agriculture.

Hydroelectric System Response to Part Load Vortex Rope Excitation

NASA Astrophysics Data System (ADS)

Alligné, S.; Nicolet, C.; Bégum, A.; Landry, C.; Gomes, J.; Avellan, F.

2016-11-01

The prediction of pressure and output power fluctuations amplitudes on Francis turbine prototype is a challenge for hydro-equipment industry since it is subjected to guarantees to ensure smooth and reliable operation of the hydro units. The European FP7 research project Hyperbole aims to setup a methodology to transpose the pressure fluctuations induced by the cavitation vortex rope on the reduced scale model to the prototype generating units. A Francis turbine unit of 444MW with a specific speed value of v = 0.29, is considered as case study. A SIMSEN model of the power station including electrical system, controllers, rotating train and hydraulic system with transposed draft tube excitation sources is setup. Based on this model, a frequency analysis of the hydroelectric system is performed to analyse potential interactions between hydraulic excitation sources and electrical components.

Continuous magnetic flux pump

NASA Technical Reports Server (NTRS)

Hildebrandt, A. F.; Elleman, D. D.; Whitmore, F. C. (Inventor)

1966-01-01

A method and means for altering the intensity of a magnetic field by transposing flux from one location to the location desired fro the magnetic field are examined. The device described includes a pair of communicating cavities formed in a block of superconducting material, is dimensioned to be insertable into one of the cavities and to substantially fill the cavity. Magnetic flux is first trapped in the cavities by establishing a magnetic field while the superconducting material is above the critical temperature at which it goes superconducting. Thereafter, the temperature of the material is reduced below the critical value, and then the exciting magnetic field may be removed. By varying the ratios of the areas of the two cavities, it is possible to produce a field having much greater flux density in the second, smaller cavity, into which the flux transposed.

Solving the corner-turning problem for large interferometers

NASA Astrophysics Data System (ADS)

Lutomirski, Andrew; Tegmark, Max; Sanchez, Nevada J.; Stein, Leo C.; Urry, W. Lynn; Zaldarriaga, Matias

2011-01-01

The so-called corner-turning problem is a major bottleneck for radio telescopes with large numbers of antennas. The problem is essentially that of rapidly transposing a matrix that is too large to store on one single device; in radio interferometry, it occurs because data from each antenna need to be routed to an array of processors each of which will handle a limited portion of the data (say, a frequency range) but requires input from each antenna. We present a low-cost solution allowing the correlator to transpose its data in real time, without contending for bandwidth, via a butterfly network requiring neither additional RAM memory nor expensive general-purpose switching hardware. We discuss possible implementations of this using FPGA, CMOS, analog logic and optical technology, and conclude that the corner-turner cost can be small even for upcoming massive radio arrays.

copia-like retrotransposons are ubiquitous among plants.

PubMed Central

Voytas, D F; Cummings, M P; Koniczny, A; Ausubel, F M; Rodermel, S R

1992-01-01

Transposable genetic elements are assumed to be a feature of all eukaryotic genomes. Their identification, however, has largely been haphazard, limited principally to organisms subjected to molecular or genetic scrutiny. We assessed the phylogenetic distribution of copia-like retrotransposons, a class of transposable element that proliferates by reverse transcription, using a polymerase chain reaction assay designed to detect copia-like element reverse transcriptase sequences. copia-like retrotransposons were identified in 64 plant species as well as the photosynthetic protist Volvox carteri. The plant species included representatives from 9 of 10 plant divisions, including bryophytes, lycopods, ferns, gymnosperms, and angiosperms. DNA sequence analysis of 29 cloned PCR products and of a maize retrotransposon cDNA confirmed the identity of these sequences as copia-like reverse transcriptase sequences, thereby demonstrating that this class of retrotransposons is a ubiquitous component of plant genomes. Images PMID:1379734

Transposable element islands facilitate adaptation to novel environments in an invasive species

PubMed Central

Schrader, Lukas; Kim, Jay W.; Ence, Daniel; Zimin, Aleksey; Klein, Antonia; Wyschetzki, Katharina; Weichselgartner, Tobias; Kemena, Carsten; Stökl, Johannes; Schultner, Eva; Wurm, Yannick; Smith, Christopher D.; Yandell, Mark; Heinze, Jürgen; Gadau, Jürgen; Oettler, Jan

2014-01-01

Adaptation requires genetic variation, but founder populations are generally genetically depleted. Here we sequence two populations of an inbred ant that diverge in phenotype to determine how variability is generated. Cardiocondyla obscurior has the smallest of the sequenced ant genomes and its structure suggests a fundamental role of transposable elements (TEs) in adaptive evolution. Accumulations of TEs (TE islands) comprising 7.18% of the genome evolve faster than other regions with regard to single-nucleotide variants, gene/exon duplications and deletions and gene homology. A non-random distribution of gene families, larvae/adult specific gene expression and signs of differential methylation in TE islands indicate intragenomic differences in regulation, evolutionary rates and coalescent effective population size. Our study reveals a tripartite interplay between TEs, life history and adaptation in an invasive species. PMID:25510865

Identification of structural variation in mouse genomes.

PubMed

Keane, Thomas M; Wong, Kim; Adams, David J; Flint, Jonathan; Reymond, Alexandre; Yalcin, Binnaz

2014-01-01

Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation.

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

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

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

Castanera, Raul; Lopez-Varas, Leticia; Borgognone, Alessandra

Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Classmore » I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.« less

The Evolution of Tyrosine-Recombinase Elements in Nematoda

PubMed Central

Szitenberg, Amir; Koutsovoulos, Georgios; Blaxter, Mark L.; Lunt, David H.

2014-01-01

Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1-like elements were found to be a derived form of another Pat1-like element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum. PMID:25197791

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

DOE PAGES

Castanera, Raul; Lopez-Varas, Leticia; Borgognone, Alessandra; ...

2016-06-13

Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Classmore » I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.« less

A novel hAT element in Bombyx mori and Rhodnius prolixus: its relationship with miniature inverted repeat transposable elements (MITEs) and horizontal transfer.

PubMed

Zhang, H-H; Shen, Y-H; Xu, H-E; Liang, H-Y; Han, M-J; Zhang, Z

2013-10-01

Comparative analysis of transposable elements (TEs) from different species can make it possible to reconstruct their history over evolutionary time. In this study, we identified a novel hAT element in Bombyx mori and Rhodnius prolixus with characteristic GGGCGGCA repeats in its subterminal region. Meanwhile, phylogenetic analysis demonstrated that the elements in these two species might represent a separate cluster of the hAT superfamily. Strikingly, a previously identified miniature inverted repeat transposable element (MITE) shared high identity with this autonomous element across the entire length, supporting the hypothesis that MITEs are derived from the internal deletion of DNA transposons. Interestingly, identity of the consensus sequences of this novel hAT element between B. mori and R. prolixus, which diverged about 370 million years ago, was as high as 96.5% over their full length (about 3.6 kb) at the nucleotide level. The patchy distribution amongst species, coupled with overall lack of intense purifying selection acting on this element, suggest that this novel hAT element might have experienced horizontal transfer between the ancestors of B. mori and R. prolixus. Our results highlight that this novel hAT element could be used as a potential tool for germline transformation of R. prolixus to control the transmission of Trypanosoma cruzi, which causes Chagas disease. © 2013 Royal Entomological Society.

Flood Frequency Analyses Using a Modified Stochastic Storm Transposition Method

NASA Astrophysics Data System (ADS)

Fang, N. Z.; Kiani, M.

2015-12-01

Research shows that areas with similar topography and climatic environment have comparable precipitation occurrences. Reproduction and realization of historical rainfall events provide foundations for frequency analysis and the advancement of meteorological studies. Stochastic Storm Transposition (SST) is a method for such a purpose and enables us to perform hydrologic frequency analyses by transposing observed historical storm events to the sites of interest. However, many previous studies in SST reveal drawbacks from simplified Probability Density Functions (PDFs) without considering restrictions for transposing rainfalls. The goal of this study is to stochastically examine the impacts of extreme events on all locations in a homogeneity zone. Since storms with the same probability of occurrence on homogenous areas do not have the identical hydrologic impacts, the authors utilize detailed precipitation parameters including the probability of occurrence of certain depth and the number of occurrence of extreme events, which are both incorporated into a joint probability function. The new approach can reduce the bias from uniformly transposing storms which erroneously increases the probability of occurrence of storms in areas with higher rainfall depths. This procedure is iterated to simulate storm events for one thousand years as the basis for updating frequency analysis curves such as IDF and FFA. The study area is the Upper Trinity River watershed including the Dallas-Fort Worth metroplex with a total area of 6,500 mi2. It is the first time that SST method is examined in such a wide scale with 20 years of radar rainfall data.

DPTEdb, an integrative database of transposable elements in dioecious plants.

PubMed

Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

2016-01-01

Dioecious plants usually harbor 'young' sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants.Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php. © The Author(s) 2016. Published by Oxford University Press.

The evolution of tyrosine-recombinase elements in Nematoda.

PubMed

Szitenberg, Amir; Koutsovoulos, Georgios; Blaxter, Mark L; Lunt, David H

2014-01-01

Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1-like elements were found to be a derived form of another Pat1-like element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum.

The structure of the regulatory region of the rat L1 (L1Rn, long interspersed repeated) DNA family of transposable elements.

PubMed Central

Furano, A V; Robb, S M; Robb, F T

1988-01-01

Here we report the DNA structure of the left 1.5 kb of two newly isolated full length members of the rat L1 DNA family (L1Rn, long interspersed repeated DNA). In contrast to earlier isolated rat L1 members, both of these contain promoter-like regions that are most likely full length. In addition, the promoter-like region of both members has undergone a partial tandem duplication. A second internal region of the left end of one of the reported members is also tandemly duplicated. The propensity of the left end of rat L1 elements to undergo this form of genetic rearrangement, as well as other structural features revealed by the present work, is discussed in light of the fact that during evolution the otherwise conserved mammalian L1 DNA families have each acquired completely different promoter-like regions. In an accompanying paper [Nur, I., Pascale, E., and Furano, A. V. (1988) Nucleic Acids Res. 16, submitted], we report that one of the rat promoter-like regions can function as a promoter in rat cells when fused to the Escherichia coli chloramphenicol acyltransferase gene. PMID:2845369

Interaction between transposable phages: cip locus of prophage D3112, responsible for inhibition of integration and transposition of the related phage B39 of Pseudomonas aeruginosa

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

Gerasimov, V.A.; Yanenko, A.S.; Akhverdyan, V.Z.

1986-04-01

Bacteriophage D3112 forms two types of PA01 (D3112) lysogens: those that partially, or completely, limit the growth of the related heteroimmune phage B39. DNA/DNA hybridization has shown that the lysogens of the first type always contain one copy of prophage D3112 (monolysogens), and the lysogens of the second type contain two or more copies of prophage D3112. Limitation of the growth of phage B39 on PA01 (D3112) lysogens is associated with the functioning of the locus of prophage D3112, designated as cip (control of interaction of phages). Using deletion derivatives of plasmid RP4::D3112, the cip locus was mapped at anmore » interval of 1.3-2.45 kb of the D3112 genome. The expression of the cip locus occurs only if the D3112 genome is at the prophage state. The function of the Cip prophage of D3112 exerts an influence on early stages of development of phage B39, decreasing the efficiency of the integration and transposition processes of phage B39.« less

Even parasites have parasites: oscillatory population dynamics of mobile genetic elements in your genome

NASA Astrophysics Data System (ADS)

Xue, Chi; Goldenfeld, Nigel

Transposable elements (TEs), or transposons, are a class of mobile genetic elements that can either move or duplicate themselves in the genome, sometimes interfering with gene expression as a result. Some TEs can code all necessary enzymes for their transposition and are thus autonomous, while non-autonomous TEs are parasitic and must depend on the machinery of autonomous ones. I present and solve a stochastic model to describe the dynamics of non-autonomous/autonomous pairs of retrotransposons in the human genome that proliferate by a copy-and-paste mechanism. We predict noise-induced persistent oscillations in their copy numbers, analogous to predator-prey dynamics in an ecosystem. We discuss if it is experimentally feasible to measure these phenomena in the laboratory and to observe them over evolutionary time through bioinformatics. This work shows that it is fruitful to regard the genome as an ecosystem that is host to diverse interacting populations. This work was partially supported by the National Science Foundation through Grant No. PHY-1430124, and by the National Aeronautics and Space Administration Astrobiology Institute (NAI) under Cooperative Agreement No. NNA13AA91A.

Gaussian entanglement revisited

NASA Astrophysics Data System (ADS)

Lami, Ludovico; Serafini, Alessio; Adesso, Gerardo

2018-02-01

We present a novel approach to the separability problem for Gaussian quantum states of bosonic continuous variable systems. We derive a simplified necessary and sufficient separability criterion for arbitrary Gaussian states of m versus n modes, which relies on convex optimisation over marginal covariance matrices on one subsystem only. We further revisit the currently known results stating the equivalence between separability and positive partial transposition (PPT) for specific classes of Gaussian states. Using techniques based on matrix analysis, such as Schur complements and matrix means, we then provide a unified treatment and compact proofs of all these results. In particular, we recover the PPT-separability equivalence for: (i) Gaussian states of 1 versus n modes; and (ii) isotropic Gaussian states. In passing, we also retrieve (iii) the recently established equivalence between separability of a Gaussian state and and its complete Gaussian extendability. Our techniques are then applied to progress beyond the state of the art. We prove that: (iv) Gaussian states that are invariant under partial transposition are necessarily separable; (v) the PPT criterion is necessary and sufficient for separability for Gaussian states of m versus n modes that are symmetric under the exchange of any two modes belonging to one of the parties; and (vi) Gaussian states which remain PPT under passive optical operations can not be entangled by them either. This is not a foregone conclusion per se (since Gaussian bound entangled states do exist) and settles a question that had been left unanswered in the existing literature on the subject. This paper, enjoyable by both the quantum optics and the matrix analysis communities, overall delivers technical and conceptual advances which are likely to be useful for further applications in continuous variable quantum information theory, beyond the separability problem.

The key role of dislocation dissociation in the plastic behaviour of single crystal nickel-based superalloy with low stacking fault energy: Three-dimensional discrete dislocation dynamics modelling

NASA Astrophysics Data System (ADS)

Huang, Minsheng; Li, Zhenhuan

2013-12-01

To model the deformation of single crystal nickel based superalloys (SCNBS) with low stacking fault energy (SFE), three-dimensional discrete dislocation dynamics (3D-DDD) is extended by incorporating dislocation dissociation mechanism. The present 3D-DDD simulations show that, consistent with the existing TEM observation, the leading partial can enter the matrix channel efficiently while the trailing partial can hardly glide into it when the dislocation dissociation is taken into account. To determine whether the dislocation dissociation can occur or not, a critical percolation stress (CPS) based criterion is suggested. According to this CPS criterion, for SCNBS there exists a critical matrix channel width. When the channel width is lower than this critical value, the dislocation tends to dissociate into an extended configuration and vice versa. To clarify the influence of dislocation dissociation on CPS, the classical Orowan formula is improved by incorporating the SFE. Moreover, the present 3D-DDD simulations also show that the yielding stress of SCNBSs with low SFE may be overestimated up to 30% if the dislocation dissociation is ignored. With dislocation dissociation being considered, the size effect due to the width of γ matrix channel and the length of γ‧ precipitates on the stress-strain responses of SCNBS can be enhanced remarkably. In addition, due to the strong constraint effect by the two-phase microstructure in SCNBS, the configuration of formed junctions is quite different from that in single phase crystals such as Cu. The present results not only provide clear understanding of the two-phase microstructure levelled microplastic mechanisms in SCNBSs with low SFE, but also help to develop new continuum-levelled constitutive laws for SCNBSs.

Principal Covariates Clusterwise Regression (PCCR): Accounting for Multicollinearity and Population Heterogeneity in Hierarchically Organized Data.

PubMed

Wilderjans, Tom Frans; Vande Gaer, Eva; Kiers, Henk A L; Van Mechelen, Iven; Ceulemans, Eva

2017-03-01

In the behavioral sciences, many research questions pertain to a regression problem in that one wants to predict a criterion on the basis of a number of predictors. Although in many cases, ordinary least squares regression will suffice, sometimes the prediction problem is more challenging, for three reasons: first, multiple highly collinear predictors can be available, making it difficult to grasp their mutual relations as well as their relations to the criterion. In that case, it may be very useful to reduce the predictors to a few summary variables, on which one regresses the criterion and which at the same time yields insight into the predictor structure. Second, the population under study may consist of a few unknown subgroups that are characterized by different regression models. Third, the obtained data are often hierarchically structured, with for instance, observations being nested into persons or participants within groups or countries. Although some methods have been developed that partially meet these challenges (i.e., principal covariates regression (PCovR), clusterwise regression (CR), and structural equation models), none of these methods adequately deals with all of them simultaneously. To fill this gap, we propose the principal covariates clusterwise regression (PCCR) method, which combines the key idea's behind PCovR (de Jong & Kiers in Chemom Intell Lab Syst 14(1-3):155-164, 1992) and CR (Späth in Computing 22(4):367-373, 1979). The PCCR method is validated by means of a simulation study and by applying it to cross-cultural data regarding satisfaction with life.

How to anticipate the assessment of the public health benefit of new medicines?

PubMed

Massol, Jacques; Puech, Alain; Boissel, Jean-Pierre

2007-01-01

The Public Health Benefit (PHB) of new medicines is a recent and French-specific criterion (October 1999 decree) which is often only partially documented in the transparency files due to a lack of timely information. At the time of the first reimbursement application for a new medicine to the "Transparency Committee", the file is exclusively based on data from randomised clinical trials. These data are generated from a global clinical development plan which was designed a long time before the new medicine's submission for reimbursement. And this plan does not systematically provide the data needed to assess the PHB. Thus, one easily understands the difficulty to anticipate and document this recent French criterion. In France, the PHB is both one of the necessary criteria for the reimbursement submission and an indicator for the national health policy management. Its assessment also helps to identify the needs and objectives of the post-registration studies (nowadays in the scope of responsibilities of the "Drug Economics Committee"). The assessment of the PHB criterion is carried through after the marketing authorization process and is an addition to it. To understand how to anticipate the assessment of the new medicines' PHB, one needs to consider how it differs from the preliminary step of the marketing authorization process. Whereas the evaluation for marketing authorization seeks to determine if the new medicine could be useful in a specific indication, the PHB assessment aims at quantifying the therapeutic benefit in a population, taking into account the reference treatments in this population. A new medicine receives a marketing authorization based on the data of the registration file which provides information on the clinical benefit of the new medicine in the populations of the trials and in the context of the trials. On the other side, the PHB looks at the effects of the new medicine at the scale of the general population, in real practice. The PHB components of a new medicine at first submission are the expected response of this new medicine to a public health need, the expected benefit on the health status of the population and ultimately the expected impact on the health care system. The benefit of a new medicine on the health status of a population is based on public health criteria which can be morbi-mortality or quality of life criteria. However, few registration files contain these public health criteria from the beginning and the predictive value of the surrogate criteria used in the trials is not always precisely assessed. It is, thus, difficult to quantify the expected benefit on these public health criteria. Moreover, the data that enable to quantify the new medicine's effects according to the various characteristics of the target population, are rarely available. Similarly, the French population epidemiological data related to the indication of the new medicine are often not available at the time of the assessment. Therefore it is difficult to evaluate the expected number of events that could be avoided if the new medicine reached the market. The authors suggest to adapt the clinical development plan for a better documentation of the PHB. They specifically recommend to integrate to the judgment criteria (endpoints) of the trials, criteria that are relevant in terms of public health, and to check for a good heterogeneity of the trial populations. They also suggest to start early enough collecting reliable national epidemiological data and the necessary elements for the assessment of the transposability of the trial results to the French population (ability to target the patients to be treated, adaptation of the healthcare system...). About the epidemiological data, the authors consider that the needs are covered in various ways depending on the diseases. To meet the needs of evaluation of the new medicines' target populations in specific indications, they recommend to use ad hoc studies as much as needed. In addition, epidemiological studies designed for market purpose with an acceptable methodology should not be systematically rejected but deserve to be presented. To be able to assess the importance of the expected theoretical benefit of a new medicine in a population, the authors underline the necessity to have access to study results with criteria related to this objective. They suggest to first define and list the criteria by disease. Regarding the representativity of the populations, it comes out that it would be advisable, but unrealistic to include in trials a population 100% representative of the population to be treated. Therefore the effect of the new medicine must be modelised (the "effect model") to be evaluated in the general population. Yet to obtain a reliable effect model, the study population must be sufficiently heterogeneous, which legitimates the demand to ensure a good population heterogeneity at the time of decision-making about trials methodology. When the criteria assessed during the development plan does not correspond to the PHB criteria, the only way to evaluate the number of events related to the PHB criterion is, again, to use modelisation. However, modelisation is only possible when the scientific literature has established a reliable correlation between the two types of criteria. In this case, the new model should be applied to a French target population to assess the expected benefit. As a conclusion, the possibilities to estimate the expected benefit of a new medicine on the health status of a specific population are currently limited. These limitations are regrettable because such an estimate is feasible without disrupting the development plans. The authors' general recommendations to update the development plans seem especially appropriate as the additions should not only be beneficial to France but to all the health authorities who would wish to assess the expected benefit of a new medicine on their territories. Anticipating the lack of clinical and epidemiological data and the lack of data that enable to evaluate the transposability of the trials results to real clinical practice is a sine qua none condition to improve the PHB assessment. The anticipation of these needs should be planned early enough by the pharmaceutical companies which could in this purpose meet the health authorities and the heads of the French public health policy in a consultation.Finally, because of the PHB's universal dimension, it is suggested that the necessary actions and publications be initiated so that the PHB can be acknowledged at the European level.

PATHOPHYSIOLOGY, DIAGNOSIS AND TREATMENTOF DUMPING SYNDROME AND ITS RELATION TO BARIATRIC SURGERY

PubMed Central

CHAVES, Yasmin da Silva; DESTEFANI, Afrânio Côgo

2016-01-01

ABSTRACT Introduction The dumping syndrome is frequent in bariatric surgery. It is probably the most common syndrome following partial or complete gastrectomy. Its prevalence in partial gastrectomy can reach up to 50%, thus it can be a significant complication arising from some types of bariatric surgeries. Objective: Critical analysis on dumping syndrome, its pathophysiology, diagnosis and treatment. Methods: A literature review was performed using the key words: 'dumping syndrome', 'bariatric surgery' and 'rapid dumping syndrome'. Inclusion criteria were: books, original works, case reports and meta-analyzes, and the exclusion criterion was literature review. Concerning the publication time, articles were screened between 1960 and May 2015. Results: The dumping syndrome is complication arising from obesity surgeries, but also can be a result of vagus nerve damage. Diagnosis is done primarily through the use of questionnaires based on scores. Conclusion: The Sigstad score and Arts survey are valid means for assessing the dumping syndrome. Initial therapy consists in the adoption of dietary measures, short acting drugs administration. PMID:27683791

Direct determination of danofloxacin and flumequine in milk by use of fluorescence spectrometry in combination with partial least-squares calibration.

