Sequence and Structure Dependent DNA-DNA Interactions

NASA Astrophysics Data System (ADS)

Kopchick, Benjamin; Qiu, Xiangyun

Molecular forces between dsDNA strands are largely dominated by electrostatics and have been extensively studied. Quantitative knowledge has been accumulated on how DNA-DNA interactions are modulated by varied biological constituents such as ions, cationic ligands, and proteins. Despite its central role in biology, the sequence of DNA has not received substantial attention and ``random'' DNA sequences are typically used in biophysical studies. However, ~50% of human genome is composed of non-random-sequence DNAs, particularly repetitive sequences. Furthermore, covalent modifications of DNA such as methylation play key roles in gene functions. Such DNAs with specific sequences or modifications often take on structures other than the canonical B-form. Here we present series of quantitative measurements of the DNA-DNA forces with the osmotic stress method on different DNA sequences, from short repeats to the most frequent sequences in genome, and to modifications such as bromination and methylation. We observe peculiar behaviors that appear to be strongly correlated with the incurred structural changes. We speculate the causalities in terms of the differences in hydration shell and DNA surface structures.

Least squares deconvolution for leak detection with a pseudo random binary sequence excitation

NASA Astrophysics Data System (ADS)

Nguyen, Si Tran Nguyen; Gong, Jinzhe; Lambert, Martin F.; Zecchin, Aaron C.; Simpson, Angus R.

2018-01-01

Leak detection and localisation is critical for water distribution system pipelines. This paper examines the use of the time-domain impulse response function (IRF) for leak detection and localisation in a pressurised water pipeline with a pseudo random binary sequence (PRBS) signal excitation. Compared to the conventional step wave generated using a single fast operation of a valve closure, a PRBS signal offers advantageous correlation properties, in that the signal has very low autocorrelation for lags different from zero and low cross correlation with other signals including noise and other interference. These properties result in a significant improvement in the IRF signal to noise ratio (SNR), leading to more accurate leak localisation. In this paper, the estimation of the system IRF is formulated as an optimisation problem in which the l2 norm of the IRF is minimised to suppress the impact of noise and interference sources. Both numerical and experimental data are used to verify the proposed technique. The resultant estimated IRF provides not only accurate leak location estimation, but also good sensitivity to small leak sizes due to the improved SNR.

A New Method for Generating Probability Tables in the Unresolved Resonance Region

DOE PAGES

Holcomb, Andrew M.; Leal, Luiz C.; Rahnema, Farzad; ...

2017-04-18

One new method for constructing probability tables in the unresolved resonance region (URR) has been developed. This new methodology is an extensive modification of the single-level Breit-Wigner (SLBW) pseudo-resonance pair sequence method commonly used to generate probability tables in the URR. The new method uses a Monte Carlo process to generate many pseudo-resonance sequences by first sampling the average resonance parameter data in the URR and then converting the sampled resonance parameters to the more robust R-matrix limited (RML) format. Furthermore, for each sampled set of pseudo-resonance sequences, the temperature-dependent cross sections are reconstructed on a small grid around themore » energy of reference using the Reich-Moore formalism and the Leal-Hwang Doppler broadening methodology. We then use the effective cross sections calculated at the energies of reference to construct probability tables in the URR. The RML cross-section reconstruction algorithm has been rigorously tested for a variety of isotopes, including 16O, 19F, 35Cl, 56Fe, 63Cu, and 65Cu. The new URR method also produced normalized cross-section factor probability tables for 238U that were found to be in agreement with current standards. The modified 238U probability tables were shown to produce results in excellent agreement with several standard benchmarks, including the IEU-MET-FAST-007 (BIG TEN), IEU-MET-FAST-003, and IEU-COMP-FAST-004 benchmarks.« less

iHyd-PseCp: Identify hydroxyproline and hydroxylysine in proteins by incorporating sequence-coupled effects into general PseAAC.

PubMed

Qiu, Wang-Ren; Sun, Bi-Qian; Xiao, Xuan; Xu, Zhao-Chun; Chou, Kuo-Chen

2016-07-12

Protein hydroxylation is a posttranslational modification (PTM), in which a CH group in Pro (P) or Lys (K) residue has been converted into a COH group, or a hydroxyl group (-OH) is converted into an organic compound. Closely associated with cellular signaling activities, this type of PTM is also involved in some major diseases, such as stomach cancer and lung cancer. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence containing many residues of P or K, which ones can be hydroxylated, and which ones cannot? With the explosive growth of protein sequences in the post-genomic age, the problem has become even more urgent. To address such a problem, we have developed a predictor called iHyd-PseCp by incorporating the sequence-coupled information into the general pseudo amino acid composition (PseAAC) and introducing the "Random Forest" algorithm to operate the calculation. Rigorous jackknife tests indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose. For the convenience of most experimental scientists, a user-friendly web-server for iHyd-PseCp has been established at http://www.jci-bioinfo.cn/iHyd-PseCp, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.

Electroacupuncture is not effective in chronic painful neuropathies.

PubMed

Penza, Paola; Bricchi, Monica; Scola, Amalia; Campanella, Angela; Lauria, Giuseppe

2011-12-01

  To investigate the analgesic efficacy of electroacupuncture (EA) in patients with chronic painful neuropathy.   Double-blind, placebo-controlled, cross-over study. Inclusion criteria were diagnosis of peripheral neuropathy, neuropathic pain (visual analog scale > 4) for at least 6 months, and stable analgesic medications for at least 3 months.   Sixteen patients were randomized into two arms to be treated with EA or pseudo-EA (placebo).   The protocol included 6 weeks of treatment, 12 weeks free of treatment, and then further 6 weeks of treatment. EA or pseudo-EA was performed weekly during each treatment period.   The primary outcome was the number of patients treated with EA achieving at least 50% of pain relief at the end of each treatment compared with pain intensity at baseline. Secondary outcomes were modification in patient's global impression of change, depression and anxiety, and quality of life.   Eleven patients were randomized to EA and five patients to pseudo-EA as the first treatment. Only one patient per group (EA and pseudo-EA) reported 50% of pain relief at the end of each treatment compared with pain intensity at baseline. Pain intensity did not differ between EA (5.7 ± 2.3 at baseline and 4.97 ± 3.23 after treatment) and pseudo-EA (4.9 ± 1.9 at baseline and 4.18 ± 2.69 after treatment). There was no difference between patients who received EA as the first treatment and patients initially treated with placebo. There was no change in the secondary outcomes.   Our results do not support the use of EA in this population of painful neuropathy patients. Further studies in larger groups of patients are warranted to confirm our observation. Wiley Periodicals, Inc.

A pseudo MS3 approach for identification of disulfide-bonded proteins: uncommon product ions and database search.

PubMed

Chen, Jianzhong; Shiyanov, Pavel; Schlager, John J; Green, Kari B

2012-02-01

It has previously been reported that disulfide and backbone bonds of native intact proteins can be concurrently cleaved using electrospray ionization (ESI) and collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). However, the cleavages of disulfide bonds result in different cysteine modifications in product ions, making it difficult to identify the disulfide-bonded proteins via database search. To solve this identification problem, we have developed a pseudo MS(3) approach by combining nozzle-skimmer dissociation (NSD) and CID on a quadrupole time-of-flight (Q-TOF) mass spectrometer using chicken lysozyme as a model. Although many of the product ions were similar to those typically seen in MS/MS spectra of enzymatically derived peptides, additional uncommon product ions were detected including c(i-1) ions (the i(th) residue being aspartic acid, arginine, lysine and dehydroalanine) as well as those from a scrambled sequence. The formation of these uncommon types of product ions, likely caused by the lack of mobile protons, were proposed to involve bond rearrangements via a six-membered ring transition state and/or salt bridge(s). A search of 20 pseudo MS(3) spectra against the Gallus gallus (chicken) database using Batch-Tag, a program originally designed for bottom up MS/MS analysis, identified chicken lysozyme as the only hit with the expectation values less than 0.02 for 12 of the spectra. The pseudo MS(3) approach may help to identify disulfide-bonded proteins and determine the associated post-translational modifications (PTMs); the confidence in the identification may be improved by incorporating the fragmentation characteristics into currently available search programs. © American Society for Mass Spectrometry, 2011

High-speed imaging using CMOS image sensor with quasi pixel-wise exposure

NASA Astrophysics Data System (ADS)

Sonoda, T.; Nagahara, H.; Endo, K.; Sugiyama, Y.; Taniguchi, R.

2017-02-01

Several recent studies in compressive video sensing have realized scene capture beyond the fundamental trade-off limit between spatial resolution and temporal resolution using random space-time sampling. However, most of these studies showed results for higher frame rate video that were produced by simulation experiments or using an optically simulated random sampling camera, because there are currently no commercially available image sensors with random exposure or sampling capabilities. We fabricated a prototype complementary metal oxide semiconductor (CMOS) image sensor with quasi pixel-wise exposure timing that can realize nonuniform space-time sampling. The prototype sensor can reset exposures independently by columns and fix these amount of exposure by rows for each 8x8 pixel block. This CMOS sensor is not fully controllable via the pixels, and has line-dependent controls, but it offers flexibility when compared with regular CMOS or charge-coupled device sensors with global or rolling shutters. We propose a method to realize pseudo-random sampling for high-speed video acquisition that uses the flexibility of the CMOS sensor. We reconstruct the high-speed video sequence from the images produced by pseudo-random sampling using an over-complete dictionary.

Beam combining and SBS suppression in white noise and pseudo-random modulated amplifiers

NASA Astrophysics Data System (ADS)

Anderson, Brian; Flores, Angel; Holten, Roger; Ehrenreich, Thomas; Dajani, Iyad

2015-03-01

White noise phase modulation (WNS) and pseudo-random binary sequence phase modulation (PRBS) are effective techniques for mitigation of nonlinear effects such as stimulated Brillouin scattering (SBS); thereby paving the way for higher power narrow linewidth fiber amplifiers. However, detailed studies comparing both coherent beam combination and the SBS suppression of these phase modulation schemes have not been reported. In this study an active fiber cutback experiment is performed comparing the enhancement factor of a PRBS and WNS broadened seed as a function of linewidth and fiber length. Furthermore, two WNS and PRBS modulated fiber lasers are coherently combined to measure and compare the fringe visibility and coherence length as a function of optical path length difference. Notably, the discrete frequency comb of PRBS modulation provides a beam combining re-coherence effect where the lasers periodically come back into phase. Significantly, this may reduce path length matching complexity in coherently combined fiber laser systems.

Autonomous choices among deterministic evolution-laws as source of uncertainty

NASA Astrophysics Data System (ADS)

Trujillo, Leonardo; Meyroneinc, Arnaud; Campos, Kilver; Rendón, Otto; Sigalotti, Leonardo Di G.

2018-03-01

We provide evidence of an extreme form of sensitivity to initial conditions in a family of one-dimensional self-ruling dynamical systems. We prove that some hyperchaotic sequences are closed-form expressions of the orbits of these pseudo-random dynamical systems. Each chaotic system in this family exhibits a sensitivity to initial conditions that encompasses the sequence of choices of the evolution rule in some collection of maps. This opens a possibility to extend current theories of complex behaviors on the basis of intrinsic uncertainty in deterministic chaos.

Pseudo-Random Number Generator Based on Coupled Map Lattices

NASA Astrophysics Data System (ADS)

Lü, Huaping; Wang, Shihong; Hu, Gang

A one-way coupled chaotic map lattice is used for generating pseudo-random numbers. It is shown that with suitable cooperative applications of both chaotic and conventional approaches, the output of the spatiotemporally chaotic system can easily meet the practical requirements of random numbers, i.e., excellent random statistical properties, long periodicity of computer realizations, and fast speed of random number generations. This pseudo-random number generator system can be used as ideal synchronous and self-synchronizing stream cipher systems for secure communications.

Pseudo CT estimation from MRI using patch-based random forest

NASA Astrophysics Data System (ADS)

Yang, Xiaofeng; Lei, Yang; Shu, Hui-Kuo; Rossi, Peter; Mao, Hui; Shim, Hyunsuk; Curran, Walter J.; Liu, Tian

2017-02-01

Recently, MR simulators gain popularity because of unnecessary radiation exposure of CT simulators being used in radiation therapy planning. We propose a method for pseudo CT estimation from MR images based on a patch-based random forest. Patient-specific anatomical features are extracted from the aligned training images and adopted as signatures for each voxel. The most robust and informative features are identified using feature selection to train the random forest. The well-trained random forest is used to predict the pseudo CT of a new patient. This prediction technique was tested with human brain images and the prediction accuracy was assessed using the original CT images. Peak signal-to-noise ratio (PSNR) and feature similarity (FSIM) indexes were used to quantify the differences between the pseudo and original CT images. The experimental results showed the proposed method could accurately generate pseudo CT images from MR images. In summary, we have developed a new pseudo CT prediction method based on patch-based random forest, demonstrated its clinical feasibility, and validated its prediction accuracy. This pseudo CT prediction technique could be a useful tool for MRI-based radiation treatment planning and attenuation correction in a PET/MRI scanner.

Analysis of heart rate and oxygen uptake kinetics studied by two different pseudo-random binary sequence work rate amplitudes.

PubMed

Drescher, U; Koschate, J; Schiffer, T; Schneider, S; Hoffmann, U

2017-06-01

The aim of the study was to compare the kinetics responses of heart rate (HR), pulmonary (V˙O 2 pulm) and predicted muscular (V˙O 2 musc) oxygen uptake between two different pseudo-random binary sequence (PRBS) work rate (WR) amplitudes both below anaerobic threshold. Eight healthy individuals performed two PRBS WR protocols implying changes between 30W and 80W and between 30W and 110W. HR and V˙O 2 pulm were measured beat-to-beat and breath-by-breath, respectively. V˙O 2 musc was estimated applying the approach of Hoffmann et al. (Eur J Appl Physiol 113: 1745-1754, 2013) considering a circulatory model for venous return and cross-correlation functions (CCF) for the kinetics analysis. HR and V˙O 2 musc kinetics seem to be independent of WR intensity (p>0.05). V˙O 2 pulm kinetics show prominent differences in the lag of the CCF maximum (39±9s; 31±4s; p<0.05). A mean difference of 14W between the PRBS WR amplitudes impacts venous return significantly, while HR and V˙O 2 musc kinetics remain unchanged. Copyright © 2017 Elsevier B.V. All rights reserved.

A perturbation method to the tent map based on Lyapunov exponent and its application

NASA Astrophysics Data System (ADS)

Cao, Lv-Chen; Luo, Yu-Ling; Qiu, Sen-Hui; Liu, Jun-Xiu

2015-10-01

Perturbation imposed on a chaos system is an effective way to maintain its chaotic features. A novel parameter perturbation method for the tent map based on the Lyapunov exponent is proposed in this paper. The pseudo-random sequence generated by the tent map is sent to another chaos function — the Chebyshev map for the post processing. If the output value of the Chebyshev map falls into a certain range, it will be sent back to replace the parameter of the tent map. As a result, the parameter of the tent map keeps changing dynamically. The statistical analysis and experimental results prove that the disturbed tent map has a highly random distribution and achieves good cryptographic properties of a pseudo-random sequence. As a result, it weakens the phenomenon of strong correlation caused by the finite precision and effectively compensates for the digital chaos system dynamics degradation. Project supported by the Guangxi Provincial Natural Science Foundation, China (Grant No. 2014GXNSFBA118271), the Research Project of Guangxi University, China (Grant No. ZD2014022), the Fund from Guangxi Provincial Key Laboratory of Multi-source Information Mining & Security, China (Grant No. MIMS14-04), the Fund from the Guangxi Provincial Key Laboratory of Wireless Wideband Communication & Signal Processing, China (Grant No. GXKL0614205), the Education Development Foundation and the Doctoral Research Foundation of Guangxi Normal University, the State Scholarship Fund of China Scholarship Council (Grant No. [2014]3012), and the Innovation Project of Guangxi Graduate Education, China (Grant No. YCSZ2015102).

An On-Demand Optical Quantum Random Number Generator with In-Future Action and Ultra-Fast Response

PubMed Central

Stipčević, Mario; Ursin, Rupert

2015-01-01

Random numbers are essential for our modern information based society e.g. in cryptography. Unlike frequently used pseudo-random generators, physical random number generators do not depend on complex algorithms but rather on a physicsal process to provide true randomness. Quantum random number generators (QRNG) do rely on a process, wich can be described by a probabilistic theory only, even in principle. Here we present a conceptualy simple implementation, which offers a 100% efficiency of producing a random bit upon a request and simultaneously exhibits an ultra low latency. A careful technical and statistical analysis demonstrates its robustness against imperfections of the actual implemented technology and enables to quickly estimate randomness of very long sequences. Generated random numbers pass standard statistical tests without any post-processing. The setup described, as well as the theory presented here, demonstrate the maturity and overall understanding of the technology. PMID:26057576

Investigating expectation effects using multiple physiological measures

PubMed Central

Siller, Alexander; Ambach, Wolfgang; Vaitl, Dieter

2015-01-01

The study aimed at experimentally investigating whether the human body can anticipate future events under improved methodological conditions. Previous studies have reported contradictory results for the phenomenon typically called presentiment. If the positive findings are accurate, they call into doubt our views about human perception, and if they are inaccurate, a plausible conventional explanation might be based on the experimental design of the previous studies, in which expectation due to item sequences was misinterpreted as presentiment. To address these points, we opted to collect several physiological variables, to test different randomization types and to manipulate subjective significance individually. For the latter, we combined a mock crime scenario, in which participants had to steal specific items, with a concealed information test (CIT), in which the participants had to conceal their knowledge when interrogated about items they had stolen or not stolen. We measured electrodermal activity, respiration, finger pulse, heart rate (HR), and reaction times. The participants (n = 154) were assigned randomly to four different groups. Items presented in the CIT were either drawn with replacement (full) or without replacement (pseudo) and were either presented category-wise (cat) or regardless of categories (nocat). To understand how these item sequences influence expectation and modulate physiological reactions, we compared the groups with respect to effect sizes for stolen vs. not stolen items. Group pseudo_cat yielded the highest effect sizes, and pseudo_nocat yielded the lowest. We could not find any evidence of presentiment but did find evidence of physiological correlates of expectation. Due to the design differing fundamentally from previous studies, these findings do not allow for conclusions on the question whether the expectation bias is being confounded with presentiment. PMID:26500600

Estimating the variance for heterogeneity in arm-based network meta-analysis.

PubMed

Piepho, Hans-Peter; Madden, Laurence V; Roger, James; Payne, Roger; Williams, Emlyn R

2018-04-19

Network meta-analysis can be implemented by using arm-based or contrast-based models. Here we focus on arm-based models and fit them using generalized linear mixed model procedures. Full maximum likelihood (ML) estimation leads to biased trial-by-treatment interaction variance estimates for heterogeneity. Thus, our objective is to investigate alternative approaches to variance estimation that reduce bias compared with full ML. Specifically, we use penalized quasi-likelihood/pseudo-likelihood and hierarchical (h) likelihood approaches. In addition, we consider a novel model modification that yields estimators akin to the residual maximum likelihood estimator for linear mixed models. The proposed methods are compared by simulation, and 2 real datasets are used for illustration. Simulations show that penalized quasi-likelihood/pseudo-likelihood and h-likelihood reduce bias and yield satisfactory coverage rates. Sum-to-zero restriction and baseline contrasts for random trial-by-treatment interaction effects, as well as a residual ML-like adjustment, also reduce bias compared with an unconstrained model when ML is used, but coverage rates are not quite as good. Penalized quasi-likelihood/pseudo-likelihood and h-likelihood are therefore recommended. Copyright © 2018 John Wiley & Sons, Ltd.

Novel pseudo-random number generator based on quantum random walks.

PubMed

Yang, Yu-Guang; Zhao, Qian-Qian

2016-02-04

In this paper, we investigate the potential application of quantum computation for constructing pseudo-random number generators (PRNGs) and further construct a novel PRNG based on quantum random walks (QRWs), a famous quantum computation model. The PRNG merely relies on the equations used in the QRWs, and thus the generation algorithm is simple and the computation speed is fast. The proposed PRNG is subjected to statistical tests such as NIST and successfully passed the test. Compared with the representative PRNG based on quantum chaotic maps (QCM), the present QRWs-based PRNG has some advantages such as better statistical complexity and recurrence. For example, the normalized Shannon entropy and the statistical complexity of the QRWs-based PRNG are 0.999699456771172 and 1.799961178212329e-04 respectively given the number of 8 bits-words, say, 16Mbits. By contrast, the corresponding values of the QCM-based PRNG are 0.999448131481064 and 3.701210794388818e-04 respectively. Thus the statistical complexity and the normalized entropy of the QRWs-based PRNG are closer to 0 and 1 respectively than those of the QCM-based PRNG when the number of words of the analyzed sequence increases. It provides a new clue to construct PRNGs and also extends the applications of quantum computation.

Novel pseudo-random number generator based on quantum random walks

PubMed Central

Yang, Yu-Guang; Zhao, Qian-Qian

2016-01-01

In this paper, we investigate the potential application of quantum computation for constructing pseudo-random number generators (PRNGs) and further construct a novel PRNG based on quantum random walks (QRWs), a famous quantum computation model. The PRNG merely relies on the equations used in the QRWs, and thus the generation algorithm is simple and the computation speed is fast. The proposed PRNG is subjected to statistical tests such as NIST and successfully passed the test. Compared with the representative PRNG based on quantum chaotic maps (QCM), the present QRWs-based PRNG has some advantages such as better statistical complexity and recurrence. For example, the normalized Shannon entropy and the statistical complexity of the QRWs-based PRNG are 0.999699456771172 and 1.799961178212329e-04 respectively given the number of 8 bits-words, say, 16Mbits. By contrast, the corresponding values of the QCM-based PRNG are 0.999448131481064 and 3.701210794388818e-04 respectively. Thus the statistical complexity and the normalized entropy of the QRWs-based PRNG are closer to 0 and 1 respectively than those of the QCM-based PRNG when the number of words of the analyzed sequence increases. It provides a new clue to construct PRNGs and also extends the applications of quantum computation. PMID:26842402

Pseudo-random dynamic address configuration (PRDAC) algorithm for mobile ad hoc networks

NASA Astrophysics Data System (ADS)

Wu, Shaochuan; Tan, Xuezhi

2007-11-01

By analyzing all kinds of address configuration algorithms, this paper provides a new pseudo-random dynamic address configuration (PRDAC) algorithm for mobile ad hoc networks. Based on PRDAC, the first node that initials this network randomly chooses a nonlinear shift register that can generates an m-sequence. When another node joins this network, the initial node will act as an IP address configuration sever to compute an IP address according to this nonlinear shift register, and then allocates this address and tell the generator polynomial of this shift register to this new node. By this means, when other node joins this network, any node that has obtained an IP address can act as a server to allocate address to this new node. PRDAC can also efficiently avoid IP conflicts and deal with network partition and merge as same as prophet address (PA) allocation and dynamic configuration and distribution protocol (DCDP). Furthermore, PRDAC has less algorithm complexity, less computational complexity and more sufficient assumption than PA. In addition, PRDAC radically avoids address conflicts and maximizes the utilization rate of IP addresses. Analysis and simulation results show that PRDAC has rapid convergence, low overhead and immune from topological structures.

Nonholonomic relativistic diffusion and exact solutions for stochastic Einstein spaces

NASA Astrophysics Data System (ADS)

Vacaru, S. I.

2012-03-01

We develop an approach to the theory of nonholonomic relativistic stochastic processes in curved spaces. The Itô and Stratonovich calculus are formulated for spaces with conventional horizontal (holonomic) and vertical (nonholonomic) splitting defined by nonlinear connection structures. Geometric models of the relativistic diffusion theory are elaborated for nonholonomic (pseudo) Riemannian manifolds and phase velocity spaces. Applying the anholonomic deformation method, the field equations in Einstein's gravity and various modifications are formally integrated in general forms, with generic off-diagonal metrics depending on some classes of generating and integration functions. Choosing random generating functions we can construct various classes of stochastic Einstein manifolds. We show how stochastic gravitational interactions with mixed holonomic/nonholonomic and random variables can be modelled in explicit form and study their main geometric and stochastic properties. Finally, the conditions when non-random classical gravitational processes transform into stochastic ones and inversely are analyzed.

de Bruijn cycles for neural decoding.

PubMed

Aguirre, Geoffrey Karl; Mattar, Marcelo Gomes; Magis-Weinberg, Lucía

2011-06-01

Stimulus counterbalance is critical for studies of neural habituation, bias, anticipation, and (more generally) the effect of stimulus history and context. We introduce de Bruijn cycles, a class of combinatorial objects, as the ideal source of pseudo-random stimulus sequences with arbitrary levels of counterbalance. Neuro-vascular imaging studies (such as BOLD fMRI) have an additional requirement imposed by the filtering and noise properties of the method: only some temporal frequencies of neural modulation are detectable. Extant methods of generating counterbalanced stimulus sequences yield neural modulations that are weakly (or not at all) detected by BOLD fMRI. We solve this limitation using a novel "path-guided" approach for the generation of de Bruijn cycles. The algorithm encodes a hypothesized neural modulation of specific temporal frequency within the seemingly random order of events. By positioning the modulation between the signal and noise bands of the neuro-vascular imaging method, the resulting sequence markedly improves detection power. These sequences may be used to study stimulus context and history effects in a manner not previously possible. Copyright © 2011 Elsevier Inc. All rights reserved.

Speech processing using maximum likelihood continuity mapping

DOEpatents

Hogden, John E.

2000-01-01

Speech processing is obtained that, given a probabilistic mapping between static speech sounds and pseudo-articulator positions, allows sequences of speech sounds to be mapped to smooth sequences of pseudo-articulator positions. In addition, a method for learning a probabilistic mapping between static speech sounds and pseudo-articulator position is described. The method for learning the mapping between static speech sounds and pseudo-articulator position uses a set of training data composed only of speech sounds. The said speech processing can be applied to various speech analysis tasks, including speech recognition, speaker recognition, speech coding, speech synthesis, and voice mimicry.

Speech processing using maximum likelihood continuity mapping

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

Hogden, J.E.

Speech processing is obtained that, given a probabilistic mapping between static speech sounds and pseudo-articulator positions, allows sequences of speech sounds to be mapped to smooth sequences of pseudo-articulator positions. In addition, a method for learning a probabilistic mapping between static speech sounds and pseudo-articulator position is described. The method for learning the mapping between static speech sounds and pseudo-articulator position uses a set of training data composed only of speech sounds. The said speech processing can be applied to various speech analysis tasks, including speech recognition, speaker recognition, speech coding, speech synthesis, and voice mimicry.

High density bit transition requirements versus the effects on BCH error correcting code. [bit synchronization

NASA Technical Reports Server (NTRS)

Ingels, F. M.; Schoggen, W. O.

1982-01-01

The design to achieve the required bit transition density for the Space Shuttle high rate multiplexes (HRM) data stream of the Space Laboratory Vehicle is reviewed. It contained a recommended circuit approach, specified the pseudo random (PN) sequence to be used and detailed the properties of the sequence. Calculations showing the probability of failing to meet the required transition density were included. A computer simulation of the data stream and PN cover sequence was provided. All worst case situations were simulated and the bit transition density exceeded that required. The Preliminary Design Review and the critical Design Review are documented. The Cover Sequence Generator (CSG) Encoder/Decoder design was constructed and demonstrated. The demonstrations were successful. All HRM and HRDM units incorporate the CSG encoder or CSG decoder as appropriate.

Laboratory complex for simulation of navigation signals of pseudosatellites

NASA Astrophysics Data System (ADS)

Ratushniak, V. N.; Gladyshev, A. B.; Sokolovskiy, A. V.; Mikhov, E. D.

2018-05-01

In the article, features of the organization, structure and questions of formation of navigation signals of pseudosatellites of the short - range navigation system based on the hardware-software complex National Instruments are considered. A software model that performs the formation and management of a pseudo-random sequence of a navigation signal and the formation and management of the format transmitted pseudosatellite navigation information is presented. The variant of constructing the transmitting equipment of the pseudosatellite base stations is provided.

Structural characterization of the N-terminal mineral modification domains from the molluscan crystal-modulating biomineralization proteins, AP7 and AP24.

PubMed

Wustman, Brandon A; Morse, Daniel E; Evans, John Spencer

2004-08-05

The AP7 and AP24 proteins represent a class of mineral-interaction polypeptides that are found in the aragonite-containing nacre layer of mollusk shell (H. rufescens). These proteins have been shown to preferentially interfere with calcium carbonate mineral growth in vitro. It is believed that both proteins play an important role in aragonite polymorph selection in the mollusk shell. Previously, we demonstrated the 1-30 amino acid (AA) N-terminal sequences of AP7 and AP24 represent mineral interaction/modification domains in both proteins, as evidenced by their ability to frustrate calcium carbonate crystal growth at step edge regions. In this present report, using free N-terminal, C(alpha)-amide "capped" synthetic polypeptides representing the 1-30 AA regions of AP7 (AP7-1 polypeptide) and AP24 (AP24-1 polypeptide) and NMR spectroscopy, we confirm that both N-terminal sequences possess putative Ca (II) interaction polyanionic sequence regions (2 x -DD- in AP7-1, -DDDED- in AP24-1) that are random coil-like in structure. However, with regard to the remaining sequences regions, each polypeptide features unique structural differences. AP7-1 possesses an extended beta-strand or polyproline type II-like structure within the A11-M10, S12-V13, and S28-I27 sequence regions, with the remaining sequence regions adopting a random-coil-like structure, a trait common to other polyelectrolyte mineral-associated polypeptide sequences. Conversely, AP24-1 possesses random coil-like structure within A1-S9 and Q14-N16 sequence regions, and evidence for turn-like, bend, or loop conformation within the G10-N13, Q17-N24, and M29-F30 sequence regions, similar to the structures identified within the putative elastomeric proteins Lustrin A and sea urchin spicule matrix proteins. The similarities and differences in AP7 and AP24 N-terminal domain structure are discussed with regard to joint AP7-AP24 protein modification of calcium carbonate growth. Copyright 2004 Wiley Periodicals, Inc.

A Systematic Prediction of Drug-Target Interactions Using Molecular Fingerprints and Protein Sequences.

PubMed

Huang, Yu-An; You, Zhu-Hong; Chen, Xing

2018-01-01

Drug-Target Interactions (DTI) play a crucial role in discovering new drug candidates and finding new proteins to target for drug development. Although the number of detected DTI obtained by high-throughput techniques has been increasing, the number of known DTI is still limited. On the other hand, the experimental methods for detecting the interactions among drugs and proteins are costly and inefficient. Therefore, computational approaches for predicting DTI are drawing increasing attention in recent years. In this paper, we report a novel computational model for predicting the DTI using extremely randomized trees model and protein amino acids information. More specifically, the protein sequence is represented as a Pseudo Substitution Matrix Representation (Pseudo-SMR) descriptor in which the influence of biological evolutionary information is retained. For the representation of drug molecules, a novel fingerprint feature vector is utilized to describe its substructure information. Then the DTI pair is characterized by concatenating the two vector spaces of protein sequence and drug substructure. Finally, the proposed method is explored for predicting the DTI on four benchmark datasets: Enzyme, Ion Channel, GPCRs and Nuclear Receptor. The experimental results demonstrate that this method achieves promising prediction accuracies of 89.85%, 87.87%, 82.99% and 81.67%, respectively. For further evaluation, we compared the performance of Extremely Randomized Trees model with that of the state-of-the-art Support Vector Machine classifier. And we also compared the proposed model with existing computational models, and confirmed 15 potential drug-target interactions by looking for existing databases. The experiment results show that the proposed method is feasible and promising for predicting drug-target interactions for new drug candidate screening based on sizeable features. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Random number generators tested on quantum Monte Carlo simulations.

PubMed

Hongo, Kenta; Maezono, Ryo; Miura, Kenichi

2010-08-01

We have tested and compared several (pseudo) random number generators (RNGs) applied to a practical application, ground state energy calculations of molecules using variational and diffusion Monte Carlo metheds. A new multiple recursive generator with 8th-order recursion (MRG8) and the Mersenne twister generator (MT19937) are tested and compared with the RANLUX generator with five luxury levels (RANLUX-[0-4]). Both MRG8 and MT19937 are proven to give the same total energy as that evaluated with RANLUX-4 (highest luxury level) within the statistical error bars with less computational cost to generate the sequence. We also tested the notorious implementation of linear congruential generator (LCG), RANDU, for comparison. (c) 2010 Wiley Periodicals, Inc.

Catalytic Activities Of [GADV]-Peptides

NASA Astrophysics Data System (ADS)

Oba, Takae; Fukushima, Jun; Maruyama, Masako; Iwamoto, Ryoko; Ikehara, Kenji

2005-10-01

We have previously postulated a novel hypothesis for the origin of life, assuming that life on the earth originated from “[GADV]-protein world”, not from the “RNA world” (see Ikehara's review, 2002). The [GADV]-protein world is constituted from peptides and proteins with random sequences of four amino acids (glycine [G], alanine [A], aspartic acid [D] and valine [V]), which accumulated by pseudo-replication of the [GADV]-proteins. To obtain evidence for the hypothesis, we produced [GADV]-peptides by repeated heat-drying of the amino acids for 30 cycles ([GADV]-P30) and examined whether the peptides have some catalytic activities or not. From the results, it was found that the [GADV]-P30 can hydrolyze several kinds of chemical bonds in molecules, such as umbelliferyl-β-D-galactoside, glycine-p-nitroanilide and bovine serum albumin. This suggests that [GADV]-P30 could play an important role in the accumulation of [GADV]-proteins through pseudo-replication, leading to the emergence of life. We further show that [GADV]-octapaptides with random sequences, but containing no cyclic compounds as diketepiperazines, have catalytic activity, hydrolyzing peptide bonds in a natural protein, bovine serum albumin. The catalytic activity of the octapeptides was much higher than the [GADV]-P30 produced through repeated heat-drying treatments. These results also support the [GADV]-protein-world hypothesis of the origin of life (see Ikehara's review, 2002). Possible steps for the emergence of life on the primitive earth are presented.

Prediction of protein S-nitrosylation sites based on adapted normal distribution bi-profile Bayes and Chou's pseudo amino acid composition.

PubMed

Jia, Cangzhi; Lin, Xin; Wang, Zhiping

2014-06-10

Protein S-nitrosylation is a reversible post-translational modification by covalent modification on the thiol group of cysteine residues by nitric oxide. Growing evidence shows that protein S-nitrosylation plays an important role in normal cellular function as well as in various pathophysiologic conditions. Because of the inherent chemical instability of the S-NO bond and the low abundance of endogenous S-nitrosylated proteins, the unambiguous identification of S-nitrosylation sites by commonly used proteomic approaches remains challenging. Therefore, computational prediction of S-nitrosylation sites has been considered as a powerful auxiliary tool. In this work, we mainly adopted an adapted normal distribution bi-profile Bayes (ANBPB) feature extraction model to characterize the distinction of position-specific amino acids in 784 S-nitrosylated and 1568 non-S-nitrosylated peptide sequences. We developed a support vector machine prediction model, iSNO-ANBPB, by incorporating ANBPB with the Chou's pseudo amino acid composition. In jackknife cross-validation experiments, iSNO-ANBPB yielded an accuracy of 65.39% and a Matthew's correlation coefficient (MCC) of 0.3014. When tested on an independent dataset, iSNO-ANBPB achieved an accuracy of 63.41% and a MCC of 0.2984, which are much higher than the values achieved by the existing predictors SNOSite, iSNO-PseAAC, the Li et al. algorithm, and iSNO-AAPair. On another training dataset, iSNO-ANBPB also outperformed GPS-SNO and iSNO-PseAAC in the 10-fold crossvalidation test.

iPhos-PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory.

PubMed

Qiu, Wang-Ren; Sun, Bi-Qian; Xiao, Xuan; Xu, Dong; Chou, Kuo-Chen

2017-05-01

Protein phosphorylation plays a critical role in human body by altering the structural conformation of a protein, causing it to become activated/deactivated, or functional modification. Given an uncharacterized protein sequence, can we predict whether it may be phosphorylated or may not? This is no doubt a very meaningful problem for both basic research and drug development. Unfortunately, to our best knowledge, so far no high throughput bioinformatics tool whatsoever has been developed to address such a very basic but important problem due to its extremely complexity and lacking sufficient training data. Here we proposed a predictor called iPhos-PseEvo by (1) incorporating the protein sequence evolutionary information into the general pseudo amino acid composition (PseAAC) via the grey system theory, (2) balancing out the skewed training datasets by the asymmetric bootstrap approach, and (3) constructing an ensemble predictor by fusing an array of individual random forest classifiers thru a voting system. Rigorous jackknife tests have indicated that very promising success rates have been achieved by iPhos-PseEvo even for such a difficult problem. A user-friendly web-server for iPhos-PseEvo has been established at http://www.jci-bioinfo.cn/iPhos-PseEvo, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. It has not escaped our notice that the formulation and approach presented here can be used to analyze many other problems in protein science as well. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Verifying Digital Components of Physical Systems: Experimental Evaluation of Test Quality

NASA Astrophysics Data System (ADS)

Laputenko, A. V.; López, J. E.; Yevtushenko, N. V.

2018-03-01

This paper continues the study of high quality test derivation for verifying digital components which are used in various physical systems; those are sensors, data transfer components, etc. We have used logic circuits b01-b010 of the package of ITC'99 benchmarks (Second Release) for experimental evaluation which as stated before, describe digital components of physical systems designed for various applications. Test sequences are derived for detecting the most known faults of the reference logic circuit using three different approaches to test derivation. Three widely used fault types such as stuck-at-faults, bridges, and faults which slightly modify the behavior of one gate are considered as possible faults of the reference behavior. The most interesting test sequences are short test sequences that can provide appropriate guarantees after testing, and thus, we experimentally study various approaches to the derivation of the so-called complete test suites which detect all fault types. In the first series of experiments, we compare two approaches for deriving complete test suites. In the first approach, a shortest test sequence is derived for testing each fault. In the second approach, a test sequence is pseudo-randomly generated by the use of an appropriate software for logic synthesis and verification (ABC system in our study) and thus, can be longer. However, after deleting sequences detecting the same set of faults, a test suite returned by the second approach is shorter. The latter underlines the fact that in many cases it is useless to spend `time and efforts' for deriving a shortest distinguishing sequence; it is better to use the test minimization afterwards. The performed experiments also show that the use of only randomly generated test sequences is not very efficient since such sequences do not detect all the faults of any type. After reaching the fault coverage around 70%, saturation is observed, and the fault coverage cannot be increased anymore. For deriving high quality short test suites, the approach that is the combination of randomly generated sequences together with sequences which are aimed to detect faults not detected by random tests, allows to reach the good fault coverage using shortest test sequences.

Comparison of tool feed influence in CNC polishing between a novel circular-random path and other pseudo-random paths.

PubMed

Takizawa, Ken; Beaucamp, Anthony

2017-09-18

A new category of circular pseudo-random paths is proposed in order to suppress repetitive patterns and improve surface waviness on ultra-precision polished surfaces. Random paths in prior research had many corners, therefore deceleration of the polishing tool affected the surface waviness. The new random path can suppress velocity changes of the polishing tool and thus restrict degradation of the surface waviness, making it suitable for applications with stringent mid-spatial-frequency requirements such as photomask blanks for EUV lithography.

Pseudo Steady-State Free Precession for MR-Fingerprinting.

PubMed

Assländer, Jakob; Glaser, Steffen J; Hennig, Jürgen

2017-03-01

This article discusses the signal behavior in the case the flip angle in steady-state free precession sequences is continuously varied as suggested for MR-fingerprinting sequences. Flip angle variations prevent the establishment of a steady state and introduce instabilities regarding to magnetic field inhomogeneities and intravoxel dephasing. We show how a pseudo steady state can be achieved, which restores the spin echo nature of steady-state free precession. Based on geometrical considerations, relationships between the flip angle, repetition and echo time are derived that suffice to the establishment of a pseudo steady state. The theory is tested with Bloch simulations as well as phantom and in vivo experiments. A typical steady-state free precession passband can be restored with the proposed conditions. The stability of the pseudo steady state is demonstrated by comparing the evolution of the signal of a single isochromat to one resulting from a spin ensemble. As confirmed by experiments, magnetization in a pseudo steady state can be described with fewer degrees of freedom compared to the original fingerprinting and the pseudo steady state results in more reliable parameter maps. The proposed conditions restore the spin-echo-like signal behavior typical for steady-state free precession in fingerprinting sequences, making this approach more robust to B 0 variations. Magn Reson Med 77:1151-1161, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Estimation of perfusion properties with MR Fingerprinting Arterial Spin Labeling.