PubMed

Murillo Pulgarín, J A; Alañón Molina, A; Boras, N

2013-03-20

A new method for the simultaneous determination of danofloxacin and flumequine in milk samples was developed by using the nonlinear variable-angle synchronous fluorescence technique to acquire data and a partial least-squares chemometric algorithm to process them. A calibration set of standard samples was designed by combination of a factorial design with two levels per factor and a central star design. Whey was used as the third component of the calibration matrix. In order to assess the goodness of the proposed method, a prediction set of 11 synthetic samples was analyzed, obtaining recovery percentages between 96.1% and 104.0%. Limits of detection, calculated by means of a new criterion, were 0.90 and 12.4 ng mL(-1) for danofloxacin and flumequine, respectively. Finally, the simultaneous determination of both fluoroquinoles in milk samples containing the analytes was successfully carried out, obtaining an average recovery percentage of 99.3 ± 4.4 for danofloxacin and 100.7 ± 4.4.

Isolation and characterization of a cDNA clone specific for avian vitellogenin II.

PubMed Central

Protter, A A; Wang, S Y; Shelness, G S; Ostapchuk, P; Williams, D L

1982-01-01

A clone for vitellogenin, a major avian, estrogen responsive egg yolk protein, was isolated from the cDNA library of estrogen-induced rooster liver. Two forms of plasma vitellogenin, vitellogenin I (VTG I) and vitellogenin II (VTG II), distinguishable on the basis of their unique partial proteolysis maps, have been characterized and their corresponding hepatic precursor forms identified. We have used this criterion to specifically characterize which vitellogenin protein had been cloned. Partial proteolysis maps of BTG I and VTG II standards, synthesized in vivo, were compared to maps of protein synthesized in vitro using RNA hybrid-selected by the vitellogenin plasmid. Eight major digest fragments were found common to the in vitro synthesized vitellogenin and the VTG II standard while no fragments were observed to correspond to the VTG I map. A restriction map of the VTG II cDNA clone permits comparison to previously described cDNA and genomic vitellogenin clones. Images PMID:6182527

Individual epigenetic variation: When, why, and so what?

USDA-ARS?s Scientific Manuscript database

Epigenetics provides a potential explanation for how environmental factors modify the risk for common diseases among individuals. Interindividual variation in DNA methylation and epigenetic regulation has been reported at specific genomic regions including transposable elements, genomically imprinte...

A new approach for annotation of transposable elements using small RNA mapping

PubMed Central

El Baidouri, Moaine; Kim, Kyung Do; Abernathy, Brian; Arikit, Siwaret; Maumus, Florian; Panaud, Olivier; Meyers, Blake C.; Jackson, Scott A.

2015-01-01

Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants. Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/ PMID:25813049

Population and clinical genetics of human transposable elements in the (post) genomic era

PubMed Central

Rishishwar, Lavanya; Wang, Lu; Clayton, Evan A.; Mariño-Ramírez, Leonardo; McDonald, John F.; Jordan, I. King

2017-01-01

ABSTRACT Recent technological developments—in genomics, bioinformatics and high-throughput experimental techniques—are providing opportunities to study ongoing human transposable element (TE) activity at an unprecedented level of detail. It is now possible to characterize genome-wide collections of TE insertion sites for multiple human individuals, within and between populations, and for a variety of tissue types. Comparison of TE insertion site profiles between individuals captures the germline activity of TEs and reveals insertion site variants that segregate as polymorphisms among human populations, whereas comparison among tissue types ascertains somatic TE activity that generates cellular heterogeneity. In this review, we provide an overview of these new technologies and explore their implications for population and clinical genetic studies of human TEs. We cover both recent published results on human TE insertion activity as well as the prospects for future TE studies related to human evolution and health. PMID:28228978

A call for benchmarking transposable element annotation methods.

PubMed

Hoen, Douglas R; Hickey, Glenn; Bourque, Guillaume; Casacuberta, Josep; Cordaux, Richard; Feschotte, Cédric; Fiston-Lavier, Anna-Sophie; Hua-Van, Aurélie; Hubley, Robert; Kapusta, Aurélie; Lerat, Emmanuelle; Maumus, Florian; Pollock, David D; Quesneville, Hadi; Smit, Arian; Wheeler, Travis J; Bureau, Thomas E; Blanchette, Mathieu

2015-01-01

DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks-that is, no standard way to measure or compare their accuracy. This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation. In the absence of standard benchmarks, toolmakers are impeded in improving their tools, annotators cannot properly assess which tools might best suit their needs, and downstream researchers cannot judge how accuracy limitations might impact their studies. We therefore propose that the TE research community create and adopt standard TE annotation benchmarks, and we call for other researchers to join the authors in making this long-overdue effort a success.

The impact of transposable elements on mammalian development.

PubMed

Garcia-Perez, Jose L; Widmann, Thomas J; Adams, Ian R

2016-11-15

Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that have a significant impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues. Importantly, the ongoing domestication and evolution of TEs appears to provide a rich source of regulatory elements, functional modules and genetic variation that fuels the evolution of mammalian developmental processes. Here, we review the functional impact that TEs exert on mammalian developmental processes and discuss how the somatic activity of TEs can influence gene regulatory networks. © 2016. Published by The Company of Biologists Ltd.

Homeland security in the C. elegans germ line: insights into the biogenesis and function of piRNAs.

PubMed

Kasper, Dionna M; Gardner, Kathryn E; Reinke, Valerie

2014-01-01

While most eukaryotic genomes contain transposable elements that can provide select evolutionary advantages to a given organism, failure to tightly control the mobility of such transposable elements can result in compromised genomic integrity of both parental and subsequent generations. Together with the Piwi subfamily of Argonaute proteins, small, non-coding Piwi-interacting RNAs (piRNAs) primarily function in the germ line to defend the genome against the potentially deleterious effects that can be caused by transposition. Here, we describe recent discoveries concerning the biogenesis and function of piRNAs in the nematode Caenorhabditis elegans, illuminating how the faithful production of these mature species can impart a robust defense mechanism for the germ line to counteract problems caused by foreign genetic elements across successive generations by contributing to the epigenetic memory of non-self vs. self.

Transposable elements in Drosophila.

PubMed

McCullers, Tabitha J; Steiniger, Mindy

2017-01-01

Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster .

The devil is in the details: Transposable element analysis of the Tasmanian devil genome.

PubMed

Nilsson, Maria A

2016-01-01

The third marsupial genome was sequenced from the Tasmanian devil ( Sarcophilus harrisii ), a species that currently is driven to extinction by a rare transmissible cancer. The transposable element (TE) landscape of the Tasmanian devil genome revealed that the main driver of retrotransposition the L ong IN terspersed E lement 1 (LINE1) seem to have become inactivated during the past 12 million years. Strangely, the S hort IN terspersed E lements (SINE), that normally hijacks the LINE1 retrotransposition system, became inactive prior to LINE1 at around 30 million years ago. The SINE inactivation was in vitro verified in several species. Here I discuss that the apparent LINE1 inactivation might be caused by a genome assembly artifact. The repetitive fraction of any genome is highly complex to assemble and the observed problems are not unique to the Tasmanian devil genome.

The devil is in the details: Transposable element analysis of the Tasmanian devil genome

PubMed Central

Nilsson, Maria A.

2016-01-01

ABSTRACT The third marsupial genome was sequenced from the Tasmanian devil (Sarcophilus harrisii), a species that currently is driven to extinction by a rare transmissible cancer. The transposable element (TE) landscape of the Tasmanian devil genome revealed that the main driver of retrotransposition the Long INterspersed Element 1 (LINE1) seem to have become inactivated during the past 12 million years. Strangely, the Short INterspersed Elements (SINE), that normally hijacks the LINE1 retrotransposition system, became inactive prior to LINE1 at around 30 million years ago. The SINE inactivation was in vitro verified in several species. Here I discuss that the apparent LINE1 inactivation might be caused by a genome assembly artifact. The repetitive fraction of any genome is highly complex to assemble and the observed problems are not unique to the Tasmanian devil genome. PMID:27066301

[The effect of modified Nance arch on treating maxillary impacted canine transposed with first premolar].

PubMed

Xu, Qing-chao; Sun, Hao; Lin, Yan; Wang, Xiu-ying; Hu, Rong-dang

2015-10-01

To explore the effect of modified Nance arch on treating maxillary canine-first premolar transposition cases, in which the anchorage and force direction were discussed. Modified Nance arch was applied to 5 cases with maxillary impacted canine-first premolar transposition. First, a lingual knot button was bonded on the surface of the canine crown. Modified Nance arch was decorated with a hook that moved horizontally and buccally. Then the location of the hook was gradually adjusted in order to move the canine cross the root of the first premolar and move the canine to the right position. At last the canine was moved downward by straight wire appliance. Five maxillary transposed canines were fully erupted in their right position, with normal pulp activity and gingival morphology. No obvious root resorption was detected. The mean treatment time was 30 months. Modified Nance arch has advantages in treating canine-first premolar transposition.

Transposable elements in Drosophila

PubMed Central

McCullers, Tabitha J.; Steiniger, Mindy

2017-01-01

ABSTRACT Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster. PMID:28580197

The priesthood of bioethics and the return of casuistry.

PubMed

Wildes, K W

1993-02-01

Several recent attempts to develop models of moral reasoning have attempted to use some form of casuistry as a way to resolve the moral controversies of clinical ethics. One of the best known models of casuistry is that of Jonsen and Toulmin who attempt to transpose a particular model of casuistry, that of Roman Catholic confessional practice, to contemporary moral disputes. This attempt is flawed in that it fails to understand both the history of the model it seeks to transpose and the morally pluralistic context of secular, postmodern society. The practice of casuistry which Jonsen and Toulmin wish to revive is a practice set in the context of a community with a shared set of moral values and structures of moral authority. Without a set of common moral values and rankings, and a moral authority to interpret cases the casuistry of the postmodern age will be pluralistic, that is, there will be many casuistries not just one.

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

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

Gordon, Sean P.; Contreras-Moreira, Bruno; Woods, Daniel P.

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely tomore » be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.« less

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.

PubMed

Gordon, Sean P; Contreras-Moreira, Bruno; Woods, Daniel P; Des Marais, David L; Burgess, Diane; Shu, Shengqiang; Stritt, Christoph; Roulin, Anne C; Schackwitz, Wendy; Tyler, Ludmila; Martin, Joel; Lipzen, Anna; Dochy, Niklas; Phillips, Jeremy; Barry, Kerrie; Geuten, Koen; Budak, Hikmet; Juenger, Thomas E; Amasino, Richard; Caicedo, Ana L; Goodstein, David; Davidson, Patrick; Mur, Luis A J; Figueroa, Melania; Freeling, Michael; Catalan, Pilar; Vogel, John P

2017-12-19

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.

Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues.

PubMed

De Cecco, Marco; Criscione, Steven W; Peterson, Abigail L; Neretti, Nicola; Sedivy, John M; Kreiling, Jill A

2013-12-01

Transposable elements (TEs) were discovered by Barbara McClintock in maize and have since been found to be ubiquitous in all living organisms. Transposition is mutagenic and organisms have evolved mechanisms to repress the activity of their endogenous TEs. Transposition in somatic cells is very low, but recent evidence suggests that it may be derepressed in some cases, such as cancer development. We have found that during normal aging several families of retrotransposable elements (RTEs) start being transcribed in mouse tissues. In advanced age the expression culminates in active transposition. These processes are counteracted by calorie restriction (CR), an intervention that slows down aging. Retrotransposition is also activated in age-associated, naturally occurring cancers in the mouse. We suggest that somatic retrotransposition is a hitherto unappreciated aging process. Mobilization of RTEs is likely to be an important contributor to the progressive dysfunction of aging cells.

Characterization of the Fb-Nof Transposable Element of Drosophila Melanogaster

PubMed Central

Harden, N.; Ashburner, M.

1990-01-01

FB-NOF is a composite transposable element of Drosophila melanogaster. It is composed of foldback sequences, of variable length, which flank a 4-kb NOF sequence with 308-bp inverted repeat termini. The NOF sequence could potentially code for a 120-kD polypeptide. The FB-NOF element is responsible for unstable mutations of the white gene (w(c) and w(DZL)) and is associated with the large TEs of G. Ising. Although most strains of D. melanogaster have 20-30 sites of FB insertion, FB-NOF elements are usually rare, many strains lack this composite element or have only one copy of it. A few strains, including w(DZL) and Basc have many (8-21) copies of FB-NOF, and these show a tendency to insert at ``hot-spots.'' These strains also have an increased number of FB elements. The DNA sequence of the NOF region associated with TE146(Z) has been determined. PMID:2174013

Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria

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

Zhou Fengfeng; Tran Thao; Xu Ying

2008-01-25

Miniature inverted-repeat transposable elements (MITEs) were first identified in plants and exerted extensive proliferations throughout eukaryotic and archaeal genomes. But very few MITEs have been characterized in bacteria. We identified a novel MITE, called Nezha, in cyanobacteria Anabaena variabilis ATCC 29413 and Nostoc sp. PCC 7120. Nezha, like most previously known MITEs in other organisms, is small in size, non-coding, carrying TIR and DR signals, and of potential to form a stable RNA secondary structure, and it tends to insert into A+T-rich regions. Recent transpositions of Nezha were observed in A. variabilis ATCC 29413 and Nostoc sp. PCC 7120, respectively.more » Nezha might have proliferated recently with aid from the transposase encoded by ISNpu3-like elements. A possible horizontal transfer event of Nezha from cyanobacteria to Polaromonas JS666 is also observed.« less

Transposable elements and G-quadruplexes.

PubMed

Kejnovsky, Eduard; Tokan, Viktor; Lexa, Matej

2015-09-01

A significant part of eukaryotic genomes is formed by transposable elements (TEs) containing not only genes but also regulatory sequences. Some of the regulatory sequences located within TEs can form secondary structures like hairpins or three-stranded (triplex DNA) and four-stranded (quadruplex DNA) conformations. This review focuses on recent evidence showing that G-quadruplex-forming sequences in particular are often present in specific parts of TEs in plants and humans. We discuss the potential role of these structures in the TE life cycle as well as the impact of G-quadruplexes on replication, transcription, translation, chromatin status, and recombination. The aim of this review is to emphasize that TEs may serve as vehicles for the genomic spread of G-quadruplexes. These non-canonical DNA structures and their conformational switches may constitute another regulatory system that, together with small and long non-coding RNA molecules and proteins, contribute to the complex cellular network resulting in the large diversity of eukaryotes.

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

DOE PAGES

Gordon, Sean P.; Contreras-Moreira, Bruno; Woods, Daniel P.; ...

2017-12-19

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely tomore » be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.« less

Transposable elements in sexual and ancient asexual taxa

PubMed Central

Arkhipova, Irina; Meselson, Matthew

2000-01-01

Sexual reproduction allows deleterious transposable elements to proliferate in populations, whereas the loss of sex, by preventing their spread, has been predicted eventually to result in a population free of such elements [Hickey, D. A. (1982) Genetics 101, 519–531]. We tested this expectation by screening representatives of a majority of animal phyla for LINE-like and gypsy-like reverse transcriptases and mariner/Tc1-like transposases. All species tested positive for reverse transcriptases except rotifers of the class Bdelloidea, the largest eukaryotic taxon in which males, hermaphrodites, and meiosis are unknown and for which ancient asexuality is supported by molecular genetic evidence. Mariner-like transposases are distributed sporadically among species and are present in bdelloid rotifers. The remarkable lack of LINE-like and gypsy-like retrotransposons in bdelloids and their ubiquitous presence in other taxa support the view that eukaryotic retrotransposons are sexually transmitted nuclear parasites and that bdelloid rotifers evolved asexually. PMID:11121049

Enhancer trap expression patterns provide a novel teaching resource.

PubMed

Geisler, Matt; Jablonska, Barbara; Springer, Patricia S

2002-12-01

A collection of Arabidopsis enhancer trap transposants has been identified for use as a teaching tool. This collection serves to assist students in understanding the patterning and organization of plant tissues and cells, and will be useful in plant anatomy, morphology, and developmental biology courses. Each transposant exhibits reporter gene expression in a specific tissue, cell type, or domain, and these lines collectively offer a glimpse of compartments of gene expression. Some compartments correspond to classical definitions of botanical anatomy and can assist in anatomical identification. Other patterns of reporter gene expression are more complex and do not necessarily correspond to known anatomical features. The sensitivity of the beta-glucuronidase histochemical stain provides the student with a colorful and direct way to visualize difficult aspects of plant development and anatomy, and provides the teacher with an invaluable tool for a practical laboratory session.

Stability of wave processes in a rotating electrically conducting fluid

NASA Astrophysics Data System (ADS)

Peregudin, S. I.; Peregudina, E. S.; Kholodova, S. E.

2018-05-01

The paper puts forward a mathematical model of dynamics of spatial large-scale motions in a rotating layer of electrically conducting incompressible perfect fluid of variable depth with due account of dissipative effects. The resulting boundary-value problem is reduced to a vector system of partial differential equations for any values of the Reynolds number. Theoretical analysis of the so-obtained analytical solution reveals the effect of the magnetic field diffusion on the stability of the wave mode — namely, with the removed external magnetic field, the diffusion of the magnetic field promotes its damping. Besides, a criterion of stability of a wave mode is obtained.

Estimation of median growth curves for children up two years old based on biresponse local linear estimator

NASA Astrophysics Data System (ADS)

Chamidah, Nur; Rifada, Marisa

2016-03-01

There is significant of the coeficient correlation between weight and height of the children. Therefore, the simultaneous model estimation is better than partial single response approach. In this study we investigate the pattern of sex difference in growth curve of children from birth up to two years of age in Surabaya, Indonesia based on biresponse model. The data was collected in a longitudinal representative sample of the Surabaya population of healthy children that consists of two response variables i.e. weight (kg) and height (cm). While a predictor variable is age (month). Based on generalized cross validation criterion, the modeling result based on biresponse model by using local linear estimator for boy and girl growth curve gives optimal bandwidth i.e 1.41 and 1.56 and the determination coefficient (R2) i.e. 99.99% and 99.98%,.respectively. Both boy and girl curves satisfy the goodness of fit criterion i.e..the determination coefficient tends to one. Also, there is difference pattern of growth curve between boy and girl. The boy median growth curves is higher than those of girl curve.

[Addictive behaviours from DSM-IV to DSM-5].

PubMed

van den Brink, W

2014-01-01

The 5th edition of the DSM was published in May, 2013. The new edition incorporates important changes in the classification of addiction. To compare the classification of addictive behaviours presented in DSM-IV with the classification presented in DSM-5 and to comment on the changes introduced into the new version. First of all, the historical developments of the concept of addiction and the classification of addictive behaviours up to DSM-IV are summarised. Then the changes that have been incorporated into DSM-5 are described. The main changes are: (1) DSM-IV substance related disorders and DSM-IV pathological gambling have been combined into one new DSM-5 category, namely 'Substance Related and Addictive Disorders'; (2) DSM-IV abuse and dependence have been combined into one new DSM-5 diagnosis, namely 'Substance Use Disorder'; (2a) the DSM-IV abuse criterion 'recurrent substance-related legal problems' and the DSM-5 criterion 'craving' has been introduced; and (2b) the criteria for (partial) remission have been sharpened. DSM-5 is an improvement on DSM-IV, but for the diagnosis of a psychiatric disorder and the treatment of a psychiatric patient, classification needs to be complemented with staging and profiling.

Data consistency criterion for selecting parameters for k-space-based reconstruction in parallel imaging.

PubMed

Nana, Roger; Hu, Xiaoping

2010-01-01

k-space-based reconstruction in parallel imaging depends on the reconstruction kernel setting, including its support. An optimal choice of the kernel depends on the calibration data, coil geometry and signal-to-noise ratio, as well as the criterion used. In this work, data consistency, imposed by the shift invariance requirement of the kernel, is introduced as a goodness measure of k-space-based reconstruction in parallel imaging and demonstrated. Data consistency error (DCE) is calculated as the sum of squared difference between the acquired signals and their estimates obtained based on the interpolation of the estimated missing data. A resemblance between DCE and the mean square error in the reconstructed image was found, demonstrating DCE's potential as a metric for comparing or choosing reconstructions. When used for selecting the kernel support for generalized autocalibrating partially parallel acquisition (GRAPPA) reconstruction and the set of frames for calibration as well as the kernel support in temporal GRAPPA reconstruction, DCE led to improved images over existing methods. Data consistency error is efficient to evaluate, robust for selecting reconstruction parameters and suitable for characterizing and optimizing k-space-based reconstruction in parallel imaging.

The consequences of ignoring measurement invariance for path coefficients in structural equation models

PubMed Central

Guenole, Nigel; Brown, Anna

2014-01-01

We report a Monte Carlo study examining the effects of two strategies for handling measurement non-invariance – modeling and ignoring non-invariant items – on structural regression coefficients between latent variables measured with item response theory models for categorical indicators. These strategies were examined across four levels and three types of non-invariance – non-invariant loadings, non-invariant thresholds, and combined non-invariance on loadings and thresholds – in simple, partial, mediated and moderated regression models where the non-invariant latent variable occupied predictor, mediator, and criterion positions in the structural regression models. When non-invariance is ignored in the latent predictor, the focal group regression parameters are biased in the opposite direction to the difference in loadings and thresholds relative to the referent group (i.e., lower loadings and thresholds for the focal group lead to overestimated regression parameters). With criterion non-invariance, the focal group regression parameters are biased in the same direction as the difference in loadings and thresholds relative to the referent group. While unacceptable levels of parameter bias were confined to the focal group, bias occurred at considerably lower levels of ignored non-invariance than was previously recognized in referent and focal groups. PMID:25278911

DNA transposon-based gene vehicles - scenes from an evolutionary drive

PubMed Central

2013-01-01

DNA transposons are primitive genetic elements which have colonized living organisms from plants to bacteria and mammals. Through evolution such parasitic elements have shaped their host genomes by replicating and relocating between chromosomal loci in processes catalyzed by the transposase proteins encoded by the elements themselves. DNA transposable elements are constantly adapting to life in the genome, and self-suppressive regulation as well as defensive host mechanisms may assist in buffering ‘cut-and-paste’ DNA mobilization until accumulating mutations will eventually restrict events of transposition. With the reconstructed Sleeping Beauty DNA transposon as a powerful engine, a growing list of transposable elements with activity in human cells have moved into biomedical experimentation and preclinical therapy as versatile vehicles for delivery and genomic insertion of transgenes. In this review, we aim to link the mechanisms that drive transposon evolution with the realities and potential challenges we are facing when adapting DNA transposons for gene transfer. We argue that DNA transposon-derived vectors may carry inherent, and potentially limiting, traits of their mother elements. By understanding in detail the evolutionary journey of transposons, from host colonization to element multiplication and inactivation, we may better exploit the potential of distinct transposable elements. Hence, parallel efforts to investigate and develop distinct, but potent, transposon-based vector systems will benefit the broad applications of gene transfer. Insight and clever optimization have shaped new DNA transposon vectors, which recently debuted in the first DNA transposon-based clinical trial. Learning from an evolutionary drive may help us create gene vehicles that are safer, more efficient, and less prone for suppression and inactivation. PMID:24320156

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

PubMed Central

Manning, Viola A.; Pandelova, Iovanna; Dhillon, Braham; Wilhelm, Larry J.; Goodwin, Stephen B.; Berlin, Aaron M.; Figueroa, Melania; Freitag, Michael; Hane, James K.; Henrissat, Bernard; Holman, Wade H.; Kodira, Chinnappa D.; Martin, Joel; Oliver, Richard P.; Robbertse, Barbara; Schackwitz, Wendy; Schwartz, David C.; Spatafora, Joseph W.; Turgeon, B. Gillian; Yandava, Chandri; Young, Sarah; Zhou, Shiguo; Zeng, Qiandong; Grigoriev, Igor V.; Ma, Li-Jun; Ciuffetti, Lynda M.

2013-01-01

Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes. PMID:23316438

Transposable Element Proliferation and Genome Expansion Are Rare in Contemporary Sunflower Hybrid Populations Despite Widespread Transcriptional Activity of LTR Retrotransposons

PubMed Central

Kawakami, Takeshi; Dhakal, Preeti; Katterhenry, Angela N.; Heatherington, Chelsea A.; Ungerer, Mark C.

2011-01-01

Hybridization is a natural phenomenon that has been linked in several organismal groups to transposable element derepression and copy number amplification. A noteworthy example involves three diploid annual sunflower species from North America that have arisen via ancient hybridization between the same two parental taxa, Helianthus annuus and H. petiolaris. The genomes of the hybrid species have undergone large-scale increases in genome size attributable to long terminal repeat (LTR) retrotransposon proliferation. The parental species that gave rise to the hybrid taxa are widely distributed, often sympatric, and contemporary hybridization between them is common. Natural H. annuus × H. petiolaris hybrid populations likely served as source populations from which the hybrid species arose and, as such, represent excellent natural experiments for examining the potential role of hybridization in transposable element derepression and proliferation in this group. In the current report, we examine multiple H. annuus × H. petiolaris hybrid populations for evidence of genome expansion, LTR retrotransposon copy number increases, and LTR retrotransposon transcriptional activity. We demonstrate that genome expansion and LTR retrotransposon proliferation are rare in contemporary hybrid populations, despite independent proliferation events that took place in the genomes of the ancient hybrid species. Interestingly, LTR retrotransposon lineages that proliferated in the hybrid species genomes remain transcriptionally active in hybrid and nonhybrid genotypes across the entire sampling area. The finding of transcriptional activity but not copy number increases in hybrid genotypes suggests that proliferation and genome expansion in contemporary hybrid populations may be mitigated by posttranscriptional mechanisms of repression. PMID:21282712

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

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

Manning, Viola A.; Pandelova, Iovanna; Dhillon, Braham

2012-08-16

Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11more » chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.« less

Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing

PubMed Central

Patel, Hardip; Forêt, Sylvain; Karlsen, Bård Ove; Jørgensen, Tor Erik; Hall-Spencer, Jason M

2018-01-01

Abstract Cnidarians harbor a variety of small regulatory RNAs that include microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), but detailed information is limited. Here, we report the identification and expression of novel miRNAs and putative piRNAs, as well as their genomic loci, in the symbiotic sea anemone Anemonia viridis. We generated a draft assembly of the A. viridis genome with putative size of 313 Mb that appeared to be composed of about 36% repeats, including known transposable elements. We detected approximately equal fractions of DNA transposons and retrotransposons. Deep sequencing of small RNA libraries constructed from A. viridis adults sampled at a natural CO2 gradient off Vulcano Island, Italy, identified 70 distinct miRNAs. Eight were homologous to previously reported miRNAs in cnidarians, whereas 62 appeared novel. Nine miRNAs were recognized as differentially expressed along the natural seawater pH gradient. We found a highly abundant and diverse population of piRNAs, with a substantial fraction showing ping–pong signatures. We identified nearly 22% putative piRNAs potentially targeting transposable elements within the A. viridis genome. The A. viridis genome appeared similar in size to that of other hexacorals with a very high divergence of transposable elements resembling that of the sea anemone genus Exaiptasia. The genome encodes and expresses a high number of small regulatory RNAs, which include novel miRNAs and piRNAs. Differentially expressed small RNAs along the seawater pH gradient indicated regulatory gene responses to environmental stressors. PMID:29385567

A variant Tc4 transposable element in the nematode C. elegans could encode a novel protein.

PubMed Central

Li, W; Shaw, J E

1993-01-01

A variant C. elegans Tc4 transposable element, Tc4-rh1030, has been sequenced and is 3483 bp long. The Tc4 element that had been analyzed previously is 1605 bp long, consists of two 774-bp nearly perfect inverted terminal repeats connected by a 57-bp loop, and lacks significant open reading frames. In Tc4-rh1030, by comparison, a 2343-bp novel sequence is present in place of a 477-bp segment in one of the inverted repeats. The novel sequence of Tc4-rh1030 is present about five times per haploid genome and is invariably associated with Tc4 elements; we have used the designation Tc4v to denote this variant subfamily of Tc4 elements. Sequence analysis of three cDNA clones suggests that a Tc4v element contains at least five exons that could encode a novel basic protein of 537 amino acid residues. On northern blots, a 1.6-kb Tc4v-specific transcript was detected in the mutator strain TR679 but not in the wild-type strain N2; Tc4 elements are known to transpose in TR679 but appear to be quiescent in N2. We have analyzed transcripts produced by an unc-33 gene that has the Tc4-rh1030 insertional mutation in its transcribed region; all or almost all of the Tc4v sequence is frequently spliced out of the mutant unc-33 transcripts, sometimes by means of non-consensus splice acceptor sites. Images PMID:8382791

Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells.

PubMed

Glinsky, Gennadi V

2018-03-01

Transposable elements have made major evolutionary impacts on creation of primate-specific and human-specific genomic regulatory loci and species-specific genomic regulatory networks (GRNs). Molecular and genetic definitions of human-specific changes to GRNs contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of diverse families of human-specific genomic regulatory loci (HSGRL) identified topologically associating domains (TADs) that are significantly enriched for HSGRL and designated rapidly evolving in human TADs. Here, the analysis of HSGRL, hESC-enriched enhancers, super-enhancers (SEs), and specific sub-TAD structures termed super-enhancer domains (SEDs) has been performed. In the hESC genome, 331 of 504 (66%) of SED-harboring TADs contain HSGRL and 68% of SEDs co-localize with HSGRL, suggesting that emergence of HSGRL may have rewired SED-associated GRNs within specific TADs by inserting novel and/or erasing existing non-coding regulatory sequences. Consequently, markedly distinct features of the principal regulatory structures of interphase chromatin evolved in the hESC genome compared to mouse: the SED quantity is 3-fold higher and the median SED size is significantly larger. Concomitantly, the overall TAD quantity is increased by 42% while the median TAD size is significantly decreased (p = 9.11E-37) in the hESC genome. Present analyses illustrate a putative global role for transposable elements and HSGRL in shaping the human-specific features of the interphase chromatin organization and functions, which are facilitated by accelerated creation of novel transcription factor binding sites and new enhancers driven by targeted placement of HSGRL at defined genomic coordinates. A trend toward the convergence of TAD and SED architectures of interphase chromatin in the hESC genome may reflect changes of 3D-folding patterns of linear chromatin fibers designed to enhance both regulatory complexity and functional precision of GRNs by creating predominantly a single gene (or a set of functionally linked genes) per regulatory domain structures. Collectively, present analyses reveal critical evolutionary contributions of transposable elements and distal enhancers to creation of thousands primate- and human-specific elements of a chromatin folding code, which defines the 3D context of interphase chromatin both restricting and facilitating biological functions of GRNs.

Generation of entanglement and its decay in a noisy environment

NASA Astrophysics Data System (ADS)

Huang, Jiehui

Entanglement plays a central role in distinguishing quantum mechanics from classical physics. Due to its fantastic properties and many potential applications in quantum information science, entanglement is attracting more and more attention. This thesis focuses on the generation of entanglement and its decay in a noisy environment. In the first experimental scheme to entangle two thermal fields, an atomic ensemble, composed of many identical four-level atoms, is employed. In the first Raman scattering, this atomic ensemble emits write signal photons after the pumping by a weak write pulse, accompanied by the transfer from one lower level to the other for some atoms. Similarly, the atomic ensemble emits read signal photons after the driving by a strong read pulse, and the ensemble turns back to its ground state after the second Raman scattering. The coherence between the two lower atomic levels plays a key role in establishing the quantum correlation between two emission fields, which is verified through the violation of Cauchy-Schwarz inequality. In particular, the controllable time delay between the two emission fields actually means the storage time of photonic information in this system, which sheds light on some potential applications, such as quantum memory. In the second experimental scheme for the generation of spatially separated multiphoton entanglement, two or more identical optical cavities are aligned along a bee-line, and a four-level atom runs through these cavities sequentially. By appropriately adjusting the passage time of the atom in each cavity or the Rabi frequency of the classical pumping laser, a photon can be generated via the interaction between the excited atom and the cavity modes. This adiabatic passage model is an effective method to map atomic coherence to photonic state in cavity QED, thus all photons in different cavities quantum-mechanically correlate with the moving atom. When a final detection is made on this atom, a generalized n-photon GHZ entangled state will be generated with certainty. Environment-induced disentanglement is another important topic in quantum optics. Based on the Peres-Horodecki criterion for separability of bipartite states, we develop the principal minor method for the verification of two-qubit entanglement. Among the fifteen principal minors (seven effective ones) of a given two-qubit state's partial transpose, if the minimum one is negative, the two-qubit state is entangled, otherwise it is separable. By applying this method to a two-qubit system under amplitude and phase dampings, we have derived the necessary and sufficient conditions for the entanglement sudden death of an initially entangled two-qubit state. Keywords: entanglement generation, atomic ensemble, two-qubit, multiphoton entanglement, cavity QED, entanglement sudden death (ESD), amplitude damping, phase damping, principal minor.

Facts about dextro-Transposition of the Great Arteries (d-TGA)

MedlinePlus

... Septal Defect Atrioventricular Septal Defect Coarctation of the Aorta D-Transposition of the Great Arteries Hypoplastic Left ... the heart – the main pulmonary artery and the aorta – are switched in position, or “transposed.” What is ...

GENETIC ENGINEERING OF ENHANCED MICROBIAL NITRIFICATION

EPA Science Inventory

Experiments were conducted to introduce genetic information in the form of antibiotic or mercuric ion resistance genes into Nitrobacter hamburgensis strain X14. The resistance genes were either stable components of broad host range plasmids or transposable genes on methods for p...

Nonlinear dynamic model for visual object tracking on Grassmann manifolds with partial occlusion handling.

PubMed

Khan, Zulfiqar Hasan; Gu, Irene Yu-Hua

2013-12-01

This paper proposes a novel Bayesian online learning and tracking scheme for video objects on Grassmann manifolds. Although manifold visual object tracking is promising, large and fast nonplanar (or out-of-plane) pose changes and long-term partial occlusions of deformable objects in video remain a challenge that limits the tracking performance. The proposed method tackles these problems with the main novelties on: 1) online estimation of object appearances on Grassmann manifolds; 2) optimal criterion-based occlusion handling for online updating of object appearances; 3) a nonlinear dynamic model for both the appearance basis matrix and its velocity; and 4) Bayesian formulations, separately for the tracking process and the online learning process, that are realized by employing two particle filters: one is on the manifold for generating appearance particles and another on the linear space for generating affine box particles. Tracking and online updating are performed in an alternating fashion to mitigate the tracking drift. Experiments using the proposed tracker on videos captured by a single dynamic/static camera have shown robust tracking performance, particularly for scenarios when target objects contain significant nonplanar pose changes and long-term partial occlusions. Comparisons with eight existing state-of-the-art/most relevant manifold/nonmanifold trackers with evaluations have provided further support to the proposed scheme.

New method for evaluation of bendability based on three-point-bending and the evolution of the cross-section moment

NASA Astrophysics Data System (ADS)

Troive, L.

2017-09-01

Friction-free 3-point bending has become a common test-method since the VDA 238-100 plate-bending test [1] was introduced. According to this test the criterion for failure is when the force suddenly drops. It was found by the author that the evolution of the cross-section moment is a more preferable measure regarding the real material response instead of the force. Beneficially, the cross-section moment gets more or less a constant maximum steady-state level when the cross-section becomes fully plastified. An expression for the moment M is presented that fulfils the criteria for energy of conservation at bending. Also an expression calculating the unit-free moment, M/Me, i.e. current moment to elastic-moment ratio, is demonstrated specifically proposed for detection of failures. The mathematical expressions are simple making it easy to transpose measured force F and stroke position S to the corresponding cross-section moment M. From that point of view it’s even possible to implement, e.g. into a conventional measurement system software, studying the cross-section moment in real-time during a test. It’s even possible to calculate other parameters such as flow-stress and shape of curvature at every stage. It has been tested on different thicknesses and grades within the range from 1.0 to 10 mm with very good results. In this paper the present model is applied on a 6.1 mm hot-rolled high strength steel from the same batch at three different conditions, i.e. directly quenched, quenched and tempered, and a third variant quench and tempered with levelling. It will be shown that very small differences in material-response can be predicted by this method.

A Burkean Perspective of Romantic Jealousy.

ERIC Educational Resources Information Center

Byers, Peggy Yuhas

Kenneth Burke's dramatistic theory of social movements can be applied to current romantic jealousy theories. Burke's dramaturgy has seven major elements: order, guilt, negation, victimage, mortification, catharsis, and redemption. These elements may all be transposed onto Burke's three critical motives: Order (status quo), Secret (differences…

Effects of Embedded Processing Tasks on Learning Outcomes.

ERIC Educational Resources Information Center

Hobbs, D. J.

1987-01-01

Describes a British study with undergraduate accountancy students which compared the quantitative and qualitative effects of three types of embedded tasks or questions--relational-semantic, transpose-semantic, and non-semantic--on learning outcomes. Variables investigated included mathematical background, recall, and comprehension. Relevance of…

Method and structure for cache aware transposition via rectangular subsections

DOEpatents

Gustavson, Fred Gehrung; Gunnels, John A

2014-02-04

A method and structure for transposing a rectangular matrix A in a computer includes subdividing the rectangular matrix A into one or more square submatrices and executing an in-place transposition for each of the square submatrices A.sub.ij.

Evolutionary Histories of Transposable Elements in the Genome of the Largest Living Marsupial Carnivore, the Tasmanian Devil

PubMed Central

Gallus, Susanne; Hallström, Björn M; Kumar, Vikas; Dodt, William G; Janke, Axel; Schumann, Gerald G; Nilsson, Maria A

2015-01-01

The largest living carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii), is the sole survivor of a lineage originating about 12 Ma. We set out to investigate the spectrum of transposable elements found in the Tasmanian devil genome, the first high-coverage genome of an Australian marsupial. Marsupial genomes have been shown to have the highest amount of transposable elements among vertebrates. We analyzed the horizontally transmitted DNA transposons OC1 and hAT-1_MEu in the Tasmanian devil genome. OC1 is present in all carnivorous marsupials, while having a very limited distribution among the remaining Australian marsupial orders. In contrast, hAT-1_MEu is present in all Australian marsupial orders, and has so far only been identified in a few placental mammals. We screened 158 introns for phylogenetically informative retrotransposons in the order Dasyuromorphia, and found that the youngest SINE (Short INterspersed Element), WSINE1, is no longer active in the subfamily Dasyuridae. The lack of detectable WSINE1 activity in this group may be due to a retrotransposon inactivation event approximately 30 Ma. We found that the Tasmanian devil genome contains a relatively low number of continuous full-length LINE-1 (Long INterspersed Element 1, L1) retrotransposons compared with the opossum genome. Furthermore, all L1 elements in the Tasmanian devil appeared to be nonfunctional. Hidden Markov Model approaches suggested that other potential sources of functional reverse transcriptase are absent from the genome. We discuss the issues associated with assembling long, highly similar L1 copies from short read Illumina data and describe how assembly artifacts can potentially lead to erroneous conclusions. PMID:25633377

Petrotectonic framework of granulites from northern part of Chilka Lake area, Eastern Ghats Belt, India: Compressional vis-à-vis transpressional tectonics

NASA Astrophysics Data System (ADS)

Das, Kaushik; Bose, Sankar; Karmakar, Subrata; Chakraborty, Supriya

2012-02-01

Granulite-facies rocks occurring north-east of the Chilka Lake anothosite (Balugan Massif) show a complex metamorphic and deformation history. The M1-D1 stage is identified only through microscopic study by the presence of S1 internal foliation shown by the M1 assemblage sillimanite-quartz-plagioclase-biotite within garnet porphyroblasts of the aluminous granulites and this fabric is obliterated in outcrop to map-scale by subsequent deformations. S2 fabric was developed at peak metamorphic condition (M2-D2) and is shown by gneissic banding present in all lithological units. S3 fabric was developed due to D3 deformation and it is tectonically transposed parallel to S2 regionally except at the hinge zone of the F3 folds. The transposed S2/S3 fabric is the regional characteristic structure of the area. The D4 event produced open upright F4 folds, but was weak enough to develop any penetrative foliation in the rocks except few spaced cleavages that developed in the quartzite/garnet-sillimanite gneiss. Petrological data suggest that the M4-D4 stage actually witnessed reactivation of the lower crust by late distinct tectonothermal event. Presence of transposed S2/S3 fabric within the anorthosite arguably suggests that the pluton was emplaced before or during the M3-D3 event. Field-based large-scale structural analyses and microfabric analyses of the granulites reveal that this terrain has been evolved through superposed folding events with two broadly perpendicular compression directions without any conclusive evidence for transpressional tectonics as argued by earlier workers. Tectonothermal history of these granulites spanning in Neoproterozoic time period is dominated by compressional tectonics with associated metamorphism at deep crust.

Derepression of the Plant Chromovirus LORE1 Induces Germline Transposition in Regenerated Plants

PubMed Central

Fukai, Eigo; Umehara, Yosuke; Sato, Shusei; Endo, Makoto; Kouchi, Hiroshi; Hayashi, Makoto; Stougaard, Jens; Hirochika, Hirohiko

2010-01-01

Transposable elements represent a large proportion of the eukaryotic genomes. Long Terminal Repeat (LTR) retrotransposons are very abundant and constitute the predominant family of transposable elements in plants. Recent studies have identified chromoviruses to be a widely distributed lineage of Gypsy elements. These elements contain chromodomains in their integrases, which suggests a preference for insertion into heterochromatin. In turn, this preference might have contributed to the patterning of heterochromatin observed in host genomes. Despite their potential importance for our understanding of plant genome dynamics and evolution, the regulatory mechanisms governing the behavior of chromoviruses and their activities remain largely uncharacterized. Here, we report a detailed analysis of the spatio-temporal activity of a plant chromovirus in the endogenous host. We examined LORE1a, a member of the endogenous chromovirus LORE1 family from the model legume Lotus japonicus. We found that this chromovirus is stochastically de-repressed in plant populations regenerated from de-differentiated cells and that LORE1a transposes in the male germline. Bisulfite sequencing of the 5′ LTR and its surrounding region suggests that tissue culture induces a loss of epigenetic silencing of LORE1a. Since LTR promoter activity is pollen specific, as shown by the analysis of transgenic plants containing an LTR::GUS fusion, we conclude that male germline-specific LORE1a transposition in pollen grains is controlled transcriptionally by its own cis-elements. New insertion sites of LORE1a copies were frequently found in genic regions and show no strong insertional preferences. These distinctive novel features of LORE1 indicate that this chromovirus has considerable potential for generating genetic and epigenetic diversity in the host plant population. Our results also define conditions for the use of LORE1a as a genetic tool. PMID:20221264

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

PubMed

Piégu, Benoît; Bire, Solenne; Arensburger, Peter; Bigot, Yves

2015-05-01

The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE). Copyright © 2015 Elsevier Inc. All rights reserved.

Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres.

PubMed

Arkhipova, Irina R; Yushenova, Irina A; Rodriguez, Fernando

2017-09-01

Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here, we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3'-end of the RNA template immediately adjacent to a hammerhead ribozyme motif. Terminon units, which can exceed 40 kb in length, display an unusually complex and diverse structure, and can form very long chains, with host genes often captured between units. As the principal polymerizing component, Terminons contain Athena reverse transcriptases previously described in bdelloid rotifers and belonging to the enigmatic group of Penelope-like elements, but can additionally accumulate multiple cooriented ORFs, including DEDDy 3'-exonucleases, GDSL esterases/lipases, GIY-YIG-like endonucleases, rolling-circle replication initiator (Rep) proteins, and putatively structural ORFs with coiled-coil motifs and transmembrane domains. The extraordinary length and complexity of Terminons and the high degree of interfamily variability in their ORF content challenge the current views on the structural organization of eukaryotic retroelements, and highlight their possible connections with the viral world and the implications for the elevated frequency of gene transfer. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Transposable element distribution, abundance and role in genome size variation in the genus Oryza.

PubMed

Zuccolo, Andrea; Sebastian, Aswathy; Talag, Jayson; Yu, Yeisoo; Kim, HyeRan; Collura, Kristi; Kudrna, Dave; Wing, Rod A

2007-08-29

The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.

Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements.

PubMed

Schartl, Manfred; Schories, Susanne; Wakamatsu, Yuko; Nagao, Yusuke; Hashimoto, Hisashi; Bertin, Chloé; Mourot, Brigitte; Schmidt, Cornelia; Wilhelm, Dagmar; Centanin, Lazaro; Guiguen, Yann; Herpin, Amaury

2018-01-29

Sex determination relies on a hierarchically structured network of genes, and is one of the most plastic processes in evolution. The evolution of sex-determining genes within a network, by neo- or sub-functionalization, also requires the regulatory landscape to be rewired to accommodate these novel gene functions. We previously showed that in medaka fish, the regulatory landscape of the master male-determining gene dmrt1bY underwent a profound rearrangement, concomitantly with acquiring a dominant position within the sex-determining network. This rewiring was brought about by the exaptation of a transposable element (TE) called Izanagi, which is co-opted to act as a silencer to turn off the dmrt1bY gene after it performed its function in sex determination. We now show that a second TE, Rex1, has been incorporated into Izanagi. The insertion of Rex1 brought in a preformed regulatory element for the transcription factor Sox5, which here functions in establishing the temporal and cell-type-specific expression pattern of dmrt1bY. Mutant analysis demonstrates the importance of Sox5 in the gonadal development of medaka, and possibly in mice, in a dmrt1bY-independent manner. Moreover, Sox5 medaka mutants have complete female-to-male sex reversal. Our work reveals an unexpected complexity in TE-mediated transcriptional rewiring, with the exaptation of a second TE into a network already rewired by a TE. We also show a dual role for Sox5 during sex determination: first, as an evolutionarily conserved regulator of germ-cell number in medaka, and second, by de novo regulation of dmrt1 transcriptional activity during primary sex determination due to exaptation of the Rex1 transposable element.

Sequence Analysis of the Genome of Carnation (Dianthus caryophyllus L.)

PubMed Central

Yagi, Masafumi; Kosugi, Shunichi; Hirakawa, Hideki; Ohmiya, Akemi; Tanase, Koji; Harada, Taro; Kishimoto, Kyutaro; Nakayama, Masayoshi; Ichimura, Kazuo; Onozaki, Takashi; Yamaguchi, Hiroyasu; Sasaki, Nobuhiro; Miyahara, Taira; Nishizaki, Yuzo; Ozeki, Yoshihiro; Nakamura, Noriko; Suzuki, Takamasa; Tanaka, Yoshikazu; Sato, Shusei; Shirasawa, Kenta; Isobe, Sachiko; Miyamura, Yoshinori; Watanabe, Akiko; Nakayama, Shinobu; Kishida, Yoshie; Kohara, Mitsuyo; Tabata, Satoshi

2014-01-01

The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. ‘Francesco’ was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568 887 315 bp, consisting of 45 088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16 644 bp and 60 737 bp, respectively, and the longest scaffold was 1 287 144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genomic sequences is available at http://carnation.kazusa.or.jp. PMID:24344172

Computer program grade 2 for the design and analysis of heat-pipe wicks

NASA Technical Reports Server (NTRS)

Eninger, J. E.; Edwards, D. K.