PubMed

Wright, Katherine L; Jiang, Yun; Ma, Dan; Noll, Douglas C; Griswold, Mark A; Gulani, Vikas; Hernandez-Garcia, Luis

2018-03-12

In this study, the acquisition of ASL data and quantification of multiple hemodynamic parameters was explored using a Magnetic Resonance Fingerprinting (MRF) approach. A pseudo-continuous ASL labeling scheme was used with pseudo-randomized timings to acquire the MRF ASL data in a 2.5 min acquisition. A large dictionary of MRF ASL signals was generated by combining a wide range of physical and hemodynamic properties with the pseudo-random MRF ASL sequence and a two-compartment model. The acquired signals were matched to the dictionary to provide simultaneous quantification of cerebral blood flow, tissue time-to-peak, cerebral blood volume, arterial time-to-peak, B 1 , and T 1. A study in seven healthy volunteers resulted in the following values across the population in grey matter (mean ± standard deviation): cerebral blood flow of 69.1 ± 6.1 ml/min/100 g, arterial time-to-peak of 1.5 ± 0.1 s, tissue time-to-peak of 1.5 ± 0.1 s, T 1 of 1634 ms, cerebral blood volume of 0.0048 ± 0.0005. The CBF measurements were compared to standard pCASL CBF estimates using a one-compartment model, and a Bland-Altman analysis showed good agreement with a minor bias. Repeatability was tested in five volunteers in the same exam session, and no statistical difference was seen. In addition to this validation, the MRF ASL acquisition's sensitivity to the physical and physiological parameters of interest was studied numerically. Copyright © 2018 Elsevier Inc. All rights reserved.

Pseudo-random tool paths for CNC sub-aperture polishing and other applications.

PubMed

Dunn, Christina R; Walker, David D

2008-11-10

In this paper we first contrast classical and CNC polishing techniques in regard to the repetitiveness of the machine motions. We then present a pseudo-random tool path for use with CNC sub-aperture polishing techniques and report polishing results from equivalent random and raster tool-paths. The random tool-path used - the unicursal random tool-path - employs a random seed to generate a pattern which never crosses itself. Because of this property, this tool-path is directly compatible with dwell time maps for corrective polishing. The tool-path can be used to polish any continuous area of any boundary shape, including surfaces with interior perforations.

Synchronization of random bit generators based on coupled chaotic lasers and application to cryptography.

PubMed

Kanter, Ido; Butkovski, Maria; Peleg, Yitzhak; Zigzag, Meital; Aviad, Yaara; Reidler, Igor; Rosenbluh, Michael; Kinzel, Wolfgang

2010-08-16

Random bit generators (RBGs) constitute an important tool in cryptography, stochastic simulations and secure communications. The later in particular has some difficult requirements: high generation rate of unpredictable bit strings and secure key-exchange protocols over public channels. Deterministic algorithms generate pseudo-random number sequences at high rates, however, their unpredictability is limited by the very nature of their deterministic origin. Recently, physical RBGs based on chaotic semiconductor lasers were shown to exceed Gbit/s rates. Whether secure synchronization of two high rate physical RBGs is possible remains an open question. Here we propose a method, whereby two fast RBGs based on mutually coupled chaotic lasers, are synchronized. Using information theoretic analysis we demonstrate security against a powerful computational eavesdropper, capable of noiseless amplification, where all parameters are publicly known. The method is also extended to secure synchronization of a small network of three RBGs.

Pulse homodyne field disturbance sensor

DOEpatents

McEwan, Thomas E.

1997-01-01

A field disturbance sensor operates with relatively low power, provides an adjustable operating range, is not hypersensitive at close range, allows co-location of multiple sensors, and is inexpensive to manufacture. The sensor includes a transmitter that transmits a sequence of transmitted bursts of electromagnetic energy. The transmitter frequency is modulated at an intermediate frequency. The sequence of bursts has a burst repetition rate, and each burst has a burst width and comprises a number of cycles at a transmitter frequency. The sensor includes a receiver which receives electromagnetic energy at the transmitter frequency, and includes a mixer which mixes a transmitted burst with reflections of the same transmitted burst to produce an intermediate frequency signal. Circuitry, responsive to the intermediate frequency signal indicates disturbances in the sensor field. Because the mixer mixes the transmitted burst with reflections of the transmitted burst, the burst width defines the sensor range. The burst repetition rate is randomly or pseudo-randomly modulated so that bursts in the sequence of bursts have a phase which varies. A second range-defining mode transmits two radio frequency bursts, where the time spacing between the bursts defines the maximum range divided by two.

Pulse homodyne field disturbance sensor

DOEpatents

McEwan, T.E.

1997-10-28

A field disturbance sensor operates with relatively low power, provides an adjustable operating range, is not hypersensitive at close range, allows co-location of multiple sensors, and is inexpensive to manufacture. The sensor includes a transmitter that transmits a sequence of transmitted bursts of electromagnetic energy. The transmitter frequency is modulated at an intermediate frequency. The sequence of bursts has a burst repetition rate, and each burst has a burst width and comprises a number of cycles at a transmitter frequency. The sensor includes a receiver which receives electromagnetic energy at the transmitter frequency, and includes a mixer which mixes a transmitted burst with reflections of the same transmitted burst to produce an intermediate frequency signal. Circuitry, responsive to the intermediate frequency signal indicates disturbances in the sensor field. Because the mixer mixes the transmitted burst with reflections of the transmitted burst, the burst width defines the sensor range. The burst repetition rate is randomly or pseudo-randomly modulated so that bursts in the sequence of bursts have a phase which varies. A second range-defining mode transmits two radio frequency bursts, where the time spacing between the bursts defines the maximum range divided by two. 12 figs.

Sequence charge decoration dictates coil-globule transition in intrinsically disordered proteins.

PubMed

Firman, Taylor; Ghosh, Kingshuk

2018-03-28

We present an analytical theory to compute conformations of heteropolymers-applicable to describe disordered proteins-as a function of temperature and charge sequence. The theory describes coil-globule transition for a given protein sequence when temperature is varied and has been benchmarked against the all-atom Monte Carlo simulation (using CAMPARI) of intrinsically disordered proteins (IDPs). In addition, the model quantitatively shows how subtle alterations of charge placement in the primary sequence-while maintaining the same charge composition-can lead to significant changes in conformation, even as drastic as a coil (swelled above a purely random coil) to globule (collapsed below a random coil) and vice versa. The theory provides insights on how to control (enhance or suppress) these changes by tuning the temperature (or solution condition) and charge decoration. As an application, we predict the distribution of conformations (at room temperature) of all naturally occurring IDPs in the DisProt database and notice significant size variation even among IDPs with a similar composition of positive and negative charges. Based on this, we provide a new diagram-of-states delineating the sequence-conformation relation for proteins in the DisProt database. Next, we study the effect of post-translational modification, e.g., phosphorylation, on IDP conformations. Modifications as little as two-site phosphorylation can significantly alter the size of an IDP with everything else being constant (temperature, salt concentration, etc.). However, not all possible modification sites have the same effect on protein conformations; there are certain "hot spots" that can cause maximal change in conformation. The location of these "hot spots" in the parent sequence can readily be identified by using a sequence charge decoration metric originally introduced by Sawle and Ghosh. The ability of our model to predict conformations (both expanded and collapsed states) of IDPs at a high-throughput level can provide valuable insights into the different mechanisms by which phosphorylation/charge mutation controls IDP function.

On the predictive control of foveal eye tracking and slow phases of optokinetic and vestibular nystagmus.

PubMed Central

Yasui, S; Young, L R

1984-01-01

Smooth pursuit and saccadic components of foveal visual tracking as well as more involuntary ocular movements of optokinetic (o.k.n.) and vestibular nystagmus slow phase components were investigated in man, with particular attention given to their possible input-adaptive or predictive behaviour. Each component in question was isolated from the eye movement records through a computer-aided procedure. The frequency response method was used with sinusoidal (predictable) and pseudo-random (unpredictable) stimuli. When the target motion was pseudo-random, the frequency response of pursuit eye movements revealed a large phase lead (up to about 90 degrees) at low stimulus frequencies. It is possible to interpret this result as a predictive effect, even though the stimulation was pseudo-random and thus 'unpredictable'. The pseudo-random-input frequency response intrinsic to the saccadic system was estimated in an indirect way from the pursuit and composite (pursuit + saccade) frequency response data. The result was fitted well by a servo-mechanism model, which has a simple anticipatory mechanism to compensate for the inherent neuromuscular saccadic delay by utilizing the retinal slip velocity signal. The o.k.n. slow phase also exhibited a predictive effect with sinusoidal inputs; however, pseudo-random stimuli did not produce such phase lead as found in the pursuit case. The vestibular nystagmus slow phase showed no noticeable sign of prediction in the frequency range examined (0 approximately 0.7 Hz), in contrast to the results of the visually driven eye movements (i.e. saccade, pursuit and o.k.n. slow phase) at comparable stimulus frequencies. PMID:6707954

Automated brain tumor segmentation using spatial accuracy-weighted hidden Markov Random Field.

PubMed

Nie, Jingxin; Xue, Zhong; Liu, Tianming; Young, Geoffrey S; Setayesh, Kian; Guo, Lei; Wong, Stephen T C

2009-09-01

A variety of algorithms have been proposed for brain tumor segmentation from multi-channel sequences, however, most of them require isotropic or pseudo-isotropic resolution of the MR images. Although co-registration and interpolation of low-resolution sequences, such as T2-weighted images, onto the space of the high-resolution image, such as T1-weighted image, can be performed prior to the segmentation, the results are usually limited by partial volume effects due to interpolation of low-resolution images. To improve the quality of tumor segmentation in clinical applications where low-resolution sequences are commonly used together with high-resolution images, we propose the algorithm based on Spatial accuracy-weighted Hidden Markov random field and Expectation maximization (SHE) approach for both automated tumor and enhanced-tumor segmentation. SHE incorporates the spatial interpolation accuracy of low-resolution images into the optimization procedure of the Hidden Markov Random Field (HMRF) to segment tumor using multi-channel MR images with different resolutions, e.g., high-resolution T1-weighted and low-resolution T2-weighted images. In experiments, we evaluated this algorithm using a set of simulated multi-channel brain MR images with known ground-truth tissue segmentation and also applied it to a dataset of MR images obtained during clinical trials of brain tumor chemotherapy. The results show that more accurate tumor segmentation results can be obtained by comparing with conventional multi-channel segmentation algorithms.

Pseudo-Random Number Generation in Children with High-Functioning Autism and Asperger's Disorder: Further Evidence for a Dissociation in Executive Functioning?

ERIC Educational Resources Information Center

Rinehart, Nicole J.; Bradshaw, John L.; Moss, Simon A.; Brereton, Avril V.; Tonge, Bruce J.

2006-01-01

The repetitive, stereotyped and obsessive behaviours, which are core diagnostic features of autism, are thought to be underpinned by executive dysfunction. This study examined executive impairment in individuals with autism and Asperger's disorder using a verbal equivalent of an established pseudo-random number generating task. Different patterns…

An algorithm to compute the sequency ordered Walsh transform

NASA Technical Reports Server (NTRS)

Larsen, H.

1976-01-01

A fast sequency-ordered Walsh transform algorithm is presented; this sequency-ordered fast transform is complementary to the sequency-ordered fast Walsh transform introduced by Manz (1972) and eliminating gray code reordering through a modification of the basic fast Hadamard transform structure. The new algorithm retains the advantages of its complement (it is in place and is its own inverse), while differing in having a decimation-in time structure, accepting data in normal order, and returning the coefficients in bit-reversed sequency order. Applications include estimation of Walsh power spectra for a random process, sequency filtering and computing logical autocorrelations, and selective bit reversing.

Calibration of the modulation transfer function of surface profilometers with binary pseudo-random test standards: expanding the application range

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

Yashchuk, Valeriy V.; Anderson, Erik H.; Barber, Samuel K.

2011-03-14

A modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) gratings and arrays [Proc. SPIE 7077-7 (2007), Opt. Eng. 47, 073602 (2008)] has been proven to be an effective MTF calibration method for a number of interferometric microscopes and a scatterometer [Nucl. Instr. and Meth. A616, 172 (2010)]. Here we report on a further expansion of the application range of the method. We describe the MTF calibration of a 6 inch phase shifting Fizeau interferometer. Beyond providing a direct measurement of the interferometer's MTF, tests with a BPR array surface have revealed an asymmetry in the instrument's datamore » processing algorithm that fundamentally limits its bandwidth. Moreover, the tests have illustrated the effects of the instrument's detrending and filtering procedures on power spectral density measurements. The details of the development of a BPR test sample suitable for calibration of scanning and transmission electron microscopes are also presented. Such a test sample is realized as a multilayer structure with the layer thicknesses of two materials corresponding to BPR sequence. The investigations confirm the universal character of the method that makes it applicable to a large variety of metrology instrumentation with spatial wavelength bandwidths from a few nanometers to hundreds of millimeters.« less

Binary pseudo-random patterned structures for modulation transfer function calibration and resolution characterization of a full-field transmission soft x-ray microscope

DOE PAGES

Yashchuk, V. V.; Fischer, P. J.; Chan, E. R.; ...

2015-12-09

We present a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) one-dimensional sequences and two-dimensional arrays as an effective method for spectral characterization in the spatial frequency domain of a broad variety of metrology instrumentation, including interferometric microscopes, scatterometers, phase shifting Fizeau interferometers, scanning and transmission electron microscopes, and at this time, x-ray microscopes. The inherent power spectral density of BPR gratings and arrays, which has a deterministic white-noise-like character, allows a direct determination of the MTF with a uniform sensitivity over the entire spatial frequency range and field of view of an instrument. We demonstrate themore » MTF calibration and resolution characterization over the full field of a transmission soft x-ray microscope using a BPR multilayer (ML) test sample with 2.8 nm fundamental layer thickness. We show that beyond providing a direct measurement of the microscope's MTF, tests with the BPRML sample can be used to fine tune the instrument's focal distance. Finally, our results confirm the universality of the method that makes it applicable to a large variety of metrology instrumentation with spatial wavelength bandwidths from a few nanometers to hundreds of millimeters.« less

Encryption method based on pseudo random spatial light modulation for single-fibre data transmission

NASA Astrophysics Data System (ADS)

Kowalski, Marcin; Zyczkowski, Marek

2017-11-01

Optical cryptosystems can provide encryption and sometimes compression simultaneously. They are increasingly attractive for information securing especially for image encryption. Our studies shown that the optical cryptosystems can be used to encrypt optical data transmission. We propose and study a new method for securing fibre data communication. The paper presents a method for optical encryption of data transmitted with a single optical fibre. The encryption process relies on pseudo-random spatial light modulation, combination of two encryption keys and the Compressed Sensing framework. A linear combination of light pulses with pseudo-random patterns provides a required encryption performance. We propose an architecture to transmit the encrypted data through the optical fibre. The paper describes the method, presents the theoretical analysis, design of physical model and results of experiment.

Red, green, blue equals 1, 2, 3: Digit-color synesthetes can use structured digit information to boost recall of color sequences.

PubMed

Teichmann, A Lina; Nieuwenstein, Mark R; Rich, Anina N

2015-01-01

Digit-color synesthetes report experiencing colors when perceiving letters and digits. The conscious experience is typically unidirectional (e.g., digits elicit colors but not vice versa) but recent evidence shows subtle bidirectional effects. We examined whether short-term memory for colors could be affected by the order of presentation reflecting more or less structure in the associated digits. We presented a stream of colored squares and asked participants to report the colors in order. The colors matched each synesthete's colors for digits 1-9 and the order of the colors corresponded either to a sequence of numbers (e.g., [red, green, blue] if 1 = red, 2 = green, 3 = blue) or no systematic sequence. The results showed that synesthetes recalled sequential color sequences more accurately than pseudo-randomized colors, whereas no such effect was found for the non-synesthetic controls. Synesthetes did not differ from non-synesthetic controls in recall of color sequences overall, providing no evidence of a general advantage in memory for serial recall of colors.

Faster heart rate and muscular oxygen uptake kinetics in type 2 diabetes patients following endurance training.

PubMed

Koschate, Jessica; Drescher, Uwe; Brinkmann, Christian; Baum, Klaus; Schiffer, Thorsten; Latsch, Joachim; Brixius, Klara; Hoffmann, Uwe

2016-11-01

Cardiorespiratory kinetics were analyzed in type 2 diabetes patients before and after a 12-week endurance exercise-training intervention. It was hypothesized that muscular oxygen uptake and heart rate (HR) kinetics would be faster after the training intervention and that this would be detectable using a standardized work rate protocol with pseudo-random binary sequences. The cardiorespiratory kinetics of 13 male sedentary, middle-aged, overweight type 2 diabetes patients (age, 60 ± 8 years; body mass index, 33 ± 4 kg·m -2 ) were tested before and after the 12-week exercise intervention. Subjects performed endurance training 3 times a week on nonconsecutive days. Pseudo-random binary sequences exercise protocols in combination with time series analysis were used to estimate kinetics. Greater maxima in cross-correlation functions (CCF max ) represent faster kinetics of the respective parameter. CCF max of muscular oxygen uptake (pre-training: 0.31 ± 0.03; post-training: 0.37 ± 0.1, P = 0.024) and CCF max of HR (pre-training: 0.25 ± 0.04; post-training: 0.29 ± 0.06, P = 0.007) as well as peak oxygen uptake (pre-training: 24.4 ± 4.7 mL·kg -1 ·min -1 ; post-training: 29.3 ± 6.5 mL·kg -1 ·min -1 , P = 0.004) increased significantly over the course of the exercise intervention. In conclusion, kinetic responses to changing work rates in the moderate-intensity range are similar to metabolic demands occurring in everyday habitual activities. Moderate endurance training accelerated the kinetic responses of HR and muscular oxygen uptake. Furthermore, the applicability of the used method to detect these accelerations was demonstrated.

Sequence charge decoration dictates coil-globule transition in intrinsically disordered proteins

NASA Astrophysics Data System (ADS)

Firman, Taylor; Ghosh, Kingshuk

2018-03-01

We present an analytical theory to compute conformations of heteropolymers—applicable to describe disordered proteins—as a function of temperature and charge sequence. The theory describes coil-globule transition for a given protein sequence when temperature is varied and has been benchmarked against the all-atom Monte Carlo simulation (using CAMPARI) of intrinsically disordered proteins (IDPs). In addition, the model quantitatively shows how subtle alterations of charge placement in the primary sequence—while maintaining the same charge composition—can lead to significant changes in conformation, even as drastic as a coil (swelled above a purely random coil) to globule (collapsed below a random coil) and vice versa. The theory provides insights on how to control (enhance or suppress) these changes by tuning the temperature (or solution condition) and charge decoration. As an application, we predict the distribution of conformations (at room temperature) of all naturally occurring IDPs in the DisProt database and notice significant size variation even among IDPs with a similar composition of positive and negative charges. Based on this, we provide a new diagram-of-states delineating the sequence-conformation relation for proteins in the DisProt database. Next, we study the effect of post-translational modification, e.g., phosphorylation, on IDP conformations. Modifications as little as two-site phosphorylation can significantly alter the size of an IDP with everything else being constant (temperature, salt concentration, etc.). However, not all possible modification sites have the same effect on protein conformations; there are certain "hot spots" that can cause maximal change in conformation. The location of these "hot spots" in the parent sequence can readily be identified by using a sequence charge decoration metric originally introduced by Sawle and Ghosh. The ability of our model to predict conformations (both expanded and collapsed states) of IDPs at a high-throughput level can provide valuable insights into the different mechanisms by which phosphorylation/charge mutation controls IDP function.

The pseudo-Boolean optimization approach to form the N-version software structure

NASA Astrophysics Data System (ADS)

Kovalev, I. V.; Kovalev, D. I.; Zelenkov, P. V.; Voroshilova, A. A.

2015-10-01

The problem of developing an optimal structure of N-version software system presents a kind of very complex optimization problem. This causes the use of deterministic optimization methods inappropriate for solving the stated problem. In this view, exploiting heuristic strategies looks more rational. In the field of pseudo-Boolean optimization theory, the so called method of varied probabilities (MVP) has been developed to solve problems with a large dimensionality. Some additional modifications of MVP have been made to solve the problem of N-version systems design. Those algorithms take into account the discovered specific features of the objective function. The practical experiments have shown the advantage of using these algorithm modifications because of reducing a search space.

An Alignment-Free Algorithm in Comparing the Similarity of Protein Sequences Based on Pseudo-Markov Transition Probabilities among Amino Acids

PubMed Central

Li, Yushuang; Yang, Jiasheng; Zhang, Yi

2016-01-01

In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences. We then apply this method into the ND5 dataset consisting of the ND5 protein sequences of 9 species, and the F10 and G11 datasets representing two of the xylanases containing glycoside hydrolase families, i.e., families 10 and 11. As a result, our method achieves a correlation coefficient of 0.962 with the canonical protein sequence aligner ClustalW in the ND5 dataset, much higher than those of other 5 popular alignment-free methods. In addition, we successfully separate the xylanases sequences in the F10 family and the G11 family and illustrate that the F10 family is more heat stable than the G11 family, consistent with a few previous studies. Moreover, we prove mathematically an identity equation involving the Pseudo-Markov transition probability vector and the amino acids content ratio vector. PMID:27918587

Lensless digital holography with diffuse illumination through a pseudo-random phase mask.

PubMed

Bernet, Stefan; Harm, Walter; Jesacher, Alexander; Ritsch-Marte, Monika

2011-12-05

Microscopic imaging with a setup consisting of a pseudo-random phase mask, and an open CMOS camera, without an imaging objective, is demonstrated. The pseudo random phase mask acts as a diffuser for an incoming laser beam, scattering a speckle pattern to a CMOS chip, which is recorded once as a reference. A sample which is afterwards inserted somewhere in the optical beam path changes the speckle pattern. A single (non-iterative) image processing step, comparing the modified speckle pattern with the previously recorded one, generates a sharp image of the sample. After a first calibration the method works in real-time and allows quantitative imaging of complex (amplitude and phase) samples in an extended three-dimensional volume. Since no lenses are used, the method is free from lens abberations. Compared to standard inline holography the diffuse sample illumination improves the axial sectioning capability by increasing the effective numerical aperture in the illumination path, and it suppresses the undesired so-called twin images. For demonstration, a high resolution spatial light modulator (SLM) is programmed to act as the pseudo-random phase mask. We show experimental results, imaging microscopic biological samples, e.g. insects, within an extended volume at a distance of 15 cm with a transverse and longitudinal resolution of about 60 μm and 400 μm, respectively.

Quantum Hash function and its application to privacy amplification in quantum key distribution, pseudo-random number generation and image encryption

NASA Astrophysics Data System (ADS)

Yang, Yu-Guang; Xu, Peng; Yang, Rui; Zhou, Yi-Hua; Shi, Wei-Min

2016-01-01

Quantum information and quantum computation have achieved a huge success during the last years. In this paper, we investigate the capability of quantum Hash function, which can be constructed by subtly modifying quantum walks, a famous quantum computation model. It is found that quantum Hash function can act as a hash function for the privacy amplification process of quantum key distribution systems with higher security. As a byproduct, quantum Hash function can also be used for pseudo-random number generation due to its inherent chaotic dynamics. Further we discuss the application of quantum Hash function to image encryption and propose a novel image encryption algorithm. Numerical simulations and performance comparisons show that quantum Hash function is eligible for privacy amplification in quantum key distribution, pseudo-random number generation and image encryption in terms of various hash tests and randomness tests. It extends the scope of application of quantum computation and quantum information.

Quantum Hash function and its application to privacy amplification in quantum key distribution, pseudo-random number generation and image encryption

PubMed Central

Yang, Yu-Guang; Xu, Peng; Yang, Rui; Zhou, Yi-Hua; Shi, Wei-Min

2016-01-01

Quantum information and quantum computation have achieved a huge success during the last years. In this paper, we investigate the capability of quantum Hash function, which can be constructed by subtly modifying quantum walks, a famous quantum computation model. It is found that quantum Hash function can act as a hash function for the privacy amplification process of quantum key distribution systems with higher security. As a byproduct, quantum Hash function can also be used for pseudo-random number generation due to its inherent chaotic dynamics. Further we discuss the application of quantum Hash function to image encryption and propose a novel image encryption algorithm. Numerical simulations and performance comparisons show that quantum Hash function is eligible for privacy amplification in quantum key distribution, pseudo-random number generation and image encryption in terms of various hash tests and randomness tests. It extends the scope of application of quantum computation and quantum information. PMID:26823196

Quantum Hash function and its application to privacy amplification in quantum key distribution, pseudo-random number generation and image encryption.

PubMed

Yang, Yu-Guang; Xu, Peng; Yang, Rui; Zhou, Yi-Hua; Shi, Wei-Min

2016-01-29

Quantum information and quantum computation have achieved a huge success during the last years. In this paper, we investigate the capability of quantum Hash function, which can be constructed by subtly modifying quantum walks, a famous quantum computation model. It is found that quantum Hash function can act as a hash function for the privacy amplification process of quantum key distribution systems with higher security. As a byproduct, quantum Hash function can also be used for pseudo-random number generation due to its inherent chaotic dynamics. Further we discuss the application of quantum Hash function to image encryption and propose a novel image encryption algorithm. Numerical simulations and performance comparisons show that quantum Hash function is eligible for privacy amplification in quantum key distribution, pseudo-random number generation and image encryption in terms of various hash tests and randomness tests. It extends the scope of application of quantum computation and quantum information.

pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes.

PubMed

Chan, Wen-Ling; Yang, Wen-Kuang; Huang, Hsien-Da; Chang, Jan-Gowth

2013-01-01

RNA interference (RNAi) is a gene silencing process within living cells, which is controlled by the RNA-induced silencing complex with a sequence-specific manner. In flies and mice, the pseudogene transcripts can be processed into short interfering RNAs (siRNAs) that regulate protein-coding genes through the RNAi pathway. Following these findings, we construct an innovative and comprehensive database to elucidate siRNA-mediated mechanism in human transcribed pseudogenes (TPGs). To investigate TPG producing siRNAs that regulate protein-coding genes, we mapped the TPGs to small RNAs (sRNAs) that were supported by publicly deep sequencing data from various sRNA libraries and constructed the TPG-derived siRNA-target interactions. In addition, we also presented that TPGs can act as a target for miRNAs that actually regulate the parental gene. To enable the systematic compilation and updating of these results and additional information, we have developed a database, pseudoMap, capturing various types of information, including sequence data, TPG and cognate annotation, deep sequencing data, RNA-folding structure, gene expression profiles, miRNA annotation and target prediction. As our knowledge, pseudoMap is the first database to demonstrate two mechanisms of human TPGs: encoding siRNAs and decoying miRNAs that target the parental gene. pseudoMap is freely accessible at http://pseudomap.mbc.nctu.edu.tw/. Database URL: http://pseudomap.mbc.nctu.edu.tw/

High-throughput and site-specific identification of 2'-O-methylation sites using ribose oxidation sequencing (RibOxi-seq).

PubMed

Zhu, Yinzhou; Pirnie, Stephan P; Carmichael, Gordon G

2017-08-01

Ribose methylation (2'- O -methylation, 2'- O Me) occurs at high frequencies in rRNAs and other small RNAs and is carried out using a shared mechanism across eukaryotes and archaea. As RNA modifications are important for ribosome maturation, and alterations in these modifications are associated with cellular defects and diseases, it is important to characterize the landscape of 2'- O -methylation. Here we report the development of a highly sensitive and accurate method for ribose methylation detection using next-generation sequencing. A key feature of this method is the generation of RNA fragments with random 3'-ends, followed by periodate oxidation of all molecules terminating in 2',3'-OH groups. This allows only RNAs harboring 2'-OMe groups at their 3'-ends to be sequenced. Although currently requiring microgram amounts of starting material, this method is robust for the analysis of rRNAs even at low sequencing depth. © 2017 Zhu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Synthesis, Improved Antisense Activity and Structural Rationale for the Divergent RNA Affinities of 3;#8242;-Fluoro Hexitol Nucleic Acid (FHNA and Ara-FHNA) Modified Oligonucleotides

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

Egli, Martin; Pallan, Pradeep S.; Allerson, Charles R.

The synthesis, biophysical, structural, and biological properties of both isomers of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with a 3'-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structuresmore » of A-type DNA duplexes modified with either monomer provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an internucleotide C-F {hor_ellipsis} H-C pseudo hydrogen bond between F3' of Ara-FHNA and C8-H of the nucleobase from the 3'-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonucleotides formulated in saline showed a potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py) {hor_ellipsis} H-C(Pu) pseudo hydrogen bonds in nucleic acid structures.« less

Sequence specificity of the human mRNA N6-adenosine methylase in vitro.

PubMed Central

Harper, J E; Miceli, S M; Roberts, R J; Manley, J L

1990-01-01

N6-adenosine methylation is a frequent modification of mRNAs and their precursors, but little is known about the mechanism of the reaction or the function of the modification. To explore these questions, we developed conditions to examine N6-adenosine methylase activity in HeLa cell nuclear extracts. Transfer of the methyl group from S-[3H methyl]-adenosylmethionine to unlabeled random copolymer RNA substrates of varying ribonucleotide composition revealed a substrate specificity consistent with a previously deduced consensus sequence, Pu[G greater than A]AC[A/C/U]. 32-P labeled RNA substrates of defined sequence were used to examine the minimum sequence requirements for methylation. Each RNA was 20 nucleotides long, and contained either the core consensus sequence GGACU, or some variation of this sequence. RNAs containing GGACU, either in single or multiple copies, were good substrates for methylation, whereas RNAs containing single base substitutions within the GGACU sequence gave dramatically reduced methylation. These results demonstrate that the N6-adenosine methylase has a strict sequence specificity, and that there is no requirement for extended sequences or secondary structures for methylation. Recognition of this sequence does not require an RNA component, as micrococcal nuclease pretreatment of nuclear extracts actually increased methylation efficiency. Images PMID:2216767

Pulse Compression Techniques for Laser Generated Ultrasound

NASA Technical Reports Server (NTRS)

Anastasi, R. F.; Madaras, E. I.

1999-01-01

Laser generated ultrasound for nondestructive evaluation has an optical power density limit due to rapid high heating that causes material damage. This damage threshold limits the generated ultrasound amplitude, which impacts nondestructive evaluation inspection capability. To increase ultrasound signal levels and improve the ultrasound signal-to-noise ratio without exceeding laser power limitations, it is possible to use pulse compression techniques. The approach illustrated here uses a 150mW laser-diode modulated with a pseudo-random sequence and signal correlation. Results demonstrate the successful generation of ultrasonic bulk waves in aluminum and graphite-epoxy composite materials using a modulated low-power laser diode and illustrate ultrasound bandwidth control.

Elastic properties of graphene: A pseudo-beam model with modified internal bending moment and its application

NASA Astrophysics Data System (ADS)

Xia, Z. M.; Wang, C. G.; Tan, H. F.

2018-04-01

A pseudo-beam model with modified internal bending moment is presented to predict elastic properties of graphene, including the Young's modulus and Poisson's ratio. In order to overcome a drawback in existing molecular structural mechanics models, which only account for pure bending (constant bending moment), the presented model accounts for linear bending moments deduced from the balance equations. Based on this pseudo-beam model, an analytical prediction is accomplished to predict the Young's modulus and Poisson's ratio of graphene based on the equation of the strain energies by using Castigliano second theorem. Then, the elastic properties of graphene are calculated compared with results available in literature, which verifies the feasibility of the pseudo-beam model. Finally, the pseudo-beam model is utilized to study the twisting wrinkling characteristics of annular graphene. Due to modifications of the internal bending moment, the wrinkling behaviors of graphene sheet are predicted accurately. The obtained results show that the pseudo-beam model has a good ability to predict the elastic properties of graphene accurately, especially the out-of-plane deformation behavior.

Pseudo-random number generator for the Sigma 5 computer

NASA Technical Reports Server (NTRS)

Carroll, S. N.

1983-01-01

A technique is presented for developing a pseudo-random number generator based on the linear congruential form. The two numbers used for the generator are a prime number and a corresponding primitive root, where the prime is the largest prime number that can be accurately represented on a particular computer. The primitive root is selected by applying Marsaglia's lattice test. The technique presented was applied to write a random number program for the Sigma 5 computer. The new program, named S:RANDOM1, is judged to be superior to the older program named S:RANDOM. For applications requiring several independent random number generators, a table is included showing several acceptable primitive roots. The technique and programs described can be applied to any computer having word length different from that of the Sigma 5.

The RANDOM computer program: A linear congruential random number generator

NASA Technical Reports Server (NTRS)

Miles, R. F., Jr.

1986-01-01

The RANDOM Computer Program is a FORTRAN program for generating random number sequences and testing linear congruential random number generators (LCGs). The linear congruential form of random number generator is discussed, and the selection of parameters of an LCG for a microcomputer described. This document describes the following: (1) The RANDOM Computer Program; (2) RANDOM.MOD, the computer code needed to implement an LCG in a FORTRAN program; and (3) The RANCYCLE and the ARITH Computer Programs that provide computational assistance in the selection of parameters for an LCG. The RANDOM, RANCYCLE, and ARITH Computer Programs are written in Microsoft FORTRAN for the IBM PC microcomputer and its compatibles. With only minor modifications, the RANDOM Computer Program and its LCG can be run on most micromputers or mainframe computers.

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

PubMed Central

Schadt, Eric E.; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H.; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A.; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types. PMID:23093720

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.

PubMed

Schadt, Eric E; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types.

Optical image encryption using chaos-based compressed sensing and phase-shifting interference in fractional wavelet domain

NASA Astrophysics Data System (ADS)

Liu, Qi; Wang, Ying; Wang, Jun; Wang, Qiong-Hua

2018-02-01

In this paper, a novel optical image encryption system combining compressed sensing with phase-shifting interference in fractional wavelet domain is proposed. To improve the encryption efficiency, the volume data of original image are decreased by compressed sensing. Then the compacted image is encoded through double random phase encoding in asymmetric fractional wavelet domain. In the encryption system, three pseudo-random sequences, generated by three-dimensional chaos map, are used as the measurement matrix of compressed sensing and two random-phase masks in the asymmetric fractional wavelet transform. It not only simplifies the keys to storage and transmission, but also enhances our cryptosystem nonlinearity to resist some common attacks. Further, holograms make our cryptosystem be immune to noises and occlusion attacks, which are obtained by two-step-only quadrature phase-shifting interference. And the compression and encryption can be achieved in the final result simultaneously. Numerical experiments have verified the security and validity of the proposed algorithm.

Calibration of the modulation transfer function of surface profilometers with binary pseudo-random test standards: Expanding the application range

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

Yashchuk, Valeriy V; Anderson, Erik H.; Barber, Samuel K.

2010-07-26

A modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) gratings and arrays [Proc. SPIE 7077-7 (2007), Opt. Eng. 47(7), 073602-1-5 (2008)] has been proven to be an effective MTF calibration method for a number of interferometric microscopes and a scatterometer [Nucl. Instr. and Meth. A 616, 172-82 (2010]. Here we report on a significant expansion of the application range of the method. We describe the MTF calibration of a 6 inch phase shifting Fizeau interferometer. Beyond providing a direct measurement of the interferometer's MTF, tests with a BPR array surface have revealed an asymmetry in the instrument'smore » data processing algorithm that fundamentally limits its bandwidth. Moreover, the tests have illustrated the effects of the instrument's detrending and filtering procedures on power spectral density measurements. The details of the development of a BPR test sample suitable for calibration of scanning and transmission electron microscopes are also presented. Such a test sample is realized as a multilayer structure with the layer thicknesses of two materials corresponding to BPR sequence. The investigations confirm the universal character of the method that makes it applicable to a large variety of metrology instrumentation with spatial wavelength bandwidths from a few nanometers to hundreds of millimeters.« less

Accelerating Pseudo-Random Number Generator for MCNP on GPU

NASA Astrophysics Data System (ADS)

Gong, Chunye; Liu, Jie; Chi, Lihua; Hu, Qingfeng; Deng, Li; Gong, Zhenghu

2010-09-01

Pseudo-random number generators (PRNG) are intensively used in many stochastic algorithms in particle simulations, artificial neural networks and other scientific computation. The PRNG in Monte Carlo N-Particle Transport Code (MCNP) requires long period, high quality, flexible jump and fast enough. In this paper, we implement such a PRNG for MCNP on NVIDIA's GTX200 Graphics Processor Units (GPU) using CUDA programming model. Results shows that 3.80 to 8.10 times speedup are achieved compared with 4 to 6 cores CPUs and more than 679.18 million double precision random numbers can be generated per second on GPU.

[A magnetic therapy apparatus with an adaptable electromagnetic spectrum for the treatment of prostatitis and gynecopathies].

PubMed

Kuz'min, A A; Meshkovskiĭ, D V; Filist, S A

2008-01-01

Problems of engineering and algorithm development of magnetic therapy apparatuses with pseudo-random radiation spectrum within the audio range for treatment of prostatitis and gynecopathies are considered. A typical design based on a PIC 16F microcontroller is suggested. It includes a keyboard, LCD indicator, audio amplifier, inducer, and software units. The problem of pseudo-random signal generation within the audio range is considered. A series of rectangular pulses is generated on a random-length interval on the basis of a three-component random vector. This series provides the required spectral characteristics of the therapeutic magnetic field and their adaptation to the therapeutic conditions and individual features of the patient.

Generation of pseudo-random numbers

NASA Technical Reports Server (NTRS)

Howell, L. W.; Rheinfurth, M. H.

1982-01-01

Practical methods for generating acceptable random numbers from a variety of probability distributions which are frequently encountered in engineering applications are described. The speed, accuracy, and guarantee of statistical randomness of the various methods are discussed.

Hybrid spread spectrum radio system

DOEpatents

Smith, Stephen F.; Dress, William B.

2010-02-02

Systems and methods are described for hybrid spread spectrum radio systems. A method includes modulating a signal by utilizing a subset of bits from a pseudo-random code generator to control an amplification circuit that provides a gain to the signal. Another method includes: modulating a signal by utilizing a subset of bits from a pseudo-random code generator to control a fast hopping frequency synthesizer; and fast frequency hopping the signal with the fast hopping frequency synthesizer, wherein multiple frequency hops occur within a single data-bit time.

Navigation Using Orthogonal Frequency Division Multiplexed Signals of Opportunity

DTIC Science & Technology

2007-09-01

transmits a 32,767 bit pseudo -random “short” code that repeats 37.5 times per second. Since the pseudo -random bit pattern and modulation scheme are... correlation process takes two “ sample windows,” both of which are ν = 16 samples wide and are spaced N = 64 samples apart, and compares them. When the...technique in (3.4) is a necessary step in order to get a more accurate estimate of the sample shift from the symbol boundary correlator in (3.1). Figure

Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat.

PubMed

Gardiner, Laura-Jayne; Bansept-Basler, Pauline; Olohan, Lisa; Joynson, Ryan; Brenchley, Rachel; Hall, Neil; O'Sullivan, Donal M; Hall, Anthony

2016-08-01

Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat-Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo-chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo-chromosomes allow us to demonstrate the application of mapping-by-sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub-genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a smaller genic region than was previously possible; associate the interval with one wheat sub-genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user-friendly community resource for phenotype mapping. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Analysis of entropy extraction efficiencies in random number generation systems

NASA Astrophysics Data System (ADS)

Wang, Chao; Wang, Shuang; Chen, Wei; Yin, Zhen-Qiang; Han, Zheng-Fu

2016-05-01

Random numbers (RNs) have applications in many areas: lottery games, gambling, computer simulation, and, most importantly, cryptography [N. Gisin et al., Rev. Mod. Phys. 74 (2002) 145]. In cryptography theory, the theoretical security of the system calls for high quality RNs. Therefore, developing methods for producing unpredictable RNs with adequate speed is an attractive topic. Early on, despite the lack of theoretical support, pseudo RNs generated by algorithmic methods performed well and satisfied reasonable statistical requirements. However, as implemented, those pseudorandom sequences were completely determined by mathematical formulas and initial seeds, which cannot introduce extra entropy or information. In these cases, “random” bits are generated that are not at all random. Physical random number generators (RNGs), which, in contrast to algorithmic methods, are based on unpredictable physical random phenomena, have attracted considerable research interest. However, the way that we extract random bits from those physical entropy sources has a large influence on the efficiency and performance of the system. In this manuscript, we will review and discuss several randomness extraction schemes that are based on radiation or photon arrival times. We analyze the robustness, post-processing requirements and, in particular, the extraction efficiency of those methods to aid in the construction of efficient, compact and robust physical RNG systems.

Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access.

PubMed

Chacón, Alejandro; Marco-Sola, Santiago; Espinosa, Antonio; Ribeca, Paolo; Moure, Juan Carlos

2015-01-01

The recent advent of high-throughput sequencing machines producing big amounts of short reads has boosted the interest in efficient string searching techniques. As of today, many mainstream sequence alignment software tools rely on a special data structure, called the FM-index, which allows for fast exact searches in large genomic references. However, such searches translate into a pseudo-random memory access pattern, thus making memory access the limiting factor of all computation-efficient implementations, both on CPUs and GPUs. Here, we show that several strategies can be put in place to remove the memory bottleneck on the GPU: more compact indexes can be implemented by having more threads work cooperatively on larger memory blocks, and a k-step FM-index can be used to further reduce the number of memory accesses. The combination of those and other optimisations yields an implementation that is able to process about two Gbases of queries per second on our test platform, being about 8 × faster than a comparable multi-core CPU version, and about 3 × to 5 × faster than the FM-index implementation on the GPU provided by the recently announced Nvidia NVBIO bioinformatics library.

Balanced PIN-TIA photoreceiver with integrated 3 dB fiber coupler for distributed fiber optic sensors

NASA Astrophysics Data System (ADS)

Datta, Shubhashish; Rajagopalan, Sruti; Lemke, Shaun; Joshi, Abhay

2014-06-01

We report a balanced PIN-TIA photoreceiver integrated with a 3 dB fiber coupler for distributed fiber optic sensors. This detector demonstrates -3 dB bandwidth >15 GHz and coupled conversion gain >65 V/W per photodiode through either input port of the 3 dB coupler, and can be operated at local oscillator power of +17 dBm. The combined common mode rejection of the balanced photoreceiver and the integrated 3 dB coupler is >20 dB. We also present measurement results with various optical stimuli, namely impulses, sinusoids, and pseudo-random sequences, which are relevant for time domain reflectometry, frequency domain reflectometry, and code correlation sensors, respectively.

Distorted estimates of implicit and explicit learning in applications of the process-dissociation procedure to the SRT task.

PubMed

Stahl, Christoph; Barth, Marius; Haider, Hilde

2015-12-01

We investigated potential biases affecting the validity of the process-dissociation (PD) procedure when applied to sequence learning. Participants were or were not exposed to a serial reaction time task (SRTT) with two types of pseudo-random materials. Afterwards, participants worked on a free or cued generation task under inclusion and exclusion instructions. Results showed that pre-experimental response tendencies, non-associative learning of location frequencies, and the usage of cue locations introduced bias to PD estimates. These biases may lead to erroneous conclusions regarding the presence of implicit and explicit knowledge. Potential remedies for these problems are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Optimal mission planning of GEO on-orbit refueling in mixed strategy

NASA Astrophysics Data System (ADS)

Chen, Xiao-qian; Yu, Jing

2017-04-01

The mission planning of GEO on-orbit refueling (OOR) in Mixed strategy is studied in this paper. Specifically, one SSc will be launched to an orbital slot near the depot when multiple GEO satellites are reaching their end of lives. The SSc replenishes fuel from the depot and then extends the lifespan of the target satellites via refueling. In the mixed scenario, only some of the target satellites could be served by the SSc, and the remaining ones will be fueled by Pseudo SScs (the target satellite which has already been refueled by the SSc and now has sufficient fuel for its operation as well as the fuel to refuel other target satellites is called Pseudo SSc here). The mission sequences and fuel mass of the SSc and Pseudo SScs, the dry mass of the SSc are used as design variables, whereas the economic benefit of the whole mission is used as design objective. The economic cost and benefit models are stated first, and then a mathematical optimization model is proposed. A comprehensive solution method involving enumeration, particle swarm optimization and modification is developed. Numerical examples are carried out to demonstrate the effectiveness of the model and solution method. Economic efficiencies of different OOR strategies are compared and discussed. The mixed strategy would perform better than the other strategies only when the target satellites satisfy some conditions. This paper presents an available mixed strategy scheme for users and analyzes its advantages and disadvantages by comparing with some other OOR strategies, providing helpful references to decision makers. The best strategy in practical applications depends on the specific demands and user preference.

Double polymer sheathed carbon nanotube supercapacitors show enhanced cycling stability

NASA Astrophysics Data System (ADS)

Zhao, Wenqi; Wang, Shanshan; Wang, Chunhui; Wu, Shiting; Xu, Wenjing; Zou, Mingchu; Ouyang, An; Cao, Anyuan; Li, Yibin

2015-12-01

Pseudo-materials are effective in boosting the specific capacitance of supercapacitors, but during service their degradation may also be very strong, causing reduced cycling stability. Here, we show that a carbon nanotube sponge grafted by two conventional pseudo-polymer layers in sequence can serve as a porous supercapacitor electrode with significantly enhanced cycling stability compared with single polymer grafting. Creating conformal polymer coatings on the nanotube surface and the resulting double-sheath configuration are important structural factors leading to the enhanced performance. Combining different polymers as double sheaths as reported here might be a potential route to circumvent the dilemma of pseudo-materials, and to simultaneously improve the capacitance and stability for various energy storage devices.Pseudo-materials are effective in boosting the specific capacitance of supercapacitors, but during service their degradation may also be very strong, causing reduced cycling stability. Here, we show that a carbon nanotube sponge grafted by two conventional pseudo-polymer layers in sequence can serve as a porous supercapacitor electrode with significantly enhanced cycling stability compared with single polymer grafting. Creating conformal polymer coatings on the nanotube surface and the resulting double-sheath configuration are important structural factors leading to the enhanced performance. Combining different polymers as double sheaths as reported here might be a potential route to circumvent the dilemma of pseudo-materials, and to simultaneously improve the capacitance and stability for various energy storage devices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05978j

PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition.

PubMed

Chen, Wei; Lei, Tian-Yu; Jin, Dian-Chuan; Lin, Hao; Chou, Kuo-Chen

2014-07-01

The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis. Copyright © 2014 Elsevier Inc. All rights reserved.

A machine-learning approach for predicting palmitoylation sites from integrated sequence-based features.

PubMed

Li, Liqi; Luo, Qifa; Xiao, Weidong; Li, Jinhui; Zhou, Shiwen; Li, Yongsheng; Zheng, Xiaoqi; Yang, Hua

2017-02-01

Palmitoylation is the covalent attachment of lipids to amino acid residues in proteins. As an important form of protein posttranslational modification, it increases the hydrophobicity of proteins, which contributes to the protein transportation, organelle localization, and functions, therefore plays an important role in a variety of cell biological processes. Identification of palmitoylation sites is necessary for understanding protein-protein interaction, protein stability, and activity. Since conventional experimental techniques to determine palmitoylation sites in proteins are both labor intensive and costly, a fast and accurate computational approach to predict palmitoylation sites from protein sequences is in urgent need. In this study, a support vector machine (SVM)-based method was proposed through integrating PSI-BLAST profile, physicochemical properties, [Formula: see text]-mer amino acid compositions (AACs), and [Formula: see text]-mer pseudo AACs into the principal feature vector. A recursive feature selection scheme was subsequently implemented to single out the most discriminative features. Finally, an SVM method was implemented to predict palmitoylation sites in proteins based on the optimal features. The proposed method achieved an accuracy of 99.41% and Matthews Correlation Coefficient of 0.9773 for a benchmark dataset. The result indicates the efficiency and accuracy of our method in prediction of palmitoylation sites based on protein sequences.

Programming and reprogramming sequence timing following high and low contextual interference practice.

PubMed

Wright, David L; Magnuson, Curt E; Black, Charles B

2005-09-01

Individuals practiced two unique discrete sequence production tasks that differed in their relative time profile in either a blocked or random practice schedule. Each participant was subsequently administered a "precuing" protocol to examine the cost of initially compiling or modifying the plan for an upcoming movement's relative timing. The findings indicated that, in general, random practice facilitated the programming of the required movement timing, and this was accomplished while exhibiting greater accuracy in movement production. Participants exposed to random practice exhibited the greatest motor programming benefit, when a modification to an already prepared movement timing profile was required. When movement timing was only partially constructed prior to the imperative signal, the individuals who were trained in blocked and random practice formats accrued a similar cost to complete the programming process. These data provide additional support for the recent claim of Immink & Wright (2001) that at least some of the benefit from experience in a random as opposed to blocked training context can be localized to superior development and implementation of the motor programming process before executing the movement.

Investigation of the performance characteristics of Doppler radar technique for aircraft collision hazard warning, phase 3

NASA Technical Reports Server (NTRS)

1972-01-01

System studies, equipment simulation, hardware development and flight tests which were conducted during the development of aircraft collision hazard warning system are discussed. The system uses a cooperative, continuous wave Doppler radar principle with pseudo-random frequency modulation. The report presents a description of the system operation and deals at length with the use of pseudo-random coding techniques. In addition, the use of mathematical modeling and computer simulation to determine the alarm statistics and system saturation characteristics in terminal area traffic of variable density is discussed.

Measuring order in disordered systems and disorder in ordered systems: Random matrix theory for isotropic and nematic liquid crystals and its perspective on pseudo-nematic domains

NASA Astrophysics Data System (ADS)

Zhao, Yan; Stratt, Richard M.

2018-05-01

Surprisingly long-ranged intermolecular correlations begin to appear in isotropic (orientationally disordered) phases of liquid crystal forming molecules when the temperature or density starts to close in on the boundary with the nematic (ordered) phase. Indeed, the presence of slowly relaxing, strongly orientationally correlated, sets of molecules under putatively disordered conditions ("pseudo-nematic domains") has been apparent for some time from light-scattering and optical-Kerr experiments. Still, a fully microscopic characterization of these domains has been lacking. We illustrate in this paper how pseudo-nematic domains can be studied in even relatively small computer simulations by looking for order-parameter tensor fluctuations much larger than one would expect from random matrix theory. To develop this idea, we show that random matrix theory offers an exact description of how the probability distribution for liquid-crystal order parameter tensors converges to its macroscopic-system limit. We then illustrate how domain properties can be inferred from finite-size-induced deviations from these random matrix predictions. A straightforward generalization of time-independent random matrix theory also allows us to prove that the analogous random matrix predictions for the time dependence of the order-parameter tensor are similarly exact in the macroscopic limit, and that relaxation behavior of the domains can be seen in the breakdown of the finite-size scaling required by that random-matrix theory.

Tailpulse signal generator

DOEpatents

Baker, John [Walnut Creek, CA; Archer, Daniel E [Knoxville, TN; Luke, Stanley John [Pleasanton, CA; Decman, Daniel J [Livermore, CA; White, Gregory K [Livermore, CA

2009-06-23

A tailpulse signal generating/simulating apparatus, system, and method designed to produce electronic pulses which simulate tailpulses produced by a gamma radiation detector, including the pileup effect caused by the characteristic exponential decay of the detector pulses, and the random Poisson distribution pulse timing for radioactive materials. A digital signal process (DSP) is programmed and configured to produce digital values corresponding to pseudo-randomly selected pulse amplitudes and pseudo-randomly selected Poisson timing intervals of the tailpulses. Pulse amplitude values are exponentially decayed while outputting the digital value to a digital to analog converter (DAC). And pulse amplitudes of new pulses are added to decaying pulses to simulate the pileup effect for enhanced realism in the simulation.

High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency.

PubMed

Takahashi, Mayumi; Wu, Xiwei; Ho, Michelle; Chomchan, Pritsana; Rossi, John J; Burnett, John C; Zhou, Jiehua

2016-09-22

The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct "biased sequences" and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the "biased sequences" was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy.

Magnetically Retrievable Catalysts for Asymmetric Synthesis

EPA Science Inventory

Surface modification of magnetic nanoparticles with chiral scaffolds for asymmetric catalytic applications is an elegant way of providing a special pseudo homogenous phase which could be separated using an external magnet. In this review, we summarize the use of magnetic nanopart...

Patterns of Stochastic Behavior in Dynamically Unstable High-Dimensional Biochemical Networks

PubMed Central

Rosenfeld, Simon

2009-01-01

The question of dynamical stability and stochastic behavior of large biochemical networks is discussed. It is argued that stringent conditions of asymptotic stability have very little chance to materialize in a multidimensional system described by the differential equations of chemical kinetics. The reason is that the criteria of asymptotic stability (Routh-Hurwitz, Lyapunov criteria, Feinberg’s Deficiency Zero theorem) would impose the limitations of very high algebraic order on the kinetic rates and stoichiometric coefficients, and there are no natural laws that would guarantee their unconditional validity. Highly nonlinear, dynamically unstable systems, however, are not necessarily doomed to collapse, as a simple Jacobian analysis would suggest. It is possible that their dynamics may assume the form of pseudo-random fluctuations quite similar to a shot noise, and, therefore, their behavior may be described in terms of Langevin and Fokker-Plank equations. We have shown by simulation that the resulting pseudo-stochastic processes obey the heavy-tailed Generalized Pareto Distribution with temporal sequence of pulses forming the set of constituent-specific Poisson processes. Being applied to intracellular dynamics, these properties are naturally associated with burstiness, a well documented phenomenon in the biology of gene expression. PMID:19838330

Measurement time and statistics for a noise thermometer with a synthetic-noise reference

NASA Astrophysics Data System (ADS)

White, D. R.; Benz, S. P.; Labenski, J. R.; Nam, S. W.; Qu, J. F.; Rogalla, H.; Tew, W. L.

2008-08-01

This paper describes methods for reducing the statistical uncertainty in measurements made by noise thermometers using digital cross-correlators and, in particular, for thermometers using pseudo-random noise for the reference signal. First, a discrete-frequency expression for the correlation bandwidth for conventional noise thermometers is derived. It is shown how an alternative frequency-domain computation can be used to eliminate the spectral response of the correlator and increase the correlation bandwidth. The corresponding expressions for the uncertainty in the measurement of pseudo-random noise in the presence of uncorrelated thermal noise are then derived. The measurement uncertainty in this case is less than that for true thermal-noise measurements. For pseudo-random sources generating a frequency comb, an additional small reduction in uncertainty is possible, but at the cost of increasing the thermometer's sensitivity to non-linearity errors. A procedure is described for allocating integration times to further reduce the total uncertainty in temperature measurements. Finally, an important systematic error arising from the calculation of ratios of statistical variables is described.

The removal of chloramphenicol from water through adsorption on activated carbon

NASA Astrophysics Data System (ADS)

Lach, Joanna; Ociepa-Kubicka, Agnieszka

2017-10-01

The presented research investigated the removal of chloramphenicol from water solutions on selected activated carbon available in three grades with different porous structure and surface chemical composition. Two models of adsorption kinetics were examined, i.e. the pseudo-first order and the pseudo-second order models. For all examined cases, the results of tests with higher value of coefficient R2 were described by the equation for pseudo-second order kinetics. The adsorption kinetics was also investigated on the activated carbons modified with ozone. The measurements were taken from the solutions with pH values of 2 and 7. Chloramphenicol was the most efficiently adsorbed on the activated carbon F-300 from the solutions with pH=7, and on the activated carbon ROW 08 Supra from the solutions with pH=2. The adsorption of this antibiotic was in the majority of cases higher from the solutions with pH=2 than pH=7. The modification of the activated carbons with ozone enhanced their adsorption capacities for chloramphenicol. The adsorption is influenced by the modification method of activated carbon (i.e. the duration of ozonation of the activated carbon solution and the solution temperature). The results were described with the Freundlich and Langmuir adsorption isotherm equations. Both models well described the obtained results (high R2 values).

A novel alignment-free method to classify protein folding types by combining spectral graph clustering with Chou's pseudo amino acid composition.

PubMed

Tripathi, Pooja; Pandey, Paras N

2017-07-07

The present work employs pseudo amino acid composition (PseAAC) for encoding the protein sequences in their numeric form. Later this will be arranged in the similarity matrix, which serves as input for spectral graph clustering method. Spectral methods are used previously also for clustering of protein sequences, but they uses pair wise alignment scores of protein sequences, in similarity matrix. The alignment score depends on the length of sequences, so clustering short and long sequences together may not good idea. Therefore the idea of introducing PseAAC with spectral clustering algorithm came into scene. We extensively tested our method and compared its performance with other existing machine learning methods. It is consistently observed that, the number of clusters that we obtained for a given set of proteins is close to the number of superfamilies in that set and PseAAC combined with spectral graph clustering shows the best classification results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Probabilistic Evaluation of Competing Climate Models

NASA Astrophysics Data System (ADS)

Braverman, A. J.; Chatterjee, S.; Heyman, M.; Cressie, N.

2017-12-01

A standard paradigm for assessing the quality of climate model simulations is to compare what these models produce for past and present time periods, to observations of the past and present. Many of these comparisons are based on simple summary statistics called metrics. Here, we propose an alternative: evaluation of competing climate models through probabilities derived from tests of the hypothesis that climate-model-simulated and observed time sequences share common climate-scale signals. The probabilities are based on the behavior of summary statistics of climate model output and observational data, over ensembles of pseudo-realizations. These are obtained by partitioning the original time sequences into signal and noise components, and using a parametric bootstrap to create pseudo-realizations of the noise sequences. The statistics we choose come from working in the space of decorrelated and dimension-reduced wavelet coefficients. We compare monthly sequences of CMIP5 model output of average global near-surface temperature anomalies to similar sequences obtained from the well-known HadCRUT4 data set, as an illustration.

PseudoBase: a database with RNA pseudoknots.

PubMed

van Batenburg, F H; Gultyaev, A P; Pleij, C W; Ng, J; Oliehoek, J

2000-01-01

PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo-knots. It can be reached at http://wwwbio. Leiden Univ.nl/ approximately Batenburg/PKB.html. This page will direct the user to a retrieval page from where a particular pseudoknot can be chosen, or to a submission page which enables the user to add pseudoknot information to the database or to an informative page that elaborates on the various aspects of the database. For each pseudoknot, 12 items are stored, e.g. the nucleotides of the region that contains the pseudoknot, the stem positions of the pseudoknot, the EMBL accession number of the sequence that contains this pseudoknot and the support that can be given regarding the reliability of the pseudoknot. Access is via a small number of steps, using 16 different categories. The development process was done by applying the evolutionary methodology for software development rather than by applying the methodology of the classical waterfall model or the more modern spiral model.

Comparing Ecological and Genetic Diversity Within the Marine Diatom Genus Pseudo-nitzschia: A Multiregional Synthesis

NASA Astrophysics Data System (ADS)

Hubbard, K.; Bruzek, S.

2016-02-01

The globally distributed marine diatom genus Pseudo-nitzschia consists of approximately 40 species, more than half of which occur in US coastal waters. Here, sensitive genetic tools targeting a variable portion of the internal transcribed spacer 1 (ITS1) region of the rRNA gene were used to assess Pseudo-nitzschia spp. diversity in more than 600 environmental DNA samples collected from US Atlantic, Pacific, and Gulf of Mexico waters. Community-based approaches employed genus-specific primers for environmental DNA fingerprinting and targeted sequencing. For the Gulf of Mexico samples especially, a nested PCR approach (with or without degenerate primers) improved resolution of species diversity. To date, more than 40 unique ITS1 amplicon sizes have been repeatedly observed in ITS1 fingerprints. Targeted sequencing of environmental DNA as well as single chains isolated from live samples indicate that many of these represent novel and known inter- and intra-specific Pseudo-nitzschia diversity. A few species (e.g., P. pungens, P. cuspidata) occur across all three regions, whereas other species and intraspecific variants occurred at local to regional spatial scales only. Generally, species frequently co-occur in complex assemblages, and transitions in Pseudo-nitzschia community composition occur seasonally, prior to bloom initiation, and across (cross-shelf, latitudinal, and vertical) environmental gradients. These observations highlight the dynamic nature of diatom community composition in the marine environment and the importance of classifying diversity at relevant ecological and/or taxonomic scales.

Binaural Simulation Experiments in the NASA Langley Structural Acoustics Loads and Transmission Facility

NASA Technical Reports Server (NTRS)

Grosveld, Ferdinand W.; Silcox, Richard (Technical Monitor)

2001-01-01

A location and positioning system was developed and implemented in the anechoic chamber of the Structural Acoustics Loads and Transmission (SALT) facility to accurately determine the coordinates of points in three-dimensional space. Transfer functions were measured between a shaker source at two different panel locations and the vibrational response distributed over the panel surface using a scanning laser vibrometer. The binaural simulation test matrix included test runs for several locations of the measuring microphones, various attitudes of the mannequin, two locations of the shaker excitation and three different shaker inputs including pulse, broadband random, and pseudo-random. Transfer functions, auto spectra, and coherence functions were acquired for the pseudo-random excitation. Time histories were acquired for the pulse and broadband random input to the shaker. The tests were repeated with a reflective surface installed. Binary data files were converted to universal format and archived on compact disk.

Local Risk-Minimization for Defaultable Claims with Recovery Process

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

Biagini, Francesca, E-mail: biagini@mathematik.uni-muenchen.de; Cretarola, Alessandra, E-mail: alessandra.cretarola@dmi.unipg.it

We study the local risk-minimization approach for defaultable claims with random recovery at default time, seen as payment streams on the random interval [0,{tau} Logical-And T], where T denotes the fixed time-horizon. We find the pseudo-locally risk-minimizing strategy in the case when the agent information takes into account the possibility of a default event (local risk-minimization with G-strategies) and we provide an application in the case of a corporate bond. We also discuss the problem of finding a pseudo-locally risk-minimizing strategy if we suppose the agent obtains her information only by observing the non-defaultable assets.

10 Gb/s operation of photonic crystal silicon optical modulators.

PubMed

Nguyen, Hong C; Sakai, Yuya; Shinkawa, Mizuki; Ishikura, Norihiro; Baba, Toshihiko

2011-07-04

We report the first experimental demonstration of 10 Gb/s modulation in a photonic crystal silicon optical modulator. The device consists of a 200 μm-long SiO2-clad photonic crystal waveguide, with an embedded p-n junction, incorporated into an asymmetric Mach-Zehnder interferometer. The device is integrated on a SOI chip and fabricated by CMOS-compatible processes. With the bias voltage set at 0 V, we measure a V(π)L < 0.056 V∙cm. Optical modulation is demonstrated by electrically driving the device with a 2(31) - 1 bit non-return-to-zero pseudo-random bit sequence signal. An open eye pattern is observed at bitrates of 10 Gb/s and 2 Gb/s, with and without pre-emphasis of the drive signal, respectively.

[Digital signal processing of a novel neuron discharge model stimulation strategy for cochlear implants].

PubMed

Yang, Yiwei; Xu, Yuejin; Miu, Jichang; Zhou, Linghong; Xiao, Zhongju

2012-10-01

To apply the classic leakage integrate-and-fire models, based on the mechanism of the generation of physiological auditory stimulation, in the information processing coding of cochlear implants to improve the auditory result. The results of algorithm simulation in digital signal processor (DSP) were imported into Matlab for a comparative analysis. Compared with CIS coding, the algorithm of membrane potential integrate-and-fire (MPIF) allowed more natural pulse discharge in a pseudo-random manner to better fit the physiological structures. The MPIF algorithm can effectively solve the problem of the dynamic structure of the delivered auditory information sequence issued in the auditory center and allowed integration of the stimulating pulses and time coding to ensure the coherence and relevance of the stimulating pulse time.

35-GHz radar sensor for automotive collision avoidance

NASA Astrophysics Data System (ADS)

Zhang, Jun

1999-07-01

This paper describes the development of a radar sensor system used for automotive collision avoidance. Because the heavy truck may have great larger radar cross section than a motorcyclist has, the radar receiver may have a large dynamic range. And multi-targets at different speed may confuse the echo spectrum causing the ambiguity between range and speed of target. To get more information about target and background and to adapt to the large dynamic range and multi-targets, a frequency modulated and pseudo- random binary sequences phase modulated continuous wave radar system is described. The analysis of this double- modulation system is given. A high-speed signal processing and data processing component are used to process and combine the data and information from echo at different direction and at every moment.

DNA based random key generation and management for OTP encryption.

PubMed

Zhang, Yunpeng; Liu, Xin; Sun, Manhui

2017-09-01

One-time pad (OTP) is a principle of key generation applied to the stream ciphering method which offers total privacy. The OTP encryption scheme has proved to be unbreakable in theory, but difficult to realize in practical applications. Because OTP encryption specially requires the absolute randomness of the key, its development has suffered from dense constraints. DNA cryptography is a new and promising technology in the field of information security. DNA chromosomes storing capabilities can be used as one-time pad structures with pseudo-random number generation and indexing in order to encrypt the plaintext messages. In this paper, we present a feasible solution to the OTP symmetric key generation and transmission problem with DNA at the molecular level. Through recombinant DNA technology, by using only sender-receiver known restriction enzymes to combine the secure key represented by DNA sequence and the T vector, we generate the DNA bio-hiding secure key and then place the recombinant plasmid in implanted bacteria for secure key transmission. The designed bio experiments and simulation results show that the security of the transmission of the key is further improved and the environmental requirements of key transmission are reduced. Analysis has demonstrated that the proposed DNA-based random key generation and management solutions are marked by high security and usability. Published by Elsevier B.V.

Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species.

PubMed

Gardiner, Laura-Jayne; Gawroński, Piotr; Olohan, Lisa; Schnurbusch, Thorsten; Hall, Neil; Hall, Anthony

2014-12-01

Mapping-by-sequencing analyses have largely required a complete reference sequence and employed whole genome re-sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re-sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early-flowering locus in einkorn wheat (Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene-rich regions of hexaploid bread wheat to design a 110-Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo-chromosomes derived from the capture probe target sequence, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval. © 2014 The Authors.The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank.

PubMed

Chen, Junjie; Guo, Mingyue; Li, Shumin; Liu, Bin

2017-11-01

As one of the most important tasks in protein sequence analysis, protein remote homology detection is critical for both basic research and practical applications. Here, we present an effective web server for protein remote homology detection called ProtDec-LTR2.0 by combining ProtDec-Learning to Rank (LTR) and pseudo protein representation. Experimental results showed that the detection performance is obviously improved. The web server provides a user-friendly interface to explore the sequence and structure information of candidate proteins and find their conserved domains by launching a multiple sequence alignment tool. The web server is free and open to all users with no login requirement at http://bioinformatics.hitsz.edu.cn/ProtDec-LTR2.0/. bliu@hit.edu.cn. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

The development of GPU-based parallel PRNG for Monte Carlo applications in CUDA Fortran

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

Kargaran, Hamed, E-mail: h-kargaran@sbu.ac.ir; Minuchehr, Abdolhamid; Zolfaghari, Ahmad

The implementation of Monte Carlo simulation on the CUDA Fortran requires a fast random number generation with good statistical properties on GPU. In this study, a GPU-based parallel pseudo random number generator (GPPRNG) have been proposed to use in high performance computing systems. According to the type of GPU memory usage, GPU scheme is divided into two work modes including GLOBAL-MODE and SHARED-MODE. To generate parallel random numbers based on the independent sequence method, the combination of middle-square method and chaotic map along with the Xorshift PRNG have been employed. Implementation of our developed PPRNG on a single GPU showedmore » a speedup of 150x and 470x (with respect to the speed of PRNG on a single CPU core) for GLOBAL-MODE and SHARED-MODE, respectively. To evaluate the accuracy of our developed GPPRNG, its performance was compared to that of some other commercially available PPRNGs such as MATLAB, FORTRAN and Miller-Park algorithm through employing the specific standard tests. The results of this comparison showed that the developed GPPRNG in this study can be used as a fast and accurate tool for computational science applications.« less

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

PubMed Central

Carlile, Thomas M.; Rojas-Duran, Maria F.; Zinshteyn, Boris; Shin, Hakyung; Bartoli, Kristen M.; Gilbert, Wendy V.

2014-01-01

Post-transcriptional modification of RNA nucleosides occurs in all living organisms. Pseudouridine, the most abundant modified nucleoside in non-coding RNAs1, enhances the function of transfer RNA and ribosomal RNA by stabilizing RNA structure2–8. mRNAs were not known to contain pseudouridine, but artificial pseudouridylation dramatically affects mRNA function – it changes the genetic code by facilitating non-canonical base pairing in the ribosome decoding center9,10. However, without evidence of naturally occurring mRNA pseudouridylation, its physiological was unclear. Here we present a comprehensive analysis of pseudouridylation in yeast and human RNAs using Pseudo-seq, a genome-wide, single-nucleotide-resolution method for pseudouridine identification. Pseudo-seq accurately identifies known modification sites as well as 100 novel sites in non-coding RNAs, and reveals hundreds of pseudouridylated sites in mRNAs. Genetic analysis allowed us to assign most of the new modification sites to one of seven conserved pseudouridine synthases, Pus1–4, 6, 7 and 9. Notably, the majority of pseudouridines in mRNA are regulated in response to environmental signals, such as nutrient deprivation in yeast and serum starvation in human cells. These results suggest a mechanism for the rapid and regulated rewiring of the genetic code through inducible mRNA modifications. Our findings reveal unanticipated roles for pseudouridylation and provide a resource for identifying the targets of pseudouridine synthases implicated in human disease11–13. PMID:25192136

High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency

PubMed Central

Takahashi, Mayumi; Wu, Xiwei; Ho, Michelle; Chomchan, Pritsana; Rossi, John J.; Burnett, John C.; Zhou, Jiehua

2016-01-01

The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct “biased sequences” and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the “biased sequences” was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy. PMID:27652575

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

PubMed Central

Thomsen, Martin Christen Frølund; Nielsen, Morten

2012-01-01

Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. The output from the server is a sequence logo and a PSSM. Seq2Logo is available at http://www.cbs.dtu.dk/biotools/Seq2Logo (14 May 2012, date last accessed). PMID:22638583

Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomes.

PubMed

Yanagi, Tomohiro; Shirasawa, Kenta; Terachi, Mayuko; Isobe, Sachiko

2017-01-01

Cultivated strawberry ( Fragaria  ×  ananassa Duch.) has homoeologous chromosomes because of allo-octoploidy. For example, two homoeologous chromosomes that belong to different sub-genome of allopolyploids have similar base sequences. Thus, when conducting de novo assembly of DNA sequences, it is difficult to determine whether these sequences are derived from the same chromosome. To avoid the difficulties associated with homoeologous chromosomes and demonstrate the possibility of sequencing allopolyploids using single chromosomes, we conducted sequence analysis using microdissected single somatic chromosomes of cultivated strawberry. Three hundred and ten somatic chromosomes of the Japanese octoploid strawberry 'Reiko' were individually selected under a light microscope using a microdissection system. DNA from 288 of the dissected chromosomes was successfully amplified using a DNA amplification kit. Using next-generation sequencing, we decoded the base sequences of the amplified DNA segments, and on the basis of mapping, we identified DNA sequences from 144 samples that were best matched to the reference genomes of the octoploid strawberry, F.  ×  ananassa , and the diploid strawberry, F. vesca . The 144 samples were classified into seven pseudo-molecules of F. vesca . The coverage rates of the DNA sequences from the single chromosome onto all pseudo-molecular sequences varied from 3 to 29.9%. We demonstrated an efficient method for sequence analysis of allopolyploid plants using microdissected single chromosomes. On the basis of our results, we believe that whole-genome analysis of allopolyploid plants can be enhanced using methodology that employs microdissected single chromosomes.

Finding Mount Everest and handling voids.

PubMed

Storch, Tobias

2011-01-01

Evolutionary algorithms (EAs) are randomized search heuristics that solve problems successfully in many cases. Their behavior is often described in terms of strategies to find a high location on Earth's surface. Unfortunately, many digital elevation models describing it contain void elements. These are elements not assigned an elevation. Therefore, we design and analyze simple EAs with different strategies to handle such partially defined functions. They are experimentally investigated on a dataset describing the elevation of Earth's surface. The largest value found by an EA within a certain runtime is measured, and the median over a few runs is computed and compared for the different EAs. For the dataset, the distribution of void elements seems to be neither random nor adversarial. They are so-called semirandomly distributed. To deepen our understanding of the behavior of the different EAs, they are theoretically considered on well-known pseudo-Boolean functions transferred to partially defined ones. These modifications are also performed in a semirandom way. The typical runtime until an optimum is found by an EA is analyzed, namely bounded from above and below, and compared for the different EAs. We figure out that for the random model it is a good strategy to assume that a void element has a worse function value than all previous elements. Whereas for the adversary model it is a good strategy to assume that a void element has the best function value of all previous elements.

SSU rDNA divergence in planktonic foraminifera: molecular taxonomy and biogeographic implications.

PubMed

André, Aurore; Quillévéré, Frédéric; Morard, Raphaël; Ujiié, Yurika; Escarguel, Gilles; de Vargas, Colomban; de Garidel-Thoron, Thibault; Douady, Christophe J

2014-01-01

The use of planktonic foraminifera in paleoceanography requires taxonomic consistency and precise assessment of the species biogeography. Yet, ribosomal small subunit (SSUr) DNA analyses have revealed that most of the modern morpho-species of planktonic foraminifera are composed of a complex of several distinct genetic types that may correspond to cryptic or pseudo-cryptic species. These genetic types are usually delimitated using partial sequences located at the 3'end of the SSUrDNA, but typically based on empirical delimitation. Here, we first use patristic genetic distances calculated within and among genetic types of the most common morpho-species to show that intra-type and inter-type genetic distances within morpho-species may significantly overlap, suggesting that genetic types have been sometimes inconsistently defined. We further apply two quantitative and independent methods, ABGD (Automatic Barcode Gap Detection) and GMYC (General Mixed Yule Coalescent) to a dataset of published and newly obtained partial SSU rDNA for a more objective assessment of the species status of these genetic types. Results of these complementary approaches are highly congruent and lead to a molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudo)cryptic species. Our results advocate for a standardized sequencing procedure allowing homogenous delimitations of (pseudo)cryptic species. On the ground of this revised taxonomic framework, we finally provide an integrative taxonomy synthesizing geographic, ecological and morphological differentiations that can occur among the genuine (pseudo)cryptic species. Due to molecular, environmental or morphological data scarcities, many aspects of our proposed integrative taxonomy are not yet fully resolved. On the other hand, our study opens up the potential for a correct interpretation of environmental sequence datasets.

SSU rDNA Divergence in Planktonic Foraminifera: Molecular Taxonomy and Biogeographic Implications

PubMed Central

André, Aurore; Quillévéré, Frédéric; Morard, Raphaël; Ujiié, Yurika; Escarguel, Gilles; de Vargas, Colomban; de Garidel-Thoron, Thibault; Douady, Christophe J.

2014-01-01

The use of planktonic foraminifera in paleoceanography requires taxonomic consistency and precise assessment of the species biogeography. Yet, ribosomal small subunit (SSUr) DNA analyses have revealed that most of the modern morpho-species of planktonic foraminifera are composed of a complex of several distinct genetic types that may correspond to cryptic or pseudo-cryptic species. These genetic types are usually delimitated using partial sequences located at the 3′end of the SSUrDNA, but typically based on empirical delimitation. Here, we first use patristic genetic distances calculated within and among genetic types of the most common morpho-species to show that intra-type and inter-type genetic distances within morpho-species may significantly overlap, suggesting that genetic types have been sometimes inconsistently defined. We further apply two quantitative and independent methods, ABGD (Automatic Barcode Gap Detection) and GMYC (General Mixed Yule Coalescent) to a dataset of published and newly obtained partial SSU rDNA for a more objective assessment of the species status of these genetic types. Results of these complementary approaches are highly congruent and lead to a molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudo)cryptic species. Our results advocate for a standardized sequencing procedure allowing homogenous delimitations of (pseudo)cryptic species. On the ground of this revised taxonomic framework, we finally provide an integrative taxonomy synthesizing geographic, ecological and morphological differentiations that can occur among the genuine (pseudo)cryptic species. Due to molecular, environmental or morphological data scarcities, many aspects of our proposed integrative taxonomy are not yet fully resolved. On the other hand, our study opens up the potential for a correct interpretation of environmental sequence datasets. PMID:25119900

Study on a novel laser target detection system based on software radio technique

NASA Astrophysics Data System (ADS)

Song, Song; Deng, Jia-hao; Wang, Xue-tian; Gao, Zhen; Sun, Ji; Sun, Zhi-hui

2008-12-01

This paper presents that software radio technique is applied to laser target detection system with the pseudo-random code modulation. Based on the theory of software radio, the basic framework of the system, hardware platform, and the implementation of the software system are detailed. Also, the block diagram of the system, DSP circuit, block diagram of the pseudo-random code generator, and soft flow diagram of signal processing are designed. Experimental results have shown that the application of software radio technique provides a novel method to realize the modularization, miniaturization and intelligence of the laser target detection system, and the upgrade and improvement of the system will become simpler, more convenient, and cheaper.

Generation of brain pseudo-CTs using an undersampled, single-acquisition UTE-mDixon pulse sequence and unsupervised clustering

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

Su, Kuan-Hao; Hu, Lingzhi; Traughber, Melanie

Purpose: MR-based pseudo-CT has an important role in MR-based radiation therapy planning and PET attenuation correction. The purpose of this study is to establish a clinically feasible approach, including image acquisition, correction, and CT formation, for pseudo-CT generation of the brain using a single-acquisition, undersampled ultrashort echo time (UTE)-mDixon pulse sequence. Methods: Nine patients were recruited for this study. For each patient, a 190-s, undersampled, single acquisition UTE-mDixon sequence of the brain was acquired (TE = 0.1, 1.5, and 2.8 ms). A novel method of retrospective trajectory correction of the free induction decay (FID) signal was performed based on point-spreadmore » functions of three external MR markers. Two-point Dixon images were reconstructed using the first and second echo data (TE = 1.5 and 2.8 ms). R2{sup ∗} images (1/T2{sup ∗}) were then estimated and were used to provide bone information. Three image features, i.e., Dixon-fat, Dixon-water, and R2{sup ∗}, were used for unsupervised clustering. Five tissue clusters, i.e., air, brain, fat, fluid, and bone, were estimated using the fuzzy c-means (FCM) algorithm. A two-step, automatic tissue-assignment approach was proposed and designed according to the prior information of the given feature space. Pseudo-CTs were generated by a voxelwise linear combination of the membership functions of the FCM. A low-dose CT was acquired for each patient and was used as the gold standard for comparison. Results: The contrast and sharpness of the FID images were improved after trajectory correction was applied. The mean of the estimated trajectory delay was 0.774 μs (max: 1.350 μs; min: 0.180 μs). The FCM-estimated centroids of different tissue types showed a distinguishable pattern for different tissues, and significant differences were found between the centroid locations of different tissue types. Pseudo-CT can provide additional skull detail and has low bias and absolute error of estimated CT numbers of voxels (−22 ± 29 HU and 130 ± 16 HU) when compared to low-dose CT. Conclusions: The MR features generated by the proposed acquisition, correction, and processing methods may provide representative clustering information and could thus be used for clinical pseudo-CT generation.« less

Inhibition of Clostridium difficile toxin A and B by 1,2-cyclohexanedione modification of an arginine residue.

PubMed

Balfanz, J; Rautenberg, P

1989-12-29

Toxin A (enterotoxin) and toxin B (cytotoxin) of Clostridium difficile were both inactivated by the arginine specific reagent 1,2-cyclohexanedione. Molecular stability during the inactivation process was demonstrated by SDS-PAGE analysis showing the same migration rates for modified and unmodified forms of the 230 kDa toxin A and of the 250 kDa toxin B. Cytotoxicity of both toxins as well as mouse lethality of the enterotoxin were drastically decreased as a result of the arginine modification. The reaction followed pseudo-first-order kinetics. Analysis of the data suggested that modification of a single arginine residue was sufficient to abolish the activity of both toxins.

Crosstalk Reduction for High-Frequency Linear-Array Ultrasound Transducers Using 1–3 Piezocomposites With Pseudo-Random Pillars

PubMed Central

Yang, Hao-Chung; Cannata, Jonathan; Williams, Jay; Shung, K. Kirk

2013-01-01

The goal of this research was to develop a novel diced 1–3 piezocomposite geometry to reduce pulse–echo ring down and acoustic crosstalk between high-frequency ultrasonic array elements. Two PZT-5H-based 1–3 composites (10 and 15 MHz) of different pillar geometries [square (SQ), 45° triangle (TR), and pseudo-random (PR)] were fabricated and then made into single-element ultrasound transducers. The measured pulse–echo waveforms and their envelopes indicate that the PR composites had the shortest −20-dB pulse length and highest sensitivity among the composites evaluated. Using these composites, 15-MHz array subapertures with a 0.95λ pitch were fabricated to assess the acoustic crosstalk between array elements. The combined electrical and acoustical crosstalk between the nearest array elements of the PR array sub-apertures (−31.8 dB at 15 MHz) was 6.5 and 2.2 dB lower than those of the SQ and the TR array subapertures, respectively. These results demonstrate that the 1–3 piezocomposite with the pseudo-random pillars may be a better choice for fabricating enhanced high-frequency linear-array ultrasound transducers; especially when mechanical dicing is used. PMID:23143580

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

V Yashchuk; R Conley; E Anderson

Verification of the reliability of metrology data from high quality X-ray optics requires that adequate methods for test and calibration of the instruments be developed. For such verification for optical surface profilometers in the spatial frequency domain, a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) gratings and arrays has been suggested [1] and [2] and proven to be an effective calibration method for a number of interferometric microscopes, a phase shifting Fizeau interferometer, and a scatterometer [5]. Here we describe the details of development of binary pseudo-random multilayer (BPRML) test samples suitable for characterization of scanningmore » (SEM) and transmission (TEM) electron microscopes. We discuss the results of TEM measurements with the BPRML test samples fabricated from a WiSi2/Si multilayer coating with pseudo-randomly distributed layers. In particular, we demonstrate that significant information about the metrological reliability of the TEM measurements can be extracted even when the fundamental frequency of the BPRML sample is smaller than the Nyquist frequency of the measurements. The measurements demonstrate a number of problems related to the interpretation of the SEM and TEM data. Note that similar BPRML test samples can be used to characterize X-ray microscopes. Corresponding work with X-ray microscopes is in progress.« less

A genetic linkage map of grape, utilizing Vitis rupestris and Vitis arizonica.