1976-01-01

This user's manual describes the revised version of the computer program GRADE(1), which designs and analyzes heat pipes with graded porosity fibrous slab wicks. The revisions are: (1) automatic calculation of the minimum condenser-end stress that will not result in an excess-liquid puddle or a liquid slug in the vapor space; (2) numerical solution of the equations describing flow in the circumferential grooves to assess the burnout criterion; (3) calculation of the contribution of excess liquid in fillets and puddles to the heat-transport; (4) calculation of the effect of partial saturation on the wick performance; and (5) calculation of the effect of vapor flow, which includes viscousinertial interactions.

A flexible model for correlated medical costs, with application to medical expenditure panel survey data.

PubMed

Chen, Jinsong; Liu, Lei; Shih, Ya-Chen T; Zhang, Daowen; Severini, Thomas A

2016-03-15

We propose a flexible model for correlated medical cost data with several appealing features. First, the mean function is partially linear. Second, the distributional form for the response is not specified. Third, the covariance structure of correlated medical costs has a semiparametric form. We use extended generalized estimating equations to simultaneously estimate all parameters of interest. B-splines are used to estimate unknown functions, and a modification to Akaike information criterion is proposed for selecting knots in spline bases. We apply the model to correlated medical costs in the Medical Expenditure Panel Survey dataset. Simulation studies are conducted to assess the performance of our method. Copyright © 2015 John Wiley & Sons, Ltd.

Characterizing entanglement with global and marginal entropic measures

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

Adesso, Gerardo; Illuminati, Fabrizio; De Siena, Silvio

2003-12-01

We qualify the entanglement of arbitrary mixed states of bipartite quantum systems by comparing global and marginal mixednesses quantified by different entropic measures. For systems of two qubits we discriminate the class of maximally entangled states with fixed marginal mixednesses, and determine an analytical upper bound relating the entanglement of formation to the marginal linear entropies. This result partially generalizes to mixed states the quantification of entanglement with marginal mixednesses holding for pure states. We identify a class of entangled states that, for fixed marginals, are globally more mixed than product states when measured by the linear entropy. Such statesmore » cannot be discriminated by the majorization criterion.« less

Binegativity of two qubits under noise

NASA Astrophysics Data System (ADS)

Sazim, Sk; Awasthi, Natasha

2018-07-01

Recently, it was argued that the binegativity might be a good quantifier of entanglement for two-qubit states. Like the concurrence and the negativity, the binegativity is also analytically computable quantifier for all two qubits. Based on numerical evidence, it was conjectured that it is a PPT (positive partial transposition) monotone and thus fulfills the criterion to be a good measure of entanglement. In this work, we investigate its behavior under noisy channels which indicate that the binegativity is decreasing monotonically with respect to increasing noise. We also find that the binegativity is closely connected to the negativity and has closed analytical form for arbitrary two qubits. Our study supports the conjecture that the binegativity is a monotone.

Damage tolerance in filament-wound graphite/epoxy pressure vessels

NASA Technical Reports Server (NTRS)

Simon, William E.; Ngueyen, Vinh D.; Chenna, Ravi K.

1995-01-01

Graphite/epoxy composites are extensively used in the aerospace and sporting goods industries due to their superior engineering properties compared to those of metals. However, graphite/epoxy is extremely susceptible to impact damage which can cause considerable and sometimes undetected reduction in strength. An inelastic impact model was developed to predict damage due to low-velocity impact. A transient dynamic finite element formulation was used in conjunction with the 3D Tsai-Wu failure criterion to determine and incorporate failure in the materials during impact. Material degradation can be adjusted from no degradation to partial degradation to full degradation. The developed software is based on an object-oriented implementation framework called Extensible Implementation Framework for Finite Elements (EIFFE).

Crack Tip Dislocation Nucleation in FCC Solids

NASA Astrophysics Data System (ADS)

Knap, J.; Sieradzki, K.

1999-02-01

We present results of molecular dynamic simulations aimed at examining crack tip dislocation emission in fcc solids. The results are analyzed in terms of recent continuum formulations of this problem. In mode II, Au, Pd, and Pt displayed a new unanticipated mechanism of crack tip dislocation emission involving the creation of a pair of Shockley partials on a slip plane one plane below the crack plane. In mode I, for all the materials examined, Rice's continuum formulation [J. Mech. Phys. Solids 40, 239 (1992)] underestimated the stress intensity for dislocation emission by almost a factor of 2. Surface stress corrections to the emission criterion brought the agreement between continuum predictions and simulations to within 20%.

Combined Studies

DTIC Science & Technology

1976-08-31

SSH, (1-1) where H viands for conjugate transpose, and S is the total signal vector recorded at an array of sensors, defined by: S...time delay, and a = a scale constant (for convenience, yet without loss of gen- erality, les us assume (|a(<l) ), The complex cepstrum x(n

Phanerochaete chrysosporium genomics

Treesearch

Luis F. Larrondo; Rafael Vicuna; Dan Cullen

2005-01-01

A high quality draft genome sequence has been generated for the lignocellulose-degrading basidiomycete Phanerochaete chrysosporium (Martinez et al. 2004). Analysis of the genome in the context of previously established genetics and physiology is presented. Transposable elements and their potential relationship to genes involved in lignin degradation are systematically...

The hobo transposable element excises and has related elements in tephritid species

USDA-ARS?s Scientific Manuscript database

Function of the Drosophila melanogaster hobo transposon in tephritid species was tested in transient embryonic excision assays by scientists at the USDA Agricultural Research Service, Center for Medical Agricultural and Veterinary Entomology, Gainesville, Florida. Wild-type and mutant strains of Ana...

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

Global mapping of transposon location.

PubMed

Gabriel, Abram; Dapprich, Johannes; Kunkel, Mark; Gresham, David; Pratt, Stephen C; Dunham, Maitreya J

2006-12-15

Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome's full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray-based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential.

Transposable Elements in Human Cancer: Causes and Consequences of Deregulation.

PubMed

Anwar, Sumadi Lukman; Wulaningsih, Wahyu; Lehmann, Ulrich

2017-05-04

Transposable elements (TEs) comprise nearly half of the human genome and play an essential role in the maintenance of genomic stability, chromosomal architecture, and transcriptional regulation. TEs are repetitive sequences consisting of RNA transposons, DNA transposons, and endogenous retroviruses that can invade the human genome with a substantial contribution in human evolution and genomic diversity. TEs are therefore firmly regulated from early embryonic development and during the entire course of human life by epigenetic mechanisms, in particular DNA methylation and histone modifications. The deregulation of TEs has been reported in some developmental diseases, as well as for different types of human cancers. To date, the role of TEs, the mechanisms underlying TE reactivation, and the interplay with DNA methylation in human cancers remain largely unexplained. We reviewed the loss of epigenetic regulation and subsequent genomic instability, chromosomal aberrations, transcriptional deregulation, oncogenic activation, and aberrations of non-coding RNAs as the potential mechanisms underlying TE deregulation in human cancers.

Transposable Elements in Human Cancer: Causes and Consequences of Deregulation

PubMed Central

Anwar, Sumadi Lukman; Wulaningsih, Wahyu; Lehmann, Ulrich

2017-01-01

Transposable elements (TEs) comprise nearly half of the human genome and play an essential role in the maintenance of genomic stability, chromosomal architecture, and transcriptional regulation. TEs are repetitive sequences consisting of RNA transposons, DNA transposons, and endogenous retroviruses that can invade the human genome with a substantial contribution in human evolution and genomic diversity. TEs are therefore firmly regulated from early embryonic development and during the entire course of human life by epigenetic mechanisms, in particular DNA methylation and histone modifications. The deregulation of TEs has been reported in some developmental diseases, as well as for different types of human cancers. To date, the role of TEs, the mechanisms underlying TE reactivation, and the interplay with DNA methylation in human cancers remain largely unexplained. We reviewed the loss of epigenetic regulation and subsequent genomic instability, chromosomal aberrations, transcriptional deregulation, oncogenic activation, and aberrations of non-coding RNAs as the potential mechanisms underlying TE deregulation in human cancers. PMID:28471386

Bursts of transposable elements as an evolutionary driving force.

PubMed

Belyayev, A

2014-12-01

A burst of transposable elements (TEs) is a massive outbreak that may cause radical genomic rebuilding. This phenomenon has been reported in connection with the formation of taxonomic groups and species and has therefore been associated with major evolutionary events in the past. Over the past few years, several research groups have discovered recent stress-induced bursts of different TEs. The events for which bursts of TEs have been recorded include domestication, polyploidy, changes in mating systems, interspecific and intergeneric hybridization and abiotic stress. Cases involving abiotic stress, particularly bursts of TEs in natural populations driven by environmental change, are of special interest because this phenomenon may underlie micro- and macro-evolutionary events and ultimately support the maintenance and generation of biological diversity. This study reviews the known cases of bursts of TEs and their possible consequences, with particular emphasis on the speciation process. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate

PubMed Central

Kimura-Yoshida, Chiharu; Yan, Kuo; Bormuth, Olga; Ding, Qiong; Nakanishi, Akiko; Sasaki, Takeshi; Hirakawa, Mika; Sumiyama, Kenta; Furuta, Yasuhide; Tarabykin, Victor; Matsuo, Isao; Okada, Norihiro

2016-01-01

Acquisition of cis-regulatory elements is a major driving force of evolution, and there are several examples of developmental enhancers derived from transposable elements (TEs). However, it remains unclear whether one enhancer element could have been produced via cooperation among multiple, yet distinct, TEs during evolution. Here we show that an evolutionarily conserved genomic region named AS3_9 comprises three TEs (AmnSINE1, X6b_DNA and MER117), inserted side-by-side, and functions as a distal enhancer for wnt5a expression during morphogenesis of the mammalian secondary palate. Functional analysis of each TE revealed step-by-step retroposition/transposition and co-option together with acquisition of a binding site for Msx1 for its full enhancer function during mammalian evolution. The present study provides a new perspective suggesting that a huge variety of TEs, in combination, could have accelerated the diversity of cis-regulatory elements involved in morphological evolution. PMID:27741242

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements.

PubMed

Lewis, Samuel H; Quarles, Kaycee A; Yang, Yujing; Tanguy, Melanie; Frézal, Lise; Smith, Stephen A; Sharma, Prashant P; Cordaux, Richard; Gilbert, Clément; Giraud, Isabelle; Collins, David H; Zamore, Phillip D; Miska, Eric A; Sarkies, Peter; Jiggins, Francis M

2018-01-01

In animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were probably present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and messenger RNAs are common among arthropods. The presence of an RNA-dependent RNA polymerase in chelicerates (horseshoe crabs, spiders and scorpions) suggests that arthropods originally used a plant-like RNA interference mechanism to silence TEs. Our results call into question the view that the ancestral role of the piRNA pathway was to protect the germline and demonstrate that small RNA silencing pathways have been repurposed for both somatic and germline functions throughout arthropod evolution.

Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome.

PubMed

Rizzon, Carène; Marais, Gabriel; Gouy, Manolo; Biémont, Christian

2002-03-01

We analyzed the distribution of 54 families of transposable elements (TEs; transposons, LTR retrotransposons, and non-LTR retrotransposons) in the chromosomes of Drosophila melanogaster, using data from the sequenced genome. The density of LTR and non-LTR retrotransposons (RNA-based elements) was high in regions with low recombination rates, but there was no clear tendency to parallel the recombination rate. However, the density of transposons (DNA-based elements) was significantly negatively correlated with recombination rate. The accumulation of TEs in regions of reduced recombination rate is compatible with selection acting against TEs, as selection is expected to be weaker in regions with lower recombination. The differences in the relationship between recombination rate and TE density that exist between chromosome arms suggest that TE distribution depends on specific characteristics of the chromosomes (chromatin structure, distribution of other sequences), the TEs themselves (transposition mechanism), and the species (reproductive system, effective population size, etc.), that have differing influences on the effect of natural selection acting against the TE insertions.

The impact of transposable elements in environmental adaptation.

PubMed

Casacuberta, Elena; González, Josefa

2013-03-01

Transposable elements (TEs) play an important role in the responsive capacity of their hosts in the face of environmental challenges. The variety of mechanisms by which TEs influence the capacity of adaptation of the host is as large as the variety of TEs and host genomes. For example, TEs might directly affect the function of individual genes, provide a mechanism for rapidly acquiring new genetic material and disseminate regulatory elements that can lead to the creation of stress-inducible regulatory networks. In this review, we summarize recent examples that are part of an increasing body of evidence suggesting a significant role of TEs in the host response to an ever-changing environment, both in prokaryote and in eukaryote organisms. We argue that in the near future, the increasing availability of genome sequences and the development of new tools to discover and analyse TE insertions will further show the relevant role of TEs in environmental adaptation. © 2013 Blackwell Publishing Ltd.

A Genome-Wide Survey of Genetic Instability by Transposition in Drosophila Hybrids

PubMed Central

Vela, Doris; Fontdevila, Antonio; Vieira, Cristina; García Guerreiro, María Pilar

2014-01-01

Hybridization between species is a genomic instability factor involved in increasing mutation rate and new chromosomal rearrangements. Evidence of a relationship between interspecific hybridization and transposable element mobilization has been reported in different organisms, but most studies are usually performed with particular TEs and do not discuss the real effect of hybridization on the whole genome. We have therefore studied whole genome instability of Drosophila interspecific hybrids, looking for the presence of new AFLP markers in hybrids. A high percentage (27–90%) of the instability markers detected corresponds to TEs belonging to classes I and II. Moreover, three transposable elements (Osvaldo, Helena and Galileo) representative of different families, showed an overall increase of transposition rate in hybrids compared to parental species. This research confirms the hypothesis that hybridization induces genomic instability by transposition bursts and suggests that genomic stress by transposition could contribute to a relaxation of mechanisms controlling TEs in the Drosophila genome. PMID:24586475

A transposable element in a NAC gene is associated with drought tolerance in maize seedlings

PubMed Central

Mao, Hude; Wang, Hongwei; Liu, Shengxue; Li, Zhigang; Yang, Xiaohong; Yan, Jianbing; Li, Jiansheng; Tran, Lam-Son Phan; Qin, Feng

2015-01-01

Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. The 82-bp MITE represses ZmNAC111 expression via RNA-directed DNA methylation and H3K9 dimethylation when heterologously expressed in Arabidopsis. Increasing ZmNAC111 expression in transgenic maize enhances drought tolerance at the seedling stage, improves water-use efficiency and induces upregulation of drought-responsive genes under water stress. The MITE insertion in the ZmNAC111 promoter appears to have occurred after maize domestication and spread among temperate germplasm. The identification of this MITE insertion provides insight into the genetic basis for natural variation in maize drought tolerance. PMID:26387805

Do morphemes matter when reading compound words with transposed letters? Evidence from eye-tracking and event-related potentials

DOE PAGES

Stites, Mallory C.; Federmeier, Kara D.; Christianson, Kiel

2016-08-06

We investigate the online processing consequences of encountering compound words with transposed letters (TLs), in order to determine if cross-morpheme TLs are more disruptive to reading than those within a single morpheme, as would be predicted by accounts of obligatory morpho-orthopgrahic decomposition. Two measures of online processing, eye movements and event-related potentials (ERPs), were collected in separate experiments. Participants read sentences containing correctly spelled compound words (cupcake), or compounds with TLs occurring either across morphemes (cucpake) or within one morpheme (cupacke). Results showed that between- and within-morpheme transpositions produced equal processing costs in both measures, in the form of longermore » reading times (Experiment 1) and a late posterior positivity (Experiment 2) that did not differ between conditions. Our findings converge to suggest that within- and between-morpheme TLs are equally disruptive to recognition, providing evidence against obligatory morpho-orthographic processing and in favour of whole-word access of English compound words during sentence reading.« less

Genomic impact of eukaryotic transposable elements

PubMed Central

2012-01-01

The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come. PMID:23171443

Genomic impact of eukaryotic transposable elements.

PubMed

Arkhipova, Irina R; Batzer, Mark A; Brosius, Juergen; Feschotte, Cédric; Moran, John V; Schmitz, Jürgen; Jurka, Jerzy

2012-11-21

The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.

FB elements can promote exon shuffling: a promoter-less white allele can be reactivated by FB mediated transposition in Drosophila melanogaster.

PubMed

Moschetti, R; Marsano, R M; Barsanti, P; Caggese, C; Caizzi, R

2004-05-01

Foldback ( FB) elements are transposable elements found in many eukaryotic genomes; they are thought to contribute significantly to genome plasticity. In Drosophila melanogaster, FBs have been shown to be involved in the transposition of large chromosomal regions and in the genetic instability of some alleles of the white gene. In this report we show that FB mediated transposition of w(67C23), a mutation that deletes the promoter of the white gene and its first exon, containing the start codon, can restore expression of the white gene. We have characterized three independent events in which a 14-kb fragment from the w(67C23) locus was transposed into an intron region in three different genes. In each case a local promoter drives the expression of white, producing a chimeric mRNA. These findings suggest that, on an evolutionary timescale, FB elements may contribute to the creation of new genes via exon shuffling.

Zaba: a novel miniature transposable element present in genomes of legume plants.

PubMed

Macas, J; Neumann, P; Pozárková, D

2003-08-01

A novel family of miniature transposable elements, named Zaba, was identified in pea (Pisum sativum) and subsequently also in other legume species using computer analysis of their DNA sequences. Zaba elements are 141-190 bp long, generate 10-bp target site duplications, and their terminal inverted repeats make up most of the sequence. Zaba elements thus resemble class 3 foldback transposons. The elements are only moderately repetitive in pea (tens to hundreds copies per haploid genome), but they are present in up to thousands of copies in the genomes of several Medicago and Vicia species. More detailed analysis of the elements from pea, including isolation of new sequences from a genomic library, revealed that a fraction of these elements are truncated, and that their last transposition probably did not occur recently. A search for Zaba sequences in EST databases showed that at least some elements are transcribed, most probably due to their association with genic regions.

Do Morphemes Matter when Reading Compound Words with Transposed Letters? Evidence from Eye-Tracking and Event-Related Potentials

PubMed Central

Stites, Mallory C.; Federmeier, Kara D.; Christianson, Kiel

2017-01-01

The current study investigates the online processing consequences of encountering compound words with transposed letters (TLs), to determine if TLs that cross morpheme boundaries are more disruptive to reading than those within a single morpheme, as would be predicted by accounts of obligatory morpho-orthopgrahic decomposition. Two measures of online processing, eye movements and event-related potentials (ERPs), were collected in separate experiments. Participants read sentences containing correctly spelled compound words (cupcake), or compounds with TLs occurring either across morpheme boundaries (cucpake) or within one morpheme (cupacke). Results showed that between- and within-morpheme transpositions produced equal processing costs in both measures, in the form of longer reading times (Experiment 1) and a late posterior positivity (Experiment 2) that did not differ between conditions. Findings converge to suggest that within- and between-morpheme TLs are equally disruptive to recognition, providing evidence against obligatory morpho-orthographic processing and in favor of whole-word access of English compound words during sentence reading. PMID:28791313

Do morphemes matter when reading compound words with transposed letters? Evidence from eye-tracking and event-related potentials

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

Stites, Mallory C.; Federmeier, Kara D.; Christianson, Kiel

We investigate the online processing consequences of encountering compound words with transposed letters (TLs), in order to determine if cross-morpheme TLs are more disruptive to reading than those within a single morpheme, as would be predicted by accounts of obligatory morpho-orthopgrahic decomposition. Two measures of online processing, eye movements and event-related potentials (ERPs), were collected in separate experiments. Participants read sentences containing correctly spelled compound words (cupcake), or compounds with TLs occurring either across morphemes (cucpake) or within one morpheme (cupacke). Results showed that between- and within-morpheme transpositions produced equal processing costs in both measures, in the form of longermore » reading times (Experiment 1) and a late posterior positivity (Experiment 2) that did not differ between conditions. Our findings converge to suggest that within- and between-morpheme TLs are equally disruptive to recognition, providing evidence against obligatory morpho-orthographic processing and in favour of whole-word access of English compound words during sentence reading.« less

Negative effect of the 5'-untranslated leader sequence on Ac transposon promoter expression.

PubMed

Scortecci, K C; Raina, R; Fedoroff, N V; Van Sluys, M A

1999-08-01

Transposable elements are used in heterologous plant hosts to clone genes by insertional mutagenesis. The Activator (Ac) transposable element has been cloned from maize, and introduced into a variety of plants. However, differences in regulation and transposition frequency have been observed between different host plants. The cause of this variability is still unknown. To better understand the activity of the Ac element, we analyzed the Ac promoter region and its 5'-untranslated leader sequence (5' UTL). Transient assays in tobacco NT1 suspension cells showed that the Ac promoter is a weak promoter and its activity was localized by deletion analyses. The data presented here indicate that the core of the Ac promoter is contained within 153 bp fragment upstream to transcription start sites. An important inhibitory effect (80%) due to the presence of the 5' UTL was found on the expression of LUC reporter gene. Here we demonstrate that the presence of the 5' UTL in the constructs reduces the expression driven by either strong or weak promoters.

Transposable elements and polyploid evolution in animals.

PubMed

Rodriguez, Fernando; Arkhipova, Irina R

2018-04-28

Polyploidy in animals is much less common than in plants, where it is thought to be pervasive in all higher plant lineages. Recent studies have highlighted the impact of polyploidization and the associated process of diploidy restoration on the evolution and speciation of selected taxonomic groups in the animal kingdom: from vertebrates represented by salmonid fishes and African clawed frogs to invertebrates represented by parasitic root-knot nematodes and bdelloid rotifers. In this review, we focus on the unique and diverse roles that transposable elements may play in these processes, from marking and diversifying subgenome-specific chromosome sets before hybridization, to influencing genome restructuring during rediploidization, to affecting subgenome-specific regulatory evolution, and occasionally providing opportunities for domestication and gene amplification to restore and improve functionality. There is still much to be learned from the future comparative genomic studies of chromosome-sized and haplotype-aware assemblies, and from postgenomic studies elucidating genetic and epigenetic regulatory phenomena across short and long evolutionary distances in the metazoan tree of life. Copyright © 2018 Elsevier Ltd. All rights reserved.

Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution

PubMed Central

Lee, Yuh Chwen G; Karpen, Gary H

2017-01-01

Transposable elements (TEs) are widespread genomic parasites, and their evolution has remained a critical question in evolutionary genomics. Here, we study the relatively unexplored epigenetic impacts of TEs and provide the first genome-wide quantification of such effects in D. melanogaster and D. simulans. Surprisingly, the spread of repressive epigenetic marks (histone H3K9me2) to nearby DNA occurs at >50% of euchromatic TEs, and can extend up to 20 kb. This results in differential epigenetic states of genic alleles and, in turn, selection against TEs. Interestingly, the lower TE content in D. simulans compared to D. melanogaster correlates with stronger epigenetic effects of TEs and higher levels of host genetic factors known to promote epigenetic silencing. Our study demonstrates that the epigenetic effects of euchromatic TEs, and host genetic factors modulating such effects, play a critical role in the evolution of TEs both within and between species. DOI: http://dx.doi.org/10.7554/eLife.25762.001 PMID:28695823

Evolution and Diversity of Transposable Elements in Vertebrate Genomes.