PubMed

Doucleff, M; Jin, Y; Gao, F; Riaz, S; Krivanek, A F; Walker, M A

2004-10-01

A genetic linkage map of grape was constructed, utilizing 116 progeny derived from a cross of two Vitis rupestris x V. arizonica interspecific hybrids, using the pseudo-testcross strategy. A total of 475 DNA markers-410 amplified fragment length polymorphism, 24 inter-simple sequence repeat, 32 random amplified polymorphic DNA, and nine simple sequence repeat markers-were used to construct the parental maps. Markers segregating 1:1 were used to construct parental framework maps with confidence levels >90% with the Plant Genome Research Initiative mapping program. In the maternal (D8909-15) map, 105 framework markers and 55 accessory markers were ordered in 17 linkage groups (756 cM). The paternal (F8909-17) map had 111 framework markers and 33 accessory markers ordered in 19 linkage groups (1,082 cM). One hundred eighty-one markers segregating 3:1 were used to connect the two parental maps' parents. This moderately dense map will be useful for the initial mapping of genes and/or QTL for resistance to the dagger nematode, Xiphinema index, and Xylella fastidiosa, the bacterial causal agent of Pierce's disease.

Model parameter estimation approach based on incremental analysis for lithium-ion batteries without using open circuit voltage

NASA Astrophysics Data System (ADS)

Wu, Hongjie; Yuan, Shifei; Zhang, Xi; Yin, Chengliang; Ma, Xuerui

2015-08-01

To improve the suitability of lithium-ion battery model under varying scenarios, such as fluctuating temperature and SoC variation, dynamic model with parameters updated realtime should be developed. In this paper, an incremental analysis-based auto regressive exogenous (I-ARX) modeling method is proposed to eliminate the modeling error caused by the OCV effect and improve the accuracy of parameter estimation. Then, its numerical stability, modeling error, and parametric sensitivity are analyzed at different sampling rates (0.02, 0.1, 0.5 and 1 s). To identify the model parameters recursively, a bias-correction recursive least squares (CRLS) algorithm is applied. Finally, the pseudo random binary sequence (PRBS) and urban dynamic driving sequences (UDDSs) profiles are performed to verify the realtime performance and robustness of the newly proposed model and algorithm. Different sampling rates (1 Hz and 10 Hz) and multiple temperature points (5, 25, and 45 °C) are covered in our experiments. The experimental and simulation results indicate that the proposed I-ARX model can present high accuracy and suitability for parameter identification without using open circuit voltage.

[Variability of nuclear 18S-25S rDNA of Gentiana lutea L. in nature and in tissue culture in vitro].

PubMed

Mel'nyk, V M; Spiridonova, K V; Andrieiev, I O; Strashniuk, N M; Kunakh, V A

2004-01-01

18S-25S rDNA sequence in genomes of G. lutea plants from different natural populations and from tissue culture has been studied with blot-hybridization method. It was shown that ribosomal repeats are represented by the variants which differ for their size and for the presence of additional HindIII restriction site. Genome of individual plant usually possesses several variants of DNA repeats. Interpopulation variability according to their quantitative ratio and to the presence of some of them has been shown. Modifications of the range of rDNA repeats not exceeding intraspecific variability were observed in callus tissues in comparison with the plants of initial population. Non-randomness of genome modifications in the course of cell adaptation to in vitro conditions makes it possible to some extent to forecast these modifications in tissue culture.

Zero-Echo-Time and Dixon Deep Pseudo-CT (ZeDD CT): Direct Generation of Pseudo-CT Images for Pelvic PET/MRI Attenuation Correction Using Deep Convolutional Neural Networks with Multiparametric MRI.

PubMed

Leynes, Andrew P; Yang, Jaewon; Wiesinger, Florian; Kaushik, Sandeep S; Shanbhag, Dattesh D; Seo, Youngho; Hope, Thomas A; Larson, Peder E Z

2018-05-01

Accurate quantification of uptake on PET images depends on accurate attenuation correction in reconstruction. Current MR-based attenuation correction methods for body PET use a fat and water map derived from a 2-echo Dixon MRI sequence in which bone is neglected. Ultrashort-echo-time or zero-echo-time (ZTE) pulse sequences can capture bone information. We propose the use of patient-specific multiparametric MRI consisting of Dixon MRI and proton-density-weighted ZTE MRI to directly synthesize pseudo-CT images with a deep learning model: we call this method ZTE and Dixon deep pseudo-CT (ZeDD CT). Methods: Twenty-six patients were scanned using an integrated 3-T time-of-flight PET/MRI system. Helical CT images of the patients were acquired separately. A deep convolutional neural network was trained to transform ZTE and Dixon MR images into pseudo-CT images. Ten patients were used for model training, and 16 patients were used for evaluation. Bone and soft-tissue lesions were identified, and the SUV max was measured. The root-mean-squared error (RMSE) was used to compare the MR-based attenuation correction with the ground-truth CT attenuation correction. Results: In total, 30 bone lesions and 60 soft-tissue lesions were evaluated. The RMSE in PET quantification was reduced by a factor of 4 for bone lesions (10.24% for Dixon PET and 2.68% for ZeDD PET) and by a factor of 1.5 for soft-tissue lesions (6.24% for Dixon PET and 4.07% for ZeDD PET). Conclusion: ZeDD CT produces natural-looking and quantitatively accurate pseudo-CT images and reduces error in pelvic PET/MRI attenuation correction compared with standard methods. © 2018 by the Society of Nuclear Medicine and Molecular Imaging.

Seminar on Understanding Digital Control and Analysis in Vibration Test Systems, part 2

NASA Technical Reports Server (NTRS)

1975-01-01

A number of techniques for dealing with important technical aspects of the random vibration control problem are described. These include the generation of pseudo-random and true random noise, the control spectrum estimation problem, the accuracy/speed tradeoff, and control correction strategies. System hardware, the operator-system interface, safety features, and operational capabilities of sophisticated digital random vibration control systems are also discussed.

A resource of single-nucleotide polymorphisms for rainbow trout generated by restriction-site associated DNA sequencing of doubled haploids

USDA-ARS?s Scientific Manuscript database

Salmonid genomes are considered to be in a pseudo-tetraploid state as a result of an evolutionarily recent genome duplication event. This situation complicates single nucleotide polymorphism (SNP) discovery in rainbow trout as many putative SNPs are actually paralogous sequence variants (PSVs) and ...

Pseudo-Bartter syndrome as the sole manifestation of cystic fibrosis in a child with 711+G>T/IVS8-5T mutation: a new face of an old disease.

PubMed

Tinsa, Faten; Hadj Fredj, Sondes; Bel Hadj, Imen; Khalsi, Fatma; Abdelhak, Sonia; Boussetta, Khadija; Messaoud, Taieb

2017-08-01

Pseudo-Bartter syndrome (PBS) describes an uncommon complication of cystic fibrosis leading to hypochloraemic, hypokalaemic metabolic alkalosis. PBS as the sole manifestation of cystic fibrosis in children is extremely rare and has never been described in patients carrying 5T variant. We report a clinical, biochemical and genetic study of a four year-old boy presenting a pseudo-Bartter syndrome as the sole manifestation of cystic fibrosis. All 27 exons and the flanking intron regions of the CFTR gene were analysed by PCR and direct sequencing. Direct sequencing was also used to analyse TG m T n and M470V polymorphisms in the patient and his parents. Two sweat tests were abnormal with elevated chloride levels at 78 and 88 mmol/L. DNA sequencing revealed a heterozygous mutation 711+1 G>T and an IVS8-T5 allele. The mutation 711+1 G>T is in trans with the IVS8-T5-TG11 allele and the child carried M470/V470 genotype. To the best of our knowledge, the genotype 711+1 G>T /IVS8-5T found in our patient is described for the first time. The role of TG11-5T-V470 allele in cases of cystic fibrosis with PB syndrome remains to be determined.

Generalized Forchheimer Flows of Isentropic Gases

NASA Astrophysics Data System (ADS)

Celik, Emine; Hoang, Luan; Kieu, Thinh

2018-03-01

We consider generalized Forchheimer flows of either isentropic gases or slightly compressible fluids in porous media. By using Muskat's and Ward's general form of the Forchheimer equations, we describe the fluid dynamics by a doubly nonlinear parabolic equation for the appropriately defined pseudo-pressure. The volumetric flux boundary condition is converted to a time-dependent Robin-type boundary condition for this pseudo-pressure. We study the corresponding initial boundary value problem, and estimate the L^∞ and W^{1,2-a} (with 0

iCar-PseCp: identify carbonylation sites in proteins by Monte Carlo sampling and incorporating sequence coupled effects into general PseAAC.

PubMed

Jia, Jianhua; Liu, Zi; Xiao, Xuan; Liu, Bingxiang; Chou, Kuo-Chen

2016-06-07

Carbonylation is a posttranslational modification (PTM or PTLM), where a carbonyl group is added to lysine (K), proline (P), arginine (R), and threonine (T) residue of a protein molecule. Carbonylation plays an important role in orchestrating various biological processes but it is also associated with many diseases such as diabetes, chronic lung disease, Parkinson's disease, Alzheimer's disease, chronic renal failure, and sepsis. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence containing many residues of K, P, R, or T, which ones can be carbonylated, and which ones cannot? To address this problem, we have developed a predictor called iCar-PseCp by incorporating the sequence-coupled information into the general pseudo amino acid composition, and balancing out skewed training dataset by Monte Carlo sampling to expand positive subset. Rigorous target cross-validations on a same set of carbonylation-known proteins indicated that the new predictor remarkably outperformed its existing counterparts. For the convenience of most experimental scientists, a user-friendly web-server for iCar-PseCp has been established at http://www.jci-bioinfo.cn/iCar-PseCp, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. It has not escaped our notice that the formulation and approach presented here can also be used to analyze many other problems in computational proteomics.

Structure and Dynamics of DNA and RNA Double Helices Obtained from the CCG and GGC Trinucleotide Repeats.

PubMed

Pan, Feng; Man, Viet Hoang; Roland, Christopher; Sagui, Celeste

2018-04-26

Expansions of both GGC and CCG sequences lead to a number of expandable, trinucleotide repeat (TR) neurodegenerative diseases. Understanding of these diseases involves, among other things, the structural characterization of the atypical DNA and RNA secondary structures. We have performed molecular dynamics simulations of (GCC) n and (GGC) n homoduplexes in order to characterize their conformations, stability, and dynamics. Each TR has two reading frames, which results in eight nonequivalent RNA/DNA homoduplexes, characterized by CpG or GpC steps between the Watson-Crick base pairs. Free energy maps for the eight homoduplexes indicate that the C-mismatches prefer anti-anti conformations, while G-mismatches prefer anti-syn conformations. Comparison between three modifications of the DNA AMBER force field shows good agreement for the mismatch free energy maps. The mismatches in DNA-GCC (but not CCG) are extrahelical, forming an extended e-motif. The mismatched duplexes exhibit characteristic sequence-dependent step twist, with strong variations in the G-rich sequences and the e-motif. The distribution of Na + is highly localized around the mismatches, especially G-mismatches. In the e-motif, there is strong Na + binding by two G(N7) atoms belonging to the pseudo GpC step created when cytosines are extruded and by extrahelical cytosines. Finally, we used a novel technique based on fast melting by means of an infrared laser pulse to classify the relative stability of the different DNA-CCG and -GGC homoduplexes.

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data.

PubMed

Duchêne, Sebastián; Duchêne, David; Holmes, Edward C; Ho, Simon Y W

2015-07-01

Rates and timescales of viral evolution can be estimated using phylogenetic analyses of time-structured molecular sequences. This involves the use of molecular-clock methods, calibrated by the sampling times of the viral sequences. However, the spread of these sampling times is not always sufficient to allow the substitution rate to be estimated accurately. We conducted Bayesian phylogenetic analyses of simulated virus data to evaluate the performance of the date-randomization test, which is sometimes used to investigate whether time-structured data sets have temporal signal. An estimate of the substitution rate passes this test if its mean does not fall within the 95% credible intervals of rate estimates obtained using replicate data sets in which the sampling times have been randomized. We find that the test sometimes fails to detect rate estimates from data with no temporal signal. This error can be minimized by using a more conservative criterion, whereby the 95% credible interval of the estimate with correct sampling times should not overlap with those obtained with randomized sampling times. We also investigated the behavior of the test when the sampling times are not uniformly distributed throughout the tree, which sometimes occurs in empirical data sets. The test performs poorly in these circumstances, such that a modification to the randomization scheme is needed. Finally, we illustrate the behavior of the test in analyses of nucleotide sequences of cereal yellow dwarf virus. Our results validate the use of the date-randomization test and allow us to propose guidelines for interpretation of its results. © The Author 2015. 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.

Study of the Kinetics and Equilibrium of the Adsorption of Oils onto Hydrophobic Jute Fiber Modified via the Sol-Gel Method.

PubMed

Lv, Na; Wang, Xiaoli; Peng, Shitao; Zhang, Huaqin; Luo, Lei

2018-05-12

A new kind of hydrophobic and oil sorbent based on jute fiber was successfully prepared by the integration of silica onto a fiber surface via the sol-gel method and subsequent hydrophobic modification with octadecyltrichlorosilane (OTS). Compared with the hydrophilic raw fiber, the modified fiber had a water contact angle (CA) of 136.2°, suggesting that the material has good hydrophobicity. Furthermore, the ability of oil in the oil/water system (taking diesel for example) to absorb was revealed by the kinetics, the isotherm equation, and the thermodynamic parameters. Adsorption behavior was kinetically investigated using pseudo first-order and pseudo second-order models. The data mostly correlated with the pseudo first-order model. The equilibrium adsorption at 298 K was assessed by using the Langmuir and Freundlich isotherm models. The Freundlich model had greater consistency with the experimental data. The obtained thermodynamic parameters demonstrate that the adsorption of diesel is spontaneous, favorable, and exothermic.

Hypoxia-induced oxidative base modifications in the VEGF hypoxia-response element are associated with transcriptionally active nucleosomes.

PubMed

Ruchko, Mykhaylo V; Gorodnya, Olena M; Pastukh, Viktor M; Swiger, Brad M; Middleton, Natavia S; Wilson, Glenn L; Gillespie, Mark N

2009-02-01

Reactive oxygen species (ROS) generated in hypoxic pulmonary artery endothelial cells cause transient oxidative base modifications in the hypoxia-response element (HRE) of the VEGF gene that bear a conspicuous relationship to induction of VEGF mRNA expression (K.A. Ziel et al., FASEB J. 19, 387-394, 2005). If such base modifications are indeed linked to transcriptional regulation, then they should be detected in HRE sequences associated with transcriptionally active nucleosomes. Southern blot analysis of the VEGF HRE associated with nucleosome fractions prepared by micrococcal nuclease digestion indicated that hypoxia redistributed some HRE sequences from multinucleosomes to transcriptionally active mono- and dinucleosome fractions. A simple PCR method revealed that VEGF HRE sequences harboring oxidative base modifications were found exclusively in mononucleosomes. Inhibition of hypoxia-induced ROS generation with myxathiozol prevented formation of oxidative base modifications but not the redistribution of HRE sequences into mono- and dinucleosome fractions. The histone deacetylase inhibitor trichostatin A caused retention of HRE sequences in compacted nucleosome fractions and prevented formation of oxidative base modifications. These findings suggest that the hypoxia-induced oxidant stress directed at the VEGF HRE requires the sequence to be repositioned into mononucleosomes and support the prospect that oxidative modifications in this sequence are an important step in transcriptional activation.

Comparing pseudo-absences generation techniques in Boosted Regression Trees models for conservation purposes: A case study on amphibians in a protected area.

PubMed

Cerasoli, Francesco; Iannella, Mattia; D'Alessandro, Paola; Biondi, Maurizio

2017-01-01

Boosted Regression Trees (BRT) is one of the modelling techniques most recently applied to biodiversity conservation and it can be implemented with presence-only data through the generation of artificial absences (pseudo-absences). In this paper, three pseudo-absences generation techniques are compared, namely the generation of pseudo-absences within target-group background (TGB), testing both the weighted (WTGB) and unweighted (UTGB) scheme, and the generation at random (RDM), evaluating their performance and applicability in distribution modelling and species conservation. The choice of the target group fell on amphibians, because of their rapid decline worldwide and the frequent lack of guidelines for conservation strategies and regional-scale planning, which instead could be provided through an appropriate implementation of SDMs. Bufo bufo, Salamandrina perspicillata and Triturus carnifex were considered as target species, in order to perform our analysis with species having different ecological and distributional characteristics. The study area is the "Gran Sasso-Monti della Laga" National Park, which hosts 15 Natura 2000 sites and represents one of the most important biodiversity hotspots in Europe. Our results show that the model calibration ameliorates when using the target-group based pseudo-absences compared to the random ones, especially when applying the WTGB. Contrarily, model discrimination did not significantly vary in a consistent way among the three approaches with respect to the tree target species. Both WTGB and RDM clearly isolate the highly contributing variables, supplying many relevant indications for species conservation actions. Moreover, the assessment of pairwise variable interactions and their three-dimensional visualization further increase the amount of useful information for protected areas' managers. Finally, we suggest the use of RDM as an admissible alternative when it is not possible to individuate a suitable set of species as a representative target-group from which the pseudo-absences can be generated.

Habitat classification modeling with incomplete data: Pushing the habitat envelope

USGS Publications Warehouse

Zarnetske, P.L.; Edwards, T.C.; Moisen, Gretchen G.

2007-01-01

Habitat classification models (HCMs) are invaluable tools for species conservation, land-use planning, reserve design, and metapopulation assessments, particularly at broad spatial scales. However, species occurrence data are often lacking and typically limited to presence points at broad scales. This lack of absence data precludes the use of many statistical techniques for HCMs. One option is to generate pseudo-absence points so that the many available statistical modeling tools can be used. Traditional techniques generate pseudoabsence points at random across broadly defined species ranges, often failing to include biological knowledge concerning the species-habitat relationship. We incorporated biological knowledge of the species-habitat relationship into pseudo-absence points by creating habitat envelopes that constrain the region from which points were randomly selected. We define a habitat envelope as an ecological representation of a species, or species feature's (e.g., nest) observed distribution (i.e., realized niche) based on a single attribute, or the spatial intersection of multiple attributes. We created HCMs for Northern Goshawk (Accipiter gentilis atricapillus) nest habitat during the breeding season across Utah forests with extant nest presence points and ecologically based pseudo-absence points using logistic regression. Predictor variables were derived from 30-m USDA Landfire and 250-m Forest Inventory and Analysis (FIA) map products. These habitat-envelope-based models were then compared to null envelope models which use traditional practices for generating pseudo-absences. Models were assessed for fit and predictive capability using metrics such as kappa, thresholdindependent receiver operating characteristic (ROC) plots, adjusted deviance (Dadj2), and cross-validation, and were also assessed for ecological relevance. For all cases, habitat envelope-based models outperformed null envelope models and were more ecologically relevant, suggesting that incorporating biological knowledge into pseudo-absence point generation is a powerful tool for species habitat assessments. Furthermore, given some a priori knowledge of the species-habitat relationship, ecologically based pseudo-absence points can be applied to any species, ecosystem, data resolution, and spatial extent. ?? 2007 by the Ecological Society of America.

In silico evidence for sequence-dependent nucleosome sliding

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

Lequieu, Joshua; Schwartz, David C.; de Pablo, Juan J.

Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nudeosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces andmore » the corresponding dynamics of nudeosome repositioning. The mechanism of nudeosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.« less

Isolation, identification, Pb(II) biosorption isotherms and kinetics of a lead adsorbing penicillium sp. MRF-1 from South Korean mine soil.

PubMed

Velmurugan, Natarajan; Hwang, Grim; Sathishkumar, Muthuswamy; Choi, Tae Kie; Lee, Kui-Jae; Oh, Byung-Taek; Lee, Yang-Soo

2010-01-01

A heavy metal contaminated soil sample collected from a mine in Chonnam Province of South Korea was found to be a source of heavy metal adsorbing biosorbents. Chemical analyses showed high contents of lead (Pb) at 357 mg/kg and cyanide (CN) at 14.6 mg/kg in the soil. The experimental results showed that Penicillium sp. MRF-1 was the best lead resistant fungus among the four individual metal tolerant fungal species isolated from the soil. Molecular characterization of Penicillium sp. MRF-1 was determined using ITS regions sequences. Effects of pH, temperature and contact time on adsorption of Pb(II) by Penicillium sp. MRF-1 were studied. Favorable conditions for maximum biosportion were found at pH 4 with 3 hr contact time. Biosorption of Pb(II) gradually increased with increasing temperature. Efficient performance of the biosorbent was described using Langmuir and Freundlich isotherms. Adsorption kinetics was studied using pseudo first-order and pseudo second-order models. Biosorbent Penicillium sp. MRF-1 showed the maximum desorption in alkali conditions. Consistent adsorption/desorption potential of the biosorbent in repetitive cycles validated the efficacy of it in large scale. SEM studies given notes on surface modification of fungal biomass under metal stress and FT-IR results showed the presence of amino groups in the surface structure of the biosorbent. In conclusion, the new biosorbent Penicillium sp. MRF-1 may potentially be used as an inexpensive, easily cultivatable material for the removal of lead from aqueous solution.

Mapping Base Modifications in DNA by Transverse-Current Sequencing

NASA Astrophysics Data System (ADS)

Alvarez, Jose R.; Skachkov, Dmitry; Massey, Steven E.; Kalitsov, Alan; Velev, Julian P.

2018-02-01

Sequencing DNA modifications and lesions, such as methylation of cytosine and oxidation of guanine, is even more important and challenging than sequencing the genome itself. The traditional methods for detecting DNA modifications are either insensitive to these modifications or require additional processing steps to identify a particular type of modification. Transverse-current sequencing in nanopores can potentially identify the canonical bases and base modifications in the same run. In this work, we demonstrate that the most common DNA epigenetic modifications and lesions can be detected with any predefined accuracy based on their tunneling current signature. Our results are based on simulations of the nanopore tunneling current through DNA molecules, calculated using nonequilibrium electron-transport methodology within an effective multiorbital model derived from first-principles calculations, followed by a base-calling algorithm accounting for neighbor current-current correlations. This methodology can be integrated with existing experimental techniques to improve base-calling fidelity.

Genetic recombination pathways and their application for genome modification of human embryonic stem cells.

PubMed

Nieminen, Mikko; Tuuri, Timo; Savilahti, Harri

2010-10-01

Human embryonic stem cells are pluripotent cells derived from early human embryo and retain a potential to differentiate into all adult cell types. They provide vast opportunities in cell replacement therapies and are expected to become significant tools in drug discovery as well as in the studies of cellular and developmental functions of human genes. The progress in applying different types of DNA recombination reactions for genome modification in a variety of eukaryotic cell types has provided means to utilize recombination-based strategies also in human embryonic stem cells. Homologous recombination-based methods, particularly those utilizing extended homologous regions and those employing zinc finger nucleases to boost genomic integration, have shown their usefulness in efficient genome modification. Site-specific recombination systems are potent genome modifiers, and they can be used to integrate DNA into loci that contain an appropriate recombination signal sequence, either naturally occurring or suitably pre-engineered. Non-homologous recombination can be used to generate random integrations in genomes relatively effortlessly, albeit with a moderate efficiency and precision. DNA transposition-based strategies offer substantially more efficient random strategies and provide means to generate single-copy insertions, thus potentiating the generation of genome-wide insertion libraries applicable in genetic screens. 2010 Elsevier Inc. All rights reserved.

tRNAmodpred: a computational method for predicting posttranscriptional modifications in tRNAs

PubMed Central

Machnicka, Magdalena A.; Dunin-Horkawicz, Stanislaw; de Crécy-Lagard, Valerie; Bujnicki, Janusz M.

2016-01-01

tRNA molecules contain numerous chemically altered nucleosides, which are formed by enzymatic modification of the primary transcripts during the complex tRNA maturation process. Some of the modifications are introduced by single reactions, while other require complex series of reactions carried out by several different enzymes. The location and distribution of various types of modifications vary greatly between different tRNA molecules, organisms and organelles. We have developed a computational method tRNAmodpred, for predicting modifications in tRNA sequences. Briefly, our method takes as an input one or more unmodified tRNA sequences and a set of protein sequences corresponding to a proteome of a cell. Subsequently it identifies homologs of known tRNA modification enzymes in the proteome, predicts tRNA modification activities and maps them onto known pathways of RNA modification from the MODOMICS database. Thereby, theoretically possible modification pathways are identified, and products of these modification reactions are proposed for query tRNAs. This method allows for predicting modification patterns for newly sequenced genomes as well as for checking tentative modification status of tRNAs from one species treated with enzymes from another source, e.g. to predict the possible modifications of eukaryotic tRNAs expressed in bacteria. tRNAmodpred is freely available as web server at http://genesilico.pl/trnamodpred/. PMID:27016142

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

Yashchuk, Valeriy V; Conley, Raymond; Anderson, Erik H

Verification of the reliability of metrology data from high quality x-ray optics requires that adequate methods for test and calibration of the instruments be developed. For such verification for optical surface profilometers in the spatial frequency domain, a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) gratings and arrays has been suggested [Proc. SPIE 7077-7 (2007), Opt. Eng. 47(7), 073602-1-5 (2008)} and proven to be an effective calibration method for a number of interferometric microscopes, a phase shifting Fizeau interferometer, and a scatterometer [Nucl. Instr. and Meth. A 616, 172-82 (2010)]. Here we describe the details ofmore » development of binary pseudo-random multilayer (BPRML) test samples suitable for characterization of scanning (SEM) and transmission (TEM) electron microscopes. We discuss the results of TEM measurements with the BPRML test samples fabricated from a WiSi2/Si multilayer coating with pseudo randomly distributed layers. In particular, we demonstrate that significant information about the metrological reliability of the TEM measurements can be extracted even when the fundamental frequency of the BPRML sample is smaller than the Nyquist frequency of the measurements. The measurements demonstrate a number of problems related to the interpretation of the SEM and TEM data. Note that similar BPRML test samples can be used to characterize x-ray microscopes. Corresponding work with x-ray microscopes is in progress.« less

Do pharmacy staff recommend evidenced-based smoking cessation products? A pseudo patron study.

PubMed

Chiang, P P C; Chapman, S

2006-06-01

To determine whether pharmacy staff recommend evidence-based smoking cessation aids. Pseudo patron visit to 50 randomly selected Sydney pharmacies where the pseudo patron enquired about the 'best' way to quit smoking and about the efficacy of a non-evidence-based cessation product, NicoBloc. Nicotine replacement therapy was universally stocked and the first product recommended by 90% of pharmacies. After prompting, 60% of pharmacies, either also recommended NicoBloc or deferred to 'customer choice'. About 34% disparaged the product. Evidence-based smoking cessation advice in Sydney pharmacies is fragile and may be compromised by commercial concerns. Smokers should be provided with independent point-of-sale summaries of evidence of cessation product effectiveness and warned about unsubstantiated claims.

Random vibration analysis of train-bridge under track irregularities and traveling seismic waves using train-slab track-bridge interaction model

NASA Astrophysics Data System (ADS)

Zeng, Zhi-Ping; Zhao, Yan-Gang; Xu, Wen-Tao; Yu, Zhi-Wu; Chen, Ling-Kun; Lou, Ping

2015-04-01

The frequent use of bridges in high-speed railway lines greatly increases the probability that trains are running on bridges when earthquakes occur. This paper investigates the random vibrations of a high-speed train traversing a slab track on a continuous girder bridge subjected to track irregularities and traveling seismic waves by the pseudo-excitation method (PEM). To derive the equations of motion of the train-slab track-bridge interaction system, the multibody dynamics and finite element method models are used for the train and the track and bridge, respectively. By assuming track irregularities to be fully coherent random excitations with time lags between different wheels and seismic accelerations to be uniformly modulated, non-stationary random excitations with time lags between different foundations, the random load vectors of the equations of motion are transformed into a series of deterministic pseudo-excitations based on PEM and the wheel-rail contact relationship. A computer code is developed to obtain the time-dependent random responses of the entire system. As a case study, the random vibration characteristics of an ICE-3 high-speed train traversing a seven-span continuous girder bridge simultaneously excited by track irregularities and traveling seismic waves are analyzed. The influence of train speed and seismic wave propagation velocity on the random vibration characteristics of the bridge and train are discussed.

iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model

PubMed Central

Lin, Wei-Zhong; Fang, Jian-An; Xiao, Xuan; Chou, Kuo-Chen

2011-01-01

DNA-binding proteins play crucial roles in various cellular processes. Developing high throughput tools for rapidly and effectively identifying DNA-binding proteins is one of the major challenges in the field of genome annotation. Although many efforts have been made in this regard, further effort is needed to enhance the prediction power. By incorporating the features into the general form of pseudo amino acid composition that were extracted from protein sequences via the “grey model” and by adopting the random forest operation engine, we proposed a new predictor, called iDNA-Prot, for identifying uncharacterized proteins as DNA-binding proteins or non-DNA binding proteins based on their amino acid sequences information alone. The overall success rate by iDNA-Prot was 83.96% that was obtained via jackknife tests on a newly constructed stringent benchmark dataset in which none of the proteins included has pairwise sequence identity to any other in a same subset. In addition to achieving high success rate, the computational time for iDNA-Prot is remarkably shorter in comparison with the relevant existing predictors. Hence it is anticipated that iDNA-Prot may become a useful high throughput tool for large-scale analysis of DNA-binding proteins. As a user-friendly web-server, iDNA-Prot is freely accessible to the public at the web-site on http://icpr.jci.edu.cn/bioinfo/iDNA-Prot or http://www.jci-bioinfo.cn/iDNA-Prot. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results. PMID:21935457

Octopus arm movements under constrained conditions: adaptation, modification and plasticity of motor primitives.

PubMed

Richter, Jonas N; Hochner, Binyamin; Kuba, Michael J

2015-04-01

The motor control of the eight highly flexible arms of the common octopus (Octopus vulgaris) has been the focus of several recent studies. Our study is the first to manage to introduce a physical constraint to an octopus arm and investigate the adaptability of stereotypical bend propagation in reaching movements and the pseudo-limb articulation during fetching. Subjects (N=6) were placed inside a transparent Perspex box with a hole at the center that allowed the insertion of a single arm. Animals had to reach out through the hole toward a target, to retrieve a food reward and fetch it. All subjects successfully adjusted their movements to the constraint without an adaptation phase. During reaching tasks, the animals showed two movement strategies: stereotypical bend propagation reachings, which were established at the hole of the Perspex box and variant waving-like movements that showed no bend propagations. During fetching movements, no complete pseudo-joint fetching was observed outside the box and subjects pulled their arms through the hole in a pull-in like movement. Our findings show that there is some flexibility in the octopus motor system to adapt to a novel situation. However, at present, it seems that these changes are more an effect of random choices between different alternative motor programs, without showing clear learning effects in the choice between the alternatives. Interestingly, animals were able to adapt the fetching movements to the physical constraint, or as an alternative explanation, they could switch the motor primitive fetching to a different motor primitive 'arm pulling'. © 2015. Published by The Company of Biologists Ltd.

UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery

PubMed Central

Mais, Christine; Wright, Jane E.; Prieto, José-Luis; Raggett, Samantha L.; McStay, Brian

2005-01-01

Human ribosomal genes (rDNA) are located in nucleolar organizer regions (NORs) on the short arms of acrocentric chromosomes. Metaphase NORs that were transcriptionally active in the previous cell cycle appear as prominent chromosomal features termed secondary constrictions that are achromatic in chromosome banding and positive in silver staining. The architectural RNA polymerase I (pol I) transcription factor UBF binds extensively across rDNA throughout the cell cycle. To determine if UBF binding underpins NOR structure, we integrated large arrays of heterologous UBF-binding sequences at ectopic sites on human chromosomes. These arrays efficiently recruit UBF even to sites outside the nucleolus and, during metaphase, form novel silver stainable secondary constrictions, termed pseudo-NORs, morphologically similar to NORs. We demonstrate for the first time that in addition to UBF the other components of the pol I machinery are found associated with sequences across the entire human rDNA repeat. Remarkably, a significant fraction of these same pol I factors are sequestered by pseudo-NORs independent of both transcription and nucleoli. Because of the heterologous nature of the sequence employed, we infer that sequestration is mediated primarily by protein–protein interactions with UBF. These results suggest that extensive binding of UBF is responsible for formation and maintenance of the secondary constriction at active NORs. Furthermore, we propose that UBF mediates recruitment of the pol I machinery to nucleoli independently of promoter elements. PMID:15598984

Open-pNovo: De Novo Peptide Sequencing with Thousands of Protein Modifications.

PubMed

Yang, Hao; Chi, Hao; Zhou, Wen-Jing; Zeng, Wen-Feng; He, Kun; Liu, Chao; Sun, Rui-Xiang; He, Si-Min

2017-02-03

De novo peptide sequencing has improved remarkably, but sequencing full-length peptides with unexpected modifications is still a challenging problem. Here we present an open de novo sequencing tool, Open-pNovo, for de novo sequencing of peptides with arbitrary types of modifications. Although the search space increases by ∼300 times, Open-pNovo is close to or even ∼10-times faster than the other three proposed algorithms. Furthermore, considering top-1 candidates on three MS/MS data sets, Open-pNovo can recall over 90% of the results obtained by any one traditional algorithm and report 5-87% more peptides, including 14-250% more modified peptides. On a high-quality simulated data set, ∼85% peptides with arbitrary modifications can be recalled by Open-pNovo, while hardly any results can be recalled by others. In summary, Open-pNovo is an excellent tool for open de novo sequencing and has great potential for discovering unexpected modifications in the real biological applications.

Analysis on pseudo excitation of random vibration for structure of time flight counter

NASA Astrophysics Data System (ADS)

Wu, Qiong; Li, Dapeng

2015-03-01

Traditional computing method is inefficient for getting key dynamical parameters of complicated structure. Pseudo Excitation Method(PEM) is an effective method for calculation of random vibration. Due to complicated and coupling random vibration in rocket or shuttle launching, the new staging white noise mathematical model is deduced according to the practical launch environment. This deduced model is applied for PEM to calculate the specific structure of Time of Flight Counter(ToFC). The responses of power spectral density and the relevant dynamic characteristic parameters of ToFC are obtained in terms of the flight acceptance test level. Considering stiffness of fixture structure, the random vibration experiments are conducted in three directions to compare with the revised PEM. The experimental results show the structure can bear the random vibration caused by launch without any damage and key dynamical parameters of ToFC are obtained. The revised PEM is similar with random vibration experiment in dynamical parameters and responses are proved by comparative results. The maximum error is within 9%. The reasons of errors are analyzed to improve reliability of calculation. This research provides an effective method for solutions of computing dynamical characteristic parameters of complicated structure in the process of rocket or shuttle launching.

Adsorption potential of a modified activated carbon for the removal of nitrogen containing compounds from model fuel

NASA Astrophysics Data System (ADS)

Anisuzzaman, S. M.; Krishnaiah, D.; Alfred, D.

2018-02-01

The purpose of this study is to find the effect of the modified activated carbon (MAC) on the adsorption activity for nitrogen containing compounds (NCC) removal from model fuel. Modification of commercial activated carbon (AC) involved impregnation with different ratios of sulfuric acid solution. Pseudo-first and pseudo-second order kinetic models were applied to study the adsorption kinetics, while the adsorption isotherms were used for the evaluation of equilibrium data. All of the experimental data were analyzed using ultraviolet-visible spectroscopy after adsorption experiment between different concentration dosage of adsorbent and model fuel. It has been found that adsorption of NCC by MAC was best fit is the Langmuir isotherm for quinoline (QUI) and Freundlich isotherm for indole (IND) with a maximum adsorption capacity of 0.13 mg/g and 0.16 mg/g respectively. Based on the experimental data, pseudo-first order exhibited the best fit for QUI with linear regression (R2) ranges from 0.0.9777 to 0.9935 and pseudo-second order exhibited the best fit for IND with linear regression (R2) ranges from 0.9701 to 0.9962. From the adsorption isotherm and kinetic studies result proven that commercial AC shows great potential in removing nitrogen.

Characterization of Apricot pseudo-chlorotic leaf spot virus, A Novel Trichovirus Isolated from Stone Fruit Trees.

PubMed

Liberti, D; Marais, A; Svanella-Dumas, L; Dulucq, M J; Alioto, D; Ragozzino, A; Rodoni, B; Candresse, T

2005-04-01

ABSTRACT A trichovirus closely related to Apple chlorotic leaf spot virus (ACLSV) was detected in symptomatic apricot and Japanese plum from Italy. The Sus2 isolate of this agent cross-reacted with anti-ACLSV polyclonal reagents but was not detected by broad-specificity anti- ACLSV monoclonal antibodies. It had particles with typical trichovirus morphology but, contrary to ACLSV, was unable to infect Chenopodium quinoa and C. amaranticolor. The sequence of its genome (7,494 nucleotides [nt], missing only approximately 30 to 40 nt of the 5' terminal sequence) and the partial sequence of another isolate were determined. The new virus has a genomic organization similar to that of ACLSV, with three open reading frames coding for a replication-associated protein (RNA-dependent RNA polymerase), a movement protein, and a capsid protein, respectively. However, it had only approximately 65 to 67% nucleotide identity with sequenced isolates of ACLSV. The differences in serology, host range, genome sequence, and phylogenetic reconstructions for all viral proteins support the idea that this agent should be considered a new virus, for which the name Apricot pseudo-chlorotic leaf spot virus (APCLSV) is proposed. APCLSV shows substantial sequence variability and has been recovered from various Prunus sources coming from seven countries, an indication that it is likely to have a wide geographical distribution.

Low power laser driver design in 28nm CMOS for on-chip and chip-to-chip optical interconnect

NASA Astrophysics Data System (ADS)

Belfiore, Guido; Szilagyi, Laszlo; Henker, Ronny; Ellinger, Frank

2015-09-01

This paper discusses the challenges and the trade-offs in the design of laser drivers for very-short distance optical communications. A prototype integrated circuit is designed and fabricated in 28 nm super-low-power CMOS technology. The power consumption of the transmitter is 17.2 mW excluding the VCSEL that in our test has a DC power consumption of 10 mW. The active area of the driver is only 0.0045 mm2. The driver can achieve an error-free (BER < 10 -12) electrical data-rate of 25 Gbit/s using a pseudo random bit sequence of 27 -1. When the driver is connected to the VCSEL module an open optical eye is reported at 15 Gbit/s. In the tested bias point the VCSEL module has a measured bandwidth of 10.7 GHz.

Optimum decoding and detection of a multiplicative amplitude-encoded watermark

NASA Astrophysics Data System (ADS)

Barni, Mauro; Bartolini, Franco; De Rosa, Alessia; Piva, Alessandro

2002-04-01

The aim of this paper is to present a novel approach to the decoding and the detection of multibit, multiplicative, watermarks embedded in the frequency domain. Watermark payload is conveyed by amplitude modulating a pseudo-random sequence, thus resembling conventional DS spread spectrum techniques. As opposed to conventional communication systems, though, the watermark is embedded within the host DFT coefficients by using a multiplicative rule. The watermark decoding technique presented in the paper is an optimum one, in that it minimizes the bit error probability. The problem of watermark presence assessment, which is often underestimated by state-of-the-art research on multibit watermarking, is addressed too, and the optimum detection rule derived according to the Neyman-Pearson criterion. Experimental results are shown both to demonstrate the validity of the theoretical analysis and to highlight the good performance of the proposed system.

An investigation of error correcting techniques for OMV and AXAF

NASA Technical Reports Server (NTRS)

Ingels, Frank; Fryer, John

1991-01-01

The original objectives of this project were to build a test system for the NASA 255/223 Reed/Solomon encoding/decoding chip set and circuit board. This test system was then to be interfaced with a convolutional system at MSFC to examine the performance of the concantinated codes. After considerable work, it was discovered that the convolutional system could not function as needed. This report documents the design, construction, and testing of the test apparatus for the R/S chip set. The approach taken was to verify the error correcting behavior of the chip set by injecting known error patterns onto data and observing the results. Error sequences were generated using pseudo-random number generator programs, with Poisson time distribution between errors and Gaussian burst lengths. Sample means, variances, and number of un-correctable errors were calculated for each data set before testing.