PubMed

Sotero-Caio, Cibele G; Platt, Roy N; Suh, Alexander; Ray, David A

2017-01-01

Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Transposition of a Ds element from a plasmid into the plant genome in Nicotiana plumbaginifolia protoplast-derived cells.

PubMed

Houba-Hérin, N; Domin, M; Pédron, J

1994-07-01

Nicotiana plumbaginifolia haploid protoplasts were co-transformed with two plasmids, one with a NPT-II/Ds element and one with a gene encoding an amino-terminal truncated Ac transposase. It is shown that Ds can efficiently transpose from extrachromosomal DNA to N. plumbaginifolia chromosomes when the Ac transposase gene is present in trans. Ds has been shown to have transposed into the plant genome in a limited number of copies (1.9 copies per genome), for 21/32 transgenic lines tested. The flanking sequences present in the original plasmid are missing in these 21 plants. In only two of 21 plants was part of the transposase construct integrated. By segregation analysis of transgenic progeny, Ds was shown to be present in the heterozygous state in 10 lines even though haploid protoplasts had been originally transformed. This observation could indicate that integration occurred after or during DNA replication that leads to protoplast diploidization.

Heterochromatin and molecular characterization of DsmarMITE transposable element in the beetle Dichotomius schiffleri (Coleoptera: Scarabaeidae).

PubMed

Xavier, Crislaine; Cabral-de-Mello, Diogo Cavalcanti; de Moura, Rita Cássia

2014-12-01

Cytogenetic studies of the Neotropical beetle genus Dichotomius (Scarabaeinae, Coleoptera) have shown dynamism for centromeric constitutive heterochromatin sequences. In the present work we studied the chromosomes and isolated repetitive sequences of Dichotomius schiffleri aiming to contribute to the understanding of coleopteran genome/chromosomal organization. Dichotomius schiffleri presented a conserved karyotype and heterochromatin distribution in comparison to other species of the genus with 2n = 18, biarmed chromosomes, and pericentromeric C-positive blocks. Similarly to heterochromatin distributional patterns, the highly and moderately repetitive DNA fraction (C 0 t-1 DNA) was detected in pericentromeric areas, contrasting with the euchromatic mapping of an isolated TE (named DsmarMITE). After structural analyses, the DsmarMITE was classified as a non-autonomous element of the type miniature inverted-repeat transposable element (MITE) with terminal inverted repeats similar to Mariner elements of insects from different orders. The euchromatic distribution for DsmarMITE indicates that it does not play a part in the dynamics of constitutive heterochromatin sequences.

Stabilization of a locally minimal forest

NASA Astrophysics Data System (ADS)

Ivanov, A. O.; Mel'nikova, A. E.; Tuzhilin, A. A.

2014-03-01

The method of partial stabilization of locally minimal networks, which was invented by Ivanov and Tuzhilin to construct examples of shortest trees with given topology, is developed. According to this method, boundary vertices of degree 2 are not added to all edges of the original locally minimal tree, but only to some of them. The problem of partial stabilization of locally minimal trees in a finite-dimensional Euclidean space is solved completely in the paper, that is, without any restrictions imposed on the number of edges remaining free of subdivision. A criterion for the realizability of such stabilization is established. In addition, the general problem of searching for the shortest forest connecting a finite family of boundary compact sets in an arbitrary metric space is formalized; it is shown that such forests exist for any family of compact sets if and only if for any finite subset of the ambient space there exists a shortest tree connecting it. The theory developed here allows us to establish further generalizations of the stabilization theorem both for arbitrary metric spaces and for metric spaces with some special properties. Bibliography: 10 titles.

Surface engineering of cardiovascular stent with endothelial cell selectivity for in vivo re-endothelialisation.

PubMed

Wei, Yu; Ji, Ying; Xiao, Lin-Lin; Lin, Quan-kui; Xu, Jian-ping; Ren, Ke-feng; Ji, Jian

2013-04-01

The in vivo endothelialisation of materials provides a promising strategy for the rapid re-endothelialisation of a cardiovascular implantation. Although many studies have focused on improving the rapid endothelialisation through the immobilisation of bioactive molecules, it should be noted that the endothelial cells (ECs) will compete with other cell types in vivo. Thus, the efforts to partially enhance the EC growth without considering the cell competition might be misleading and meaningless in vivo. In this study, we demonstrated that the competitive growth of human umbilical vein endothelial cells (HUVECs) over human aortic smooth muscle cells (HASMCs) could be increased through the synergic action of the nonspecific resistance to phosphorylcholine and the specific recognition of the REDV peptide. Further in vivo data indicate that the competitive ability of ECs over SMCs, instead of the number of ECs, is a significantly more important criterion for the development of a pure endothelial layer in vivo and thus the attainment of a better anti-restenosis effect. Consequently, the surface tailoring of a stent to obtain high endothelial cell selectivity is likely an effective design criterion for in situ endothelialisation and a possible future solution for the problem of in-stent restenosis. Copyright © 2013 Elsevier Ltd. All rights reserved.

[Conversion disorder: from DSM IV to DSM 5 or from a psychiatric to a neurological diagnosis].

PubMed

Vermeulen, M; Willems, M H A

2015-01-01

According to one of the diagnostic criteria of the dsm iv for conversion disorder there has to be a temporal relationship between psychological factors and the onset, or the worsening, of the symptoms. This criterion has been omitted in the dsm-5. Another criterion, namely that the symptoms are not produced intentionally, has also been abandoned. A new recommendation is that therapists should look for neurological symptoms that support the diagnosis. To investigate whether studies support the changes in the criteria. We searched literature using PubMed. When the symptoms first appear, trauma or stress in 37% of patients is of a physical rather than a psychological nature. Different forms of stress were found in equal proportions (20%) in patients with or without conversion disorder. There are no specific stressors, except possibly in patients with dysphonia. The percentages of childhood abuse vary widely, namely from 0 to 85%. The characteristic phenomenon of 'la belle indifference' occurs in only 3% of patients with conversion disorder versus only 2% of controls. Most of the 'positive' clinical tests for partial paralysis and sensory and gait disorders are highly specific. There are no reliable tests for distinguishing conversion disorder from simulation. The changes of the criteria are supported by recent studies.

A Mathematical Proof of the Vortex Shedding Mechanism

NASA Astrophysics Data System (ADS)

Boghosian, Michael; Cassel, Kevin

2015-11-01

A novel mechanism leading to vortex splitting and subsequent shedding that is valid for both inviscid or viscous flows and external, internal, or wall-bounded flows is described. The mechanism, termed the Vortex-Shedding Mechanism (VSM), is simple and intuitive, requiring only two coincident conditions in the flow: (1) the existence of a location with zero momentum and (2) the presence of a net force having a positive divergence. Previous simulations of various flows have demonstrated the VSM numerically. Here, we present a mathematical proof of the VSM that is shown to be both a necessary and sufficient condition for a vortex splitting event in any two-dimensional, incompressible flow. The proof includes relating the positive divergence of the net force, condition (2) above, with the second invariant of the velocity gradient tensor, i.e. the Q-criterion. It is shown that the Q-criterion is identical to the determinant of the Hessian matrix for the streamfunction. As a result, the second-partial-derivative test on this Hessian matrix can provide a qualitative description on the behavior of the streamfunction, and thus vortices or recirculation regions, near critical points. Supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health (R01 DK90769).

Insertional mutagenesis using Tnt1 retrotransposon in potato

USDA-ARS?s Scientific Manuscript database

Potato is the third most important food crop in the world. However, genetics and genomics research of potato has lagged behind many major crop species due to its autotetraploidy and a highly heterogeneous genome. Insertional mutagenesis using T-DNA or transposable elements, which is available in sev...

Coordinated Control of a Planar Dual-Crane Non-Fully Restrained System

DTIC Science & Technology

2008-12-01

Support Over-The-Shore (HSOTS) 2007 in Puerto Quetzal , Guatemala. . . . . . . . . . . . . . 30 Figure 27. Reference frame and coordinate definitions...2007 in Puerto Quetzal , Guatemala. 30 require the construction an inverse of the Jacobian, but rather the transpose only. It is noted that the effector

Young Children Reinvent Arithmetic: Implications of Piaget's Theory.

ERIC Educational Resources Information Center

Kamii, Constance Kazuko; DeClark, Georgia

In the foreword to this book, Inhelder states that its essential contribution is that "it transposed to actual reality Piaget's central epistemological thesis according to which mathematical thought is, from its most elementary manifestations, the product of the subject's activity that he characterized by the term 'reflective…

Method of optimizing performance of Rankine cycle power plants

DOEpatents

Pope, William L.; Pines, Howard S.; Doyle, Padraic A.; Silvester, Lenard F.

1982-01-01

A method for efficiently operating a Rankine cycle power plant (10) to maximize fuel utilization efficiency or energy conversion efficiency or minimize costs by selecting a turbine (22) fluid inlet state which is substantially in the area adjacent and including the transposed critical temperature line (46).

Management of abortion complications at a rural hospital in Uganda: a quality assessment by a partially completed criterion-based audit.

PubMed

Mellerup, Natja; Sørensen, Bjarke L; Kuriigamba, Gideon K; Rudnicki, Martin

2015-09-20

Complications of unsafe abortion are a major contributor to maternal deaths in developing countries. This study aimed to evaluate the clinical assessment for life-threatening complications and the following management in women admitted with complications from abortions at a rural hospital in Uganda. A partially completed criterion-based audit was conducted comparing actual to optimal care. The audit criteria cover initial clinical assessment of vital signs and management of common severe complications such as sepsis and haemorrhage. Sepsis shall be managed by immediate evacuation of the uterus and antibiotics in relation to and after surgical management. Shock by aggressive rehydration followed by evacuation. In total 238 women admitted between January 2007 and April 2012 were included. Complications were categorized as incomplete, threatened, inevitable, missed or septic abortion and by trimester. Actual management was compared to the audit criteria and presented by descriptive statistics. Fifty six per cent of the women were in second trimester. Abortion complications were distributed as follows: 53 % incomplete abortions, 28 % threatened abortions, 12 % inevitable abortions, 4 % missed abortions and 3 % septic abortions. Only one of 238 cases met all criteria of optimal clinical assessment and management. Thus, vital signs were measured in 3 %, antibiotic criteria was met in 59 % of the cases, intravenous fluid resuscitation was administered to 35 % of women with hypotension and pain was managed in 87 % of the cases. Sharp curettage was used in 69 % of those surgically evacuated and manual vacuum aspiration in 14 %. In total 3 % of the abortions were categorized as unsafe. Two of eight women with septic abortion had evacuation performed during admission-day, one woman died due to septic abortion and one from severe haemorrhage. Guidelines were not followed and suboptimal assessment or management was observed in all but one case. This was especially due to missing documentation of vital signs necessary to diagnose life-threatening complications, poor fluid resuscitation at signs of shock, and delayed evacuation of septic abortion.

Miniature inverted-repeat transposable element identification and genetic marker development in Agrostis

USDA-ARS?s Scientific Manuscript database

Creeping bentgrass (Agrostis stolonifera L.) is an important species to the turfgrass industry because of its adaptation for use in high quality turf stands such as golf course putting greens, tees, and fairways. A. stolonifera is a highly outcrossing allotetraploid making genetic marker developmen...

Transposable element junctions in marker development and genomic characterization of barley

USDA-ARS?s Scientific Manuscript database

Barley is a model plant in genomic studies of Triticeae species. A complete barley genome sequence will facilitate not only barley breeding programs, but also those for related species. However, the large genome size and high repetitive sequence content complicate the barley genome assembly. The ma...

62. The Return of Educational Radio?

ERIC Educational Resources Information Center

Berman, Sally D.

2008-01-01

This paper examines one of the traditional technologies of distance education, radio, and presents examples of educational and community radio usage in Asia and Africa. Instead of merely transposing western approaches to distance education in developing countries, it is suggested that the developed world can learn from uses of radio in developing…

Method of optimizing performance of Rankine cycle power plants. [US DOE Patent

DOEpatents

Pope, W.L.; Pines, H.S.; Doyle, P.A.; Silvester, L.F.

1980-06-23

A method is described for efficiently operating a Rankine cycle power plant to maximize fuel utilization efficiency or energy conversion efficiency or minimize costs by selecting a turbine fluid inlet state which is substantially on the area adjacent and including the transposed critical temperature line.

Analysis of a MULE-cyanide hydratase gene fusion in Verticillium dahliae

USDA-ARS?s Scientific Manuscript database

The genome of the phytopathogenic fungus Verticillium dahliae encodes numerous Class II “cut-and-paste” transposable elements, including those of a small group of MULE transposons. We have previously identified a fusion event between a MULE transposon sequence and sequence encoding a cyanide hydrata...

Research on Frequency Transposition for Hearing Aids. Final Report.

ERIC Educational Resources Information Center

Gengel, Roy W.; Pickett, J. M.

Reported were studies measuring residual auditory capacities of deaf persons and investigating hearing aids which transpose speech to lower frequencies where deaf persons may have better hearing. Studies on temporal and frequency discrimination indicated that the duration of a signal may have a differential effect on its detectability by…

Transposon based functional characterization of soybean genes

USDA-ARS?s Scientific Manuscript database

Type II transposable elements that use cut and paste mechanism for jumping from one genomic region to another is ideal in tagging and cloning genes. Precise excision from an insertion site in a mutant gene leads to regaining the wild-type function. Thus, function of a gene can be established based o...

Verbal and Visual Translation of Mayakovsky's and Lissitsky's "For Reading Out Loud."

ERIC Educational Resources Information Center

Lange, Martha Scotford

1988-01-01

Explores difficulties in translating and understanding visual poetry created by a linguistically different culture. Provides historical context and analyzes the design process of El Lissitzky's typographic presentation of Vladimir Mayakovsky's poems. Transposes the visual wordplays found in the original Cyrillic typography into the Roman alphabet.…

REACTIVATION POTENTIAL OF EPIGENETICALLY INACTIVE MU TRANSPOSABLE ELEMENTS OF ZEA MAYS L. DECREASES IN SUCCESSIVE GENERATIONS. (R824900)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Comparisons of Historical versus Synthetic Weather Inputs to Watershed Models and their Effect on Pollutant Loads

USDA-ARS?s Scientific Manuscript database

Synthetic weather generators are important for continuous-simulation of agricultural watersheds for risk analyses of downstream water quality. Many watersheds are sparsely or totally ungauged and daily weather must either be transposed or augmented. Since water quality models must recognize runoff...

Leading Performance: Transposing Musicianship into the Leadership Debate

ERIC Educational Resources Information Center

Bush, Marie

2011-01-01

This article reflects the personal experiences of its author: a musician, teacher and current leader in the secondary independent sector. It provides an initial exploration of the link between leadership and musicianship, pivoting on the concept of performance and how specific socialised and embedded skills and experiences developed through…

Higher-speed coronal mass ejections and their geoeffectiveness

NASA Astrophysics Data System (ADS)

Singh, A. K.; Bhargawa, Asheesh; Tonk, Apeksha

2018-06-01

We have attempted to examine the ability of coronal mass ejections to cause geoeffectiveness. To that end, we have investigated total 571 cases of higher-speed (> 1000 km/s) coronal mass ejection events observed during the years 1996-2012. On the basis of angular width (W) of observance, events of coronal mass ejection were further classified as front-side or halo coronal mass ejections (W = 360°); back-side halo coronal mass ejections (W = 360°); partial halo (120°< W < 360°) and non-halo (W < 120°). From further analysis, we found that front halo coronal mass ejections were much faster and more geoeffective in comparison of partial halo and non-halo coronal mass ejections. We also inferred that the front-sided halo coronal mass ejections were 67.1% geoeffective while geoeffectiveness of partial halo coronal mass ejections and non-halo coronal mass ejections were found to be 44.2% and 56.6% respectively. During the same period of observation, 43% of back-sided CMEs showed geoeffectiveness. We have also investigated some events of coronal mass ejections having speed > 2500 km/s as a case study. We have concluded that mere speed of coronal mass ejection and their association with solar flares or solar activity were not mere criterion for producing geoeffectiveness but angular width of coronal mass ejections and their originating position also played a key role.

Optimizing pattern recognition-based control for partial-hand prosthesis application.

PubMed

Earley, Eric J; Adewuyi, Adenike A; Hargrove, Levi J

2014-01-01

Partial-hand amputees often retain good residual wrist motion, which is essential for functional activities involving use of the hand. Thus, a crucial design criterion for a myoelectric, partial-hand prosthesis control scheme is that it allows the user to retain residual wrist motion. Pattern recognition (PR) of electromyographic (EMG) signals is a well-studied method of controlling myoelectric prostheses. However, wrist motion degrades a PR system's ability to correctly predict hand-grasp patterns. We studied the effects of (1) window length and number of hand-grasps, (2) static and dynamic wrist motion, and (3) EMG muscle source on the ability of a PR-based control scheme to classify functional hand-grasp patterns. Our results show that training PR classifiers with both extrinsic and intrinsic muscle EMG yields a lower error rate than training with either group by itself (p<0.001); and that training in only variable wrist positions, with only dynamic wrist movements, or with both variable wrist positions and movements results in lower error rates than training in only the neutral wrist position (p<0.001). Finally, our results show that both an increase in window length and a decrease in the number of grasps available to the classifier significantly decrease classification error (p<0.001). These results remained consistent whether the classifier selected or maintained a hand-grasp.

Cox Regression Models with Functional Covariates for Survival Data.

PubMed

Gellar, Jonathan E; Colantuoni, Elizabeth; Needham, Dale M; Crainiceanu, Ciprian M

2015-06-01

We extend the Cox proportional hazards model to cases when the exposure is a densely sampled functional process, measured at baseline. The fundamental idea is to combine penalized signal regression with methods developed for mixed effects proportional hazards models. The model is fit by maximizing the penalized partial likelihood, with smoothing parameters estimated by a likelihood-based criterion such as AIC or EPIC. The model may be extended to allow for multiple functional predictors, time varying coefficients, and missing or unequally-spaced data. Methods were inspired by and applied to a study of the association between time to death after hospital discharge and daily measures of disease severity collected in the intensive care unit, among survivors of acute respiratory distress syndrome.

Noise Considerations for V/STOL Transports

NASA Technical Reports Server (NTRS)

Kenyon, George C.

1968-01-01

Noise consideration may well be as important a factor in future aircraft concept selection as such economic factors as operating cost and profitability. The impact of noise on some of the design and operational aspects of future V/STOL transports is examined in detail, including consideration of configuration, attitude-control system, lift system, and terminal flight pattern. Extended vertical rise of VTOL aircraft as a method of limiting the intense noise exposure to the terminal area is shown to be only partially effective as well as costly. Comparisons are made of noise contours for conceptual V/STOL transports for several PNdB criteria. The variation in extent of affected area with configuration and criterion emphasizes the importance of establishing an "acceptable" noise level for "city-center" operation.

The Distributed Criterion Design

ERIC Educational Resources Information Center

McDougall, Dennis

2006-01-01

This article describes and illustrates a novel form of the changing criterion design called the distributed criterion design, which represents perhaps the first advance in the changing criterion design in four decades. The distributed criterion design incorporates elements of the multiple baseline and A-B-A-B designs and is well suited to applied…

An Elasto-Plastic Damage Model for Rocks Based on a New Nonlinear Strength Criterion

NASA Astrophysics Data System (ADS)

Huang, Jingqi; Zhao, Mi; Du, Xiuli; Dai, Feng; Ma, Chao; Liu, Jingbo

2018-05-01

The strength and deformation characteristics of rocks are the most important mechanical properties for rock engineering constructions. A new nonlinear strength criterion is developed for rocks by combining the Hoek-Brown (HB) criterion and the nonlinear unified strength criterion (NUSC). The proposed criterion takes account of the intermediate principal stress effect against HB criterion, as well as being nonlinear in the meridian plane against NUSC. Only three parameters are required to be determined by experiments, including the two HB parameters σ c and m i . The failure surface of the proposed criterion is continuous, smooth and convex. The proposed criterion fits the true triaxial test data well and performs better than the other three existing criteria. Then, by introducing the Geological Strength Index, the proposed criterion is extended to rock masses and predicts the test data well. Finally, based on the proposed criterion, a triaxial elasto-plastic damage model for intact rock is developed. The plastic part is based on the effective stress, whose yield function is developed by the proposed criterion. For the damage part, the evolution function is assumed to have an exponential form. The performance of the constitutive model shows good agreement with the results of experimental tests.

Analysis of augmented aircraft flying qualities through application of the Neal-Smith criterion

NASA Technical Reports Server (NTRS)

Bailey, R. E.; Smith, R. E.

1981-01-01

The Neal-Smith criterion is examined for possible applications in the evaluation of augmented fighter aircraft flying qualities. Longitudinal and lateral flying qualities are addressed. Based on the application of several longitudinal flying qualities data bases, revisions are proposed to the original criterion. Examples are given which show the revised criterion to be a good discriminator of pitch flying qualities. Initial results of lateral flying qualities evaluation through application of the Neal-Smith criterion are poor. Lateral aircraft configurations whose flying qualities are degraded by roll ratcheting effects map into the Level 1 region of the criterion. A third dimension of the criterion for flying qualities specification is evident. Additional criteria are proposed to incorporate this dimension into the criterion structure for flying qualities analysis.

Perspectives on Quality Assurance in Higher Education in Norway

ERIC Educational Resources Information Center

Lycke, Kirsten Hofgaard

2004-01-01

Quality assurance is well known internationally but the notion is relatively new in Norway. To understand some of the issues and dilemmas that emerge in the Norwegian reception of quality assurance in higher education, this article traces how quality assurance is gaining its form and how international trends are understood, transposed and adopted…

Instep island flaps.

PubMed

Reading, G

1984-12-01

The instep island flap is safe and useful. It is based on branches of the posterior tibial artery and can be a musculocutaneous or a direct fasciocutaneous island flap. Sensory branches of the digital nerves may be transposed with the flap. There is a wide arc of transposition and the flap has survived even in very difficult circumstances.

The Tgm9-induced indexed insertional mutant collection to conduct community-based reverse genetics studies in soybean

USDA-ARS?s Scientific Manuscript database

Until now, functional analyses of soybean genes have been very arduous because of the lack of a rapid transformation procedure. Recently identified the active endogenous type II transposable element, Tgm9, excises from insertion sites and restores wild-type phenotypes. Thus, this element provides a ...

Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification

USDA-ARS?s Scientific Manuscript database

Verticillium dahliae (Vd) and Verticillium albo-atrum (Va) are cosmopolitan soil fungi causing very disruptive vascular diseases on a wide range of crop plants. To date, no sexual stage has been identified in either microorganism suggesting that somatic mutation is a major force in generating geneti...

Shock Compression of Metal Crystals: A Comparison of Eulerian and Lagrangian Elastic-Plastic Theories

DTIC Science & Technology

2014-11-01

incorporate the right Cauchy–Green strain tensor E, a function of the ( elas - tic) deformation gradient and its transpose. Such theories have been used...been compared for several anisotropic metallic single crystals (Al, Cu and Mg), with elas - tic constants of up to order four included. Differences

A Model Plant for a Biology Curriculum: Spider Flower ("Cleome Hasslerana L.")

ERIC Educational Resources Information Center

Marquard, Robert D.; Steinback, Rebecca

2009-01-01

Major advances in fundamental science are developed using model systems. Classic examples of model systems include Mendel's work with the common garden pea ("Pisium sativa"), classic inheritance work by Morgan with the fruit fly ("Drosophila"), developmental studies with the nematode ("C. elegans"), and transposable elements in maize ("Zea…

Design and Simulation of a Nano-Satellite Attitude Determination System

DTIC Science & Technology

2009-12-01

SimTime); 119 2. Attitude Matrix %# eml function att = ATT( quat ) %% Making Attitude Matrix att = transpose(XI(quat)) * PSI(quat); return...3. XI %# eml function xi = XI( quat ) %% Making Xi Matrix xi = [ quat(4...eye(3) + SKEW(quat(1:3,1)) ; - quat(1:3,1)’ ]; return %---------------------------------------------------------------------- 4. PSI %# eml

Evolutionary conservation, diversity and specificity of LTR retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison

USDA-ARS?s Scientific Manuscript database

The availability of complete or nearly complete genome sequences from several plant species permits detailed discovery and cross-species comparison of transposable elements (TEs) at the whole genome level. We initially investigated 510 LTR-retrotransposon (LTR-RT) families that are comprised of 32,...

Substituted-Letter and Transposed-Letter Effects in a Masked Priming Paradigm with French Developing Readers and Dyslexics

ERIC Educational Resources Information Center

Lete, Bernard; Fayol, Michel

2013-01-01

The aim of the study was to undertake a behavioral investigation of the development of automatic orthographic processing during reading acquisition in French. Following Castles and colleagues' 2007 study ("Journal of Experimental Child Psychology, 97," 165-182) and their lexical tuning hypothesis framework, substituted-letter and…

The Immersive LearningScape--Knowledge Transposed: Learning Globally, Applying Locally

ERIC Educational Resources Information Center

Jimenez-Eliaeson, Tomas

2011-01-01

In an increasingly global world, where events in one corner of the world simultaneously affect other remote areas of the planet, global competition is becoming a continuously evolving phenomenon. Competition is also increasingly becoming an individual endeavor. Individual's own knowledge and skills will be the differentiators in a global economy.…

The landscape of transposable elements in the finished genome of the fungal wheat pathogen Mycosphaerella graminicola

USDA-ARS?s Scientific Manuscript database

Repetitive sequence analysis has become an integral part of genome sequencing projects in addition to gene identification and annotation. Identification of repeats is important not only because it improves gene prediction, but also because of the role that repetitive sequences play in determining th...

Scaling GDL for Multi-cores to Process Planck HFI Beams Monte Carlo on HPC

NASA Astrophysics Data System (ADS)

Coulais, A.; Schellens, M.; Duvert, G.; Park, J.; Arabas, S.; Erard, S.; Roudier, G.; Hivon, E.; Mottet, S.; Laurent, B.; Pinter, M.; Kasradze, N.; Ayad, M.

2014-05-01

After reviewing the majors progress done in GDL -now in 0.9.4- on performance and plotting capabilities since ADASS XXI paper (Coulais et al. 2012), we detail how a large code for Planck HFI beams Monte Carlo was successfully transposed from IDL to GDL on HPC.

ERP Evidence of Hemispheric Independence in Visual Word Recognition

ERIC Educational Resources Information Center

Nemrodov, Dan; Harpaz, Yuval; Javitt, Daniel C.; Lavidor, Michal

2011-01-01

This study examined the capability of the left hemisphere (LH) and the right hemisphere (RH) to perform a visual recognition task independently as formulated by the Direct Access Model (Fernandino, Iacoboni, & Zaidel, 2007). Healthy native Hebrew speakers were asked to categorize nouns and non-words (created from nouns by transposing two middle…

The correlation between thermal comfort in buildings and fashion products.

PubMed

Giesel, Aline; de Mello Souza, Patrícia

2012-01-01

This article is about thermal comfort in the wearable product. The research correlates fashion and architecture, in so far as it elects the brise soleil - an architectural element capable of regulating temperature and ventilation inside buildings - as a study referential, in trying to transpose and adapt its mechanisms to the wearable apparel.

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

Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon.

PubMed

Mitra, Rupak; Li, Xianghong; Kapusta, Aurélie; Mayhew, David; Mitra, Robi D; Feschotte, Cédric; Craig, Nancy L

2013-01-02

A revelation of the genomic age has been the contributions of the mobile DNA segments called transposable elements to chromosome structure, function, and evolution in virtually all organisms. Substantial fractions of vertebrate genomes derive from transposable elements, being dominated by retroelements that move via RNA intermediates. Although many of these elements have been inactivated by mutation, several active retroelements remain. Vertebrate genomes also contain substantial quantities and a high diversity of cut-and-paste DNA transposons, but no active representative of this class has been identified in mammals. Here we show that a cut-and-paste element called piggyBat, which has recently invaded the genome of the little brown bat (Myotis lucifugus) and is a member of the piggyBac superfamily, is active in its native form in transposition assays in bat and human cultured cells, as well as in the yeast Saccharomyces cerevisiae. Our study suggests that some DNA transposons are still actively shaping some mammalian genomes and reveals an unprecedented opportunity to study the mechanism, regulation, and genomic impact of cut-and-paste transposition in a natural mammalian host.

Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor.

PubMed

Fu, Yu; Kawabe, Akira; Etcheverry, Mathilde; Ito, Tasuku; Toyoda, Atsushi; Fujiyama, Asao; Colot, Vincent; Tarutani, Yoshiaki; Kakutani, Tetsuji

2013-08-28

Transposable elements (TEs) have a major impact on genome evolution, but they are potentially deleterious, and most of them are silenced by epigenetic mechanisms, such as DNA methylation. Here, we report the characterization of a TE encoding an activity to counteract epigenetic silencing by the host. In Arabidopsis thaliana, we identified a mobile copy of the Mutator-like element (MULE) with degenerated terminal inverted repeats (TIRs). This TE, named Hiun (Hi), is silent in wild-type plants, but it transposes when DNA methylation is abolished. When a Hi transgene was introduced into the wild-type background, it induced excision of the endogenous Hi copy, suggesting that Hi is the autonomously mobile copy. In addition, the transgene induced loss of DNA methylation and transcriptional activation of the endogenous Hi. Most importantly, the trans-activation of Hi depends on a Hi-encoded protein different from the conserved transposase. Proteins related to this anti-silencing factor, which we named VANC, are widespread in the non-TIR MULEs and may have contributed to the recent success of these TEs in natural Arabidopsis populations.

DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis.

PubMed

Dinh, Thanh Theresa; Gao, Lei; Liu, Xigang; Li, Dongming; Li, Shengben; Zhao, Yuanyuan; O'Leary, Michael; Le, Brandon; Schmitz, Robert J; Manavella, Pablo A; Manavella, Pablo; Li, Shaofang; Weigel, Detlef; Pontes, Olga; Ecker, Joseph R; Chen, Xuemei

2014-07-01

RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) are related transcriptional silencing mechanisms that target transposable elements (TEs) and repeats to maintain genome stability in plants. RdDM is mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α) was able to de-repress LUCL by reducing its DNA methylation and H3K9me2 levels. Further studies with Arabidopsis top1α mutants showed that TOP1α silences endogenous RdDM loci by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at TEs and repeats. This study assigned a new role in epigenetic silencing to an enzyme that affects DNA topology.

The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine?

PubMed

Arensburger, Peter; Piégu, Benoît; Bigot, Yves

2016-01-01

Transposable element (TE) science has been significantly influenced by the pioneering ideas of David Finnegan near the end of the last century, as well as by the classification systems that were subsequently developed. Today, whole genome TE annotation is mostly done using tools that were developed to aid gene annotation rather than to specifically study TEs. We argue that further progress in the TE field is impeded both by current TE classification schemes and by a failure to recognize that TE biology is fundamentally different from that of multicellular organisms. Novel genome wide TE annotation methods are helping to redefine our understanding of TE sequence origins and evolution. We briefly discuss some of these new methods as well as ideas for possible alternative classification schemes. Our hope is to encourage the formation of a society to organize a larger debate on these questions and to promote the adoption of standards for annotation and an improved TE classification.

ARGONAUTE9-dependent silencing of transposable elements in pericentromeric regions of Arabidopsis.

PubMed

Durán-Figueroa, Noé; Vielle-Calzada, Jean-Philippe

2010-11-01

Recent evidence indicates that the establishment of the haploid phase of the plant life cycle requires epigenetic mechanisms that control reproductive cell fate. We previously showed that in Arabidopsis thaliana (Arabidopsis) mutations in ARGONAUTE9 (AGO9) result in defective cell specification during megasporogenesis. AGO9 preferentially interacts with 24 nucleotide (nt) small RNAs (sRNAs) derived from transposable elements (TEs), and its sporophytic activity is required to silence TEs in the female gametophyte. Here we show that AGO9 can bind in vitro to 24 nt sRNAs corresponding to Athila retrotransposons expressed in the ovule prior to pollination. We also show that AGO9 is necessary to inactivate a significant proportion of long terminal repeat retrotransposons (LTRs) in the ovule, and that its predominant TE targets are located in the pericentromeric regions of all 5 chromosomes, suggesting a link between the AGO9-dependent sRNA pathway and heterochromatin formation. Our extended results point towards the existence of a tissue-specific mechanism of sRNA-dependent TE silencing in the ovule.

Horizontal acquisition of transposable elements and viral sequences: patterns and consequences.

PubMed

Gilbert, Clément; Feschotte, Cédric

2018-04-01

It is becoming clear that most eukaryotic transposable elements (TEs) owe their evolutionary success in part to horizontal transfer events, which enable them to invade new species. Recent large-scale studies are beginning to unravel the mechanisms and ecological factors underlying this mode of transmission. Viruses are increasingly recognized as vectors in the process but also as a direct source of genetic material horizontally acquired by eukaryotic organisms. Because TEs and endogenous viruses are major catalysts of variation and innovation in genomes, we argue that horizontal inheritance has had a more profound impact in eukaryotic evolution than is commonly appreciated. To support this proposal, we compile a list of examples, including some previously unrecognized, whereby new host functions and phenotypes can be directly attributed to horizontally acquired TE or viral sequences. We predict that the number of examples will rapidly grow in the future as the prevalence of horizontal transfer in the life cycle of TEs becomes even more apparent, firmly establishing this form of non-Mendelian inheritance as a consequential facet of eukaryotic evolution. Copyright © 2018 Elsevier Ltd. All rights reserved.

Inferring transposons activity chronology by TRANScendence - TEs database and de-novo mining tool.

PubMed

Startek, Michał Piotr; Nogły, Jakub; Gromadka, Agnieszka; Grzebelus, Dariusz; Gambin, Anna

2017-10-16

The constant progress in sequencing technology leads to ever increasing amounts of genomic data. In the light of current evidence transposable elements (TEs for short) are becoming useful tools for learning about the evolution of host genome. Therefore the software for genome-wide detection and analysis of TEs is of great interest. Here we describe the computational tool for mining, classifying and storing TEs from newly sequenced genomes. This is an online, web-based, user-friendly service, enabling users to upload their own genomic data, and perform de-novo searches for TEs. The detected TEs are automatically analyzed, compared to reference databases, annotated, clustered into families, and stored in TEs repository. Also, the genome-wide nesting structure of found elements are detected and analyzed by new method for inferring evolutionary history of TEs. We illustrate the functionality of our tool by performing a full-scale analyses of TE landscape in Medicago truncatula genome. TRANScendence is an effective tool for the de-novo annotation and classification of transposable elements in newly-acquired genomes. Its streamlined interface makes it well-suited for evolutionary studies.

Prediction of Francis Turbine Prototype Part Load Pressure and Output Power Fluctuations with Hydroelectric Model

NASA Astrophysics Data System (ADS)

Alligné, S.; Nicolet, C.; Béguin, A.; Landry, C.; Gomes, J.; Avellan, F.

2017-04-01

The prediction of pressure and output power fluctuations amplitudes on Francis turbine prototype is a challenge for hydro-equipment industry since it is subjected to guarantees to ensure smooth and reliable operation of the hydro units. The European FP7 research project Hyperbole aims to setup a methodology to transpose the pressure fluctuations induced by the cavitation vortex rope from the reduced scale model to the prototype generating units. A Francis turbine unit of 444MW with a specific speed value of ν = 0.29, is considered as case study. A SIMSEN model of the power station including electrical system, controllers, rotating train and hydraulic system with transposed draft tube excitation sources is setup. Based on this model, a frequency analysis of the hydroelectric system is performed for all technologies to analyse potential interactions between hydraulic excitation sources and electrical components. Three technologies have been compared: the classical fixed speed configuration with Synchronous Machine (SM) and the two variable speed technologies which are Doubly Fed Induction Machine (DFIM) and Full Size Frequency Converter (FSFC).

SimulaTE: simulating complex landscapes of transposable elements of populations.

PubMed

Kofler, Robert

2018-04-15

Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results. To address this problem, we developed SimulaTE a tool that generates TE landscapes for populations using a newly developed domain specific language (DSL). The simple syntax of our DSL allows for easily building even complex TE landscapes that have, for example, nested, truncated and highly diverged TE insertions. Reads may be simulated for the populations using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). The comparison between the expected (i.e. simulated) and the observed results will guide researchers in finding the most suitable approach for a particular research question. SimulaTE is implemented in Python and available at https://sourceforge.net/projects/simulates/. Manual https://sourceforge.net/p/simulates/wiki/Home/#manual; Test data and tutorials https://sourceforge.net/p/simulates/wiki/Home/#walkthrough; Validation https://sourceforge.net/p/simulates/wiki/Home/#validation. robert.kofler@vetmeduni.ac.at.

Massive contribution of transposable elements to mammalian regulatory sequences.

PubMed

Rayan, Nirmala Arul; Del Rosario, Ricardo C H; Prabhakar, Shyam

2016-09-01

Barbara McClintock discovered the existence of transposable elements (TEs) in the late 1940s and initially proposed that they contributed to the gene regulatory program of higher organisms. This controversial idea gained acceptance only much later in the 1990s, when the first examples of TE-derived promoter sequences were uncovered. It is now known that half of the human genome is recognizably derived from TEs. It is thus important to understand the scope and nature of their contribution to gene regulation. Here, we provide a timeline of major discoveries in this area and discuss how transposons have revolutionized our understanding of mammalian genomes, with a special emphasis on the massive contribution of TEs to primate evolution. Our analysis of primate-specific functional elements supports a simple model for the rate at which new functional elements arise in unique and TE-derived DNA. Finally, we discuss some of the challenges and unresolved questions in the field, which need to be addressed in order to fully characterize the impact of TEs on gene regulation, evolution and disease processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improved maize reference genome with single-molecule technologies.

PubMed

Jiao, Yinping; Peluso, Paul; Shi, Jinghua; Liang, Tiffany; Stitzer, Michelle C; Wang, Bo; Campbell, Michael S; Stein, Joshua C; Wei, Xuehong; Chin, Chen-Shan; Guill, Katherine; Regulski, Michael; Kumari, Sunita; Olson, Andrew; Gent, Jonathan; Schneider, Kevin L; Wolfgruber, Thomas K; May, Michael R; Springer, Nathan M; Antoniou, Eric; McCombie, W Richard; Presting, Gernot G; McMullen, Michael; Ross-Ibarra, Jeffrey; Dawe, R Kelly; Hastie, Alex; Rank, David R; Ware, Doreen

2017-06-22

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.

piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells

PubMed Central

Pezic, Dubravka; Manakov, Sergei A.; Sachidanandam, Ravi; Aravin, Alexei A.

2014-01-01

Transposable elements (TEs) occupy a large fraction of metazoan genomes and pose a constant threat to genomic integrity. This threat is particularly critical in germ cells, as changes in the genome that are induced by TEs will be transmitted to the next generation. Small noncoding piwi-interacting RNAs (piRNAs) recognize and silence a diverse set of TEs in germ cells. In mice, piRNA-guided transposon repression correlates with establishment of CpG DNA methylation on their sequences, yet the mechanism and the spectrum of genomic targets of piRNA silencing are unknown. Here we show that in addition to DNA methylation, the piRNA pathway is required to maintain a high level of the repressive H3K9me3 histone modification on long interspersed nuclear elements (LINEs) in germ cells. piRNA-dependent chromatin repression targets exclusively full-length elements of actively transposing LINE families, demonstrating the remarkable ability of the piRNA pathway to recognize active elements among the large number of genomic transposon fragments. PMID:24939875

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

Lyakh, Dmitry I.

An efficient parallel tensor transpose algorithm is suggested for shared-memory computing units, namely, multicore CPU, Intel Xeon Phi, and NVidia GPU. The algorithm operates on dense tensors (multidimensional arrays) and is based on the optimization of cache utilization on x86 CPU and the use of shared memory on NVidia GPU. From the applied side, the ultimate goal is to minimize the overhead encountered in the transformation of tensor contractions into matrix multiplications in computer implementations of advanced methods of quantum many-body theory (e.g., in electronic structure theory and nuclear physics). A particular accent is made on higher-dimensional tensors that typicallymore » appear in the so-called multireference correlated methods of electronic structure theory. Depending on tensor dimensionality, the presented optimized algorithms can achieve an order of magnitude speedup on x86 CPUs and 2-3 times speedup on NVidia Tesla K20X GPU with respect to the na ve scattering algorithm (no memory access optimization). Furthermore, the tensor transpose routines developed in this work have been incorporated into a general-purpose tensor algebra library (TAL-SH).« less

An On-Chip Learning Neuromorphic Autoencoder With Current-Mode Transposable Memory Read and Virtual Lookup Table.

PubMed

Cho, Hwasuk; Son, Hyunwoo; Seong, Kihwan; Kim, Byungsub; Park, Hong-June; Sim, Jae-Yoon

2018-02-01

This paper presents an IC implementation of on-chip learning neuromorphic autoencoder unit in a form of rate-based spiking neural network. With a current-mode signaling scheme embedded in a 500 × 500 6b SRAM-based memory, the proposed architecture achieves simultaneous processing of multiplications and accumulations. In addition, a transposable memory read for both forward and backward propagations and a virtual lookup table are also proposed to perform an unsupervised learning of restricted Boltzmann machine. The IC is fabricated using 28-nm CMOS process and is verified in a three-layer network of encoder-decoder pair for training and recovery of images with two-dimensional pixels. With a dataset of 50 digits, the IC shows a normalized root mean square error of 0.078. Measured energy efficiencies are 4.46 pJ per synaptic operation for inference and 19.26 pJ per synaptic weight update for learning, respectively. The learning performance is also estimated by simulations if the proposed hardware architecture is extended to apply to a batch training of 60 000 MNIST datasets.

Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.)

PubMed Central

Benjak, Andrej; Boué, Stéphanie; Forneck, Astrid

2009-01-01

Miniature inverted-repeat transposable elements (MITEs) are a particular type of defective class II transposons present in genomes as highly homogeneous populations of small elements. Their high copy number and close association to genes make their potential impact on gene evolution particularly relevant. Here, we present a detailed analysis of the MITE families directly related to grapevine “cut-and-paste” transposons. Our results show that grapevine MITEs have transduplicated and amplified genomic sequences, including gene sequences and fragments of other mobile elements. Our results also show that although some of the MITE families were already present in the ancestor of the European and American Vitis wild species, they have been amplified and have been actively transposing accompanying grapevine domestication and breeding. We show that MITEs are abundant in grapevine and some of them are frequently inserted within the untranslated regions of grapevine genes. MITE insertions are highly polymorphic among grapevine cultivars, which frequently generate transcript variability. The data presented here show that MITEs have greatly contributed to the grapevine genetic diversity which has been used for grapevine domestication and breeding. PMID:20333179

The Ecological Genomics of Fungi: Repeated Elements in Filamentous Fungi with a Focus on Wood-Decay Fungi

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

Murat, Claude; Payen, Thibaut; Petitpierre, Denis

2013-01-01

In the last decade, the genome of several dozen filamentous fungi have been sequenced. Interestingly, vast diversity in genome size was observed (Fig. 2.1) with 14-fold differences between the 9 Mb of the human pathogenic dandruff fungus (Malassezia globosa; Xu, Saunders, et al., 2007) and the 125 Mb of the ectomycorrhizal black truffle of P rigord (Tuber melanosporum; Martin, Kohler, et al., 2010). Recently, Raffaele and Kamoun (2012) highlighted that the genomes of several lineages of filamentous plant pathogens have been shaped by repeat-driven expansion. Indeed, repeated elements are ubiquitous in all prokaryote and eukaryote genomes; however, their frequencies canmore » vary from just a minor percentage of the genome to more that 60 percent of the genome. Repeated elements can be classified in two major types: satellites DNA and transposable elements. In this chapter, the different types of repeated elements and how these elements can impact genome and gene repertoire will be described. Also, an intriguing link between the transposable elements richness and diversity and the ecological niche will be highlighted.« less

Reduced transposed flicker noise in microwave oscillators using gaas-based feedforward amplifiers.

PubMed

Everard, Jeremy K A; Broomfield, Carl D

2007-06-01

Transposed flicker noise reduction and removal is demonstrated in 7.6 GHz microwave oscillators for offsets greater than 10 kHz. This is achieved by using a GaAs-based feedforward power amplifier as the oscillation-sustaining stage and incorporating a limiter and resonator elsewhere in the loop. 20 dB noise suppression is demonstrated at 12.5 kHz offset when the error correcting amplifier is switched on. Three oscillator pairs have been built. A transmission line feedback oscillator with a Qo of 180 and two sapphire-based, dielectric resonator oscillators (DROs) with a Qo of 44,500. The difference between the two DROs is a change in the limiter threshold power level of 10 dB. The phase noise rolls-off at (1/f)(2) for offsets greater than 10 kHz for the transmission line oscillator and is set by the thermal noise to within 0-1 dB of the theoretical minimum. The noise performance of the DROs is within 6-12 dB of the theory. Possible reasons for this discrepancy are presented.

What makes up plant genomes: The vanishing line between transposable elements and genes.

PubMed

Zhao, Dongyan; Ferguson, Ann A; Jiang, Ning

2016-02-01

The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes. Copyright © 2015 Elsevier B.V. All rights reserved.

The Role of Transposable Elements in Speciation

PubMed Central

Serrato-Capuchina, Antonio; Matute, Daniel R.

2018-01-01

Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species. PMID:29762547

Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs

PubMed Central

Zhao, Siming; Luo, Kaixuan; Pavlovic, Bryan J; Karimi, Mohammad M; Stephens, Matthew

2018-01-01

Transposable elements (TEs) comprise almost half of primate genomes and their aberrant regulation can result in deleterious effects. In pluripotent stem cells, rapidly evolving KRAB-ZNF genes target TEs for silencing by H3K9me3. To investigate the evolution of TE silencing, we performed H3K9me3 ChIP-seq experiments in induced pluripotent stem cells from 10 human and 7 chimpanzee individuals. We identified four million orthologous TEs and found the SVA and ERV families to be marked most frequently by H3K9me3. We found little evidence of inter-species differences in TE silencing, with as many as 82% of putatively silenced TEs marked at similar levels in humans and chimpanzees. TEs that are preferentially silenced in one species are a similar age to those silenced in both species and are not more likely to be associated with expression divergence of nearby orthologous genes. Our data suggest limited species-specificity of TE silencing across 6 million years of primate evolution. PMID:29648536

Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice.