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

PubMed Central

Ji, Zhicheng; Ji, Hongkai

2016-01-01

When analyzing single-cell RNA-seq data, constructing a pseudo-temporal path to order cells based on the gradual transition of their transcriptomes is a useful way to study gene expression dynamics in a heterogeneous cell population. Currently, a limited number of computational tools are available for this task, and quantitative methods for comparing different tools are lacking. Tools for Single Cell Analysis (TSCAN) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis. TSCAN uses a cluster-based minimum spanning tree (MST) approach to order cells. Cells are first grouped into clusters and an MST is then constructed to connect cluster centers. Pseudo-time is obtained by projecting each cell onto the tree, and the ordered sequence of cells can be used to study dynamic changes of gene expression along the pseudo-time. Clustering cells before MST construction reduces the complexity of the tree space. This often leads to improved cell ordering. It also allows users to conveniently adjust the ordering based on prior knowledge. TSCAN has a graphical user interface (GUI) to support data visualization and user interaction. Furthermore, quantitative measures are developed to objectively evaluate and compare different pseudo-time reconstruction methods. TSCAN is available at https://github.com/zji90/TSCAN and as a Bioconductor package. PMID:27179027

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.

PubMed

Ji, Zhicheng; Ji, Hongkai

2016-07-27

When analyzing single-cell RNA-seq data, constructing a pseudo-temporal path to order cells based on the gradual transition of their transcriptomes is a useful way to study gene expression dynamics in a heterogeneous cell population. Currently, a limited number of computational tools are available for this task, and quantitative methods for comparing different tools are lacking. Tools for Single Cell Analysis (TSCAN) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis. TSCAN uses a cluster-based minimum spanning tree (MST) approach to order cells. Cells are first grouped into clusters and an MST is then constructed to connect cluster centers. Pseudo-time is obtained by projecting each cell onto the tree, and the ordered sequence of cells can be used to study dynamic changes of gene expression along the pseudo-time. Clustering cells before MST construction reduces the complexity of the tree space. This often leads to improved cell ordering. It also allows users to conveniently adjust the ordering based on prior knowledge. TSCAN has a graphical user interface (GUI) to support data visualization and user interaction. Furthermore, quantitative measures are developed to objectively evaluate and compare different pseudo-time reconstruction methods. TSCAN is available at https://github.com/zji90/TSCAN and as a Bioconductor package. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Investigation of modulation parameters in multiplexing gas chromatography.

PubMed

Trapp, Oliver

2010-10-22

Combination of information technology and separation sciences opens a new avenue to achieve high sample throughputs and therefore is of great interest to bypass bottlenecks in catalyst screening of parallelized reactors or using multitier well plates in reaction optimization. Multiplexing gas chromatography utilizes pseudo-random injection sequences derived from Hadamard matrices to perform rapid sample injections which gives a convoluted chromatogram containing the information of a single sample or of several samples with similar analyte composition. The conventional chromatogram is obtained by application of the Hadamard transform using the known injection sequence or in case of several samples an averaged transformed chromatogram is obtained which can be used in a Gauss-Jordan deconvolution procedure to obtain all single chromatograms of the individual samples. The performance of such a system depends on the modulation precision and on the parameters, e.g. the sequence length and modulation interval. Here we demonstrate the effects of the sequence length and modulation interval on the deconvoluted chromatogram, peak shapes and peak integration for sequences between 9-bit (511 elements) and 13-bit (8191 elements) and modulation intervals Δt between 5 s and 500 ms using a mixture of five components. It could be demonstrated that even for high-speed modulation at time intervals of 500 ms the chromatographic information is very well preserved and that the separation efficiency can be improved by very narrow sample injections. Furthermore this study shows that the relative peak areas in multiplexed chromatograms do not deviate from conventionally recorded chromatograms. Copyright © 2010 Elsevier B.V. All rights reserved.

Demonstration of Johnson noise thermometry with all-superconducting quantum voltage noise source

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

Yamada, Takahiro, E-mail: yamada-takahiro@aist.go.jp; Urano, Chiharu; Maezawa, Masaaki

We present a Johnson noise thermometry (JNT) system based on an integrated quantum voltage noise source (IQVNS) that has been fully implemented using superconducting circuit technology. To enable precise measurement of Boltzmann's constant, an IQVNS chip was designed to produce intrinsically calculable pseudo-white noise to calibrate the JNT system. On-chip real-time generation of pseudo-random codes via simple circuits produced pseudo-voltage noise with a harmonic tone interval of less than 1 Hz, which was one order of magnitude finer than the harmonic tone interval of conventional quantum voltage noise sources. We estimated a value for Boltzmann's constant experimentally by performing JNT measurementsmore » at the temperature of the triple point of water using the IQVNS chip.« less

Analysis of backward error recovery for concurrent processes with recovery blocks

NASA Technical Reports Server (NTRS)

Shin, K. G.; Lee, Y. H.

1982-01-01

Three different methods of implementing recovery blocks (RB's). These are the asynchronous, synchronous, and the pseudo recovery point implementations. Pseudo recovery points so that unbounded rollback may be avoided while maintaining process autonomy are proposed. Probabilistic models for analyzing these three methods under standard assumptions in computer performance analysis, i.e., exponential distributions for related random variables were developed. The interval between two successive recovery lines for asynchronous RB's mean loss in computation power for the synchronized method, and additional overhead and rollback distance in case PRP's are used were estimated.

Two-dimensional optoelectronic interconnect-processor and its operational bit error rate

NASA Astrophysics Data System (ADS)

Liu, J. Jiang; Gollsneider, Brian; Chang, Wayne H.; Carhart, Gary W.; Vorontsov, Mikhail A.; Simonis, George J.; Shoop, Barry L.

2004-10-01

Two-dimensional (2-D) multi-channel 8x8 optical interconnect and processor system were designed and developed using complementary metal-oxide-semiconductor (CMOS) driven 850-nm vertical-cavity surface-emitting laser (VCSEL) arrays and the photodetector (PD) arrays with corresponding wavelengths. We performed operation and bit-error-rate (BER) analysis on this free-space integrated 8x8 VCSEL optical interconnects driven by silicon-on-sapphire (SOS) circuits. Pseudo-random bit stream (PRBS) data sequence was used in operation of the interconnects. Eye diagrams were measured from individual channels and analyzed using a digital oscilloscope at data rates from 155 Mb/s to 1.5 Gb/s. Using a statistical model of Gaussian distribution for the random noise in the transmission, we developed a method to compute the BER instantaneously with the digital eye-diagrams. Direct measurements on this interconnects were also taken on a standard BER tester for verification. We found that the results of two methods were in the same order and within 50% accuracy. The integrated interconnects were investigated in an optoelectronic processing architecture of digital halftoning image processor. Error diffusion networks implemented by the inherently parallel nature of photonics promise to provide high quality digital halftoned images.

Comparison of Decisions Quality of Heuristic Methods with Limited Depth-First Search Techniques in the Graph Shortest Path Problem

NASA Astrophysics Data System (ADS)

Vatutin, Eduard

2017-12-01

The article deals with the problem of analysis of effectiveness of the heuristic methods with limited depth-first search techniques of decision obtaining in the test problem of getting the shortest path in graph. The article briefly describes the group of methods based on the limit of branches number of the combinatorial search tree and limit of analyzed subtree depth used to solve the problem. The methodology of comparing experimental data for the estimation of the quality of solutions based on the performing of computational experiments with samples of graphs with pseudo-random structure and selected vertices and arcs number using the BOINC platform is considered. It also shows description of obtained experimental results which allow to identify the areas of the preferable usage of selected subset of heuristic methods depending on the size of the problem and power of constraints. It is shown that the considered pair of methods is ineffective in the selected problem and significantly inferior to the quality of solutions that are provided by ant colony optimization method and its modification with combinatorial returns.

The gradient boosting algorithm and random boosting for genome-assisted evaluation in large data sets.

PubMed

González-Recio, O; Jiménez-Montero, J A; Alenda, R

2013-01-01

In the next few years, with the advent of high-density single nucleotide polymorphism (SNP) arrays and genome sequencing, genomic evaluation methods will need to deal with a large number of genetic variants and an increasing sample size. The boosting algorithm is a machine-learning technique that may alleviate the drawbacks of dealing with such large data sets. This algorithm combines different predictors in a sequential manner with some shrinkage on them; each predictor is applied consecutively to the residuals from the committee formed by the previous ones to form a final prediction based on a subset of covariates. Here, a detailed description is provided and examples using a toy data set are included. A modification of the algorithm called "random boosting" was proposed to increase predictive ability and decrease computation time of genome-assisted evaluation in large data sets. Random boosting uses a random selection of markers to add a subsequent weak learner to the predictive model. These modifications were applied to a real data set composed of 1,797 bulls genotyped for 39,714 SNP. Deregressed proofs of 4 yield traits and 1 type trait from January 2009 routine evaluations were used as dependent variables. A 2-fold cross-validation scenario was implemented. Sires born before 2005 were used as a training sample (1,576 and 1,562 for production and type traits, respectively), whereas younger sires were used as a testing sample to evaluate predictive ability of the algorithm on yet-to-be-observed phenotypes. Comparison with the original algorithm was provided. The predictive ability of the algorithm was measured as Pearson correlations between observed and predicted responses. Further, estimated bias was computed as the average difference between observed and predicted phenotypes. The results showed that the modification of the original boosting algorithm could be run in 1% of the time used with the original algorithm and with negligible differences in accuracy and bias. This modification may be used to speed the calculus of genome-assisted evaluation in large data sets such us those obtained from consortiums. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Pseudo progression identification of glioblastoma with dictionary learning.

PubMed

Zhang, Jian; Yu, Hengyong; Qian, Xiaohua; Liu, Keqin; Tan, Hua; Yang, Tielin; Wang, Maode; Li, King Chuen; Chan, Michael D; Debinski, Waldemar; Paulsson, Anna; Wang, Ge; Zhou, Xiaobo

2016-06-01

Although the use of temozolomide in chemoradiotherapy is effective, the challenging clinical problem of pseudo progression has been raised in brain tumor treatment. This study aims to distinguish pseudo progression from true progression. Between 2000 and 2012, a total of 161 patients with glioblastoma multiforme (GBM) were treated with chemoradiotherapy at our hospital. Among the patients, 79 had their diffusion tensor imaging (DTI) data acquired at the earliest diagnosed date of pseudo progression or true progression, and 23 had both DTI data and genomic data. Clinical records of all patients were kept in good condition. Volumetric fractional anisotropy (FA) images obtained from the DTI data were decomposed into a sequence of sparse representations. Then, a feature selection algorithm was applied to extract the critical features from the feature matrix to reduce the size of the feature matrix and to improve the classification accuracy. The proposed approach was validated using the 79 samples with clinical DTI data. Satisfactory results were obtained under different experimental conditions. The area under the receiver operating characteristic (ROC) curve (AUC) was 0.87 for a given dictionary with 1024 atoms. For the subgroup of 23 samples, genomics data analysis was also performed. Results implied further perspective on pseudo progression classification. The proposed method can determine pseudo progression and true progression with improved accuracy. Laboring segmentation is no longer necessary because this skillfully designed method is not sensitive to tumor location. Copyright © 2016 Elsevier Ltd. All rights reserved.

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

PubMed

Pilkington, Sarah M; Crowhurst, Ross; Hilario, Elena; Nardozza, Simona; Fraser, Lena; Peng, Yongyan; Gunaseelan, Kularajathevan; Simpson, Robert; Tahir, Jibran; Deroles, Simon C; Templeton, Kerry; Luo, Zhiwei; Davy, Marcus; Cheng, Canhong; McNeilage, Mark; Scaglione, Davide; Liu, Yifei; Zhang, Qiong; Datson, Paul; De Silva, Nihal; Gardiner, Susan E; Bassett, Heather; Chagné, David; McCallum, John; Dzierzon, Helge; Deng, Cecilia; Wang, Yen-Yi; Barron, Lorna; Manako, Kelvina; Bowen, Judith; Foster, Toshi M; Erridge, Zoe A; Tiffin, Heather; Waite, Chethi N; Davies, Kevin M; Grierson, Ella P; Laing, William A; Kirk, Rebecca; Chen, Xiuyin; Wood, Marion; Montefiori, Mirco; Brummell, David A; Schwinn, Kathy E; Catanach, Andrew; Fullerton, Christina; Li, Dawei; Meiyalaghan, Sathiyamoorthy; Nieuwenhuizen, Niels; Read, Nicola; Prakash, Roneel; Hunter, Don; Zhang, Huaibi; McKenzie, Marian; Knäbel, Mareike; Harris, Alastair; Allan, Andrew C; Gleave, Andrew; Chen, Angela; Janssen, Bart J; Plunkett, Blue; Ampomah-Dwamena, Charles; Voogd, Charlotte; Leif, Davin; Lafferty, Declan; Souleyre, Edwige J F; Varkonyi-Gasic, Erika; Gambi, Francesco; Hanley, Jenny; Yao, Jia-Long; Cheung, Joey; David, Karine M; Warren, Ben; Marsh, Ken; Snowden, Kimberley C; Lin-Wang, Kui; Brian, Lara; Martinez-Sanchez, Marcela; Wang, Mindy; Ileperuma, Nadeesha; Macnee, Nikolai; Campin, Robert; McAtee, Peter; Drummond, Revel S M; Espley, Richard V; Ireland, Hilary S; Wu, Rongmei; Atkinson, Ross G; Karunairetnam, Sakuntala; Bulley, Sean; Chunkath, Shayhan; Hanley, Zac; Storey, Roy; Thrimawithana, Amali H; Thomson, Susan; David, Charles; Testolin, Raffaele; Huang, Hongwen; Hellens, Roger P; Schaffer, Robert J

2018-04-16

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Estimation of the transmissivity of thin leaky-confined aquifers from single-well pumping tests

NASA Astrophysics Data System (ADS)

Worthington, Paul F.

1981-01-01

Data from the quasi-equilibrium phases of a step-drawdown test are used to evaluate the coefficient of non-linear head losses subject to the assumption of a constant effective well radius. After applying a well-loss correction to the observed drawdowns of the first step, an approximation method is used to estimate a pseudo-transmissivity of the aquifer from a single value of time-variant drawdown. The pseudo-transmissivities computed for each of a sequence of values of time pass through a minimum when there is least manifestation of casing-storage and leakage effects, phenomena to which pumping-test data of this kind are particularly susceptible. This minimum pseudo-transmissivity, adjusted for partial penetration effects where appropriate, constitutes the best possible estimate of aquifer transmissivity. The ease of application of the overall procedure is illustrated by a practical example.

"iSS-Hyb-mRMR": Identification of splicing sites using hybrid space of pseudo trinucleotide and pseudo tetranucleotide composition.

PubMed

Iqbal, Muhammad; Hayat, Maqsood

2016-05-01

Gene splicing is a vital source of protein diversity. Perfectly eradication of introns and joining exons is the prominent task in eukaryotic gene expression, as exons are usually interrupted by introns. Identification of splicing sites through experimental techniques is complicated and time-consuming task. With the avalanche of genome sequences generated in the post genomic age, it remains a complicated and challenging task to develop an automatic, robust and reliable computational method for fast and effective identification of splicing sites. In this study, a hybrid model "iSS-Hyb-mRMR" is proposed for quickly and accurately identification of splicing sites. Two sample representation methods namely; pseudo trinucleotide composition (PseTNC) and pseudo tetranucleotide composition (PseTetraNC) were used to extract numerical descriptors from DNA sequences. Hybrid model was developed by concatenating PseTNC and PseTetraNC. In order to select high discriminative features, minimum redundancy maximum relevance algorithm was applied on the hybrid feature space. The performance of these feature representation methods was tested using various classification algorithms including K-nearest neighbor, probabilistic neural network, general regression neural network, and fitting network. Jackknife test was used for evaluation of its performance on two benchmark datasets S1 and S2, respectively. The predictor, proposed in the current study achieved an accuracy of 93.26%, sensitivity of 88.77%, and specificity of 97.78% for S1, and the accuracy of 94.12%, sensitivity of 87.14%, and specificity of 98.64% for S2, respectively. It is observed, that the performance of proposed model is higher than the existing methods in the literature so for; and will be fruitful in the mechanism of RNA splicing, and other research academia. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Pseudo-random generator based on Chinese Remainder Theorem

NASA Astrophysics Data System (ADS)

Bajard, Jean Claude; Hördegen, Heinrich

2009-08-01

Pseudo-Random Generators (PRG) are fundamental in cryptography. Their use occurs at different level in cipher protocols. They need to verify some properties for being qualified as robust. The NIST proposes some criteria and a tests suite which gives informations on the behavior of the PRG. In this work, we present a PRG constructed from the conversion between further residue systems of representation of the elements of GF(2)[X]. In this approach, we use some pairs of co-prime polynomials of degree k and a state vector of 2k bits. The algebraic properties are broken by using different independent pairs during the process. Since this method is reversible, we also can use it as a symmetric crypto-system. We evaluate the cost of a such system, taking into account that some operations are commonly implemented on crypto-processors. We give the results of the different NIST Tests and we explain this choice compare to others found in the literature. We describe the behavior of this PRG and explain how the different rounds are chained for ensuring a fine secure randomness.

Properties of Protein Drug Target Classes

PubMed Central

Bull, Simon C.; Doig, Andrew J.

2015-01-01

Accurate identification of drug targets is a crucial part of any drug development program. We mined the human proteome to discover properties of proteins that may be important in determining their suitability for pharmaceutical modulation. Data was gathered concerning each protein’s sequence, post-translational modifications, secondary structure, germline variants, expression profile and drug target status. The data was then analysed to determine features for which the target and non-target proteins had significantly different values. This analysis was repeated for subsets of the proteome consisting of all G-protein coupled receptors, ion channels, kinases and proteases, as well as proteins that are implicated in cancer. Machine learning was used to quantify the proteins in each dataset in terms of their potential to serve as a drug target. This was accomplished by first inducing a random forest that could distinguish between its targets and non-targets, and then using the random forest to quantify the drug target likeness of the non-targets. The properties that can best differentiate targets from non-targets were primarily those that are directly related to a protein’s sequence (e.g. secondary structure). Germline variants, expression levels and interactions between proteins had minimal discriminative power. Overall, the best indicators of drug target likeness were found to be the proteins’ hydrophobicities, in vivo half-lives, propensity for being membrane bound and the fraction of non-polar amino acids in their sequences. In terms of predicting potential targets, datasets of proteases, ion channels and cancer proteins were able to induce random forests that were highly capable of distinguishing between targets and non-targets. The non-target proteins predicted to be targets by these random forests comprise the set of the most suitable potential future drug targets, and should therefore be prioritised when building a drug development programme. PMID:25822509

Artificial Intelligence, DNA Mimicry, and Human Health.

PubMed

Stefano, George B; Kream, Richard M

2017-08-14

The molecular evolution of genomic DNA across diverse plant and animal phyla involved dynamic registrations of sequence modifications to maintain existential homeostasis to increasingly complex patterns of environmental stressors. As an essential corollary, driver effects of positive evolutionary pressure are hypothesized to effect concerted modifications of genomic DNA sequences to meet expanded platforms of regulatory controls for successful implementation of advanced physiological requirements. It is also clearly apparent that preservation of updated registries of advantageous modifications of genomic DNA sequences requires coordinate expansion of convergent cellular proofreading/error correction mechanisms that are encoded by reciprocally modified genomic DNA. Computational expansion of operationally defined DNA memory extends to coordinate modification of coding and previously under-emphasized noncoding regions that now appear to represent essential reservoirs of untapped genetic information amenable to evolutionary driven recruitment into the realm of biologically active domains. Additionally, expansion of DNA memory potential via chemical modification and activation of noncoding sequences is targeted to vertical augmentation and integration of an expanded cadre of transcriptional and epigenetic regulatory factors affecting linear coding of protein amino acid sequences within open reading frames.

Computed tomography synthesis from magnetic resonance images in the pelvis using multiple random forests and auto-context features

NASA Astrophysics Data System (ADS)

Andreasen, Daniel; Edmund, Jens M.; Zografos, Vasileios; Menze, Bjoern H.; Van Leemput, Koen

2016-03-01

In radiotherapy treatment planning that is only based on magnetic resonance imaging (MRI), the electron density information usually obtained from computed tomography (CT) must be derived from the MRI by synthesizing a so-called pseudo CT (pCT). This is a non-trivial task since MRI intensities are neither uniquely nor quantitatively related to electron density. Typical approaches involve either a classification or regression model requiring specialized MRI sequences to solve intensity ambiguities, or an atlas-based model necessitating multiple registrations between atlases and subject scans. In this work, we explore a machine learning approach for creating a pCT of the pelvic region from conventional MRI sequences without using atlases. We use a random forest provided with information about local texture, edges and spatial features derived from the MRI. This helps to solve intensity ambiguities. Furthermore, we use the concept of auto-context by sequentially training a number of classification forests to create and improve context features, which are finally used to train a regression forest for pCT prediction. We evaluate the pCT quality in terms of the voxel-wise error and the radiologic accuracy as measured by water-equivalent path lengths. We compare the performance of our method against two baseline pCT strategies, which either set all MRI voxels in the subject equal to the CT value of water, or in addition transfer the bone volume from the real CT. We show an improved performance compared to both baseline pCTs suggesting that our method may be useful for MRI-only radiotherapy.

Spreading Sequence System for Full Connectivity Relay Network

NASA Technical Reports Server (NTRS)

Kwon, Hyuck M. (Inventor); Pham, Khanh D. (Inventor); Yang, Jie (Inventor)

2018-01-01

Fully connected uplink and downlink fully connected relay network systems using pseudo-noise spreading and despreading sequences subjected to maximizing the signal-to-interference-plus-noise ratio. The relay network systems comprise one or more transmitting units, relays, and receiving units connected via a communication network. The transmitting units, relays, and receiving units each may include a computer for performing the methods and steps described herein and transceivers for transmitting and/or receiving signals. The computer encodes and/or decodes communication signals via optimum adaptive PN sequences found by employing Cholesky decompositions and singular value decompositions (SVD). The PN sequences employ channel state information (CSI) to more effectively and more securely computing the optimal sequences.

Prediction protein structural classes with pseudo-amino acid composition: approximate entropy and hydrophobicity pattern.

PubMed

Zhang, Tong-Liang; Ding, Yong-Sheng; Chou, Kuo-Chen

2008-01-07

Compared with the conventional amino acid (AA) composition, the pseudo-amino acid (PseAA) composition as originally introduced for protein subcellular location prediction can incorporate much more information of a protein sequence, so as to remarkably enhance the power of using a discrete model to predict various attributes of a protein. In this study, based on the concept of PseAA composition, the approximate entropy and hydrophobicity pattern of a protein sequence are used to characterize the PseAA components. Also, the immune genetic algorithm (IGA) is applied to search the optimal weight factors in generating the PseAA composition. Thus, for a given protein sequence sample, a 27-D (dimensional) PseAA composition is generated as its descriptor. The fuzzy K nearest neighbors (FKNN) classifier is adopted as the prediction engine. The results thus obtained in predicting protein structural classification are quite encouraging, indicating that the current approach may also be used to improve the prediction quality of other protein attributes, or at least can play a complimentary role to the existing methods in the relevant areas. Our algorithm is written in Matlab that is available by contacting the corresponding author.

Common position of indels that cause deviations from canonical genome organization in different measles virus strains.

PubMed

Ivancic-Jelecki, Jelena; Slovic, Anamarija; Šantak, Maja; Tešović, Goran; Forcic, Dubravko

2016-07-29

The canonical genome organization of measles virus (MV) is characterized by total size of 15 894 nucleotides (nts) and defined length of every genomic region, both coding and non-coding. Only rarely have reports of strains possessing non-canonical genomic properties (possessing indels, with or without the change of total genome length) been published. The observed mutations are mutually compensatory in a sense that the total genome length remains polyhexameric. Although programmed and highly precise pseudo-templated nucleotide additions during transcription are inherent to polymerases of all viruses belonging to family Paramyxoviridae, a similar mechanism that would serve to non-randomly correct genome length, if an indel has occurred during replication, has so far not been described in the context of a complete virus genome. We compiled all complete MV genomic sequences (64 in total) available in open access sequence databases. Multiple sequence comparisons and phylogenetic analyses were performed with the aim of exploring whether non-recombinant and non-evolutionary linked measles strains that show deviations from canonical genome organization possess a common genetic characteristic. In 11 MV sequences we detected deviations from canonical genome organization due to short indels located within homopolymeric stretches or next to them. In nine out of 11 identified non-canonical MV sequences, a common feature was observed: one mutation, either an insertion or a deletion, was located in a 28 nts long region in F gene 5' untranslated region (positions 5051-5078 in genomic cDNA of canonical strains). This segment is composed of five tandemly linked homopolymeric stretches, its consensus sequence is G6-7C7-8A6-7G1-3C5-6. Although none of the mononucleotide repeats within this segment has fixed length, the total number of nts in canonical strains is always 28. These nine non-canonical strains, as well as the tenth (not mutated in 5051-5078 segment), can be grouped in three clusters, based on their passage histories/epidemiological data/genetic similarities. There are no indications that the 3 clusters are evolutionary linked, other than the fact that they all belong to clade D. A common narrow genomic region was found to be mutated in different, non-related, wild type strains suggesting that this region might have a function in non-random genome length corrections occurring during MV replication.

Genetic variation for pseudo-self-compatibility in self-incompatible populations of Leavenworthia alabamica (Brassicaceae).

PubMed

Baldwin, Sarah J; Schoen, Daniel J

2017-01-01

Self-incompatibility (SI) promotes outcrossing, but transitions to self-compatibility (SC) are frequent. Population genetic theory describing the breakdown of SI to SC suggests that, under most conditions, populations should be composed of either SI or SC individuals. Under a narrow range of conditions, theory suggests that SI may persist alongside reduced expression of SI (pseudo-SI, PSI) in mixed-mating populations. We studied genetic variation for PSI segregating in four SI populations of Leavenworthia alabamica by measurement of the heritability of pollen tube number after self-pollination. We tested for the role of the S-locus in this variation by sequencing seven S-alleles from plants with high pseudo-SC (PSC) and testing for the co-segregation of these alleles with PSC. We found a continuous distribution of PSC in all populations and 90% of plants exhibited PSC. The heritability ranged from 0.39 to 0.57. All seven S-alleles from plants with high PSC exhibited trans-specific polymorphism, and no stop codons were observed within the c. 600-bp region sequenced. One of these S-alleles was directly associated with the inheritance of PSC. We conclude that heritable variation in PSC is largely a result of genetic variation in the signaling cascade downstream of the S-locus reaction, together with the presence of one leaky S-allele. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

The Random Telegraph Signal Behavior of Intermittently Stuck Bits in SDRAMs

NASA Astrophysics Data System (ADS)

Chugg, Andrew Michael; Burnell, Andrew J.; Duncan, Peter H.; Parker, Sarah; Ward, Jonathan J.

2009-12-01

This paper reports behavior analogous to the Random Telegraph Signal (RTS) seen in the leakage currents from radiation induced hot pixels in Charge Coupled Devices (CCDs), but in the context of stuck bits in Synchronous Dynamic Random Access Memories (SDRAMs). Our analysis suggests that pseudo-random sticking and unsticking of the SDRAM bits is due to thermally induced fluctuations in leakage current through displacement damage complexes in depletion regions that were created by high-energy neutron and proton interactions. It is shown that the number of observed stuck bits increases exponentially with temperature, due to the general increase in the leakage currents through the damage centers with temperature. Nevertheless, some stuck bits are seen to pseudo-randomly stick and unstick in the context of a continuously rising trend of temperature, thus demonstrating that their damage centers can exist in multiple widely spaced, discrete levels of leakage current, which is highly consistent with RTS. This implies that these intermittently stuck bits (ISBs) are a displacement damage phenomenon and are unrelated to microdose issues, which is confirmed by the observation that they also occur in unbiased irradiation. Finally, we note that observed variations in the periodicity of the sticking and unsticking behavior on several timescales is most readily explained by multiple leakage current pathways through displacement damage complexes spontaneously and independently opening and closing under the influence of thermal vibrations.

Sex difference in human fingertip recognition of micron-level randomness as unpleasant.

PubMed

Nakatani, M; Kawasoe, T; Denda, M

2011-08-01

We investigated sex difference in evaluation, using the human fingertip, of the tactile impressions of three different micron-scale patterns laser-engraved on plastic plates. There were two ordered (periodical) patterns consisting of ripples on a scale of a few micrometres and one pseudo-random (non-periodical) pattern; these patterns were considered to mimic the surface geometry of healthy and damaged human hair, respectively. In the first experiment, 10 women and 10 men ran a fingertip over each surface and determined which of the three plates felt most unpleasant. All 10 female participants reported the random pattern, but not the ordered patterns, as unpleasant, whereas the majority of the male participants did not. In the second experiment, 9 of 10 female participants continued to report the pseudo-random pattern as unpleasant even after their fingertip had been coated with a collodion membrane. In the third experiment, participants were asked to evaluate the magnitude of the tactile impression for each pattern. The results again indicated that female participants tend to report a greater magnitude of unpleasantness than male participants. Our findings indicate that the female participants could readily detect microgeometric surface characteristics and that they evaluated the random pattern as more unpleasant. Possible physical and perceptual mechanisms involved are discussed. © 2011 The Authors. ICS © 2011 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Undesirable Choice Biases with Small Differences in the Spatial Structure of Chance Stimulus Sequences.

PubMed

Herrera, David; Treviño, Mario

2015-01-01

In two-alternative discrimination tasks, experimenters usually randomize the location of the rewarded stimulus so that systematic behavior with respect to irrelevant stimuli can only produce chance performance on the learning curves. One way to achieve this is to use random numbers derived from a discrete binomial distribution to create a 'full random training schedule' (FRS). When using FRS, however, sporadic but long laterally-biased training sequences occur by chance and such 'input biases' are thought to promote the generation of laterally-biased choices (i.e., 'output biases'). As an alternative, a 'Gellerman-like training schedule' (GLS) can be used. It removes most input biases by prohibiting the reward from appearing on the same location for more than three consecutive trials. The sequence of past rewards obtained from choosing a particular discriminative stimulus influences the probability of choosing that same stimulus on subsequent trials. Assuming that the long-term average ratio of choices matches the long-term average ratio of reinforcers, we hypothesized that a reduced amount of input biases in GLS compared to FRS should lead to a reduced production of output biases. We compared the choice patterns produced by a 'Rational Decision Maker' (RDM) in response to computer-generated FRS and GLS training sequences. To create a virtual RDM, we implemented an algorithm that generated choices based on past rewards. Our simulations revealed that, although the GLS presented fewer input biases than the FRS, the virtual RDM produced more output biases with GLS than with FRS under a variety of test conditions. Our results reveal that the statistical and temporal properties of training sequences interacted with the RDM to influence the production of output biases. Thus, discrete changes in the training paradigms did not translate linearly into modifications in the pattern of choices generated by a RDM. Virtual RDMs could be further employed to guide the selection of proper training schedules for perceptual decision-making studies.

New scene change control scheme based on pseudoskipped picture

NASA Astrophysics Data System (ADS)

Lee, Youngsun; Lee, Jinwhan; Chang, Hyunsik; Nam, Jae Y.

1997-01-01

A new scene change control scheme which improves the video coding performance for sequences that have many scene changed pictures is proposed in this paper. The scene changed pictures except intra-coded picture usually need more bits than normal pictures in order to maintain constant picture quality. The major idea of this paper is how to obtain extra bits which are needed to encode scene changed pictures. We encode a B picture which is located before a scene changed picture like a skipped picture. We call such a B picture as a pseudo-skipped picture. By generating the pseudo-skipped picture like a skipped picture. We call such a B picture as a pseudo-skipped picture. By generating the pseudo-skipped picture, we can save some bits and they are added to the originally allocated target bits to encode the scene changed picture. The simulation results show that the proposed algorithm improves encoding performance about 0.5 to approximately 2.0 dB of PSNR compared to MPEG-2 TM5 rate controls scheme. In addition, the suggested algorithm is compatible with MPEG-2 video syntax and the picture repetition is not recognizable.

Exome Sequencing of 18 Chinese Families with Congenital Cataracts: A New Sight of the NHS Gene

PubMed Central

Sun, Wenmin; Xiao, Xueshan; Li, Shiqiang; Guo, Xiangming; Zhang, Qingjiong

2014-01-01

Purpose The aim of this study was to investigate the mutation spectrum and frequency of 34 known genes in 18 Chinese families with congenital cataracts. Methods Genomic DNA and clinical data was collected from 18 families with congenital cataracts. Variations in 34 cataract-associated genes were screened by whole exome sequencing and then validated by Sanger sequencing. Results Eleven candidate variants in seven of the 34 genes were detected by exome sequencing and then confirmed by Sanger sequencing, including two variants predicted to be benign and the other pathogenic mutations. The nine mutations were present in 9 of the 18 (50%) families with congenital cataracts. Of the four families with mutations in the X-linked NHS gene, no other abnormalities were recorded except for cataract, in which a pseudo-dominant inheritance form was suggested, as female carriers also had different forms of cataracts. Conclusion This study expands the mutation spectrum and frequency of genes responsible for congenital cataract. Mutation in NHS is a common cause of nonsyndromic congenital cataract with pseudo-autosomal dominant inheritance. Combined with our previous studies, a genetic basis could be identified in 67.6% of families with congenital cataracts in our case series, in which mutations in genes encoding crystallins, genes encoding connexins, and NHS are responsible for 29.4%, 14.7%, and 11.8% of families, respectively. Our results suggest that mutations in NHS are the common cause of congenital cataract, both syndromic and nonsyndromic. PMID:24968223

Hybrid lentivirus-phiC31-int-NLS vector allows site-specific recombination in murine and human cells but induces DNA damage.

PubMed

Grandchamp, Nicolas; Altémir, Dorothée; Philippe, Stéphanie; Ursulet, Suzanna; Pilet, Héloïse; Serre, Marie-Claude; Lenain, Aude; Serguera, Che; Mallet, Jacques; Sarkis, Chamsy

2014-01-01

Gene transfer allows transient or permanent genetic modifications of cells for experimental or therapeutic purposes. Gene delivery by HIV-derived lentiviral vector (LV) is highly effective but the risk of insertional mutagenesis is important and the random/uncontrollable integration of the DNA vector can deregulate the cell transcriptional activity. Non Integrative Lentiviral Vectors (NILVs) solve this issue in non-dividing cells, but they do not allow long term expression in dividing cells. In this context, obtaining stable expression while avoiding the problems inherent to unpredictable DNA vector integration requires the ability to control the integration site. One possibility is to use the integrase of phage phiC31 (phiC31-int) which catalyzes efficient site-specific recombination between the attP site in the phage genome and the chromosomal attB site of its Streptomyces host. Previous studies showed that phiC31-int is active in many eukaryotic cells, such as murine or human cells, and directs the integration of a DNA substrate into pseudo attP sites (pattP) which are homologous to the native attP site. In this study, we combined the efficiency of NILV for gene delivery and the specificity of phiC31-int for DNA substrate integration to engineer a hybrid tool for gene transfer with the aim of allowing long term expression in dividing and non-dividing cells preventing genotoxicity. We demonstrated the feasibility to target NILV integration in human and murine pattP sites with a dual NILV vectors system: one which delivers phiC31-int, the other which constitute the substrate containing an attB site in its DNA sequence. These promising results are however alleviated by the occurrence of significant DNA damages. Further improvements are thus required to prevent chromosomal rearrangements for a therapeutic use of the system. However, its use as a tool for experimental applications such as transgenesis is already applicable.

Fingerprints of Modified RNA Bases from Deep Sequencing Profiles.

PubMed

Kietrys, Anna M; Velema, Willem A; Kool, Eric T

2017-11-29

Posttranscriptional modifications of RNA bases are not only found in many noncoding RNAs but have also recently been identified in coding (messenger) RNAs as well. They require complex and laborious methods to locate, and many still lack methods for localized detection. Here we test the ability of next-generation sequencing (NGS) to detect and distinguish between ten modified bases in synthetic RNAs. We compare ultradeep sequencing patterns of modified bases, including miscoding, insertions and deletions (indels), and truncations, to unmodified bases in the same contexts. The data show widely varied responses to modification, ranging from no response, to high levels of mutations, insertions, deletions, and truncations. The patterns are distinct for several of the modifications, and suggest the future use of ultradeep sequencing as a fingerprinting strategy for locating and identifying modifications in cellular RNAs.

Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae.

PubMed

Rosinski-Chupin, Isabelle; Sauvage, Elisabeth; Sismeiro, Odile; Villain, Adrien; Da Cunha, Violette; Caliot, Marie-Elise; Dillies, Marie-Agnès; Trieu-Cuot, Patrick; Bouloc, Philippe; Lartigue, Marie-Frédérique; Glaser, Philippe

2015-05-30

Streptococcus agalactiae, or Group B Streptococcus, is a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. In an effort to reconstruct the transcriptional networks involved in S. agalactiae physiology and pathogenesis, we performed an extensive and robust characterization of its transcriptome through a combination of differential RNA-sequencing in eight different growth conditions or genetic backgrounds and strand-specific RNA-sequencing. Our study identified 1,210 transcription start sites (TSSs) and 655 transcript ends as well as 39 riboswitches and cis-regulatory regions, 39 cis-antisense non-coding RNAs and 47 small RNAs potentially acting in trans. Among these putative regulatory RNAs, ten were differentially expressed in response to an acid stress and two riboswitches sensed directly or indirectly the pH modification. Strikingly, 15% of the TSSs identified were associated with the incorporation of pseudo-templated nucleotides, showing that reiterative transcription is a pervasive process in S. agalactiae. In particular, 40% of the TSSs upstream genes involved in nucleotide metabolism show reiterative transcription potentially regulating gene expression, as exemplified for pyrG and thyA encoding the CTP synthase and the thymidylate synthase respectively. This comprehensive map of the transcriptome at the single nucleotide resolution led to the discovery of new regulatory mechanisms in S. agalactiae. It also provides the basis for in depth analyses of transcriptional networks in S. agalactiae and of the regulatory role of reiterative transcription following variations of intra-cellular nucleotide pools.

Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

PubMed

Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

2016-06-07

As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparative study on kinetic adsorption of Cu(II), Cd(II) and Ni(II) ions from aqueous solutions using activated sludge and dried sludge

NASA Astrophysics Data System (ADS)

Ong, Soon-An; Toorisaka, Eiichi; Hirata, Makoto; Hano, Tadashi

2013-03-01

The adsorption of Cu(II), Cd(II) and Ni(II) ions from aqueous solutions by activated sludge and dried sludge was investigated under laboratory conditions to assess its potential in removing metal ions. The adsorption behavior of metal ions onto activated sludge and dried sludge was analyzed with Weber-Morris intra-particle diffusion model, Lagergren first-order model and pseudo second-order model. The rate constant of intra-particle diffusion on activated sludge and dried sludge increased in the sequence of Cu(II) > Ni(II) > Cd(II). According to the regression coefficients, it was observed that the kinetic adsorption data can fit better by the pseudo second-order model compared to the first-order Lagergren model with R 2 > 0.997. The adsorption capacities of metal ions onto activated sludge and dried sludge followed the sequence Ni(II) ≈ Cu(II) > Cd(II) and Cu(II) > Ni(II) > Cd(II).

Local Random Quantum Circuits are Approximate Polynomial-Designs

NASA Astrophysics Data System (ADS)

Brandão, Fernando G. S. L.; Harrow, Aram W.; Horodecki, Michał

2016-09-01

We prove that local random quantum circuits acting on n qubits composed of O( t 10 n 2) many nearest neighbor two-qubit gates form an approximate unitary t-design. Previously it was unknown whether random quantum circuits were a t-design for any t > 3. The proof is based on an interplay of techniques from quantum many-body theory, representation theory, and the theory of Markov chains. In particular we employ a result of Nachtergaele for lower bounding the spectral gap of frustration-free quantum local Hamiltonians; a quasi-orthogonality property of permutation matrices; a result of Oliveira which extends to the unitary group the path-coupling method for bounding the mixing time of random walks; and a result of Bourgain and Gamburd showing that dense subgroups of the special unitary group, composed of elements with algebraic entries, are ∞-copy tensor-product expanders. We also consider pseudo-randomness properties of local random quantum circuits of small depth and prove that circuits of depth O( t 10 n) constitute a quantum t-copy tensor-product expander. The proof also rests on techniques from quantum many-body theory, in particular on the detectability lemma of Aharonov, Arad, Landau, and Vazirani. We give applications of the results to cryptography, equilibration of closed quantum dynamics, and the generation of topological order. In particular we show the following pseudo-randomness property of generic quantum circuits: Almost every circuit U of size O( n k ) on n qubits cannot be distinguished from a Haar uniform unitary by circuits of size O( n ( k-9)/11) that are given oracle access to U.

Experimental demonstration of localized Brillouin gratings with low off-peak reflectivity established by perfect Golomb codes.

PubMed

Antman, Yair; Yaron, Lior; Langer, Tomi; Tur, Moshe; Levanon, Nadav; Zadok, Avi

2013-11-15

Dynamic Brillouin gratings (DBGs), inscribed by comodulating two writing pump waves with a perfect Golomb code, are demonstrated and characterized experimentally. Compared with pseudo-random bit sequence (PRBS) modulation of the pump waves, the Golomb code provides lower off-peak reflectivity due to the unique properties of its cyclic autocorrelation function. Golomb-coded DBGs allow the long variable delay of one-time probe waveforms with higher signal-to-noise ratios, and without averaging. As an example, the variable delay of return-to-zero, on-off keyed data at a 1 Gbit/s rate, by as much as 10 ns, is demonstrated successfully. The eye diagram of the reflected waveform remains open, whereas PRBS modulation of the pump waves results in a closed eye. The variable delay of data at 2.5 Gbit/s is reported as well, with a marginally open eye diagram. The experimental results are in good agreement with simulations.

Data series embedding and scale invariant statistics.

PubMed

Michieli, I; Medved, B; Ristov, S

2010-06-01

Data sequences acquired from bio-systems such as human gait data, heart rate interbeat data, or DNA sequences exhibit complex dynamics that is frequently described by a long-memory or power-law decay of autocorrelation function. One way of characterizing that dynamics is through scale invariant statistics or "fractal-like" behavior. For quantifying scale invariant parameters of physiological signals several methods have been proposed. Among them the most common are detrended fluctuation analysis, sample mean variance analyses, power spectral density analysis, R/S analysis, and recently in the realm of the multifractal approach, wavelet analysis. In this paper it is demonstrated that embedding the time series data in the high-dimensional pseudo-phase space reveals scale invariant statistics in the simple fashion. The procedure is applied on different stride interval data sets from human gait measurements time series (Physio-Bank data library). Results show that introduced mapping adequately separates long-memory from random behavior. Smaller gait data sets were analyzed and scale-free trends for limited scale intervals were successfully detected. The method was verified on artificially produced time series with known scaling behavior and with the varying content of noise. The possibility for the method to falsely detect long-range dependence in the artificially generated short range dependence series was investigated. (c) 2009 Elsevier B.V. All rights reserved.

DNA Barcoding through Quaternary LDPC Codes

PubMed Central

Tapia, Elizabeth; Spetale, Flavio; Krsticevic, Flavia; Angelone, Laura; Bulacio, Pilar

2015-01-01

For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH) or have intrinsic poor error correcting abilities (Hamming). Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC) codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10−2 per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10−9 at the expense of a rate of read losses just in the order of 10−6. PMID:26492348

DNA Barcoding through Quaternary LDPC Codes.

PubMed

Tapia, Elizabeth; Spetale, Flavio; Krsticevic, Flavia; Angelone, Laura; Bulacio, Pilar

2015-01-01

For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH) or have intrinsic poor error correcting abilities (Hamming). Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC) codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10(-2) per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10(-9) at the expense of a rate of read losses just in the order of 10(-6).

A pseudo-thermodynamic description of dispersion for nanocomposites

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

Jin, Yan; Beaucage, Gregory; Vogtt, Karsten

Dispersion in polymer nanocomposites is determined by the kinetics of mixing and chemical affinity. Compounds like reinforcing filler/elastomer blends display some similarity to colloidal solutions in that the filler particles are close to randomly dispersed through processing. It is attractive to apply a pseudo-thermodynamic approach taking advantage of this analogy between the kinetics of mixing for polymer compounds and thermally driven dispersion for colloids. In order to demonstrate this pseudo-thermodynamic approach, two polybutadienes and one polyisoprene were milled with three carbon blacks and two silicas. These samples were examined using small-angle x-ray scattering as a function of filler concentration tomore » determine a pseudo-second order virial coefficient, A2, which is used as an indicator for compatibility of the filler and polymer. It is found that A2 follows the expected behavior with lower values for smaller primary particles indicating that smaller particles are less compatible and more difficult to mix. The measured values of A2 can be used to specify repulsive interaction potentials for coarse grain DPD simulations of filler/elastomer systems. In addition, new methods to quantify the filler percolation threshold and filler mesh size as a function of filler concentration are obtained. Moreover, the results represent a new approach to understanding and predicting compatibility in polymer nanocomposites based on a pseudo-thermodynamic approach.« less

A pseudo-thermodynamic description of dispersion for nanocomposites

DOE PAGES

Jin, Yan; Beaucage, Gregory; Vogtt, Karsten; ...

2017-09-18

Dispersion in polymer nanocomposites is determined by the kinetics of mixing and chemical affinity. Compounds like reinforcing filler/elastomer blends display some similarity to colloidal solutions in that the filler particles are close to randomly dispersed through processing. It is attractive to apply a pseudo-thermodynamic approach taking advantage of this analogy between the kinetics of mixing for polymer compounds and thermally driven dispersion for colloids. In order to demonstrate this pseudo-thermodynamic approach, two polybutadienes and one polyisoprene were milled with three carbon blacks and two silicas. These samples were examined using small-angle x-ray scattering as a function of filler concentration tomore » determine a pseudo-second order virial coefficient, A2, which is used as an indicator for compatibility of the filler and polymer. It is found that A2 follows the expected behavior with lower values for smaller primary particles indicating that smaller particles are less compatible and more difficult to mix. The measured values of A2 can be used to specify repulsive interaction potentials for coarse grain DPD simulations of filler/elastomer systems. In addition, new methods to quantify the filler percolation threshold and filler mesh size as a function of filler concentration are obtained. Moreover, the results represent a new approach to understanding and predicting compatibility in polymer nanocomposites based on a pseudo-thermodynamic approach.« less

Hydroxyapatite-binding peptides for bone growth and inhibition

DOEpatents

Bertozzi, Carolyn R [Berkeley, CA; Song, Jie [Shrewsbury, MA; Lee, Seung-Wuk [Walnut Creek, CA

2011-09-20

Hydroxyapatite (HA)-binding peptides are selected using combinatorial phage library display. Pseudo-repetitive consensus amino acid sequences possessing periodic hydroxyl side chains in every two or three amino acid sequences are obtained. These sequences resemble the (Gly-Pro-Hyp).sub.x repeat of human type I collagen, a major component of extracellular matrices of natural bone. A consistent presence of basic amino acid residues is also observed. The peptides are synthesized by the solid-phase synthetic method and then used for template-driven HA-mineralization. Microscopy reveal that the peptides template the growth of polycrystalline HA crystals .about.40 nm in size.

Pseudo-random properties of a linear congruential generator investigated by b-adic diaphony

NASA Astrophysics Data System (ADS)

Stoev, Peter; Stoilova, Stanislava

2017-12-01

In the proposed paper we continue the study of the diaphony, defined in b-adic number system, and we extend it in different directions. We investigate this diaphony as a tool for estimation of the pseudorandom properties of some of the most used random number generators. This is done by evaluating the distribution of specially constructed two-dimensional nets on the base of the obtained random numbers. The aim is to see how the generated numbers are suitable for calculations in some numerical methods (Monte Carlo etc.).

Music performance and the perception of key.

PubMed

Thompson, W F; Cuddy, L L

1997-02-01

The effect of music performance on perceived key movement was examined. Listeners judged key movement in sequences presented without performance expression (mechanical) in Experiment 1 and with performance expression in Experiment 2. Modulation distance varied. Judgments corresponded to predictions based on the cycle of fifths and toroidal models of key relatedness, with the highest correspondence for performed versions with the toroidal model. In Experiment 3, listeners compared mechanical sequences with either performed sequences or modifications of performed sequences. Modifications preserved expressive differences between chords, but not between voices. Predictions from Experiments 1 and 2 held only for performed sequences, suggesting that differences between voices are informative of key movement. Experiment 4 confirmed that modifications did not disrupt musicality. Analyses of performances further suggested a link between performance expression and key.

Design of pseudo-symmetric high bit rate, bend insensitive optical fiber applicable for high speed FTTH

NASA Astrophysics Data System (ADS)

Makouei, Somayeh; Koozekanani, Z. D.

2014-12-01

In this paper, with sophisticated modification on modal-field distribution and introducing new design procedure, the single-mode fiber with ultra-low bending-loss and pseudo-symmetric high bit-rate of uplink and downlink, appropriate for fiber-to-the-home (FTTH) operation is presented. The bending-loss reduction and dispersion management are done by the means of Genetic Algorithm. The remarkable feature of this methodology is designing a bend-insensitive fiber without reduction of core radius and MFD. Simulation results show bending loss of 1.27×10-2 dB/turn at 1.55 μm for 5 mm curvature radius. The MFD and Aeff are 9.03 μm and 59.11 μm2. Moreover, the upstream and downstream bit-rates are approximately 2.38 Gbit/s-km and 3.05 Gbit/s-km.

Influence of 5-N-carboxamide modifications on the thermodynamic stability of oligonucleotides

PubMed Central

Wolk, Steven K.; Shoemaker, Richard K.; Mayfield, Wes S.; Mestdagh, Andrew L.; Janjic, Nebojsa

2015-01-01

We have recently shown that the incorporation of modified nucleotides such as 5-N-carboxamide-deoxyuridines into random nucleic acid libraries improves success rates in SELEX experiments and facilitates the identification of ligands with slow off-rates. Here we report the impact of these modifications on the thermodynamic stability of both duplexes and intramolecular ‘single-stranded’ structures. Within duplexes, large, hydrophobic naphthyl groups were destabilizing relative to the all natural DNA duplex, while the hydrophilic groups exhibited somewhat improved duplex stability. All of the significant changes in stability were driven by opposing contributions from the enthalpic and entropic terms. In contrast, both benzyl and naphthyl modifications stabilized intramolecular single-stranded structures relative to their natural DNA analogs, consistent with the notion that intramolecular folding allows formation of novel, stabilizing hydrophobic interactions. Imino proton NMR data provided evidence that elements of the folded structure form at temperatures well below the Tm, with a melting transition that is distinctly less cooperative when compared to duplex DNA. Although there are no data to suggest that the unmodified DNA sequences fold into structures similar to their modified analogs, this still represents clear evidence that these modifications impart thermodynamic stability to the folded structure not achievable with unmodified DNA. PMID:26438535

Cre/lox-Recombinase-Mediated Cassette Exchange for Reversible Site-Specific Genomic Targeting of the Disease Vector, Aedes aegypti.

PubMed

Häcker, Irina; Harrell Ii, Robert A; Eichner, Gerrit; Pilitt, Kristina L; O'Brochta, David A; Handler, Alfred M; Schetelig, Marc F

2017-03-07

Site-specific genome modification (SSM) is an important tool for mosquito functional genomics and comparative gene expression studies, which contribute to a better understanding of mosquito biology and are thus a key to finding new strategies to eliminate vector-borne diseases. Moreover, it allows for the creation of advanced transgenic strains for vector control programs. SSM circumvents the drawbacks of transposon-mediated transgenesis, where random transgene integration into the host genome results in insertional mutagenesis and variable position effects. We applied the Cre/lox recombinase-mediated cassette exchange (RMCE) system to Aedes aegypti, the vector of dengue, chikungunya, and Zika viruses. In this context we created four target site lines for RMCE and evaluated their fitness costs. Cre-RMCE is functional in a two-step mechanism and with good efficiency in Ae. aegypti. The advantages of Cre-RMCE over existing site-specific modification systems for Ae. aegypti, phiC31-RMCE and CRISPR, originate in the preservation of the recombination sites, which 1) allows successive modifications and rapid expansion or adaptation of existing systems by repeated targeting of the same site; and 2) provides reversibility, thus allowing the excision of undesired sequences. Thereby, Cre-RMCE complements existing genomic modification tools, adding flexibility and versatility to vector genome targeting.

Oligo/Polynucleotide-Based Gene Modification: Strategies and Therapeutic Potential

PubMed Central

Sargent, R. Geoffrey; Kim, Soya

2011-01-01

Oligonucleotide- and polynucleotide-based gene modification strategies were developed as an alternative to transgene-based and classical gene targeting-based gene therapy approaches for treatment of genetic disorders. Unlike the transgene-based strategies, oligo/polynucleotide gene targeting approaches maintain gene integrity and the relationship between the protein coding and gene-specific regulatory sequences. Oligo/polynucleotide-based gene modification also has several advantages over classical vector-based homologous recombination approaches. These include essentially complete homology to the target sequence and the potential to rapidly engineer patient-specific oligo/polynucleotide gene modification reagents. Several oligo/polynucleotide-based approaches have been shown to successfully mediate sequence-specific modification of genomic DNA in mammalian cells. The strategies involve the use of polynucleotide small DNA fragments, triplex-forming oligonucleotides, and single-stranded oligodeoxynucleotides to mediate homologous exchange. The primary focus of this review will be on the mechanistic aspects of the small fragment homologous replacement, triplex-forming oligonucleotide-mediated, and single-stranded oligodeoxynucleotide-mediated gene modification strategies as it relates to their therapeutic potential. PMID:21417933

Finsler-type modification of the Coulomb law

NASA Astrophysics Data System (ADS)

Itin, Yakov; Lämmerzahl, Claus; Perlick, Volker

2014-12-01

Finsler geometry is a natural generalization of pseudo-Riemannian geometry. It can be motivated e.g. by a modified version of the Ehlers-Pirani-Schild axiomatic approach to space-time theory. Also, some scenarios of quantum gravity suggest a modified dispersion relation which could be phrased in terms of Finsler geometry. On a Finslerian space-time, the universality of free fall is still satisfied but local Lorentz invariance is violated in a way not covered by standard Lorentz invariance violation schemes. In this paper we consider a Finslerian modification of Maxwell's equations. The corrections to the Coulomb potential and to the hydrogen energy levels are computed. We find that the Finsler metric corrections yield a splitting of the energy levels. Experimental data provide bounds for the Finsler parameters.

Modification of zeolite 4A for use as an adsorbent for glyphosate and as an antibacterial agent for water.

PubMed

Zavareh, Siamak; Farrokhzad, Zahra; Darvishi, Farshad

2018-07-15

The aim of this work was to design a low cost adsorbent for efficient and selective removal of glyphosate from water at neutral pH conditions. For this purpose, zeolite 4A, a locally abundant and cheap mineral material, was ion-exchanged with Cu 2+ to produce Cu-zeolite 4A. The FTIR results revealed that the modification has no important effect on chemical structure of zeolite 4A. After modification, highly crystalline zeolite 4A was converted to amorphous Cu-zeolite 4A according to XRD studies. The SEM images showed spherical-like particles with porous surfaces for Cu-zeolite 4A compared to cubic particles with smooth surfaces for zeolite 4A. Adsorption equilibrium data were well fitted with non-linear forms of Langmuir, Freundlich and Temkin isotherms. The maximum adsorption capacity for Cu-zeolite 4A was calculated to be 112.7 mg g -1 based on the Langmuir model. The adsorption of glyphosate by the modified adsorbent had fast kinetics fitted both pseudo-first-order and pseudo-second-order models. A mechanism based on chemical adsorption was proposed for the removal process. The modified adsorbent had a good selectivity to glyphosate over natural waters common cations and anions. It also showed desired regeneration ability as an important feature for practical uses. The potential use of the developed material as antibacterial agent for water disinfection filters was also investigated by MIC method. Relatively strong antibacterial activity was observed for Cu-zeolite 4A against Gram-positive and Gram-negative model bacteria while zeolite 4A had no antibacterial properties. No release of Cu 2+ to aqueous solutions was detected as unique feature of the developed material. Copyright © 2018 Elsevier Inc. All rights reserved.

Using Bioacoustical Methodologies to Evaluate Equine Hearing Capabilities and Cognition

NASA Astrophysics Data System (ADS)

Makepeace, Shawn

The field of Bioacoustics is an emerging field of science that investigates various aspects of animal audiology and communication. More recently, audiological means have been used to evaluate the cognitive abilities of animals using event related brain potentials (ERP's). The Mismatch Negativity (MMN) component of the ERP is considered a cognitive neuroelectric phenomenon since it is generated in the area of the cortex that is responsible for evaluating sound stimuli including the ability to discriminate. Such discrimination produces a negative-going waveform with a relative latency of about 150-250 msec when elicited with auditory stimuli in human adults. The MMN response is elicited by use of the oddball paradigm in which two different tones are presented in pseudo-random order. The purpose of this study was to determine if elicitation of the MMN is achievable in the horse by use of current equipment in a non-clinical setting such as a barn. During the course of this experiment, it became obvious that the major challenge was the excessive amount of noise that inundated the waveforms thereby making any specific waves even remotely discernible. Attempts were made to improve the signal-to-noise ratio (SNR) by modifications to the testing unit and the addition of several in-line and digital filters. However, even with these modifications, the MMN response still could not be identifiable within the noise of the waveforms. Therefore, the matter of whether or not the horse elicits a MMN response should be revised to if it is even feasible to elicit a MMN response in these animals.

Pseudo Random Stimulus Response of Combustion Systems.

DTIC Science & Technology

1980-01-01

is also 7 applicable to the coalescence/dispersion (C/D) micromixing model In the C/D model, micromixing is simulated by considering the reacting...the turbulent fluctuations on the local heat release rate. Thus the micromixing ’noise’ measurements will not be valid, however, deductions

Variable word length encoder reduces TV bandwith requirements

NASA Technical Reports Server (NTRS)

Sivertson, W. E., Jr.

1965-01-01

Adaptive variable resolution encoding technique provides an adaptive compression pseudo-random noise signal processor for reducing television bandwidth requirements. Complementary processors are required in both the transmitting and receiving systems. The pretransmission processor is analog-to-digital, while the postreception processor is digital-to-analog.

Even and odd normalized zero modes in random interacting Majorana models respecting the parity P and the time-reversal-symmetry T

NASA Astrophysics Data System (ADS)

Monthus, Cécile

2018-06-01

For random interacting Majorana models where the only symmetries are the parity P and the time-reversal-symmetry T, various approaches are compared to construct exact even and odd normalized zero modes Γ in finite size, i.e. Hermitian operators that commute with the Hamiltonian, that square to the identity, and that commute (even) or anticommute (odd) with the parity P. Even normalized zero-modes are well known under the name of ‘pseudo-spins’ in the field of many-body-localization or more precisely ‘local integrals of motion’ (LIOMs) in the many-body-localized-phase where the pseudo-spins happens to be spatially localized. Odd normalized zero-modes are popular under the name of ‘Majorana zero modes’ or ‘strong zero modes’. Explicit examples for small systems are described in detail. Applications to real-space renormalization procedures based on blocks containing an odd number of Majorana fermions are also discussed.

Random network model of electrical conduction in two-phase rock

NASA Astrophysics Data System (ADS)

Fuji-ta, Kiyoshi; Seki, Masayuki; Ichiki, Masahiro

2018-05-01

We developed a cell-type lattice model to clarify the interconnected conductivity mechanism of two-phase rock. We quantified electrical conduction networks in rock and evaluated electrical conductivity models of the two-phase interaction. Considering the existence ratio of conductive and resistive cells in the model, we generated natural matrix cells simulating a natural mineral distribution pattern, using Mersenne Twister random numbers. The most important and prominent feature of the model simulation is a drastic increase in the pseudo-conductivity index for conductor ratio R > 0.22. This index in the model increased from 10-4 to 100 between R = 0.22 and 0.9, a change of four orders of magnitude. We compared our model responses with results from previous model studies. Although the pseudo-conductivity computed by the model differs slightly from that of the previous model, model responses can account for the conductivity change. Our modeling is thus effective for quantitatively estimating the degree of interconnection of rock and minerals.

First international two-way satellite time and frequency transfer experiment employing dual pseudo-random noise codes.

PubMed

Tseng, Wen-Hung; Huang, Yi-Jiun; Gotoh, Tadahiro; Hobiger, Thomas; Fujieda, Miho; Aida, Masanori; Li, Tingyu; Lin, Shinn-Yan; Lin, Huang-Tien; Feng, Kai-Ming

2012-03-01

Two-way satellite time and frequency transfer (TWSTFT) is one of the main techniques used to compare atomic time scales over long distances. To both improve the precision of TWSTFT and decrease the satellite link fee, a new software-defined modem with dual pseudo-random noise (DPN) codes has been developed. In this paper, we demonstrate the first international DPN-based TWSTFT experiment over a period of 6 months. The results of DPN exhibit excellent performance, which is competitive with the Global Positioning System (GPS) precise point positioning (PPP) technique in the short-term and consistent with the conventional TWSTFT in the long-term. Time deviations of less than 75 ps are achieved for averaging times from 1 s to 1 d. Moreover, the DPN data has less diurnal variation than that of the conventional TWSTFT. Because the DPN-based system has advantages of higher precision and lower bandwidth cost, it is one of the most promising methods to improve international time-transfer links.

Applications of statistical physics and information theory to the analysis of DNA sequences

NASA Astrophysics Data System (ADS)

Grosse, Ivo

2000-10-01

DNA carries the genetic information of most living organisms, and the of genome projects is to uncover that genetic information. One basic task in the analysis of DNA sequences is the recognition of protein coding genes. Powerful computer programs for gene recognition have been developed, but most of them are based on statistical patterns that vary from species to species. In this thesis I address the question if there exist universal statistical patterns that are different in coding and noncoding DNA of all living species, regardless of their phylogenetic origin. In search for such species-independent patterns I study the mutual information function of genomic DNA sequences, and find that it shows persistent period-three oscillations. To understand the biological origin of the observed period-three oscillations, I compare the mutual information function of genomic DNA sequences to the mutual information function of stochastic model sequences. I find that the pseudo-exon model is able to reproduce the mutual information function of genomic DNA sequences. Moreover, I find that a generalization of the pseudo-exon model can connect the existence and the functional form of long-range correlations to the presence and the length distributions of coding and noncoding regions. Based on these theoretical studies I am able to find an information-theoretical quantity, the average mutual information (AMI), whose probability distributions are significantly different in coding and noncoding DNA, while they are almost identical in all studied species. These findings show that there exist universal statistical patterns that are different in coding and noncoding DNA of all studied species, and they suggest that the AMI may be used to identify genes in different living species, irrespective of their taxonomic origin.

High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements.

PubMed

Lim, Haw Chuan; Braun, Michael J

2016-09-01

Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27-43). On average, 66.2% of the reads mapped to the pseudo-reference genome of each species. Of these mapped reads, an average of 52.7% was identified as PCR or optical duplicates. We achieved deeper effective sequencing for historical samples (122.7×) compared to modern samples (23.5×). The number of nucleotide sites with at least 8× sequencing depth was high, with averages ranging from 0.89 × 10(6)  bp (Arachnothera, modern samples) to 1.98 × 10(6)  bp (Stachyris, modern samples). Linear regression revealed that the amount of sequence data obtained from each historical sample (represented by per cent of the pseudo-reference genome recovered with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013) related to how recently the sample was collected. We observed characteristic post-mortem damage in the DNA of historical samples. However, we were able to reduce the error rate significantly by truncating ends of reads during read mapping (local alignment) and conducting stringent SNP and genotype filtering. © 2016 John Wiley & Sons Ltd.

Extracting random numbers from quantum tunnelling through a single diode.

PubMed

Bernardo-Gavito, Ramón; Bagci, Ibrahim Ethem; Roberts, Jonathan; Sexton, James; Astbury, Benjamin; Shokeir, Hamzah; McGrath, Thomas; Noori, Yasir J; Woodhead, Christopher S; Missous, Mohamed; Roedig, Utz; Young, Robert J

2017-12-19

Random number generation is crucial in many aspects of everyday life, as online security and privacy depend ultimately on the quality of random numbers. Many current implementations are based on pseudo-random number generators, but information security requires true random numbers for sensitive applications like key generation in banking, defence or even social media. True random number generators are systems whose outputs cannot be determined, even if their internal structure and response history are known. Sources of quantum noise are thus ideal for this application due to their intrinsic uncertainty. In this work, we propose using resonant tunnelling diodes as practical true random number generators based on a quantum mechanical effect. The output of the proposed devices can be directly used as a random stream of bits or can be further distilled using randomness extraction algorithms, depending on the application.

The risk of harmful algal blooms (HABs) in the oyster-growing estuaries of New South Wales, Australia.

PubMed

Ajani, Penelope; Brett, Steve; Krogh, Martin; Scanes, Peter; Webster, Grant; Armand, Leanne

2013-06-01

The spatial and temporal variability of potentially harmful phytoplankton was examined in the oyster-growing estuaries of New South Wales. Forty-five taxa from 31 estuaries were identified from 2005 to 2009. Harmful species richness was latitudinally graded for rivers, with increasing number of taxa southward. There were significant differences (within an estuary) in harmful species abundance and richness for 11 of 21 estuaries tested. Where differences were observed, these were predominately due to species belonging to the Pseudo-nitzschia delicatissima group, Dinophysis acuminata, Dictyocha octonaria and Prorocentrum cordatum with a consistent upstream versus downstream pattern emerging. Temporal (seasonal or interannual) patterns in harmful phytoplankton within and among estuaries were highly variable. Examination of harmful phytoplankton in relation to recognised estuary disturbance measures revealed species abundance correlated to estuary modification levels and flushing time, with modified, slow flushing estuaries having higher abundance. Harmful species richness correlated with bioregion, estuary modification levels and estuary class, with southern, unmodified lakes demonstrating greater species density. Predicting how these risk taxa and risk zones may change with further estuary disturbance and projected climate warming will require more focused, smaller scale studies aimed at a deeper understanding of species-specific ecology and bloom mechanisms. Coupled with this consideration, there is an imperative for further taxonomic, ecological and toxicological investigations into poorly understood taxa (e.g. Pseudo-nitzschia).

Effects of intensity and order of stimuli presentation on AEPs: an analysis of the consistency of EP augmenting/reducing in the auditory modality.

PubMed

Carrillo-de-la-Peña, M T

1999-05-01

(1) To achieve a better understanding of the intensity dependence function of AEPs recorded at fronto-central and temporal electrode sites; (2) To assess the possible influence of the order of stimuli presentation on this function; and (3) To investigate if a subject's AEPs augmenting or reducing (A/R) tendency is consistent throughout two intra-session runs. Two sequences of 288 stimuli of different intensities (60, 80, 90 and 110 dB SPL) were delivered to 29 psychology students. In the first run, stimuli were presented in 4 consecutive blocks of 72 tones of each intensity, either in an ascendant (from lowest to loudest stimuli) or descendent (from loudest to lowest) way. In the second run, a pseudo-randomized sequence of stimuli of the 4 intensities was presented. (1) AEPs recorded at fronto-central electrodes showed a stronger intensity dependence than those recorded at temporal leads; (2) The delivery of tones of different intensities in an aleatory sequence provoked higher amplitudes at Fz and Cz - especially for the loudest tones - but not at temporal leads; (3) The individual's AEP responses to stimuli of increasing intensity are highly consistent throughout two intra-session runs. The different findings obtained for the fronto-central N1P2 and the T complex in relation to the effect of intensity and order of stimuli presentation may be explained in terms of the cortical origin of those components. The higher amplitudes found with an aleatory sequence, especially for the highest intensity stimuli, may reflect that these stimuli capture the subject's attention and provoke an enhancement of the N1 component. The implications of the present results for investigation into A/R and the clinical relevance of this phenomenon are discussed.

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

PubMed Central

Carvalho, Alexandra T P; Gouveia, Leonor; Kanna, Charan Raju; Wärmländer, Sebastian K T S; Platts, Jamie A; Kamerlin, Shina Caroline Lynn

2014-01-01

We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding. PMID:25625845

Scope of Various Random Number Generators in Ant System Approach for TSP

NASA Technical Reports Server (NTRS)

Sen, S. K.; Shaykhian, Gholam Ali

2007-01-01

Experimented on heuristic, based on an ant system approach for traveling Salesman problem, are several quasi and pseudo-random number generators. This experiment is to explore if any particular generator is most desirable. Such an experiment on large samples has the potential to rank the performance of the generators for the foregoing heuristic. This is just to seek an answer to the controversial performance ranking of the generators in probabilistic/statically sense.

Molecular basis of length polymorphism in the human zeta-globin gene complex.

PubMed Central

Goodbourn, S E; Higgs, D R; Clegg, J B; Weatherall, D J

1983-01-01

The length polymorphism between the human zeta-globin gene and its pseudogene is caused by an allele-specific variation in the copy number of a tandemly repeating 36-base-pair sequence. This sequence is related to a tandemly repeated 14-base-pair sequence in the 5' flanking region of the human insulin gene, which is known to cause length polymorphism, and to a repetitive sequence in intervening sequence (IVS) 1 of the pseudo-zeta-globin gene. Evidence is presented that the latter is also of variable length, probably because of differences in the copy number of the tandem repeat. The homology between the three length polymorphisms may be an indication of the presence of a more widespread group of related sequences in the human genome, which might be useful for generalized linkage studies. PMID:6308667

Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing

DTIC Science & Technology

2010-08-25

or intentional genetic modifications that circumvent the targets of the detection assays or in the case of a biological attack using an antibiotic ...genetic changes conferring antibiotic resistance can be deciphered rapidly and accurately using WGS. We demonstrate the utility of Roche 454...Rapid Identification of Genetic Modifications in Bacillus anthracis Using Whole Genome Draft Sequences Generated by 454 Pyrosequencing Peter E. Chen1

Direct Detection and Sequencing of Damaged DNA Bases

PubMed Central

2011-01-01

Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time (SMRT®) DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications. PMID:22185597

Direct detection and sequencing of damaged DNA bases.

PubMed

Clark, Tyson A; Spittle, Kristi E; Turner, Stephen W; Korlach, Jonas

2011-12-20

Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time (SMRT®) DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications.

A study of high density bit transition requirements versus the effects on BCH error correcting coding

NASA Technical Reports Server (NTRS)

Ingels, F.; Schoggen, W. O.

1981-01-01

Several methods for increasing bit transition densities in a data stream are summarized, discussed in detail, and compared against constraints imposed by the 2 MHz data link of the space shuttle high rate multiplexer unit. These methods include use of alternate pulse code modulation waveforms, data stream modification by insertion, alternate bit inversion, differential encoding, error encoding, and use of bit scramblers. The psuedo-random cover sequence generator was chosen for application to the 2 MHz data link of the space shuttle high rate multiplexer unit. This method is fully analyzed and a design implementation proposed.

Application of global positioning system to determination of tectonic plate movements and crustal deformations

NASA Technical Reports Server (NTRS)

Anderle, R. J.

1978-01-01

It is shown that pseudo-range measurements to four GPS satellites based on correlation of the pseudo random code transmissions from the satellites can be used to determine the relative position of ground stations which are separated by several hundred kilometers to a precision at the centimeter level. Carrier signal measurements during the course of passage of satellites over a pair of stations also yield centimeter precision in the relative position, but oscillator instabilities limit the accuracy. The accuracy of solutions based on either type of data is limited by unmodeled tropospheric refraction effects which would reach 5 centimeters at low elevation angles for widely separated stations.

Expression of homing endonuclease gene and insertion-like element in sea anemone mitochondrial genomes: Lesson learned from Anemonia viridis.

PubMed

Chi, Sylvia Ighem; Urbarova, Ilona; Johansen, Steinar D

2018-04-30

The mitochondrial genomes of sea anemones are dynamic in structure. Invasion by genetic elements, such as self-catalytic group I introns or insertion-like sequences, contribute to sea anemone mitochondrial genome expansion and complexity. By using next generation sequencing we investigated the complete mtDNAs and corresponding transcriptomes of the temperate sea anemone Anemonia viridis and its closer tropical relative Anemonia majano. Two versions of fused homing endonuclease gene (HEG) organization were observed among the Actiniidae sea anemones; in-frame gene fusion and pseudo-gene fusion. We provided support for the pseudo-gene fusion organization in Anemonia species, resulting in a repressed HEG from the COI-884 group I intron. orfA, a putative protein-coding gene with insertion-like features, was present in both Anemonia species. Interestingly, orfA and COI expression were significantly up-regulated upon long-term environmental stress corresponding to low seawater pH conditions. This study provides new insights to the dynamics of sea anemone mitochondrial genome structure and function. Copyright © 2018 Elsevier B.V. All rights reserved.

Identification of immunoglobulins using Chou's pseudo amino acid composition with feature selection technique.

PubMed

Tang, Hua; Chen, Wei; Lin, Hao

2016-04-01

Immunoglobulins, also called antibodies, are a group of cell surface proteins which are produced by the immune system in response to the presence of a foreign substance (called antigen). They play key roles in many medical, diagnostic and biotechnological applications. Correct identification of immunoglobulins is crucial to the comprehension of humoral immune function. With the avalanche of protein sequences identified in postgenomic age, it is highly desirable to develop computational methods to timely identify immunoglobulins. In view of this, we designed a predictor called "IGPred" by formulating protein sequences with the pseudo amino acid composition into which nine physiochemical properties of amino acids were incorporated. Jackknife cross-validated results showed that 96.3% of immunoglobulins and 97.5% of non-immunoglobulins can be correctly predicted, indicating that IGPred holds very high potential to become a useful tool for antibody analysis. For the convenience of most experimental scientists, a web-server for IGPred was established at http://lin.uestc.edu.cn/server/IGPred. We believe that the web-server will become a powerful tool to study immunoglobulins and to guide related experimental validations.

Hide and vanish: data sets where the most parsimonious tree is known but hard to find, and their implications for tree search methods.

PubMed

Goloboff, Pablo A

2014-10-01

Three different types of data sets, for which the uniquely most parsimonious tree can be known exactly but is hard to find with heuristic tree search methods, are studied. Tree searches are complicated more by the shape of the tree landscape (i.e. the distribution of homoplasy on different trees) than by the sheer abundance of homoplasy or character conflict. Data sets of Type 1 are those constructed by Radel et al. (2013). Data sets of Type 2 present a very rugged landscape, with narrow peaks and valleys, but relatively low amounts of homoplasy. For such a tree landscape, subjecting the trees to TBR and saving suboptimal trees produces much better results when the sequence of clipping for the tree branches is randomized instead of fixed. An unexpected finding for data sets of Types 1 and 2 is that starting a search from a random tree instead of a random addition sequence Wagner tree may increase the probability that the search finds the most parsimonious tree; a small artificial example where these probabilities can be calculated exactly is presented. Data sets of Type 3, the most difficult data sets studied here, comprise only congruent characters, and a single island with only one most parsimonious tree. Even if there is a single island, missing entries create a very flat landscape which is difficult to traverse with tree search algorithms because the number of equally parsimonious trees that need to be saved and swapped to effectively move around the plateaus is too large. Minor modifications of the parameters of tree drifting, ratchet, and sectorial searches allow travelling around these plateaus much more efficiently than saving and swapping large numbers of equally parsimonious trees with TBR. For these data sets, two new related criteria for selecting taxon addition sequences in Wagner trees (the "selected" and "informative" addition sequences) produce much better results than the standard random or closest addition sequences. These new methods for Wagner trees and for moving around plateaus can be useful when analyzing phylogenomic data sets formed by concatenation of genes with uneven taxon representation ("sparse" supermatrices), which are likely to present a tree landscape with extensive plateaus. Copyright © 2014 Elsevier Inc. All rights reserved.

Computational Models for Belief Revision, Group Decision-Making and Cultural Shifts

DTIC Science & Technology

2010-10-25

34social" networks; the green numbers are pseudo-trees or artificial (non-social) constructions. The dashed blue line indicates the range of Erdos- Renyi ...non-social networks such as Erdos- Renyi random graphs or the more passive non-cognitive spreading of disease or information flow, As mentioned

pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC.

PubMed

Jia, Jianhua; Zhang, Liuxia; Liu, Zi; Xiao, Xuan; Chou, Kuo-Chen

2016-10-15

Sumoylation is a post-translational modification (PTM) process, in which small ubiquitin-related modifier (SUMO) is attaching by covalent bonds to substrate protein. It is critical to many different biological processes such as replicating genome, expressing gene, localizing and stabilizing proteins; unfortunately, it is also involved with many major disorders including Alzheimer's and Parkinson's diseases. Therefore, for both basic research and drug development, it is important to identify the sumoylation sites in proteins. To address such a problem, we developed a predictor called pSumo-CD by incorporating the sequence-coupled information into the general pseudo-amino acid composition (PseAAC) and introducing the covariance discriminant (CD) algorithm, in which a bias-adjustment term, which has the function to automatically adjust the errors caused by the bias due to the imbalance of training data, had been incorporated. Rigorous cross-validations indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose. For the convenience of most experimental scientists, a user-friendly web-server for pSumo-CD has been established at http://www.jci-bioinfo.cn/pSumo-CD, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. jjia@gordonlifescience.org, xxiao@gordonlifescience.org or kcchou@gordonlifescience.orgSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Modified Theoretical Model of Intrinsic Hardness of Crystalline Solids

PubMed Central

Dai, Fu-Zhi; Zhou, Yanchun

2016-01-01

Super-hard materials have been extensively investigated due to their practical importance in numerous industrial applications. To stimulate the design and exploration of new super-hard materials, microscopic models that elucidate the fundamental factors controlling hardness are desirable. The present work modified the theoretical model of intrinsic hardness proposed by Gao. In the modification, we emphasize the critical role of appropriately decomposing a crystal to pseudo-binary crystals, which should be carried out based on the valence electron population of each bond. After modification, the model becomes self-consistent and predicts well the hardness values of many crystals, including crystals composed of complex chemical bonds. The modified model provides fundamental insights into the nature of hardness, which can facilitate the quest for intrinsic super-hard materials. PMID:27604165

A Secure, Intelligent, and Smart-Sensing Approach for Industrial System Automation and Transmission over Unsecured Wireless Networks

PubMed Central

Shahzad, Aamir; Lee, Malrey; Xiong, Neal Naixue; Jeong, Gisung; Lee, Young-Keun; Choi, Jae-Young; Mahesar, Abdul Wheed; Ahmad, Iftikhar

2016-01-01

In Industrial systems, Supervisory control and data acquisition (SCADA) system, the pseudo-transport layer of the distributed network protocol (DNP3) performs the functions of the transport layer and network layer of the open systems interconnection (OSI) model. This study used a simulation design of water pumping system, in-which the network nodes are directly and wirelessly connected with sensors, and are monitored by the main controller, as part of the wireless SCADA system. This study also intends to focus on the security issues inherent in the pseudo-transport layer of the DNP3 protocol. During disassembly and reassembling processes, the pseudo-transport layer keeps track of the bytes sequence. However, no mechanism is available that can verify the message or maintain the integrity of the bytes in the bytes received/transmitted from/to the data link layer or in the send/respond from the main controller/sensors. To properly and sequentially keep track of the bytes, a mechanism is required that can perform verification while bytes are received/transmitted from/to the lower layer of the DNP3 protocol or the send/respond to/from field sensors. For security and byte verification purposes, a mechanism needs to be proposed for the pseudo-transport layer, by employing cryptography algorithm. A dynamic choice security buffer (SB) is designed and employed during the security development. To achieve the desired goals of the proposed study, a pseudo-transport layer stack model is designed using the DNP3 protocol open library and the security is deployed and tested, without changing the original design. PMID:26950129

A Secure, Intelligent, and Smart-Sensing Approach for Industrial System Automation and Transmission over Unsecured Wireless Networks.

PubMed

Shahzad, Aamir; Lee, Malrey; Xiong, Neal Naixue; Jeong, Gisung; Lee, Young-Keun; Choi, Jae-Young; Mahesar, Abdul Wheed; Ahmad, Iftikhar

2016-03-03

In Industrial systems, Supervisory control and data acquisition (SCADA) system, the pseudo-transport layer of the distributed network protocol (DNP3) performs the functions of the transport layer and network layer of the open systems interconnection (OSI) model. This study used a simulation design of water pumping system, in-which the network nodes are directly and wirelessly connected with sensors, and are monitored by the main controller, as part of the wireless SCADA system. This study also intends to focus on the security issues inherent in the pseudo-transport layer of the DNP3 protocol. During disassembly and reassembling processes, the pseudo-transport layer keeps track of the bytes sequence. However, no mechanism is available that can verify the message or maintain the integrity of the bytes in the bytes received/transmitted from/to the data link layer or in the send/respond from the main controller/sensors. To properly and sequentially keep track of the bytes, a mechanism is required that can perform verification while bytes are received/transmitted from/to the lower layer of the DNP3 protocol or the send/respond to/from field sensors. For security and byte verification purposes, a mechanism needs to be proposed for the pseudo-transport layer, by employing cryptography algorithm. A dynamic choice security buffer (SB) is designed and employed during the security development. To achieve the desired goals of the proposed study, a pseudo-transport layer stack model is designed using the DNP3 protocol open library and the security is deployed and tested, without changing the original design.