PubMed

Song, Xianwei; Cao, Xiaofeng

2017-04-01

Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice (Oryza sativa) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

A cis-regulatory sequence driving metabolic insecticide resistance in mosquitoes: functional characterisation and signatures of selection.

PubMed

Wilding, Craig S; Smith, Ian; Lynd, Amy; Yawson, Alexander Egyir; Weetman, David; Paine, Mark J I; Donnelly, Martin J

2012-09-01

Although cytochrome P450 (CYP450) enzymes are frequently up-regulated in mosquitoes resistant to insecticides, no regulatory motifs driving these expression differences with relevance to wild populations have been identified. Transposable elements (TEs) are often enriched upstream of those CYP450s involved in insecticide resistance, leading to the assumption that they contribute regulatory motifs that directly underlie the resistance phenotype. A partial CuRE1 (Culex Repetitive Element 1) transposable element is found directly upstream of CYP9M10, a cytochrome P450 implicated previously in larval resistance to permethrin in the ISOP450 strain of Culex quinquefasciatus, but is absent from the equivalent genomic region of a susceptible strain. Via expression of CYP9M10 in Escherichia coli we have now demonstrated time- and NADPH-dependant permethrin metabolism, prerequisites for confirmation of a role in metabolic resistance, and through qPCR shown that CYP9M10 is >20-fold over-expressed in ISOP450 compared to a susceptible strain. In a fluorescent reporter assay the region upstream of CYP9M10 from ISOP450 drove 10× expression compared to the equivalent region (lacking CuRE1) from the susceptible strain. Close correspondence with the gene expression fold-change implicates the upstream region including CuRE1 as a cis-regulatory element involved in resistance. Only a single CuRE1 bearing allele, identical to the CuRE1 bearing allele in the resistant strain, is found throughout Sub-Saharan Africa, in contrast to the diversity encountered in non-CuRE1 alleles. This suggests a single origin and subsequent spread due to selective advantage. CuRE1 is detectable using a simple diagnostic. When applied to C. quinquefasciatus larvae from Ghana we have demonstrated a significant association with permethrin resistance in multiple field sites (mean Odds Ratio = 3.86) suggesting this marker has relevance to natural populations of vector mosquitoes. However, when CuRE1 was excised from the allele used in the reporter assay through fusion PCR, expression was unaffected, indicating that the TE has no direct role in resistance and hence that CuRE1 is acting only as a marker of an as yet unidentified regulatory motif in the association analysis. This suggests that a re-evaluation of the assumption that TEs contribute regulatory motifs involved in gene expression may be necessary. Copyright © 2012 Elsevier Ltd. All rights reserved.

Time to Criterion: An Experimental Study.

ERIC Educational Resources Information Center

Anderson, Lorin W.

The purpose of the study was to investigate the magnitude of individual differences in time-to-criterion and the stability of these differences. Time-to-criterion was defined in two ways: the amount of elapsed time required to attain the criterion level and the amount of on-task time required to attain the criterion level. Ninety students were…

Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements.

PubMed

Guérin, Frédéric; Arnaiz, Olivier; Boggetto, Nicole; Denby Wilkes, Cyril; Meyer, Eric; Sperling, Linda; Duharcourt, Sandra

2017-04-26

DNA elimination is developmentally programmed in a wide variety of eukaryotes, including unicellular ciliates, and leads to the generation of distinct germline and somatic genomes. The ciliate Paramecium tetraurelia harbors two types of nuclei with different functions and genome structures. The transcriptionally inactive micronucleus contains the complete germline genome, while the somatic macronucleus contains a reduced genome streamlined for gene expression. During development of the somatic macronucleus, the germline genome undergoes massive and reproducible DNA elimination events. Availability of both the somatic and germline genomes is essential to examine the genome changes that occur during programmed DNA elimination and ultimately decipher the mechanisms underlying the specific removal of germline-limited sequences. We developed a novel experimental approach that uses flow cell imaging and flow cytometry to sort subpopulations of nuclei to high purity. We sorted vegetative micronuclei and macronuclei during development of P. tetraurelia. We validated the method by flow cell imaging and by high throughput DNA sequencing. Our work establishes the proof of principle that developing somatic macronuclei can be sorted from a complex biological sample to high purity based on their size, shape and DNA content. This method enabled us to sequence, for the first time, the germline DNA from pure micronuclei and to identify novel transposable elements. Sequencing the germline DNA confirms that the Pgm domesticated transposase is required for the excision of all ~45,000 Internal Eliminated Sequences. Comparison of the germline DNA and unrearranged DNA obtained from PGM-silenced cells reveals that the latter does not provide a faithful representation of the germline genome. We developed a flow cytometry-based method to purify P. tetraurelia nuclei to high purity and provided quality control with flow cell imaging and high throughput DNA sequencing. We identified 61 germline transposable elements including the first Paramecium retrotransposons. This approach paves the way to sequence the germline genomes of P. aurelia sibling species for future comparative genomic studies.

Paleotemperature reconstruction from mammalian phosphate δ18O records - an alternative view on data processing

NASA Astrophysics Data System (ADS)

Skrzypek, Grzegorz; Sadler, Rohan; Wiśniewski, Andrzej

2017-04-01

The stable oxygen isotope composition of phosphates (δ18O) extracted from mammalian bone and teeth material is commonly used as a proxy for paleotemperature. Historically, several different analytical and statistical procedures for determining air paleotemperatures from the measured δ18O of phosphates have been applied. This inconsistency in both stable isotope data processing and the application of statistical procedures has led to large and unwanted differences between calculated results. This study presents the uncertainty associated with two of the most commonly used regression methods: least squares inverted fit and transposed fit. We assessed the performance of these methods by designing and applying calculation experiments to multiple real-life data sets, calculating in reverse temperatures, and comparing them with true recorded values. Our calculations clearly show that the mean absolute errors are always substantially higher for the inverted fit (a causal model), with the transposed fit (a predictive model) returning mean values closer to the measured values (Skrzypek et al. 2015). The predictive models always performed better than causal models, with 12-65% lower mean absolute errors. Moreover, the least-squares regression (LSM) model is more appropriate than Reduced Major Axis (RMA) regression for calculating the environmental water stable oxygen isotope composition from phosphate signatures, as well as for calculating air temperature from the δ18O value of environmental water. The transposed fit introduces a lower overall error than the inverted fit for both the δ18O of environmental water and Tair calculations; therefore, the predictive models are more statistically efficient than the causal models in this instance. The direct comparison of paleotemperature results from different laboratories and studies may only be achieved if a single method of calculation is applied. Reference Skrzypek G., Sadler R., Wiśniewski A., 2016. Reassessment of recommendations for processing mammal phosphate δ18O data for paleotemperature reconstruction. Palaeogeography, Palaeoclimatology, Palaeoecology 446, 162-167.

Characterization of three active transposable elements recently inserted in three independent DFR-A alleles and one high-copy DNA transposon isolated from the Pink allele of the ANS gene in onion (Allium cepa L.).

PubMed

Kim, Sunggil; Park, Jee Young; Yang, Tae-Jin

2015-06-01

Intact retrotransposon and DNA transposons inserted in a single gene were characterized in onions (Allium cepa) and their transcription and copy numbers were estimated in this study. While analyzing diverse onion germplasm, large insertions in the DFR-A gene encoding dihydroflavonol 4-reductase (DFR) involved in the anthocyanin biosynthesis pathway were found in two accessions. A 5,070-bp long terminal repeat (LTR) retrotransposon inserted in the active DFR-A (R4) allele was identified from one of the large insertions and designated AcCOPIA1. An intact ORF encoded typical domains of copia-like LTR retrotransposons. However, AcCOPIA1 contained atypical 'TG' and 'TA' dinucleotides at the ends of the LTRs. A 4,615-bp DNA transposon was identified in the other large insertion. This DNA transposon, designated AcCACTA1, contained an ORF coding for a transposase showing homology with the CACTA superfamily transposable elements (TEs). Another 5,073-bp DNA transposon was identified from the DFR-A (TRN) allele. This DNA transposon, designated AchAT1, belonged to the hAT superfamily with short 4-bp terminal inverted repeats (TIRs). Finally, a 6,258-bp non-autonomous DNA transposon, designated AcPINK, was identified in the ANS-p allele encoding anthocyanidin synthase, the next downstream enzyme to DFR in the anthocyanin biosynthesis pathway. AcPINK also possessed very short 3-bp TIRs. Active transcription of AcCOPIA1, AcCACTA1, and AchAT1 was observed through RNA-Seq analysis and RT-PCR. The copy numbers of AcPINK estimated by mapping the genomic DNA reads produced by NextSeq 500 were predominantly high compared with the other TEs. A series of evidence indicated that these TEs might have transposed in these onion genes very recently, providing a stepping stone for elucidation of enormously large-sized onion genome structure.

Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes

PubMed Central

Chen, Song; Li, Xianchun

2007-01-01

Background Transposons, i.e. transposable elements (TEs), are the major internal spontaneous mutation agents for the variability of eukaryotic genomes. To address the general issue of whether transposons mediate genomic changes in environment-adaptation genes, we scanned two alleles per each of the six xenobiotic-metabolizing Helicoverpa zea cytochrome P450 loci, including CYP6B8, CYP6B27, CYP321A1, CYP321A2, CYP9A12v3 and CYP9A14, for the presence of transposon insertions by genome walking and sequence analysis. We also scanned thirteen Drosophila melanogaster P450s genes for TE insertions by in silico mapping and literature search. Results Twelve novel transposons, including LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), MITEs (miniature inverted-repeat transposable elements), one full-length transib-like transposon, and one full-length Tcl-like DNA transpson, are identified from the alleles of the six H. zea P450 genes. The twelve transposons are inserted into the 5'flanking region, 3'flanking region, exon, or intron of the six environment-adaptation P450 genes. In D. melanogaster, seven out of the eight Drosophila P450s (CYP4E2, CYP6A2, CYP6A8, CYP6A9, CYP6G1, CYP6W1, CYP12A4, CYP12D1) implicated in insecticide resistance are associated with a variety of transposons. By contrast, all the five Drosophila P450s (CYP302A1, CYP306A1, CYP307A1, CYP314A1 and CYP315A1) involved in ecdysone biosynthesis and developmental regulation are free of TE insertions. Conclusion These results indicate that TEs are selectively retained within or in close proximity to xenobiotic-metabolizing P450 genes. PMID:17381843

Minos as a novel Tc1/mariner-type transposable element for functional genomic analysis in Aspergillus nidulans.

PubMed

Evangelinos, Minoas; Anagnostopoulos, Gerasimos; Karvela-Kalogeraki, Iliana; Stathopoulou, Panagiota M; Scazzocchio, Claudio; Diallinas, George

2015-08-01

Transposons constitute powerful genetic tools for gene inactivation, exon or promoter trapping and genome analyses. The Minos element from Drosophila hydei, a Tc1/mariner-like transposon, has proved as a very efficient tool for heterologous transposition in several metazoa. In filamentous fungi, only a handful of fungal-specific transposable elements have been exploited as genetic tools, with the impala Tc1/mariner element from Fusarium oxysporum being the most successful. Here, we developed a two-component transposition system to manipulate Minos transposition in Aspergillus nidulans (AnMinos). Our system allows direct selection of transposition events based on re-activation of niaD, a gene necessary for growth on nitrate as a nitrogen source. On average, among 10(8) conidiospores, we obtain up to ∼0.8×10(2) transposition events leading to the expected revertant phenotype (niaD(+)), while ∼16% of excision events lead to AnMinos loss. Characterized excision footprints consisted of the four terminal bases of the transposon flanked by the TA target duplication and led to no major DNA rearrangements. AnMinos transposition depends on the presence of its homologous transposase. Its frequency was not significantly affected by temperature, UV irradiation or the transcription status of the original integration locus (niaD). Importantly, transposition is dependent on nkuA, encoding an enzyme essential for non-homologous end joining of DNA in double-strand break repair. AnMinos proved to be an efficient tool for functional analysis as it seems to transpose in different genomic loci positions in all chromosomes, including a high proportion of integration events within or close to genes. We have used Minos to obtain morphological and toxic analogue resistant mutants. Interestingly, among morphological mutants some seem to be due to Minos-elicited over-expression of specific genes, rather than gene inactivation. Copyright © 2015 Elsevier Inc. All rights reserved.

Transposable elements generate population-specific insertional patterns and allelic variation in genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides).

PubMed

Domb, Katherine; Keidar, Danielle; Yaakov, Beery; Khasdan, Vadim; Kashkush, Khalil

2017-10-27

Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic variation between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the impact of population-unique/specific TE insertions on structure and expression of genes. We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases, the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat. For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.

Insights into the transposable mobilome of Paracoccus spp. (Alphaproteobacteria).

PubMed

Dziewit, Lukasz; Baj, Jadwiga; Szuplewska, Magdalena; Maj, Anna; Tabin, Mateusz; Czyzkowska, Anna; Skrzypczyk, Grazyna; Adamczuk, Marcin; Sitarek, Tomasz; Stawinski, Piotr; Tudek, Agnieszka; Wanasz, Katarzyna; Wardal, Ewa; Piechucka, Ewa; Bartosik, Dariusz

2012-01-01

Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial evolution.

Insights into the Transposable Mobilome of Paracoccus spp. (Alphaproteobacteria)

PubMed Central

Dziewit, Lukasz; Baj, Jadwiga; Szuplewska, Magdalena; Maj, Anna; Tabin, Mateusz; Czyzkowska, Anna; Skrzypczyk, Grazyna; Adamczuk, Marcin; Sitarek, Tomasz; Stawinski, Piotr; Tudek, Agnieszka; Wanasz, Katarzyna; Wardal, Ewa; Piechucka, Ewa; Bartosik, Dariusz

2012-01-01

Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial evolution. PMID:22359677

On the degree conjecture for separability of multipartite quantum states

NASA Astrophysics Data System (ADS)

Hassan, Ali Saif M.; Joag, Pramod S.

2008-01-01

We settle the so-called degree conjecture for the separability of multipartite quantum states, which are normalized graph Laplacians, first given by Braunstein et al. [Phys. Rev. A 73, 012320 (2006)]. The conjecture states that a multipartite quantum state is separable if and only if the degree matrix of the graph associated with the state is equal to the degree matrix of the partial transpose of this graph. We call this statement to be the strong form of the conjecture. In its weak version, the conjecture requires only the necessity, that is, if the state is separable, the corresponding degree matrices match. We prove the strong form of the conjecture for pure multipartite quantum states using the modified tensor product of graphs defined by Hassan and Joag [J. Phys. A 40, 10251 (2007)], as both necessary and sufficient condition for separability. Based on this proof, we give a polynomial-time algorithm for completely factorizing any pure multipartite quantum state. By polynomial-time algorithm, we mean that the execution time of this algorithm increases as a polynomial in m, where m is the number of parts of the quantum system. We give a counterexample to show that the conjecture fails, in general, even in its weak form, for multipartite mixed states. Finally, we prove this conjecture, in its weak form, for a class of multipartite mixed states, giving only a necessary condition for separability.

Sequence analysis of the genome of carnation (Dianthus caryophyllus L.).

PubMed

Yagi, Masafumi; Kosugi, Shunichi; Hirakawa, Hideki; Ohmiya, Akemi; Tanase, Koji; Harada, Taro; Kishimoto, Kyutaro; Nakayama, Masayoshi; Ichimura, Kazuo; Onozaki, Takashi; Yamaguchi, Hiroyasu; Sasaki, Nobuhiro; Miyahara, Taira; Nishizaki, Yuzo; Ozeki, Yoshihiro; Nakamura, Noriko; Suzuki, Takamasa; Tanaka, Yoshikazu; Sato, Shusei; Shirasawa, Kenta; Isobe, Sachiko; Miyamura, Yoshinori; Watanabe, Akiko; Nakayama, Shinobu; Kishida, Yoshie; Kohara, Mitsuyo; Tabata, Satoshi

2014-06-01

The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. 'Francesco' was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568,887,315 bp, consisting of 45,088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16,644 bp and 60,737 bp, respectively, and the longest scaffold was 1,287,144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼ 98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genomic sequences is available at http://carnation.kazusa.or.jp. © The Author 2013. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch.

PubMed

Meile, Lukas; Croll, Daniel; Brunner, Patrick C; Plissonneau, Clémence; Hartmann, Fanny E; McDonald, Bruce A; Sánchez-Vallet, Andrea

2018-04-25

Cultivar-strain specificity in the wheat-Zymoseptoria tritici pathosystem determines the infection outcome and is controlled by resistance genes on the host side, many of which have been identified. On the pathogen side, however, the molecular determinants of specificity remain largely unknown. We used genetic mapping, targeted gene disruption and allele swapping to characterise the recognition of the new avirulence factor Avr3D1. We then combined population genetic and comparative genomic analyses to characterise the evolutionary trajectory of Avr3D1. Avr3D1 is specifically recognised by wheat cultivars harbouring the Stb7 resistance gene, triggering a strong defence response without preventing pathogen infection and reproduction. Avr3D1 resides in a cluster of putative effector genes located in a genome region populated by independent transposable element insertions. The gene was present in all 132 investigated strains and is highly polymorphic, with 30 different protein variants identified. We demonstrated that specific amino acid substitutions in Avr3D1 led to evasion of recognition. These results demonstrate that quantitative resistance and gene-for-gene interactions are not mutually exclusive. Localising avirulence genes in highly plastic genomic regions probably facilitates accelerated evolution that enables escape from recognition by resistance proteins. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

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

Pairolero, P.C.; Arnold, P.G.

In this article, we review our experience during the past 9 years with 205 consecutive thoracic wall reconstructions. The 100 female and 105 male patients ranged in age from 12 to 85 years (mean, 53.4 years). One hundred fourteen patients had thoracic wall tumors, 56 had radiation necrosis, 56 had infected median sternotomy wounds, and 8 had costochondritis. Twenty-nine of these patients had combinations of the aforementioned conditions. One hundred seventy-eight patients underwent skeletal resection. A mean of 5.4 ribs were resected in 142 patients. Total or partial sternectomies were performed in 60. Skeletal defects were closed with prosthetic materialmore » in 66 patients and with autogenous ribs in 12. One hundred sixty-eight patients underwent 244 muscle flap procedures: 149 pectoralis major, 56 latissimus dorsi, 14 rectus abdominis, 13 serratus anterior, 8 external oblique, 2 trapezius, and 2 advancement of diaphragm. The omentum was transposed in 20 patients. The mean number of operations per patient was 1.9 (range, 1 to 8). The mean duration of hospitalization was 16.5 days. One perioperative death occurred (at 29 days). Four patients required tracheostomy. During a mean follow-up of 32.4 months, there were 49 late deaths, predominantly due to malignant disease. All 204 patients who were alive 30 days after operation had excellent surgical results at last follow-up examination or at the time of death due to causes unrelated to the reconstructive procedure.« less

The 5S rDNA in two Abracris grasshoppers (Ommatolampidinae: Acrididae): molecular and chromosomal organization.

PubMed

Bueno, Danilo; Palacios-Gimenez, Octavio Manuel; Martí, Dardo Andrea; Mariguela, Tatiane Casagrande; Cabral-de-Mello, Diogo Cavalcanti

2016-08-01

The 5S ribosomal DNA (rDNA) sequences are subject of dynamic evolution at chromosomal and molecular levels, evolving through concerted and/or birth-and-death fashion. Among grasshoppers, the chromosomal location for this sequence was established for some species, but little molecular information was obtained to infer evolutionary patterns. Here, we integrated data from chromosomal and nucleotide sequence analysis for 5S rDNA in two Abracris species aiming to identify evolutionary dynamics. For both species, two arrays were identified, a larger sequence (named type-I) that consisted of the entire 5S rDNA gene plus NTS (non-transcribed spacer) and a smaller (named type-II) with truncated 5S rDNA gene plus short NTS that was considered a pseudogene. For type-I sequences, the gene corresponding region contained the internal control region and poly-T motif and the NTS presented partial transposable elements. Between the species, nucleotide differences for type-I were noticed, while type-II was identical, suggesting pseudogenization in a common ancestor. At chromosomal point to view, the type-II was placed in one bivalent, while type-I occurred in multiple copies in distinct chromosomes. In Abracris, the evolution of 5S rDNA was apparently influenced by the chromosomal distribution of clusters (single or multiple location), resulting in a mixed mechanism integrating concerted and birth-and-death evolution depending on the unit.

The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees

PubMed Central

Wan, KangKang; Zhang, Zhong; Pang, Xiaoming; Yin, Xiao; Bai, Yang; Sun, Xiaoqing; Gao, Lizhi; Li, Ruiqiang; Zhang, Jinbo

2016-01-01

Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar ‘Junzao’ and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of ‘Dongzao’, a fresh jujube, was ~86.5 Mb larger than that of the ‘Junzao’, partially due to the recent insertions of transposable elements in the ‘Dongzao’ genome. We constructed eight proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two sister families in the order Rosales, and elucidated the evolutionary processes that have shaped the genome structures of modern jujubes. Population structure analysis revealed the complex genetic background of jujubes resulting from extensive hybridizations between jujube and its wild relatives. Notably, several key genes that control fruit organic acid metabolism and sugar content were identified in the selective sweep regions. We also identified S-locus genes controlling gametophytic self-incompatibility and investigated haplotype patterns of the S locus in the jujube genomes, which would provide a guideline for parent selection for jujube crossbreeding. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication. PMID:28005948

Aging as an Epigenetic Phenomenon

PubMed Central

Ashapkin, Vasily V.; Kutueva, Lyudmila I.; Vanyushin, Boris F.

2017-01-01

Introduction: Hypermethylation of genes associated with promoter CpG islands, and hypomethylation of CpG poor genes, repeat sequences, transposable elements and intergenic genome sections occur during aging in mammals. Methylation levels of certain CpG sites display strict correlation to age and could be used as “epigenetic clock” to predict biological age. Multi-substrate deacetylases SIRT1 and SIRT6 affect aging via locus-specific modulations of chromatin structure and activity of multiple regulatory proteins involved in aging. Random errors in DNA methylation and other epigenetic marks during aging increase the transcriptional noise, and thus lead to enhanced phenotypic variation between cells of the same tissue. Such variation could cause progressive organ dysfunction observed in aged individuals. Multiple experimental data show that induction of NF-κB regulated gene sets occurs in various tissues of aged mammals. Upregulation of multiple miRNAs occurs at mid age leading to downregulation of enzymes and regulatory proteins involved in basic cellular functions, such as DNA repair, oxidative phosphorylation, intermediate metabolism, and others. Conclusion: Strong evidence shows that all epigenetic systems contribute to the lifespan control in various organisms. Similar to other cell systems, epigenome is prone to gradual degradation due to the genome damage, stressful agents, and other aging factors. But unlike mutations and other kinds of the genome damage, age-related epigenetic changes could be fully or partially reversed to a “young” state. PMID:29081695

The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees.