MO-F-CAMPUS-J-05: Toward MRI-Only Radiotherapy: Novel Tissue Segmentation and Pseudo-CT Generation Techniques Based On T1 MRI Sequences

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

Aouadi, S; McGarry, M; Hammoud, R

Purpose: To develop and validate a 4 class tissue segmentation approach (air cavities, background, bone and soft-tissue) on T1 -weighted brain MRI and to create a pseudo-CT for MRI-only radiation therapy verification. Methods: Contrast-enhanced T1-weighted fast-spin-echo sequences (TR = 756ms, TE= 7.152ms), acquired on a 1.5T GE MRI-Simulator, are used.MRIs are firstly pre-processed to correct for non uniformity using the non parametric, non uniformity intensity normalization algorithm. Subsequently, a logarithmic inverse scaling log(1/image) is applied, prior to segmentation, to better differentiate bone and air from soft-tissues. Finally, the following method is enrolled to classify intensities into air cavities, background, bonemore » and soft-tissue:Thresholded region growing with seed points in image corners is applied to get a mask of Air+Bone+Background. The background is, afterward, separated by the scan-line filling algorithm. The air mask is extracted by morphological opening followed by a post-processing based on knowledge about air regions geometry. The remaining rough bone pre-segmentation is refined by applying 3D geodesic active contours; bone segmentation evolves by the sum of internal forces from contour geometry and external force derived from image gradient magnitude.Pseudo-CT is obtained by assigning −1000HU to air and background voxels, performing linear mapping of soft-tissue MR intensities in [-400HU, 200HU] and inverse linear mapping of bone MR intensities in [200HU, 1000HU]. Results: Three brain patients having registered MRI and CT are used for validation. CT intensities classification into 4 classes is performed by thresholding. Dice and misclassification errors are quantified. Correct classifications for soft-tissue, bone, and air are respectively 89.67%, 77.8%, and 64.5%. Dice indices are acceptable for bone (0.74) and soft-tissue (0.91) but low for air regions (0.48). Pseudo-CT produces DRRs with acceptable clinical visual agreement to CT-based DRR. Conclusion: The proposed approach makes it possible to use T1-weighted MRI to generate accurate pseudo-CT from 4-class segmentation.« less

Atlas-guided generation of pseudo-CT images for MRI-only and hybrid PET-MRI-guided radiotherapy treatment planning.

PubMed

Arabi, Hossein; Koutsouvelis, Nikolaos; Rouzaud, Michel; Miralbell, Raymond; Zaidi, Habib

2016-09-07

Magnetic resonance imaging (MRI)-guided attenuation correction (AC) of positron emission tomography (PET) data and/or radiation therapy (RT) treatment planning is challenged by the lack of a direct link between MRI voxel intensities and electron density. Therefore, even if this is not a trivial task, a pseudo-computed tomography (CT) image must be predicted from MRI alone. In this work, we propose a two-step (segmentation and fusion) atlas-based algorithm focusing on bone tissue identification to create a pseudo-CT image from conventional MRI sequences and evaluate its performance against the conventional MRI segmentation technique and a recently proposed multi-atlas approach. The clinical studies consisted of pelvic CT, PET and MRI scans of 12 patients with loco-regionally advanced rectal disease. In the first step, bone segmentation of the target image is optimized through local weighted atlas voting. The obtained bone map is then used to assess the quality of deformed atlases to perform voxel-wise weighted atlas fusion. To evaluate the performance of the method, a leave-one-out cross-validation (LOOCV) scheme was devised to find optimal parameters for the model. Geometric evaluation of the produced pseudo-CT images and quantitative analysis of the accuracy of PET AC were performed. Moreover, a dosimetric evaluation of volumetric modulated arc therapy photon treatment plans calculated using the different pseudo-CT images was carried out and compared to those produced using CT images serving as references. The pseudo-CT images produced using the proposed method exhibit bone identification accuracy of 0.89 based on the Dice similarity metric compared to 0.75 achieved by the other atlas-based method. The superior bone extraction resulted in a mean standard uptake value bias of  -1.5  ±  5.0% (mean  ±  SD) in bony structures compared to  -19.9  ±  11.8% and  -8.1  ±  8.2% achieved by MRI segmentation-based (water-only) and atlas-guided AC. Dosimetric evaluation using dose volume histograms and the average difference between minimum/maximum absorbed doses revealed a mean error of less than 1% for the both target volumes and organs at risk. Two-dimensional (2D) gamma analysis of the isocenter dose distributions at 1%/1 mm criterion revealed pass rates of 91.40  ±  7.56%, 96.00  ±  4.11% and 97.67  ±  3.6% for MRI segmentation, atlas-guided and the proposed methods, respectively. The proposed method generates accurate pseudo-CT images from conventional Dixon MRI sequences with improved bone extraction accuracy. The approach is promising for potential use in PET AC and MRI-only or hybrid PET/MRI-guided RT treatment planning.

Atlas-guided generation of pseudo-CT images for MRI-only and hybrid PET-MRI-guided radiotherapy treatment planning

NASA Astrophysics Data System (ADS)

Arabi, Hossein; Koutsouvelis, Nikolaos; Rouzaud, Michel; Miralbell, Raymond; Zaidi, Habib

2016-09-01

Magnetic resonance imaging (MRI)-guided attenuation correction (AC) of positron emission tomography (PET) data and/or radiation therapy (RT) treatment planning is challenged by the lack of a direct link between MRI voxel intensities and electron density. Therefore, even if this is not a trivial task, a pseudo-computed tomography (CT) image must be predicted from MRI alone. In this work, we propose a two-step (segmentation and fusion) atlas-based algorithm focusing on bone tissue identification to create a pseudo-CT image from conventional MRI sequences and evaluate its performance against the conventional MRI segmentation technique and a recently proposed multi-atlas approach. The clinical studies consisted of pelvic CT, PET and MRI scans of 12 patients with loco-regionally advanced rectal disease. In the first step, bone segmentation of the target image is optimized through local weighted atlas voting. The obtained bone map is then used to assess the quality of deformed atlases to perform voxel-wise weighted atlas fusion. To evaluate the performance of the method, a leave-one-out cross-validation (LOOCV) scheme was devised to find optimal parameters for the model. Geometric evaluation of the produced pseudo-CT images and quantitative analysis of the accuracy of PET AC were performed. Moreover, a dosimetric evaluation of volumetric modulated arc therapy photon treatment plans calculated using the different pseudo-CT images was carried out and compared to those produced using CT images serving as references. The pseudo-CT images produced using the proposed method exhibit bone identification accuracy of 0.89 based on the Dice similarity metric compared to 0.75 achieved by the other atlas-based method. The superior bone extraction resulted in a mean standard uptake value bias of  -1.5  ±  5.0% (mean  ±  SD) in bony structures compared to  -19.9  ±  11.8% and  -8.1  ±  8.2% achieved by MRI segmentation-based (water-only) and atlas-guided AC. Dosimetric evaluation using dose volume histograms and the average difference between minimum/maximum absorbed doses revealed a mean error of less than 1% for the both target volumes and organs at risk. Two-dimensional (2D) gamma analysis of the isocenter dose distributions at 1%/1 mm criterion revealed pass rates of 91.40  ±  7.56%, 96.00  ±  4.11% and 97.67  ±  3.6% for MRI segmentation, atlas-guided and the proposed methods, respectively. The proposed method generates accurate pseudo-CT images from conventional Dixon MRI sequences with improved bone extraction accuracy. The approach is promising for potential use in PET AC and MRI-only or hybrid PET/MRI-guided RT treatment planning.

Advanced Sine Wave Modulation of Continuous Wave Laser System for Atmospheric CO2 Differential Absorption Measurements

NASA Technical Reports Server (NTRS)

Campbell, Joel F.; Lin, Bing; Nehrir, Amin R.

2014-01-01

NASA Langley Research Center in collaboration with ITT Exelis have been experimenting with Continuous Wave (CW) laser absorption spectrometer (LAS) as a means of performing atmospheric CO2 column measurements from space to support the Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS) mission.Because range resolving Intensity Modulated (IM) CW lidar techniques presented here rely on matched filter correlations, autocorrelation properties without side lobes or other artifacts are highly desirable since the autocorrelation function is critical for the measurements of lidar return powers, laser path lengths, and CO2 column amounts. In this paper modulation techniques are investigated that improve autocorrelation properties. The modulation techniques investigated in this paper include sine waves modulated by maximum length (ML) sequences in various hardware configurations. A CW lidar system using sine waves modulated by ML pseudo random noise codes is described, which uses a time shifting approach to separate channels and make multiple, simultaneous online/offline differential absorption measurements. Unlike the pure ML sequence, this technique is useful in hardware that is band pass filtered as the IM sine wave carrier shifts the main power band. Both amplitude and Phase Shift Keying (PSK) modulated IM carriers are investigated that exibit perfect autocorrelation properties down to one cycle per code bit. In addition, a method is presented to bandwidth limit the ML sequence based on a Gaussian filter implemented in terms of Jacobi theta functions that does not seriously degrade the resolution or introduce side lobes as a means of reducing aliasing and IM carrier bandwidth.

Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes

PubMed Central

Chand, Mahesh Kumar; Nirwan, Neha; Diffin, Fiona M.; van Aelst, Kara; Kulkarni, Manasi; Pernstich, Christian; Szczelkun, Mark D.; Saikrishnan, Kayarat

2015-01-01

Endonucleolytic double-strand DNA break production requires separate strand cleavage events. Although catalytic mechanisms for simple dimeric endonucleases are available, there are many complex nuclease machines which are poorly understood in comparison. Here we studied the single polypeptide Type ISP restriction-modification (RM) enzymes, which cleave random DNA between distant target sites when two enzymes collide following convergent ATP-driven translocation. We report the 2.7 Angstroms resolution X-ray crystal structure of a Type ISP enzyme-DNA complex, revealing that both the helicase-like ATPase and nuclease are unexpectedly located upstream of the direction of translocation, inconsistent with simple nuclease domain-dimerization. Using single-molecule and biochemical techniques, we demonstrate that each ATPase remodels its DNA-protein complex and translocates along DNA without looping it, leading to a collision complex where the nuclease domains are distal. Sequencing of single cleavage events suggests a previously undescribed endonuclease model, where multiple, stochastic strand nicking events combine to produce DNA scission. PMID:26389736

Minimizing effects of methodological decisions on interpretation and prediction in species distribution studies: An example with background selection

USGS Publications Warehouse

Jarnevich, Catherine S.; Talbert, Marian; Morisette, Jeffrey T.; Aldridge, Cameron L.; Brown, Cynthia; Kumar, Sunil; Manier, Daniel; Talbert, Colin; Holcombe, Tracy R.

2017-01-01

Evaluating the conditions where a species can persist is an important question in ecology both to understand tolerances of organisms and to predict distributions across landscapes. Presence data combined with background or pseudo-absence locations are commonly used with species distribution modeling to develop these relationships. However, there is not a standard method to generate background or pseudo-absence locations, and method choice affects model outcomes. We evaluated combinations of both model algorithms (simple and complex generalized linear models, multivariate adaptive regression splines, Maxent, boosted regression trees, and random forest) and background methods (random, minimum convex polygon, and continuous and binary kernel density estimator (KDE)) to assess the sensitivity of model outcomes to choices made. We evaluated six questions related to model results, including five beyond the common comparison of model accuracy assessment metrics (biological interpretability of response curves, cross-validation robustness, independent data accuracy and robustness, and prediction consistency). For our case study with cheatgrass in the western US, random forest was least sensitive to background choice and the binary KDE method was least sensitive to model algorithm choice. While this outcome may not hold for other locations or species, the methods we used can be implemented to help determine appropriate methodologies for particular research questions.

A Combinatorial H4 Tail Library to Explore the Histone Code

PubMed Central

Garske, Adam L.; Craciun, Gheorghe; Denu, John M.

2008-01-01

Histone modifications modulate chromatin structure and function. A posttranslational modification-randomized, combinatorial library based on the first twenty-one residues of histone H4 was designed for systematic examination of proteins that interpret a histone code. The 800-member library represented all permutations of most known modifications within the N-terminal tail of histone H4. To determine its utility in a protein-binding assay, the on-bead library was screened with an antibody directed against phosphoserine 1 of H4. Among the hits, 59/60 sequences were phosphorylated at S1, while 30/30 of those selected from the non-hits were unphosphorylated. A 512-member version of the library was then used to determine the binding specificity of the double tudor domain of hJMJD2A, a histone demethylase involved in transcriptional repression. Global linear least squares fitting of modifications from the identified peptides (40 hits and 34 non-hits) indicated that methylation of K20 was the primary determinant for binding, but that phosphorylation/acetylation on neighboring sites attenuated the interaction. To validate the on-bead screen, isothermal titration calorimetry was performed with thirteen H4 peptides. Dissociation constants ranged from 1 mM - 1μM and corroborated the screening results. The general approach should be useful for probing the specificity of any histone-binding protein. PMID:18616348

Development and Analysis of Hybrid Thermoelectric Refrigerator Systems

NASA Astrophysics Data System (ADS)

Saifizi, M.; Zakaria, M. S.; Yaacob, Sazali; Wan, Khairunizam

2018-03-01

Thermoelectric module (TEM) is a type of solid-state devices which has the capability to maintain the accuracy of small temperature variation application. In this study, a hybrid thermoelectric refrigerator system is introduced by utilizing TEMs; direct and air to air thermoelectric heat pump to cool down and maintain low temperature for vaccines storage. Two different materials which are aluminum and stainless steel are used as container in hybrid thermoelectric refrigerator (HTER) configuration to investigate the response of every system in transient and steady state mode. A proper temperature sensor calibration technique is implemented to make certain real time data acquisition of the systems are not affected very much from the noise generated. From step response analysis, it is indicated that HTER I (aluminum) has rapid settling time from transient to steady state than HTER II (stainless steel) since aluminum has better thermal conductivity as compared to stainless steel. It is found that HTER I is better in cooling capability with the same input current instead of HTER II which required a longer time to achieve steady state mode. Besides, in Pseudo Random Binary Sequence (PRBS) response analysis injected to both systems shows HTER I is very sensitive to current input as the sequence length of HTER I is shorter than HTER II. However both systems depict the varying temperature in the range of 4 oC due to differences in thermal conductivity of container.

Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins.

PubMed Central

Zhu, H.; Braun, W.

1999-01-01

A statistical analysis of a representative data set of 169 known protein structures was used to analyze the specificity of residue interactions between spatial neighboring strands in beta-sheets. Pairwise potentials were derived from the frequency of residue pairs in nearest contact, second nearest and third nearest contacts across neighboring beta-strands compared to the expected frequency of residue pairs in a random model. A pseudo-energy function based on these statistical pairwise potentials recognized native beta-sheets among possible alternative pairings. The native pairing was found within the three lowest energies in 73% of the cases in the training data set and in 63% of beta-sheets in a test data set of 67 proteins, which were not part of the training set. The energy function was also used to detect tripeptides, which occur frequently in beta-sheets of native proteins. The majority of native partners of tripeptides were distributed in a low energy range. Self-correcting distance geometry (SECODG) calculations using distance constraints sets derived from possible low energy pairing of beta-strands uniquely identified the native pairing of the beta-sheet in pancreatic trypsin inhibitor (BPTI). These results will be useful for predicting the structure of proteins from their amino acid sequence as well as for the design of proteins containing beta-sheets. PMID:10048326

Robust statistical methods for impulse noise suppressing of spread spectrum induced polarization data, with application to a mine site, Gansu province, China

NASA Astrophysics Data System (ADS)

Liu, Weiqiang; Chen, Rujun; Cai, Hongzhu; Luo, Weibin

2016-12-01

In this paper, we investigated the robust processing of noisy spread spectrum induced polarization (SSIP) data. SSIP is a new frequency domain induced polarization method that transmits pseudo-random m-sequence as source current where m-sequence is a broadband signal. The potential information at multiple frequencies can be obtained through measurement. Removing the noise is a crucial problem for SSIP data processing. Considering that if the ordinary mean stack and digital filter are not capable of reducing the impulse noise effectively in SSIP data processing, the impact of impulse noise will remain in the complex resistivity spectrum that will affect the interpretation of profile anomalies. We implemented a robust statistical method to SSIP data processing. The robust least-squares regression is used to fit and remove the linear trend from the original data before stacking. The robust M estimate is used to stack the data of all periods. The robust smooth filter is used to suppress the residual noise for data after stacking. For robust statistical scheme, the most appropriate influence function and iterative algorithm are chosen by testing the simulated data to suppress the outliers' influence. We tested the benefits of the robust SSIP data processing using examples of SSIP data recorded in a test site beside a mine in Gansu province, China.

Emergence of Sequence Type 779 Methicillin-Resistant Staphylococcus aureus Harboring a Novel Pseudo Staphylococcal Cassette Chromosome mec (SCCmec)-SCC-SCCCRISPR Composite Element in Irish Hospitals

PubMed Central

Kinnevey, Peter M.; Shore, Anna C.; Brennan, Grainne I.; Sullivan, Derek J.; Ehricht, Ralf; Monecke, Stefan; Slickers, Peter

2013-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) has been a major cause of nosocomial infection in Irish hospitals for 4 decades, and replacement of predominant MRSA clones has occurred several times. An MRSA isolate recovered in 2006 as part of a larger study of sporadic MRSA exhibited a rare spa (t878) and multilocus sequence (ST779) type and was nontypeable by PCR- and DNA microarray-based staphylococcal cassette chromosome mec (SCCmec) element typing. Whole-genome sequencing revealed the presence of a novel 51-kb composite island (CI) element with three distinct domains, each flanked by direct repeat and inverted repeat sequences, including (i) a pseudo SCCmec element (16.3 kb) carrying mecA with a novel mec class region, a fusidic acid resistance gene (fusC), and two copper resistance genes (copB and copC) but lacking ccr genes; (ii) an SCC element (17.5 kb) carrying a novel ccrAB4 allele; and (iii) an SCC element (17.4 kb) carrying a novel ccrC allele and a clustered regularly interspaced short palindromic repeat (CRISPR) region. The novel CI was subsequently identified by PCR in an additional 13 t878/ST779 MRSA isolates, six from bloodstream infections, recovered between 2006 and 2011 in 11 hospitals. Analysis of open reading frames (ORFs) carried by the CI showed amino acid sequence similarity of 44 to 100% to ORFs from S. aureus and coagulase-negative staphylococci (CoNS). These findings provide further evidence of genetic transfer between S. aureus and CoNS and show how this contributes to the emergence of novel SCCmec elements and MRSA strains. Ongoing surveillance of this MRSA strain is warranted and will require updating of currently used SCCmec typing methods. PMID:23147725

Comprehensive Analysis of Protein Modifications by Top-down Mass Spectrometry

PubMed Central

Zhang, Han; Ge, Ying

2012-01-01

Mass spectrometry (MS)-based proteomics is playing an increasingly important role in cardiovascular research. Proteomics includes not only identification and quantification of proteins, but also the characterization of protein modifications such as post-translational modifications and sequence variants. The conventional bottom-up approach, involving proteolytic digestion of proteins into small peptides prior to MS analysis, is routinely used for protein identification and quantification with high throughput and automation. Nevertheless, it has limitations in the analysis of protein modifications mainly due to the partial sequence coverage and loss of connections among modifications on disparate portions of a protein. An alternative approach, top-down MS, has emerged as a powerful tool for the analysis of protein modifications. The top-down approach analyzes whole proteins directly, providing a “bird’s eye” view of all existing modifications. Subsequently, each modified protein form can be isolated and fragmented in the mass spectrometer to locate the modification site. The incorporation of the non-ergodic dissociation methods such as electron capture dissociation (ECD) greatly enhances the top-down capabilities. ECD is especially useful for mapping labile post-translational modifications which are well-preserved during the ECD fragmentation process. Top-down MS with ECD has been successfully applied to cardiovascular research with the unique advantages in unraveling the molecular complexity, quantifying modified protein forms, complete mapping of modifications with full sequence coverage, discovering unexpected modifications, and identifying and quantifying positional isomers and determining the order of multiple modifications. Nevertheless, top-down MS still needs to overcome some technical challenges to realize its full potential. Herein, we reviewed the advantages and challenges of top-down methodology with a focus on its application in cardiovascular research. PMID:22187450

[Absorption of Uranium with Tea Oil Tree Sawdust Modified by Succinic Acid].

PubMed

Zhang, Xiao-feng; Chen, Di-yun; Peng, Yan; Liu, Yong-sheng; Xiong, Xue-ying

2015-05-01

In order to explore how the modification of succinic acid improves the adsorption of tea oil tree sawdust for uranium, the tea oil tree sawdust was modified by succinic acid, after the pretreatments of crushing, screening, alkalization and acidification. Infrared analysis indicated carboxylic acid groups and ester groups were added to the sawdust after modification, and scanning electron microscope demonstrated after modification the appearance of tea oil tree sawdust was transferred from the structure like compact and straight stripped into the structure like loose and wrinkled leaves, which meant modification increased its inner pores. By the static experiments, effects of reaction time between adsorbent and solvent, dosage of adsorbent, temperature, pH value and initial concentration of uranium were investigated. The results showed that after the modification by succinic acid, the absorption rate of tea oil tree sawdust for uranium increased significantly by about 20% in 12.5 mg · L(-1) initial concentration uranium solution. Adsorption equilibrium was achieved within 180 min, and the kinetic data can be well described by the pseudo-second-order kinetic model. The experimental adsorption isotherm followed the Langmuir and Freundlich models. In addition, the maximum adsorption amounts of tea oil tree sawdust after modification calculated from Langmuir equation raised from 21.413 3 to 31.545 7 mg · g(-1) at 35°C and pH 4.0.

Generating random numbers by means of nonlinear dynamic systems

NASA Astrophysics Data System (ADS)

Zang, Jiaqi; Hu, Haojie; Zhong, Juhua; Luo, Duanbin; Fang, Yi

2018-07-01

To introduce the randomness of a physical process to students, a chaotic pendulum experiment was opened in East China University of Science and Technology (ECUST) on the undergraduate level in the physics department. It was shown chaotic motion could be initiated through adjusting the operation of a chaotic pendulum. By using the data of the angular displacements of chaotic motion, random binary numerical arrays can be generated. To check the randomness of generated numerical arrays, the NIST Special Publication 800-20 method was adopted. As a result, it was found that all the random arrays which were generated by the chaotic motion could pass the validity criteria and some of them were even better than the quality of pseudo-random numbers generated by a computer. Through the experiments, it is demonstrated that chaotic pendulum can be used as an efficient mechanical facility in generating random numbers, and can be applied in teaching random motion to the students.

77 FR 30367 - Defense Federal Acquisition Regulation Supplement: Order of Application for Modifications (DFARS...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-22

... sequence of modifications to a contract or order, a method for determining the order of application for... application for modifications. (a) Circumstances may exist in which the numeric order of the modifications to... date and the same signature date, procuring contracting office modifications will be applied in numeric...

Prediction of protein structural classes by Chou's pseudo amino acid composition: approached using continuous wavelet transform and principal component analysis.

PubMed

Li, Zhan-Chao; Zhou, Xi-Bin; Dai, Zong; Zou, Xiao-Yong

2009-07-01

A prior knowledge of protein structural classes can provide useful information about its overall structure, so it is very important for quick and accurate determination of protein structural class with computation method in protein science. One of the key for computation method is accurate protein sample representation. Here, based on the concept of Chou's pseudo-amino acid composition (AAC, Chou, Proteins: structure, function, and genetics, 43:246-255, 2001), a novel method of feature extraction that combined continuous wavelet transform (CWT) with principal component analysis (PCA) was introduced for the prediction of protein structural classes. Firstly, the digital signal was obtained by mapping each amino acid according to various physicochemical properties. Secondly, CWT was utilized to extract new feature vector based on wavelet power spectrum (WPS), which contains more abundant information of sequence order in frequency domain and time domain, and PCA was then used to reorganize the feature vector to decrease information redundancy and computational complexity. Finally, a pseudo-amino acid composition feature vector was further formed to represent primary sequence by coupling AAC vector with a set of new feature vector of WPS in an orthogonal space by PCA. As a showcase, the rigorous jackknife cross-validation test was performed on the working datasets. The results indicated that prediction quality has been improved, and the current approach of protein representation may serve as a useful complementary vehicle in classifying other attributes of proteins, such as enzyme family class, subcellular localization, membrane protein types and protein secondary structure, etc.

Determining the Location of DNA Modification and Mutation Caused by UVB Light in Skin Cancer

DTIC Science & Technology

2015-09-01

Award Number: W81XWH-12-1-0333 TITLE: Determining the Location of DNA Modification and Mutation Caused by UVB Light in Skin Cancer PRINCIPAL...COVERED 15 Aug 2012 – 14 Aug 2015 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER W81XWH-12-1-0333 Determining the Location of DNA Modification and Mutation ...sequencing libraries generated for both yeast and human cells show pyrimidine bias on the 5’ end, indicating that we are sequencing the dimers

Conditional poliovirus mutants made by random deletion mutagenesis of infectious cDNA.

PubMed Central

Kirkegaard, K; Nelsen, B

1990-01-01

Small deletions were introduced into DNA plasmids bearing cDNA copies of Mahoney type 1 poliovirus RNA. The procedure used was similar to that of P. Hearing and T. Shenk (J. Mol. Biol. 167:809-822, 1983), with modifications designed to introduce only one lesion randomly into each DNA molecule. Methods to map small deletions in either large DNA or RNA molecules were employed. Two poliovirus mutants, VP1-101 and VP1-102, were selected from mutagenized populations on the basis of their host range phenotype, showing a large reduction in the relative numbers of plaques on CV1 and HeLa cells compared with wild-type virus. The deletions borne by the mutant genomes were mapped to the region encoding the amino terminus of VP1. That these lesions were responsible for the mutant phenotypes was substantiated by reintroduction of the sequenced lesions into a wild-type poliovirus cDNA by deoxyoligonucleotide-directed mutagenesis. The deletion of nucleotides encoding amino acids 8 and 9 of VP1 was responsible for the VP1-101 phenotype; the VP1-102 defect was caused by the deletion of the sequences encoding the first four amino acids of VP1. The peptide sequence at the VP1-VP3 proteolytic cleavage site was altered from glutamine-glycine to glutamine-methionine in VP1-102; this apparently did not alter the proteolytic cleavage pattern. The biochemical defects resulting from these mutations are discussed in the accompanying report. Images PMID:2152811

Faster Bit-Parallel Algorithms for Unordered Pseudo-tree Matching and Tree Homeomorphism

NASA Astrophysics Data System (ADS)

Kaneta, Yusaku; Arimura, Hiroki

In this paper, we consider the unordered pseudo-tree matching problem, which is a problem of, given two unordered labeled trees P and T, finding all occurrences of P in T via such many-one embeddings that preserve node labels and parent-child relationship. This problem is closely related to tree pattern matching problem for XPath queries with child axis only. If m > w , we present an efficient algorithm that solves the problem in O(nm log(w)/w) time using O(hm/w + mlog(w)/w) space and O(m log(w)) preprocessing on a unit-cost arithmetic RAM model with addition, where m is the number of nodes in P, n is the number of nodes in T, h is the height of T, and w is the word length. We also discuss a modification of our algorithm for the unordered tree homeomorphism problem, which corresponds to a tree pattern matching problem for XPath queries with descendant axis only.

Pseudo-cat's eye for improved tilt-immune interferometry.

PubMed

Speake, Clive C; Bradshaw, Miranda J

2015-08-20

We present a new simple optical design for a cat's eye retroreflector. We describe the design of the new optical configuration and its use in tilt-immune interferometry where it enables the tracking of the displacement of a plane target mirror with minimum sensitivity to its tilt about axes orthogonal to the interferometer's optical axis. In this application the new cat's eye does not behave as a perfect retroreflector and we refer to it as a "pseudo"-cat's eye (PCE). The device allows, for the first time, tilt-immune interferometric displacement measurements in cases where the nominal distance to the target mirror is significantly larger than the length of the cat's eye. We describe the general optical characteristics of the PCE and compare its performance in our application with that of a conventional cat's eye optical configuration using ABCD matrices and Zemax analyses. We further suggest a simple modification to the design that would enable the PCE to behave as a perfect cat's eye, and this design may provide an advantageous solution for other applications.

Sequence tagging reveals unexpected modifications in toxicoproteomics

PubMed Central

Dasari, Surendra; Chambers, Matthew C.; Codreanu, Simona G.; Liebler, Daniel C.; Collins, Ben C.; Pennington, Stephen R.; Gallagher, William M.; Tabb, David L.

2010-01-01

Toxicoproteomic samples are rich in posttranslational modifications (PTMs) of proteins. Identifying these modifications via standard database searching can incur significant performance penalties. Here we describe the latest developments in TagRecon, an algorithm that leverages inferred sequence tags to identify modified peptides in toxicoproteomic data sets. TagRecon identifies known modifications more effectively than the MyriMatch database search engine. TagRecon outperformed state of the art software in recognizing unanticipated modifications from LTQ, Orbitrap, and QTOF data sets. We developed user-friendly software for detecting persistent mass shifts from samples. We follow a three-step strategy for detecting unanticipated PTMs in samples. First, we identify the proteins present in the sample with a standard database search. Next, identified proteins are interrogated for unexpected PTMs with a sequence tag-based search. Finally, additional evidence is gathered for the detected mass shifts with a refinement search. Application of this technology on toxicoproteomic data sets revealed unintended cross-reactions between proteins and sample processing reagents. Twenty five proteins in rat liver showed signs of oxidative stress when exposed to potentially toxic drugs. These results demonstrate the value of mining toxicoproteomic data sets for modifications. PMID:21214251

The impact of metformin, oral contraceptives, and lifestyle modification on polycystic ovary syndrome in obese adolescent women in two randomized, placebo-controlled clinical trials.

PubMed

Hoeger, Kathleen; Davidson, Kristen; Kochman, Lynda; Cherry, Tracy; Kopin, Laurie; Guzick, David S

2008-11-01

Polycystic ovary syndrome (PCOS) presents in adolescence, and obesity is a common finding. The benefits and risks of alternate approaches to the management of PCOS in obese adolescent women are not clear. We investigated the effects of metformin, oral contraceptives (OCs), and/or lifestyle modification in obese adolescent women with PCOS. Two small, randomized, placebo-controlled clinical trials were performed. A total of 79 obese adolescent women with PCOS participated. In the single treatment trial, subjects were randomized to metformin, placebo, a lifestyle modification program, or OC. In the combined treatment trial, all subjects received lifestyle modification and OC and were randomized to metformin or placebo. Serum concentrations of androgens and lipids were measured. Lifestyle modification alone resulted in a 59% reduction in free androgen index with a 122% increase in SHBG. OC resulted in a significant decrease in total testosterone (44%) and free androgen index (86%) but also resulted in an increase in C-reactive protein (39.7%) and cholesterol (14%). The combination of lifestyle modification, OC, and metformin resulted in a 55% decrease in total testosterone, as compared to 33% with combined treatment and placebo, a 4% reduction in waist circumference, and a significant increase in HDL (46%). In these preliminary trials, both lifestyle modification and OCs significantly reduce androgens and increase SHBG in obese adolescents with PCOS. Metformin, in combination with lifestyle modification and OC, reduces central adiposity, reduces total testosterone, and increases HDL, but does not enhance overall weight reduction.

RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

PubMed Central

Grosjean, Henri; Gaspin, Christine; Marck, Christian; Decatur, Wayne A; de Crécy-Lagard, Valérie

2008-01-01

Background Naturally occurring RNAs contain numerous enzymatically altered nucleosides. Differences in RNA populations (RNomics) and pattern of RNA modifications (Modomics) depends on the organism analyzed and are two of the criteria that distinguish the three kingdoms of life. If the genomic sequences of the RNA molecules can be derived from whole genome sequence information, the modification profile cannot and requires or direct sequencing of the RNAs or predictive methods base on the presence or absence of the modifications genes. Results By employing a comparative genomics approach, we predicted almost all of the genes coding for the t+rRNA modification enzymes in the mesophilic moderate halophile Haloferax volcanii. These encode both guide RNAs and enzymes. Some are orthologous to previously identified genes in Archaea, Bacteria or in Saccharomyces cerevisiae, but several are original predictions. Conclusion The number of modifications in t+rRNAs in the halophilic archaeon is surprisingly low when compared with other Archaea or Bacteria, particularly the hyperthermophilic organisms. This may result from the specific lifestyle of halophiles that require high intracellular salt concentration for survival. This salt content could allow RNA to maintain its functional structural integrity with fewer modifications. We predict that the few modifications present must be particularly important for decoding, accuracy of translation or are modifications that cannot be functionally replaced by the electrostatic interactions provided by the surrounding salt-ions. This analysis also guides future experimental validation work aiming to complete the understanding of the function of RNA modifications in Archaeal translation. PMID:18844986

Improving tRNAscan-SE Annotation Results via Ensemble Classifiers.

PubMed

Zou, Quan; Guo, Jiasheng; Ju, Ying; Wu, Meihong; Zeng, Xiangxiang; Hong, Zhiling

2015-11-01

tRNAScan-SE is a tRNA detection program that is widely used for tRNA annotation; however, the false positive rate of tRNAScan-SE is unacceptable for large sequences. Here, we used a machine learning method to try to improve the tRNAScan-SE results. A new predictor, tRNA-Predict, was designed. We obtained real and pseudo-tRNA sequences as training data sets using tRNAScan-SE and constructed three different tRNA feature sets. We then set up an ensemble classifier, LibMutil, to predict tRNAs from the training data. The positive data set of 623 tRNA sequences was obtained from tRNAdb 2009 and the negative data set was the false positive tRNAs predicted by tRNAscan-SE. Our in silico experiments revealed a prediction accuracy rate of 95.1 % for tRNA-Predict using 10-fold cross-validation. tRNA-Predict was developed to distinguish functional tRNAs from pseudo-tRNAs rather than to predict tRNAs from a genome-wide scan. However, tRNA-Predict can work with the output of tRNAscan-SE, which is a genome-wide scanning method, to improve the tRNAscan-SE annotation results. The tRNA-Predict web server is accessible at http://datamining.xmu.edu.cn/∼gjs/tRNA-Predict. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-beam range imager for autonomous operations

NASA Technical Reports Server (NTRS)

Marzwell, Neville I.; Lee, H. Sang; Ramaswami, R.

1993-01-01

For space operations from the Space Station Freedom the real time range imager will be very valuable in terms of refuelling, docking as well as space exploration operations. For these applications as well as many other robotics and remote ranging applications, a small potable, power efficient, robust range imager capable of a few tens of km ranging with 10 cm accuracy is needed. The system developed is based on a well known pseudo-random modulation technique applied to a laser transmitter combined with a novel range resolution enhancement technique. In this technique, the transmitter is modulated by a relatively low frequency of an order of a few MHz to enhance the signal to noise ratio and to ease the stringent systems engineering requirements while accomplishing a very high resolution. The desired resolution cannot easily be attained by other conventional approaches. The engineering model of the system is being designed to obtain better than 10 cm range accuracy simply by implementing a high precision clock circuit. In this paper we present the principle of the pseudo-random noise (PN) lidar system and the results of the proof of experiment.

Multi-kW coherent combining of fiber lasers seeded with pseudo random phase modulated light

NASA Astrophysics Data System (ADS)

Flores, Angel; Ehrehreich, Thomas; Holten, Roger; Anderson, Brian; Dajani, Iyad

2016-03-01

We report efficient coherent beam combining of five kilowatt-class fiber amplifiers with a diffractive optical element (DOE). Based on a master oscillator power amplifier (MOPA) configuration, the amplifiers were seeded with pseudo random phase modulated light. Each non-polarization maintaining fiber amplifier was optically path length matched and provides approximately 1.2 kW of near diffraction-limited output power (measured M2<1.1). Consequently, a low power sample of each laser was utilized for active linear polarization control. A low power sample of the combined beam after the DOE provided an error signal for active phase locking which was performed via Locking of Optical Coherence by Single-Detector Electronic-Frequency Tagging (LOCSET). After phase stabilization, the beams were coherently combined via the 1x5 DOE. A total combined output power of 4.9 kW was achieved with 82% combining efficiency and excellent beam quality (M2<1.1). The intrinsic DOE splitter loss was 5%. Similarly, losses due in part to non-ideal polarization, ASE content, uncorrelated wavefront errors, and misalignment errors contributed to the efficiency reduction.

Hybrid Topological Lie-Hamiltonian Learning in Evolving Energy Landscapes

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

In this Chapter, a novel bidirectional algorithm for hybrid (discrete + continuous-time) Lie-Hamiltonian evolution in adaptive energy landscape-manifold is designed and its topological representation is proposed. The algorithm is developed within a geometrically and topologically extended framework of Hopfield's neural nets and Haken's synergetics (it is currently designed in Mathematica, although with small changes it could be implemented in Symbolic C++ or any other computer algebra system). The adaptive energy manifold is determined by the Hamiltonian multivariate cost function H, based on the user-defined vehicle-fleet configuration matrix W, which represents the pseudo-Riemannian metric tensor of the energy manifold. Search for the global minimum of H is performed using random signal differential Hebbian adaptation. This stochastic gradient evolution is driven (or, pulled-down) by `gravitational forces' defined by the 2nd Lie derivatives of H. Topological changes of the fleet matrix W are observed during the evolution and its topological invariant is established. The evolution stops when the W-topology breaks down into several connectivity-components, followed by topology-breaking instability sequence (i.e., a series of phase transitions).

On the adaptivity and complexity embedded into differential evolution

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

Senkerik, Roman; Pluhacek, Michal; Jasek, Roman

2016-06-08

This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performedmore » on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.« less

The Hilbert-Huang Transform-Based Denoising Method for the TEM Response of a PRBS Source Signal

NASA Astrophysics Data System (ADS)

Hai, Li; Guo-qiang, Xue; Pan, Zhao; Hua-sen, Zhong; Khan, Muhammad Younis

2016-08-01

The denoising process is critical in processing transient electromagnetic (TEM) sounding data. For the full waveform pseudo-random binary sequences (PRBS) response, an inadequate noise estimation may result in an erroneous interpretation. We consider the Hilbert-Huang transform (HHT) and its application to suppress the noise in the PRBS response. The focus is on the thresholding scheme to suppress the noise and the analysis of the signal based on its Hilbert time-frequency representation. The method first decomposes the signal into the intrinsic mode function, and then, inspired by the thresholding scheme in wavelet analysis; an adaptive and interval thresholding is conducted to set to zero all the components in intrinsic mode function which are lower than a threshold related to the noise level. The algorithm is based on the characteristic of the PRBS response. The HHT-based denoising scheme is tested on the synthetic and field data with the different noise levels. The result shows that the proposed method has a good capability in denoising and detail preservation.

Spatial and temporal plasticity of chromatin during programmed DNA-reorganization in Stylonychia macronuclear development

PubMed Central

Postberg, Jan; Heyse, Katharina; Cremer, Marion; Cremer, Thomas; Lipps, Hans J

2008-01-01

Background: In this study we exploit the unique genome organization of ciliates to characterize the biological function of histone modification patterns and chromatin plasticity for the processing of specific DNA sequences during a nuclear differentiation process. Ciliates are single-cell eukaryotes containing two morphologically and functionally specialized types of nuclei, the somatic macronucleus and the germline micronucleus. In the course of sexual reproduction a new macronucleus develops from a micronuclear derivative. During this process specific DNA sequences are eliminated from the genome, while sequences that will be transcribed in the mature macronucleus are retained. Results: We show by immunofluorescence microscopy, Western analyses and chromatin immunoprecipitation (ChIP) experiments that each nuclear type establishes its specific histone modification signature. Our analyses reveal that the early macronuclear anlage adopts a permissive chromatin state immediately after the fusion of two heterochromatic germline micronuclei. As macronuclear development progresses, repressive histone modifications that specify sequences to be eliminated are introduced de novo. ChIP analyses demonstrate that permissive histone modifications are associated with sequences that will be retained in the new macronucleus. Furthermore, our data support the hypothesis that a PIWI-family protein is involved in a transnuclear cross-talk and in the RNAi-dependent control of developmental chromatin reorganization. Conclusion: Based on these data we present a comprehensive analysis of the spatial and temporal pattern of histone modifications during this nuclear differentiation process. Results obtained in this study may also be relevant for our understanding of chromatin plasticity during metazoan embryogenesis. PMID:19014664

Study of pseudo noise CW diode laser for ranging applications

NASA Technical Reports Server (NTRS)

Lee, Hyo S.; Ramaswami, Ravi

1992-01-01

A new Pseudo Random Noise (PN) modulated CW diode laser radar system is being developed for real time ranging of targets at both close and large distances (greater than 10 KM) to satisy a wide range of applications: from robotics to future space applications. Results from computer modeling and statistical analysis, along with some preliminary data obtained from a prototype system, are presented. The received signal is averaged for a short time to recover the target response function. It is found that even with uncooperative targets, based on the design parameters used (200-mW laser and 20-cm receiver), accurate ranging is possible up to about 15 KM, beyond which signal to noise ratio (SNR) becomes too small for real time analog detection.

On the joint spectral density of bivariate random sequences. Thesis Technical Report No. 21

NASA Technical Reports Server (NTRS)

Aalfs, David D.

1995-01-01

For univariate random sequences, the power spectral density acts like a probability density function of the frequencies present in the sequence. This dissertation extends that concept to bivariate random sequences. For this purpose, a function called the joint spectral density is defined that represents a joint probability weighing of the frequency content of pairs of random sequences. Given a pair of random sequences, the joint spectral density is not uniquely determined in the absence of any constraints. Two approaches to constraining the sequences are suggested: (1) assume the sequences are the margins of some stationary random field, (2) assume the sequences conform to a particular model that is linked to the joint spectral density. For both approaches, the properties of the resulting sequences are investigated in some detail, and simulation is used to corroborate theoretical results. It is concluded that under either of these two constraints, the joint spectral density can be computed from the non-stationary cross-correlation.