PubMed

Huang, Jian; Zhang, Chunmei; Zhao, Xing; Fei, Zhangjun; Wan, KangKang; Zhang, Zhong; Pang, Xiaoming; Yin, Xiao; Bai, Yang; Sun, Xiaoqing; Gao, Lizhi; Li, Ruiqiang; Zhang, Jinbo; Li, Xingang

2016-12-01

Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar 'Junzao' and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the 'Junzao', partially due to the recent insertions of transposable elements in the 'Dongzao' genome. We constructed eight proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two sister families in the order Rosales, and elucidated the evolutionary processes that have shaped the genome structures of modern jujubes. Population structure analysis revealed the complex genetic background of jujubes resulting from extensive hybridizations between jujube and its wild relatives. Notably, several key genes that control fruit organic acid metabolism and sugar content were identified in the selective sweep regions. We also identified S-locus genes controlling gametophytic self-incompatibility and investigated haplotype patterns of the S locus in the jujube genomes, which would provide a guideline for parent selection for jujube crossbreeding. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication.

qPR: An adaptive partial-report procedure based on Bayesian inference.

PubMed

Baek, Jongsoo; Lesmes, Luis Andres; Lu, Zhong-Lin

2016-08-01

Iconic memory is best assessed with the partial report procedure in which an array of letters appears briefly on the screen and a poststimulus cue directs the observer to report the identity of the cued letter(s). Typically, 6-8 cue delays or 600-800 trials are tested to measure the iconic memory decay function. Here we develop a quick partial report, or qPR, procedure based on a Bayesian adaptive framework to estimate the iconic memory decay function with much reduced testing time. The iconic memory decay function is characterized by an exponential function and a joint probability distribution of its three parameters. Starting with a prior of the parameters, the method selects the stimulus to maximize the expected information gain in the next test trial. It then updates the posterior probability distribution of the parameters based on the observer's response using Bayesian inference. The procedure is reiterated until either the total number of trials or the precision of the parameter estimates reaches a certain criterion. Simulation studies showed that only 100 trials were necessary to reach an average absolute bias of 0.026 and a precision of 0.070 (both in terms of probability correct). A psychophysical validation experiment showed that estimates of the iconic memory decay function obtained with 100 qPR trials exhibited good precision (the half width of the 68.2% credible interval = 0.055) and excellent agreement with those obtained with 1,600 trials of the conventional method of constant stimuli procedure (RMSE = 0.063). Quick partial-report relieves the data collection burden in characterizing iconic memory and makes it possible to assess iconic memory in clinical populations.

Multi-probe-based resonance-frequency electrical impedance spectroscopy for detection of suspicious breast lesions: improving performance using partial ROC optimization

NASA Astrophysics Data System (ADS)

Lederman, Dror; Zheng, Bin; Wang, Xingwei; Wang, Xiao Hui; Gur, David

2011-03-01

We have developed a multi-probe resonance-frequency electrical impedance spectroscope (REIS) system to detect breast abnormalities. Based on assessing asymmetry in REIS signals acquired between left and right breasts, we developed several machine learning classifiers to classify younger women (i.e., under 50YO) into two groups of having high and low risk for developing breast cancer. In this study, we investigated a new method to optimize performance based on the area under a selected partial receiver operating characteristic (ROC) curve when optimizing an artificial neural network (ANN), and tested whether it could improve classification performance. From an ongoing prospective study, we selected a dataset of 174 cases for whom we have both REIS signals and diagnostic status verification. The dataset includes 66 "positive" cases recommended for biopsy due to detection of highly suspicious breast lesions and 108 "negative" cases determined by imaging based examinations. A set of REIS-based feature differences, extracted from the two breasts using a mirror-matched approach, was computed and constituted an initial feature pool. Using a leave-one-case-out cross-validation method, we applied a genetic algorithm (GA) to train the ANN with an optimal subset of features. Two optimization criteria were separately used in GA optimization, namely the area under the entire ROC curve (AUC) and the partial area under the ROC curve, up to a predetermined threshold (i.e., 90% specificity). The results showed that although the ANN optimized using the entire AUC yielded higher overall performance (AUC = 0.83 versus 0.76), the ANN optimized using the partial ROC area criterion achieved substantially higher operational performance (i.e., increasing sensitivity level from 28% to 48% at 95% specificity and/ or from 48% to 58% at 90% specificity).

qPR: An adaptive partial-report procedure based on Bayesian inference

PubMed Central

Baek, Jongsoo; Lesmes, Luis Andres; Lu, Zhong-Lin

2016-01-01

Iconic memory is best assessed with the partial report procedure in which an array of letters appears briefly on the screen and a poststimulus cue directs the observer to report the identity of the cued letter(s). Typically, 6–8 cue delays or 600–800 trials are tested to measure the iconic memory decay function. Here we develop a quick partial report, or qPR, procedure based on a Bayesian adaptive framework to estimate the iconic memory decay function with much reduced testing time. The iconic memory decay function is characterized by an exponential function and a joint probability distribution of its three parameters. Starting with a prior of the parameters, the method selects the stimulus to maximize the expected information gain in the next test trial. It then updates the posterior probability distribution of the parameters based on the observer's response using Bayesian inference. The procedure is reiterated until either the total number of trials or the precision of the parameter estimates reaches a certain criterion. Simulation studies showed that only 100 trials were necessary to reach an average absolute bias of 0.026 and a precision of 0.070 (both in terms of probability correct). A psychophysical validation experiment showed that estimates of the iconic memory decay function obtained with 100 qPR trials exhibited good precision (the half width of the 68.2% credible interval = 0.055) and excellent agreement with those obtained with 1,600 trials of the conventional method of constant stimuli procedure (RMSE = 0.063). Quick partial-report relieves the data collection burden in characterizing iconic memory and makes it possible to assess iconic memory in clinical populations. PMID:27580045

Criterion-free measurement of motion transparency perception at different speeds

PubMed Central

Rocchi, Francesca; Ledgeway, Timothy; Webb, Ben S.

2018-01-01

Transparency perception often occurs when objects within the visual scene partially occlude each other or move at the same time, at different velocities across the same spatial region. Although transparent motion perception has been extensively studied, we still do not understand how the distribution of velocities within a visual scene contribute to transparent perception. Here we use a novel psychophysical procedure to characterize the distribution of velocities in a scene that give rise to transparent motion perception. To prevent participants from adopting a subjective decision criterion when discriminating transparent motion, we used an “odd-one-out,” three-alternative forced-choice procedure. Two intervals contained the standard—a random-dot-kinematogram with dot speeds or directions sampled from a uniform distribution. The other interval contained the comparison—speeds or directions sampled from a distribution with the same range as the standard, but with a notch of different widths removed. Our results suggest that transparent motion perception is driven primarily by relatively slow speeds, and does not emerge when only very fast speeds are present within a visual scene. Transparent perception of moving surfaces is modulated by stimulus-based characteristics, such as the separation between the means of the overlapping distributions or the range of speeds presented within an image. Our work illustrates the utility of using objective, forced-choice methods to reveal the mechanisms underlying motion transparency perception. PMID:29614154

Differentiating corporal punishment from physical abuse in the prediction of lifetime aggression.

PubMed

King, Alan R; Ratzak, Abrianna; Ballantyne, Sage; Knutson, Shane; Russell, Tiffany D; Pogalz, Colton R; Breen, Cody M

2018-05-01

Corporal punishment and parental physical abuse often co-occur during upbringing, making it difficult to differentiate their selective impacts on psychological functioning. Associations between corporal punishment and a number of lifetime aggression indicators were examined in this study after efforts to control the potential influence of various forms of co-occurring maltreatment (parental physical abuse, childhood sexual abuse, sibling abuse, peer bullying, and observed parental violence). College students (N = 1,136) provided retrospective self-reports regarding their history of aggression and levels of exposure to childhood corporal punishment and maltreatment experiences. Analyses focused on three hypotheses: 1) The odds of experiencing childhood physical abuse would be higher among respondents reporting frequent corporal punishment during upbringing; 2) Corporal punishment scores would predict the criterion aggression indices after control of variance associated with childhood maltreatment; 3) Aggression scores would be higher among respondents classified in the moderate and elevated corporal punishment risk groups. Strong support was found for the first hypothesis since the odds of childhood physical abuse recollections were higher (OR = 65.3) among respondents who experienced frequent (>60 total disciplinary acts) corporal punishment during upbringing. Partial support was found for the second and third hypotheses. Dimensional and categorical corporal punishment scores were associated significantly with half of the criterion measures. These findings support efforts to dissuade reliance on corporal punishment to manage child behavior. © 2018 Wiley Periodicals, Inc.

High-Temperature Oxidation Behavior of Iridium-Rhenium Alloys

NASA Technical Reports Server (NTRS)

Reed, Brian D.

1995-01-01

The life-limiting mechanism for radiation-cooled rockets made from iridium-coated rhenium (Ir/Re) is the diffusion of Re into the Ir layer and the subsequent oxidation of the resulting Ir-Re alloy from the inner surface. In a previous study, a life model for Ir/Re rockets was developed. It incorporated Ir-Re diffusion and oxidation data to predict chamber lifetimes as a function of temperature and oxygen partial pressure. Oxidation testing at 1540 deg C suggested that a 20-wt percent Re concentration at the inner wall surface should be established as the failure criterion. The present study was performed to better define Ir-oxidation behavior as a function of Re concentration and to supplement the data base for the life model. Samples ranging from pure Ir to Ir-40 wt percent Re (Ir-40Re) were tested at 1500 deg C, in two different oxygen environments. There were indications that the oxidation rate of the Ir-Re alloy increased significantly when it went from a single-phase solid solution to a two-phase mixture, as was suggested in previous work. However, because of testing anomalies in this study, there were not enough dependable oxidation data to definitively raise the Ir/Re rocket failure criterion from 20-wt percent Re to a Re concentration corresponding to entry into the two-phase region.

A Reconsideration of the Extension Strain Criterion for Fracture and Failure of Rock

NASA Astrophysics Data System (ADS)

Wesseloo, J.; Stacey, T. R.

2016-12-01

The complex behaviours of rocks and rock masses have presented paradoxes to the rock engineer, including the fracturing of seemingly strong rock under low stress conditions, which often occurs near excavation boundaries. The extension strain criterion was presented as a fracture initiation criterion under these conditions (Stacey in Int J Rock Mech Min Sci 18:469-474, 1981). This criterion has been used successfully by some and criticised by others. In this paper, we review the literature on the extension strain criterion and present a case for the correct interpretation of the criterion and the conditions suitable for its use. We argue that the extension strain criterion can also be used to provide an indication of damage level under conditions of relatively low confining stress. We also present an augmentation of the criterion, the ultimate extension strain, which is applicable under extensional loading conditions when σ 2 is similar in magnitude to σ 1.

Strength-based criterion shifts in recognition memory.

PubMed

Singer, Murray

2009-10-01

In manipulations of stimulus strength between lists, a more lenient signal detection criterion is more frequently applied to a weak than to a strong stimulus class. However, with randomly intermixed weak and strong test probes, such a criterion shift often does not result. A procedure that has yielded delay-based within-list criterion shifts was applied to strength manipulations in recognition memory for categorized word lists. When participants made semantic ratings about each stimulus word, strength-based criterion shifts emerged regardless of whether words from pairs of categories were studied in separate blocks (Experiment 1) or in intermixed blocks (Experiment 2). In Experiment 3, the criterion shift persisted under the semantic-rating study task, but not under rote memorization. These findings suggest that continually adjusting the recognition decision criterion is cognitively feasible. They provide a technique for manipulating the criterion shift, and they identify competing theoretical accounts of these effects.

Global surface-based cloud observation for ISCCP

NASA Technical Reports Server (NTRS)

1994-01-01

Visual observations of cloud cover are hindered at night due to inadequate illumination of the clouds. This usually leads to an underestimation of the average cloud cover at night, especially for the amounts of middle and high clouds, in climatologies on surface observations. The diurnal cycles of cloud amounts, if based on all the surface observations, are therefore in error, but they can be obtained more accurately if the nighttime observations are screened to select those made under sufficient moonlight. Ten years of nighttime weather observations from the northern hemisphere in December were classified according to the illuminance of moonlight or twilight on the cloud tops, and a threshold level of illuminance was determined, above which the clouds are apparently detected adequately. This threshold corresponds to light from a full moon at an elevation angle of 6 degrees or from a partial moon at higher elevation, or twilight from the sun less than 9 degrees below the horizon. It permits the use of about 38% of the observations made with the sun below the horizon. The computed diurnal cycles of total cloud cover are altered considerably when this moonlight criterion is imposed. Maximum cloud cover over much of the ocean is now found to be at night or in the morning, whereas computations obtained without benefit of the moonlight criterion, as in our published atlases, showed the time of maximum to be noon or early afternoon in many regions. Cloud cover is greater at night than during the day over the open oceans far from the continents, particularly in summer. However, near noon maxima are still evident in the coastal regions, so that the global annual average oceanic cloud cover is still slightly greater during the day than at night, by 0.3%. Over land, where daytime maxima are still obtained but with reduced amplitude, average cloud cover is 3.3% greater during the daytime. The diurnal cycles of total cloud cover we obtain are compared with those of ISCCP for a few regions; they are generally in better agreement if the moonlight criterion is imposed on the surface observations. Using the moonlight criterion, we have analyzed ten years (1982-1991) of surface weather observations over land and ocean, worldwide, for total cloud cover and for the frequency of occurrence of clear sky, fog and precipitation The global average cloud cover (average of day and night) is about 2% higher if we impose the moonlight criterion than if we use all observations. The difference is greater in winter than in summer, because of the fewer hours of darkness in the summer. The amplitude of the annual cycle of total cloud cover over the Arctic Ocean and at the South Pole is diminished by a few percent when the moonlight criterion is imposed. The average cloud cover for 1982-1991 is found to be 55% for northern hemisphere land, 53% for southern hemisphere land, 66% for northern hemisphere ocean, and 70% for southern hemisphere ocean, giving a global average of 64%. The global average for daytime is 64.6% for nighttime 63.3%.

Numerical simulation of the casting process of titanium removable partial denture frameworks.

PubMed

Wu, Menghuai; Wagner, Ingo; Sahm, Peter R; Augthun, Michael

2002-03-01

The objective of this work was to study the filling incompleteness and porosity defects in titanium removal partial denture frameworks by means of numerical simulation. Two frameworks, one for lower jaw and one for upper jaw, were chosen according to dentists' recommendation to be simulated. Geometry of the frameworks were laser-digitized and converted into a simulation software (MAGMASOFT). Both mold filling and solidification of the castings with different sprue designs (e.g. tree, ball, and runner-bar) were numerically calculated. The shrinkage porosity was quantitatively predicted by a feeding criterion, the potential filling defect and gas pore sensitivity were estimated based on the filling and solidification results. A satisfactory sprue design with process parameters was finally recommended for real casting trials (four replica for each frameworks). All the frameworks were successfully cast. Through X-ray radiographic inspections it was found that all the castings were acceptably sound except for only one case in which gas bubbles were detected in the grasp region of the frame. It is concluded that numerical simulation aids to achieve understanding of the casting process and defect formation in titanium frameworks, hence to minimize the risk of producing defect casting by improving the sprue design and process parameters.

Precise Point Positioning with Partial Ambiguity Fixing.

PubMed

Li, Pan; Zhang, Xiaohong

2015-06-10

Reliable and rapid ambiguity resolution (AR) is the key to fast precise point positioning (PPP). We propose a modified partial ambiguity resolution (PAR) method, in which an elevation and standard deviation criterion are first used to remove the low-precision ambiguity estimates for AR. Subsequently the success rate and ratio-test are simultaneously used in an iterative process to increase the possibility of finding a subset of decorrelated ambiguities which can be fixed with high confidence. One can apply the proposed PAR method to try to achieve an ambiguity-fixed solution when full ambiguity resolution (FAR) fails. We validate this method using data from 450 stations during DOY 021 to 027, 2012. Results demonstrate the proposed PAR method can significantly shorten the time to first fix (TTFF) and increase the fixing rate. Compared with FAR, the average TTFF for PAR is reduced by 14.9% for static PPP and 15.1% for kinematic PPP. Besides, using the PAR method, the average fixing rate can be increased from 83.5% to 98.2% for static PPP, from 80.1% to 95.2% for kinematic PPP respectively. Kinematic PPP accuracy with PAR can also be significantly improved, compared to that with FAR, due to a higher fixing rate.

Precise Point Positioning with Partial Ambiguity Fixing

PubMed Central

Li, Pan; Zhang, Xiaohong

2015-01-01

Reliable and rapid ambiguity resolution (AR) is the key to fast precise point positioning (PPP). We propose a modified partial ambiguity resolution (PAR) method, in which an elevation and standard deviation criterion are first used to remove the low-precision ambiguity estimates for AR. Subsequently the success rate and ratio-test are simultaneously used in an iterative process to increase the possibility of finding a subset of decorrelated ambiguities which can be fixed with high confidence. One can apply the proposed PAR method to try to achieve an ambiguity-fixed solution when full ambiguity resolution (FAR) fails. We validate this method using data from 450 stations during DOY 021 to 027, 2012. Results demonstrate the proposed PAR method can significantly shorten the time to first fix (TTFF) and increase the fixing rate. Compared with FAR, the average TTFF for PAR is reduced by 14.9% for static PPP and 15.1% for kinematic PPP. Besides, using the PAR method, the average fixing rate can be increased from 83.5% to 98.2% for static PPP, from 80.1% to 95.2% for kinematic PPP respectively. Kinematic PPP accuracy with PAR can also be significantly improved, compared to that with FAR, due to a higher fixing rate. PMID:26067196

Selecting the optimum number of partial least squares components for the calibration of attenuated total reflectance-mid-infrared spectra of undesigned kerosene samples.

PubMed

Gómez-Carracedo, M P; Andrade, J M; Rutledge, D N; Faber, N M

2007-03-07

Selecting the correct dimensionality is critical for obtaining partial least squares (PLS) regression models with good predictive ability. Although calibration and validation sets are best established using experimental designs, industrial laboratories cannot afford such an approach. Typically, samples are collected in an (formally) undesigned way, spread over time and their measurements are included in routine measurement processes. This makes it hard to evaluate PLS model dimensionality. In this paper, classical criteria (leave-one-out cross-validation and adjusted Wold's criterion) are compared to recently proposed alternatives (smoothed PLS-PoLiSh and a randomization test) to seek out the optimum dimensionality of PLS models. Kerosene (jet fuel) samples were measured by attenuated total reflectance-mid-IR spectrometry and their spectra where used to predict eight important properties determined using reference methods that are time-consuming and prone to analytical errors. The alternative methods were shown to give reliable dimensionality predictions when compared to external validation. By contrast, the simpler methods seemed to be largely affected by the largest changes in the modeling capabilities of the first components.

Steady flow rate to a partially penetrating well with seepage face in an unconfined aquifer

NASA Astrophysics Data System (ADS)

Behrooz-Koohenjani, Siavash; Samani, Nozar; Kompani-Zare, Mazda

2011-06-01

The flow rate to fully screened, partially penetrating wells in an unconfined aquifer is numerically simulated using MODFLOW 2000, taking into account the flow from the seepage face and decrease in saturated thickness of the aquifer towards the well. A simple three-step method is developed to find the top of the seepage face and hence the seepage-face length. The method is verified by comparing it with the results of previous predictive methods. The results show that the component of flow through the seepage face can supply a major portion of the total pumping rate. Variations in flow rate as a function of the penetration degree, elevation of the water level in the well and the distance to the far constant head boundary are investigated and expressed in terms of dimensionless curves and equations. These curves and equations can be used to design the degree of penetration for which the allowable steady pumping rate is attained for a given elevation of water level in the well. The designed degree of penetration or flow rate will assure the sustainability of the aquifer storage, and can be used as a management criterion for issuing drilling well permits by groundwater protection authorities.

Evaluation of Regression Models of Balance Calibration Data Using an Empirical Criterion

NASA Technical Reports Server (NTRS)

Ulbrich, Norbert; Volden, Thomas R.

2012-01-01

An empirical criterion for assessing the significance of individual terms of regression models of wind tunnel strain gage balance outputs is evaluated. The criterion is based on the percent contribution of a regression model term. It considers a term to be significant if its percent contribution exceeds the empirical threshold of 0.05%. The criterion has the advantage that it can easily be computed using the regression coefficients of the gage outputs and the load capacities of the balance. First, a definition of the empirical criterion is provided. Then, it is compared with an alternate statistical criterion that is widely used in regression analysis. Finally, calibration data sets from a variety of balances are used to illustrate the connection between the empirical and the statistical criterion. A review of these results indicated that the empirical criterion seems to be suitable for a crude assessment of the significance of a regression model term as the boundary between a significant and an insignificant term cannot be defined very well. Therefore, regression model term reduction should only be performed by using the more universally applicable statistical criterion.

Three-year clinical performance of cast gold vs ceramic partial crowns.

PubMed

Federlin, M; Wagner, J; Männer, T; Hiller, K-A; Schmalz, G

2007-12-01

Cast gold partial crowns (CGPC) and partial ceramic crowns (PCC) are both accepted for restoring posterior teeth with extended lesions today. However, as esthetics in dentistry becomes increasingly important, CGPC are being progressively replaced by PCC. The aim of the present prospective split-mouth study was the comparison of the clinical performance of PCC and CGPC after 3 years of clinical service. Twenty-eight patients (11 men and 17 women) participated in the 3-year recall with a total of 56 restorations. In each patient, one CGPC (Degulor C) and one PCC (Vita Mark II ceramic/Cerec III) had been inserted at baseline. CGPC were placed using a zinc phosphate cement (Harvard); PCC were adhesively luted (Variolink II/Excite). All restorations were clinically assessed using modified US Public Health Service (USPHS) criteria at baseline, 1 year, 2 years, and 3 years after insertion. Twenty-eight CGPC and 14 PCC were placed in molars, and 14 PCC were placed in premolars. Early data were reported previously under the same study design. After 3 years, the evaluation according to USPHS criteria revealed no statistically significant differences between both types of restorations with the exception of marginal adaptation and marginal discoloration: A statistically significant difference within the PCC group (baseline/3 years) was determined for the criterion marginal adaptation. For the 3-year recall period, overall failure was 0% for CGPC and 6.9% for PCC. At 3 years, PCC meet American Dental Association Acceptance Guidelines criteria for tooth-colored restorative materials for posterior teeth.

Disentangling the Developmental Trajectories of Letter Position and Letter Identity Coding Using Masked Priming

ERIC Educational Resources Information Center

Kezilas, Yvette; McKague, Meredith; Kohnen, Saskia; Badcock, Nicholas A.; Castles, Anne

2017-01-01

Masked transposed-letter (TL) priming effects have been used to index letter position processing over the course of reading development. Whereas some studies have reported an increase in TL priming over development, others have reported a decrease. These findings have led to the development of 2 somewhat contradictory accounts of letter position…

Transposed-Letter Effects in Reading: Evidence from Eye Movements and Parafoveal Preview

ERIC Educational Resources Information Center

Johnson, Rebecca L.; Perea, Manuel; Rayner, Keith

2007-01-01

Three eye movement experiments were conducted to examine the role of letter identity and letter position during reading. Before fixating on a target word within each sentence, readers were provided with a parafoveal preview that differed in the amount of useful letter identity and letter position information it provided. In Experiments 1 and 2,…