Image encryption using random sequence generated from generalized information domain

NASA Astrophysics Data System (ADS)

Xia-Yan, Zhang; Guo-Ji, Zhang; Xuan, Li; Ya-Zhou, Ren; Jie-Hua, Wu

2016-05-01

A novel image encryption method based on the random sequence generated from the generalized information domain and permutation-diffusion architecture is proposed. The random sequence is generated by reconstruction from the generalized information file and discrete trajectory extraction from the data stream. The trajectory address sequence is used to generate a P-box to shuffle the plain image while random sequences are treated as keystreams. A new factor called drift factor is employed to accelerate and enhance the performance of the random sequence generator. An initial value is introduced to make the encryption method an approximately one-time pad. Experimental results show that the random sequences pass the NIST statistical test with a high ratio and extensive analysis demonstrates that the new encryption scheme has superior security.

True random numbers from amplified quantum vacuum.

PubMed

Jofre, M; Curty, M; Steinlechner, F; Anzolin, G; Torres, J P; Mitchell, M W; Pruneri, V

2011-10-10

Random numbers are essential for applications ranging from secure communications to numerical simulation and quantitative finance. Algorithms can rapidly produce pseudo-random outcomes, series of numbers that mimic most properties of true random numbers while quantum random number generators (QRNGs) exploit intrinsic quantum randomness to produce true random numbers. Single-photon QRNGs are conceptually simple but produce few random bits per detection. In contrast, vacuum fluctuations are a vast resource for QRNGs: they are broad-band and thus can encode many random bits per second. Direct recording of vacuum fluctuations is possible, but requires shot-noise-limited detectors, at the cost of bandwidth. We demonstrate efficient conversion of vacuum fluctuations to true random bits using optical amplification of vacuum and interferometry. Using commercially-available optical components we demonstrate a QRNG at a bit rate of 1.11 Gbps. The proposed scheme has the potential to be extended to 10 Gbps and even up to 100 Gbps by taking advantage of high speed modulation sources and detectors for optical fiber telecommunication devices.

Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry.

PubMed

Kirpekar, F; Douthwaite, S; Roepstorff, P

2000-02-01

We present a method to screen RNA for posttranscriptional modifications based on Matrix Assisted Laser Desorption/Ionization mass spectrometry (MALDI-MS). After the RNA is digested to completion with a nucleotide-specific RNase, the fragments are analyzed by mass spectrometry. A comparison of the observed mass data with the data predicted from the gene sequence identifies fragments harboring modified nucleotides. Fragments larger than dinucleotides were valuable for the identification of posttranscriptional modifications. A more refined mapping of RNA modifications can be obtained by using two RNases in parallel combined with further fragmentation by Post Source Decay (PSD). This approach allows fast and sensitive screening of a purified RNA for posttranscriptional modification, and has been applied on 5S rRNA from two thermophilic microorganisms, the bacterium Bacillus stearothermophilus and the archaeon Sulfolobus acidocaldarius, as well as the halophile archaea Halobacterium halobium and Haloarcula marismortui. One S. acidocaldarius posttranscriptional modification was identified and was further characterized by PSD as a methylation of cytidine32. The modified C is located in a region that is clearly conserved with respect to both sequence and position in B. stearothermophilus and H. halobium and to some degree also in H. marismortui. However, no analogous modification was identified in the latter three organisms. We further find that the 5' end of H. halobium 5S rRNA is dephosphorylated, in contrast to the other 5S rRNA species investigated. The method additionally gives an immediate indication of whether the expected RNA sequence is in agreement with the observed fragment masses. Discrepancies with two of the published 5S rRNA sequences were identified and are reported here.

Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry.

PubMed Central

Kirpekar, F; Douthwaite, S; Roepstorff, P

2000-01-01

We present a method to screen RNA for posttranscriptional modifications based on Matrix Assisted Laser Desorption/Ionization mass spectrometry (MALDI-MS). After the RNA is digested to completion with a nucleotide-specific RNase, the fragments are analyzed by mass spectrometry. A comparison of the observed mass data with the data predicted from the gene sequence identifies fragments harboring modified nucleotides. Fragments larger than dinucleotides were valuable for the identification of posttranscriptional modifications. A more refined mapping of RNA modifications can be obtained by using two RNases in parallel combined with further fragmentation by Post Source Decay (PSD). This approach allows fast and sensitive screening of a purified RNA for posttranscriptional modification, and has been applied on 5S rRNA from two thermophilic microorganisms, the bacterium Bacillus stearothermophilus and the archaeon Sulfolobus acidocaldarius, as well as the halophile archaea Halobacterium halobium and Haloarcula marismortui. One S. acidocaldarius posttranscriptional modification was identified and was further characterized by PSD as a methylation of cytidine32. The modified C is located in a region that is clearly conserved with respect to both sequence and position in B. stearothermophilus and H. halobium and to some degree also in H. marismortui. However, no analogous modification was identified in the latter three organisms. We further find that the 5' end of H. halobium 5S rRNA is dephosphorylated, in contrast to the other 5S rRNA species investigated. The method additionally gives an immediate indication of whether the expected RNA sequence is in agreement with the observed fragment masses. Discrepancies with two of the published 5S rRNA sequences were identified and are reported here. PMID:10688367

Transfer of perceptual-motor training and the space adaptation syndrome

NASA Technical Reports Server (NTRS)

Kennedy, R. S.; Berbaum, K. S.; Williams, M. C.; Brannan, J.; Welch, R. B.

1987-01-01

Perceptual cue conflict may be the basis for the symptoms which are experienced by space travelers in microgravity conditions. Recovery has been suggested to take place after perceptual modification or reinterpretation. To elucidate this process, 10 subjects who repeatedly experienced a visual/vestibular conflict over trials and days, were tested in a similar but not identical perceptual situation (pseudo-Coriolis) to determine whether any savings in perceptual adaptation had occurred as compared to an unpracticed control group (N = 40). The practiced subjects experienced lessening dizziness and ataxia within and over sessions.

UAV Control on the Basis of 3D Landmark Bearing-Only Observations.

PubMed

Karpenko, Simon; Konovalenko, Ivan; Miller, Alexander; Miller, Boris; Nikolaev, Dmitry

2015-11-27

The article presents an approach to the control of a UAV on the basis of 3D landmark observations. The novelty of the work is the usage of the 3D RANSAC algorithm developed on the basis of the landmarks' position prediction with the aid of a modified Kalman-type filter. Modification of the filter based on the pseudo-measurements approach permits obtaining unbiased UAV position estimation with quadratic error characteristics. Modeling of UAV flight on the basis of the suggested algorithm shows good performance, even under significant external perturbations.

TDRSS telecommunications system, PN code analysis

NASA Technical Reports Server (NTRS)

Dixon, R.; Gold, R.; Kaiser, F.

1976-01-01

The pseudo noise (PN) codes required to support the TDRSS telecommunications services are analyzed and the impact of alternate coding techniques on the user transponder equipment, the TDRSS equipment, and all factors that contribute to the acquisition and performance of these telecommunication services is assessed. Possible alternatives to the currently proposed hybrid FH/direct sequence acquisition procedures are considered and compared relative to acquisition time, implementation complexity, operational reliability, and cost. The hybrid FH/direct sequence technique is analyzed and rejected in favor of a recommended approach which minimizes acquisition time and user transponder complexity while maximizing probability of acquisition and overall link reliability.

KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system

PubMed Central

Chin, V.; Valinluck, V.; Magaki, S.; Ryu, J.

2004-01-01

KpnBI is a restriction-modification (R-M) system recognized in the GM236 strain of Klebsiella pneumoniae. Here, the KpnBI modification genes were cloned into a plasmid using a modification expression screening method. The modification genes that consist of both hsdM (2631 bp) and hsdS (1344 bp) genes were identified on an 8.2 kb EcoRI chromosomal fragment. These two genes overlap by one base and share the same promoter located upstream of the hsdM gene. Using recently developed plasmid R-M tests and a computer program RM Search, the DNA recognition sequence for the KpnBI enzymes was identified as a new 8 nt sequence containing one degenerate base with a 6 nt spacer, CAAANNNNNNRTCA. From Dam methylation and HindIII sensitivity tests, the methylation loci were predicted to be the italicized third adenine in the 5′ specific region and the adenine opposite the italicized thymine in the 3′ specific region. Combined with previous sequence data for hsdR, we concluded that the KpnBI system is a typical type I R-M system. The deduced amino acid sequences of the three subunits of the KpnBI system show only limited homologies (25 to 33% identity) at best, to the four previously categorized type I families (IA, IB, IC, and ID). Furthermore, their identity scores to other uncharacterized putative genome type I sequences were 53% at maximum. Therefore, we propose that KpnBI is the prototype of a new ‘type IE’ family. PMID:15475385

On the design of random metasurface based devices.

PubMed

Dupré, Matthieu; Hsu, Liyi; Kanté, Boubacar

2018-05-08

Metasurfaces are generally designed by placing scatterers in periodic or pseudo-periodic grids. We propose and discuss design rules for functional metasurfaces with randomly placed anisotropic elements that randomly sample a well-defined phase function. By analyzing the focusing performance of random metasurface lenses as a function of their density and the density of the phase-maps used to design them, we find that the performance of 1D metasurfaces is mostly governed by their density while 2D metasurfaces strongly depend on both the density and the near-field coupling configuration of the surface. The proposed approach is used to design all-polarization random metalenses at near infrared frequencies. Challenges, as well as opportunities of random metasurfaces compared to periodic ones are discussed. Our results pave the way to new approaches in the design of nanophotonic structures and devices from lenses to solar energy concentrators.

Calculating Nozzle Side Loads using Acceleration Measurements of Test-Based Models

NASA Technical Reports Server (NTRS)

Brown, Andrew M.; Ruf, Joe

2007-01-01

As part of a NASA/MSFC research program to evaluate the effect of different nozzle contours on the well-known but poorly characterized "side load" phenomena, we attempt to back out the net force on a sub-scale nozzle during cold-flow testing using acceleration measurements. Because modeling the test facility dynamics is problematic, new techniques for creating a "pseudo-model" of the facility and nozzle directly from modal test results are applied. Extensive verification procedures were undertaken, resulting in a loading scale factor necessary for agreement between test and model based frequency response functions. Side loads are then obtained by applying a wide-band random load onto the system model, obtaining nozzle response PSD's, and iterating both the amplitude and frequency of the input until a good comparison of the response with the measured response PSD for a specific time point is obtained. The final calculated loading can be used to compare different nozzle profiles for assessment during rocket engine nozzle development and as a basis for accurate design of the nozzle and engine structure to withstand these loads. The techniques applied within this procedure have extensive applicability to timely and accurate characterization of all test fixtures used for modal test.A viewgraph presentation on a model-test based pseudo-model used to calculate side loads on rocket engine nozzles is included. The topics include: 1) Side Loads in Rocket Nozzles; 2) Present Side Loads Research at NASA/MSFC; 3) Structural Dynamic Model Generation; 4) Pseudo-Model Generation; 5) Implementation; 6) Calibration of Pseudo-Model Response; 7) Pseudo-Model Response Verification; 8) Inverse Force Determination; 9) Results; and 10) Recent Work.

Parallelization of a Monte Carlo particle transport simulation code

NASA Astrophysics Data System (ADS)

Hadjidoukas, P.; Bousis, C.; Emfietzoglou, D.

2010-05-01

We have developed a high performance version of the Monte Carlo particle transport simulation code MC4. The original application code, developed in Visual Basic for Applications (VBA) for Microsoft Excel, was first rewritten in the C programming language for improving code portability. Several pseudo-random number generators have been also integrated and studied. The new MC4 version was then parallelized for shared and distributed-memory multiprocessor systems using the Message Passing Interface. Two parallel pseudo-random number generator libraries (SPRNG and DCMT) have been seamlessly integrated. The performance speedup of parallel MC4 has been studied on a variety of parallel computing architectures including an Intel Xeon server with 4 dual-core processors, a Sun cluster consisting of 16 nodes of 2 dual-core AMD Opteron processors and a 200 dual-processor HP cluster. For large problem size, which is limited only by the physical memory of the multiprocessor server, the speedup results are almost linear on all systems. We have validated the parallel implementation against the serial VBA and C implementations using the same random number generator. Our experimental results on the transport and energy loss of electrons in a water medium show that the serial and parallel codes are equivalent in accuracy. The present improvements allow for studying of higher particle energies with the use of more accurate physical models, and improve statistics as more particles tracks can be simulated in low response time.

A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects

PubMed Central

Bramsen, Jesper B.; Pakula, Malgorzata M.; Hansen, Thomas B.; Bus, Claus; Langkjær, Niels; Odadzic, Dalibor; Smicius, Romualdas; Wengel, Suzy L.; Chattopadhyaya, Jyoti; Engels, Joachim W.; Herdewijn, Piet; Wengel, Jesper; Kjems, Jørgen

2010-01-01

Small interfering RNAs (siRNAs) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent miRNA-like behavior. Such off-target effects are primarily mediated by the sequence-specific interaction between the siRNA seed regions (position 2–8 of either siRNA strand counting from the 5′-end) and complementary sequences in the 3′UTR of (off-) targets. It was previously shown that chemical modification of siRNAs can reduce off-targeting but only very few modifications have been tested leaving more to be identified. Here we developed a luciferase reporter-based assay suitable to monitor siRNA off-targeting in a high throughput manner using stable cell lines. We investigated the impact of chemically modifying single nucleotide positions within the siRNA seed on siRNA function and off-targeting using 10 different types of chemical modifications, three different target sequences and three siRNA concentrations. We found several differently modified siRNAs to exercise reduced off-targeting yet incorporation of the strongly destabilizing unlocked nucleic acid (UNA) modification into position 7 of the siRNA most potently reduced off-targeting for all tested sequences. Notably, such position-specific destabilization of siRNA–target interactions did not significantly reduce siRNA potency and is therefore well suited for future siRNA designs especially for applications in vivo where siRNA concentrations, expectedly, will be low. PMID:20453030

Exploring bacterial epigenomics in the next-generation sequencing era: a new approach for an emerging frontier.

PubMed

Chen, Poyin; Jeannotte, Richard; Weimer, Bart C

2014-05-01

Epigenetics has an important role for the success of foodborne pathogen persistence in diverse host niches. Substantial challenges exist in determining DNA methylation to situation-specific phenotypic traits. DNA modification, mediated by restriction-modification systems, functions as an immune response against antagonistic external DNA, and bacteriophage-acquired methyltransferases (MTase) and orphan MTases - those lacking the cognate restriction endonuclease - facilitate evolution of new phenotypes via gene expression modulation via DNA and RNA modifications, including methylation and phosphorothioation. Recent establishment of large-scale genome sequencing projects will result in a significant increase in genome availability that will lead to new demands for data analysis including new predictive bioinformatics approaches that can be verified with traditional scientific rigor. Sequencing technologies that detect modification coupled with mass spectrometry to discover new adducts is a powerful tactic to study bacterial epigenetics, which is poised to make novel and far-reaching discoveries that link biological significance and the bacterial epigenome. Copyright © 2014 Elsevier Ltd. All rights reserved.

Engineering of a DNA Polymerase for Direct m6 A Sequencing.

PubMed

Aschenbrenner, Joos; Werner, Stephan; Marchand, Virginie; Adam, Martina; Motorin, Yuri; Helm, Mark; Marx, Andreas

2018-01-08

Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N 6 -methyladenosine (m 6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m 6 A-containing RNA prior to sequencing, since m 6 A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m 6 A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for N 6 -methylation. We identified a mutant that exhibits increased misincorporation opposite m 6 A compared to unmodified A. Application of the generated DNA polymerase in next-generation sequencing allowed the identification of m 6 A sites directly from the sequencing data of untreated RNA samples. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Random Numbers and Monte Carlo Methods

NASA Astrophysics Data System (ADS)

Scherer, Philipp O. J.

Many-body problems often involve the calculation of integrals of very high dimension which cannot be treated by standard methods. For the calculation of thermodynamic averages Monte Carlo methods are very useful which sample the integration volume at randomly chosen points. After summarizing some basic statistics, we discuss algorithms for the generation of pseudo-random numbers with given probability distribution which are essential for all Monte Carlo methods. We show how the efficiency of Monte Carlo integration can be improved by sampling preferentially the important configurations. Finally the famous Metropolis algorithm is applied to classical many-particle systems. Computer experiments visualize the central limit theorem and apply the Metropolis method to the traveling salesman problem.

An electrocorticographic BCI using code-based VEP for control in video applications: a single-subject study

PubMed Central

Kapeller, Christoph; Kamada, Kyousuke; Ogawa, Hiroshi; Prueckl, Robert; Scharinger, Josef; Guger, Christoph

2014-01-01

A brain-computer-interface (BCI) allows the user to control a device or software with brain activity. Many BCIs rely on visual stimuli with constant stimulation cycles that elicit steady-state visual evoked potentials (SSVEP) in the electroencephalogram (EEG). This EEG response can be generated with a LED or a computer screen flashing at a constant frequency, and similar EEG activity can be elicited with pseudo-random stimulation sequences on a screen (code-based BCI). Using electrocorticography (ECoG) instead of EEG promises higher spatial and temporal resolution and leads to more dominant evoked potentials due to visual stimulation. This work is focused on BCIs based on visual evoked potentials (VEP) and its capability as a continuous control interface for augmentation of video applications. One 35 year old female subject with implanted subdural grids participated in the study. The task was to select one out of four visual targets, while each was flickering with a code sequence. After a calibration run including 200 code sequences, a linear classifier was used during an evaluation run to identify the selected visual target based on the generated code-based VEPs over 20 trials. Multiple ECoG buffer lengths were tested and the subject reached a mean online classification accuracy of 99.21% for a window length of 3.15 s. Finally, the subject performed an unsupervised free run in combination with visual feedback of the current selection. Additionally, an algorithm was implemented that allowed to suppress false positive selections and this allowed the subject to start and stop the BCI at any time. The code-based BCI system attained very high online accuracy, which makes this approach very promising for control applications where a continuous control signal is needed. PMID:25147509

Characterizing resonant component in speech: A different view of tracking fundamental frequency

NASA Astrophysics Data System (ADS)

Dong, Bin

2017-05-01

Inspired by the nonlinearity and nonstationarity and the modulations in speech, Hilbert-Huang Transform and cyclostationarity analysis are employed to investigate the speech resonance in vowel in sequence. Cyclostationarity analysis is not directly manipulated on the target vowel, but on its intrinsic mode functions one by one. Thanks to the equivalence between the fundamental frequency in speech and the cyclic frequency in cyclostationarity analysis, the modulation intensity distributions of the intrinsic mode functions provide much information for the estimation of the fundamental frequency. To highlight the relationship between frequency and time, the pseudo-Hilbert spectrum is proposed to replace the Hilbert spectrum here. After contrasting the pseudo-Hilbert spectra of and the modulation intensity distributions of the intrinsic mode functions, it finds that there is usually one intrinsic mode function which works as the fundamental component of the vowel. Furthermore, the fundamental frequency of the vowel can be determined by tracing the pseudo-Hilbert spectrum of its fundamental component along the time axis. The later method is more robust to estimate the fundamental frequency, when meeting nonlinear components. Two vowels [a] and [i], picked up from a speech database FAU Aibo Emotion Corpus, are applied to validate the above findings.

Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

DOEpatents

Studier, F. William

1995-04-18

Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient.

Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

DOEpatents

Studier, F.W.

1995-04-18

Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient. 2 figs.

The coalescent process in models with selection and recombination.

PubMed

Hudson, R R; Kaplan, N L

1988-11-01

The statistical properties of the process describing the genealogical history of a random sample of genes at a selectively neutral locus which is linked to a locus at which natural selection operates are investigated. It is found that the equations describing this process are simple modifications of the equations describing the process assuming that the two loci are completely linked. Thus, the statistical properties of the genealogical process for a random sample at a neutral locus linked to a locus with selection follow from the results obtained for the selected locus. Sequence data from the alcohol dehydrogenase (Adh) region of Drosophila melanogaster are examined and compared to predictions based on the theory. It is found that the spatial distribution of nucleotide differences between Fast and Slow alleles of Adh is very similar to the spatial distribution predicted if balancing selection operates to maintain the allozyme variation at the Adh locus. The spatial distribution of nucleotide differences between different Slow alleles of Adh do not match the predictions of this simple model very well.

Yeast One-Hybrid Gγ Recruitment System for Identification of Protein Lipidation Motifs

PubMed Central

Fukuda, Nobuo; Doi, Motomichi; Honda, Shinya

2013-01-01

Fatty acids and isoprenoids can be covalently attached to a variety of proteins. These lipid modifications regulate protein structure, localization and function. Here, we describe a yeast one-hybrid approach based on the Gγ recruitment system that is useful for identifying sequence motifs those influence lipid modification to recruit proteins to the plasma membrane. Our approach facilitates the isolation of yeast cells expressing lipid-modified proteins via a simple and easy growth selection assay utilizing G-protein signaling that induces diploid formation. In the current study, we selected the N-terminal sequence of Gα subunits as a model case to investigate dual lipid modification, i.e., myristoylation and palmitoylation, a modification that is widely conserved from yeast to higher eukaryotes. Our results suggest that both lipid modifications are required for restoration of G-protein signaling. Although we could not differentiate between myristoylation and palmitoylation, N-terminal position 7 and 8 play some critical role. Moreover, we tested the preference for specific amino-acid residues at position 7 and 8 using library-based screening. This new approach will be useful to explore protein-lipid associations and to determine the corresponding sequence motifs. PMID:23922919

Common fold in helix–hairpin–helix proteins

PubMed Central

Shao, Xuguang; Grishin, Nick V.

2000-01-01

Helix–hairpin–helix (HhH) is a widespread motif involved in non-sequence-specific DNA binding. The majority of HhH motifs function as DNA-binding modules, however, some of them are used to mediate protein–protein interactions or have acquired enzymatic activity by incorporating catalytic residues (DNA glycosylases). From sequence and structural analysis of HhH-containing proteins we conclude that most HhH motifs are integrated as a part of a five-helical domain, termed (HhH)2 domain here. It typically consists of two consecutive HhH motifs that are linked by a connector helix and displays pseudo-2-fold symmetry. (HhH)2 domains show clear structural integrity and a conserved hydrophobic core composed of seven residues, one residue from each α-helix and each hairpin, and deserves recognition as a distinct protein fold. In addition to known HhH in the structures of RuvA, RadA, MutY and DNA-polymerases, we have detected new HhH motifs in sterile alpha motif and barrier-to-autointegration factor domains, the α-subunit of Escherichia coli RNA-polymerase, DNA-helicase PcrA and DNA glyco­s­y­lases. Statistically significant sequence similarity of HhH motifs and pronounced structural conservation argue for homology between (HhH)2 domains in different protein families. Our analysis helps to clarify how non-symmetric protein motifs bind to the double helix of DNA through the formation of a pseudo-2-fold symmetric (HhH)2 functional unit. PMID:10908318

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

PubMed Central

Lin, Hao; Deng, En-Ze; Ding, Hui; Chen, Wei; Chou, Kuo-Chen

2014-01-01

The σ54 promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the σ54 promoters. Here, a predictor called ‘iPro54-PseKNC’ was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called ‘pseudo k-tuple nucleotide composition’, which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the σ54 promoters. PMID:25361964

A protocol of histone modification-based mechanistic study of acupuncture in patients with stable angina pectoris.

PubMed

Wang, Ning; Lu, Sheng-Feng; Chen, Hui; Wang, Jian-Fei; Fu, Shu-Ping; Hu, Chen-Jun; Yang, Yi; Liang, Fan-Rong; Zhu, Bing-Mei

2015-04-30

Angina pectoris (Angina) is a medical condition related to myocardial ischemia. Although acupuncture has been widely accepted as a clinical approach for angina, there is no sufficient evidence of its effectiveness against this syndrome, and its mechanisms have not yet been well elucidated. We develop this protocol to confirm the clinical efficacy of electro-acupuncture on stable angina pectoris by needling on acupoint Neiguan (PC6). Furthermore, we employ high-throughput sequencing technology to investigate the gene expression profiling and determine involvement of histone modifications in the regulation of genes after electro-acupuncture treatment. A randomized, controlled, double-blinded (assessor and patients) trial will be carried out. Sixty participants will be randomly assigned to two acupuncture treatment groups and one control group in a 1:1:1 ratio. Participants in acupuncture groups will receive 12 sessions of electro-acupuncture treatment across 4 weeks, followed by a 12-week randomization period. The acupuncture groups are divided into Neiguan (PC6) on Pericardium Meridian of Hand-jueyin or a non-acupoint. The primary clinical measure of effect is the frequency of angina attacks between these groups for four weeks after randomization. RNAs are extracted from peripheral neutrophils collected from all participants on day 0, day 30, and week 16, and are processed to RNA-Seq. We then investigate profiles of histone modifications by ChIP-Seq, for H3 Lysine 4 (H3K4me) and acetylation of H3 Lysine 27 (H3K27ac), in the presence or absence of acupuncture treatment. This study determines the efficacy and mechanisms of electro-acupuncture on stable angina pectoris. We focus on effectiveness of acupuncture on alleviating symptoms of myocardial ischemia and the gene regulation and the chromatin remodeling marks, including H3K4me1, H3K4me2, and H3K27ac, which could be key factors for regulating gene expressions caused by electro-acupuncture treatment at Neiguan. This is the first genome-wide study of electro-acupuncture treatment in angina patients, and will provide valuable information for future studies in the fields of acupuncture and its underlying mechanisms. Fourteen patients have been recruited since recruitment opened in November of 2012. This study is scheduled to end in November of 2014. ChiCTR-TRC-12002668.

Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition.

PubMed

Shen, Hong-Bin; Chou, Kuo-Chen

2005-11-25

The nucleus is the brain of eukaryotic cells that guides the life processes of the cell by issuing key instructions. For in-depth understanding of the biochemical process of the nucleus, the knowledge of localization of nuclear proteins is very important. With the avalanche of protein sequences generated in the post-genomic era, it is highly desired to develop an automated method for fast annotating the subnuclear locations for numerous newly found nuclear protein sequences so as to be able to timely utilize them for basic research and drug discovery. In view of this, a novel approach is developed for predicting the protein subnuclear location. It is featured by introducing a powerful classifier, the optimized evidence-theoretic K-nearest classifier, and using the pseudo amino acid composition [K.C. Chou, PROTEINS: Structure, Function, and Genetics, 43 (2001) 246], which can incorporate a considerable amount of sequence-order effects, to represent protein samples. As a demonstration, identifications were performed for 370 nuclear proteins among the following 9 subnuclear locations: (1) Cajal body, (2) chromatin, (3) heterochromatin, (4) nuclear diffuse, (5) nuclear pore, (6) nuclear speckle, (7) nucleolus, (8) PcG body, and (9) PML body. The overall success rates thus obtained by both the re-substitution test and jackknife cross-validation test are significantly higher than those by existing classifiers on the same working dataset. It is anticipated that the powerful approach may also become a useful high throughput vehicle to bridge the huge gap occurring in the post-genomic era between the number of gene sequences in databases and the number of gene products that have been functionally characterized. The OET-KNN classifier will be available at www.pami.sjtu.edu.cn/people/hbshen.

Improved pan-specific MHC class I peptide-binding predictions using a novel representation of the MHC-binding cleft environment.

PubMed

Carrasco Pro, S; Zimic, M; Nielsen, M

2014-02-01

Major histocompatibility complex (MHC) molecules play a key role in cell-mediated immune responses presenting bounded peptides for recognition by the immune system cells. Several in silico methods have been developed to predict the binding affinity of a given peptide to a specific MHC molecule. One of the current state-of-the-art methods for MHC class I is NetMHCpan, which has a core ingredient for the representation of the MHC class I molecule using a pseudo-sequence representation of the binding cleft amino acid environment. New and large MHC-peptide-binding data sets are constantly being made available, and also new structures of MHC class I molecules with a bound peptide have been published. In order to test if the NetMHCpan method can be improved by integrating this novel information, we created new pseudo-sequence definitions for the MHC-binding cleft environment from sequence and structural analyses of different MHC data sets including human leukocyte antigen (HLA), non-human primates (chimpanzee, macaque and gorilla) and other animal alleles (cattle, mouse and swine). From these constructs, we showed that by focusing on MHC sequence positions found to be polymorphic across the MHC molecules used to train the method, the NetMHCpan method achieved a significant increase in the predictive performance, in particular, of non-human MHCs. This study hence showed that an improved performance of MHC-binding methods can be achieved not only by the accumulation of more MHC-peptide-binding data but also by a refined definition of the MHC-binding environment including information from non-human species. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Q-learning residual analysis: application to the effectiveness of sequences of antipsychotic medications for patients with schizophrenia.

PubMed

Ertefaie, Ashkan; Shortreed, Susan; Chakraborty, Bibhas

2016-06-15

Q-learning is a regression-based approach that uses longitudinal data to construct dynamic treatment regimes, which are sequences of decision rules that use patient information to inform future treatment decisions. An optimal dynamic treatment regime is composed of a sequence of decision rules that indicate how to optimally individualize treatment using the patients' baseline and time-varying characteristics to optimize the final outcome. Constructing optimal dynamic regimes using Q-learning depends heavily on the assumption that regression models at each decision point are correctly specified; yet model checking in the context of Q-learning has been largely overlooked in the current literature. In this article, we show that residual plots obtained from standard Q-learning models may fail to adequately check the quality of the model fit. We present a modified Q-learning procedure that accommodates residual analyses using standard tools. We present simulation studies showing the advantage of the proposed modification over standard Q-learning. We illustrate this new Q-learning approach using data collected from a sequential multiple assignment randomized trial of patients with schizophrenia. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Fusion of GFP to the M.EcoKI DNA methyltransferase produces a new probe of Type I DNA restriction and modification enzymes

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

Chen, Kai; Roberts, Gareth A.; Stephanou, Augoustinos S.

2010-07-23

Research highlights: {yields} Successful fusion of GFP to M.EcoKI DNA methyltransferase. {yields} GFP located at C-terminal of sequence specificity subunit does not later enzyme activity. {yields} FRET confirms structural model of M.EcoKI bound to DNA. -- Abstract: We describe the fusion of enhanced green fluorescent protein to the C-terminus of the HsdS DNA sequence-specificity subunit of the Type I DNA modification methyltransferase M.EcoKI. The fusion expresses well in vivo and assembles with the two HsdM modification subunits. The fusion protein functions as a sequence-specific DNA methyltransferase protecting DNA against digestion by the EcoKI restriction endonuclease. The purified enzyme shows Foerstermore » resonance energy transfer to fluorescently-labelled DNA duplexes containing the target sequence and to fluorescently-labelled ocr protein, a DNA mimic that binds to the M.EcoKI enzyme. Distances determined from the energy transfer experiments corroborate the structural model of M.EcoKI.« less

77 FR 74631 - General Services Administration Acquisition Regulation: Modifications (Multiple Award Schedules...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-17

...-0001; Sequence 21] General Services Administration Acquisition Regulation: Modifications (Multiple... Modifications (Multiple Award Schedule). DATES: Submit comments on or before: February 15, 2013. FOR FURTHER INFORMATION CONTACT: Ms. Dana Munson, General Services Acquisition Policy Division, GSA, (202) 357-9652 or...

Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

PubMed Central

2011-01-01

Background Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Results Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. In addition, 341,984 ESTs were generated from ES and PES internodes of genotype 773 using the GS FLX Titanium platform. The first alfalfa (Medicago sativa) gene index (MSGI 1.0) was assembled using the Sanger ESTs available from GenBank, the GS FLX Titanium EST sequences, and the de novo assembled Illumina sequences. MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1,294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Out of 55 SNPs randomly selected for experimental validation, 47 (85%) were polymorphic between the two genotypes. We also identified numerous allelic variations within each genotype. Digital gene expression analysis identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Conclusions Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a forage crop and cellulosic feedstock. PMID:21504589

Error reduction study employing a pseudo-random binary sequence for use in acoustic pyrometry of gases

NASA Astrophysics Data System (ADS)

Ewan, B. C. R.; Ireland, S. N.

2000-12-01

Acoustic pyrometry uses the temperature dependence of sound speed in materials to measure temperature. This is normally achieved by measuring the transit time for a sound signal over a known path length and applying the material relation between temperature and velocity to extract an "average" temperature. Sources of error associated with the measurement of mean transit time are discussed in implementing the technique in gases, one of the principal causes being background noise in typical industrial environments. A number of transmitted signal and processing strategies which can be used in the area are examined and the expected error in mean transit time associated with each technique is quantified. Transmitted signals included pulses, pure frequencies, chirps, and pseudorandom binary sequences (prbs), while processing involves edge detection and correlation. Errors arise through the misinterpretation of the positions of edge arrival or correlation peaks due to instantaneous deviations associated with background noise and these become more severe as signal to noise amplitude ratios decrease. Population errors in the mean transit time are estimated for the different measurement strategies and it is concluded that PRBS combined with correlation can provide the lowest errors when operating in high noise environments. The operation of an instrument based on PRBS transmitted signals is described and test results under controlled noise conditions are presented. These confirm the value of the strategy and demonstrate that measurements can be made with signal to noise amplitude ratios down to 0.5.

A sensitive mass spectrometric method for hypothesis-driven detection of peptide post-translational modifications: multiple reaction monitoring-initiated detection and sequencing (MIDAS).

PubMed

Unwin, Richard D; Griffiths, John R; Whetton, Anthony D

2009-01-01

The application of a targeted mass spectrometric workflow to the sensitive identification of post-translational modifications is described. This protocol employs multiple reaction monitoring (MRM) to search for all putative peptides specifically modified in a target protein. Positive MRMs trigger an MS/MS experiment to confirm the nature and site of the modification. This approach, termed MIDAS (MRM-initiated detection and sequencing), is more sensitive than approaches using neutral loss scanning or precursor ion scanning methodologies, due to a more efficient use of duty cycle along with a decreased background signal associated with MRM. We describe the use of MIDAS for the identification of phosphorylation, with a typical experiment taking just a couple of hours from obtaining a peptide sample. With minor modifications, the MIDAS method can be applied to other protein modifications or unmodified peptides can be used as a MIDAS target.

A Simple Method for Visualization of Locus-Specific H4K20me1 Modifications in Living Caenorhabditis elegans Single Cells.

PubMed

Shinkai, Yoichi; Kuramochi, Masahiro; Doi, Motomichi

2018-05-03

Recently, advances in next-generation sequencing technologies have enabled genome-wide analyses of epigenetic modifications; however, it remains difficult to analyze the states of histone modifications at a single-cell resolution in living multicellular organisms because of the heterogeneity within cellular populations. Here we describe a simple method to visualize histone modifications on the specific sequence of target locus at a single-cell resolution in living Caenorhabditis elegans , by combining the LacO/LacI system and a genetically-encoded H4K20me1-specific probe, "mintbody". We demonstrate that Venus-labeled mintbody and mTurquoise2-labeled LacI can co-localize on an artificial chromosome carrying both the target locus and LacO sequences, where H4K20me1 marks the target locus. We demonstrate that our visualization method can precisely detect H4K20me1 depositions on the her-1 gene sequences on the artificial chromosome, to which the dosage compensation complex binds to regulate sex determination. The degree of H4K20me1 deposition on the her-1 sequences on the artificial chromosome correlated strongly with sex, suggesting that, using the artificial chromosome, this method can reflect context-dependent changes of H4K20me1 on endogenous genomes. Furthermore, we demonstrate live imaging of H4K20me1 depositions on the artificial chromosome. Combined with ChIP assays, this mintbody-LacO/LacI visualization method will enable analysis of developmental and context-dependent alterations of locus-specific histone modifications in specific cells and elucidation of the underlying molecular mechanisms. Copyright © 2018, G3: Genes, Genomes, Genetics.

IT-26IDENTIFICATION OF PSEUDO-PROGRESSION IN NEW DIAGNOSED GLIOBLASTOMA (GBM) IN A RANDOMIZED PHASE 2 OF ICT-107: MRI AND PATHOLOGY CORRELATION

PubMed Central

Phuphanich, Surasak; Yu, John; Bannykh, Serguei; Zhu, Jay-Jiguang

2014-01-01

BACKGROUND: Previously reports of pseudo-progression in patients with brain tumor after therapeutic vaccines in pediatric and adult glioma (Pollack, JCO online on June 2, 2014 and Okada, JCO Jan 20, 2011; 29: 330-336) demonstrated that RANO criteria for tumor progression may not be adequate for immunotherapy trials. Similar observations were also seen in other checkpoint inhibitor in melanoma and NSLSC. METHODS: We identified 2 patients, who developed tumor progression by RANO criteria, underwent surgery following enrollment in a phase 2 randomized ICT-107 (an autologous vaccine consisting of patient dendritic cells pulsed with peptides from AIM-2, TRP-2, HER2/neu, IL-13Ra2, gp100, MAGE1) after radiation and Temozolomide (TMZ). RESULTS: The first case is a 69 years old Chinese male, who underwent 1st surgery of gross total resection right occipital GBM on 10/26/2011. Subsequently he received 19 cycles of TMZ and 9 vaccines/placebo. MRI from 7/2/2013 showed enhancement surrounding surgical cavity. After 2nd surgery, pathology showed only rare residual tumor cells with macrophages and positive CD 8 cells. He continued on this vaccine program and MRI showed more progression with finger-like extension into parietal lobe 4 months later. The 3rd surgery also showed extensive reactive changes with no active tumor cells. For 2nd case, a 62 years old male, who underwent first surgery on 7/11/2011 of right temporal lobe, developed 2 areas of enhancement after 6 cycles of TMZ and 7 vaccines/placebo on 4/18/2012. With 2nd surgery, pathology showed reactive gliosis without active tumor. The subject continued in this trial. CONCLUSION: Pseudo-progression was confirmed by pathology in these 2 patients at 20 and 9 months which were delayed comparing to pseudo-progression observed in patients treated with concurrent XRT/TMZ (3-6 months). Future iRANO criteria development is essential for immunotherapy trials. Accurately identifying and managing such patients is necessary to avoid premature termination of therapy.

Test surfaces useful for calibration of surface profilometers

DOEpatents

Yashchuk, Valeriy V; McKinney, Wayne R; Takacs, Peter Z

2013-12-31

The present invention provides for test surfaces and methods for calibration of surface profilometers, including interferometric and atomic force microscopes. Calibration is performed using a specially designed test surface, or the Binary Pseudo-random (BPR) grating (array). Utilizing the BPR grating (array) to measure the power spectral density (PSD) spectrum, the profilometer is calibrated by determining the instrumental modulation transfer.

PSO algorithm enhanced with Lozi Chaotic Map - Tuning experiment

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

Pluhacek, Michal; Senkerik, Roman; Zelinka, Ivan

2015-03-10

In this paper it is investigated the effect of tuning of control parameters of the Lozi Chaotic Map employed as a chaotic pseudo-random number generator for the particle swarm optimization algorithm. Three different benchmark functions are selected from the IEEE CEC 2013 competition benchmark set. The Lozi map is extensively tuned and the performance of PSO is evaluated.

A cryptographic hash function based on chaotic network automata

NASA Astrophysics Data System (ADS)

Machicao, Jeaneth; Bruno, Odemir M.

2017-12-01

Chaos theory has been used to develop several cryptographic methods relying on the pseudo-random properties extracted from simple nonlinear systems such as cellular automata (CA). Cryptographic hash functions (CHF) are commonly used to check data integrity. CHF “compress” arbitrary long messages (input) into much smaller representations called hash values or message digest (output), designed to prevent the ability to reverse the hash values into the original message. This paper proposes a chaos-based CHF inspired on an encryption method based on chaotic CA rule B1357-S2468. Here, we propose an hybrid model that combines CA and networks, called network automata (CNA), whose chaotic spatio-temporal outputs are used to compute a hash value. Following the Merkle and Damgård model of construction, a portion of the message is entered as the initial condition of the network automata, so that the rest parts of messages are iteratively entered to perturb the system. The chaotic network automata shuffles the message using flexible control parameters, so that the generated hash value is highly sensitive to the message. As demonstrated in our experiments, the proposed model has excellent pseudo-randomness and sensitivity properties with acceptable performance when compared to conventional hash functions.

Cooperation of Deterministic Dynamics and Random Noise in Production of Complex Syntactical Avian Song Sequences: A Neural Network Model

PubMed Central

Yamashita, Yuichi; Okumura, Tetsu; Okanoya, Kazuo; Tani, Jun

2011-01-01

How the brain learns and generates temporal sequences is a fundamental issue in neuroscience. The production of birdsongs, a process which involves complex learned sequences, provides researchers with an excellent biological model for this topic. The Bengalese finch in particular learns a highly complex song with syntactical structure. The nucleus HVC (HVC), a premotor nucleus within the avian song system, plays a key role in generating the temporal structures of their songs. From lesion studies, the nucleus interfacialis (NIf) projecting to the HVC is considered one of the essential regions that contribute to the complexity of their songs. However, the types of interaction between the HVC and the NIf that can produce complex syntactical songs remain unclear. In order to investigate the function of interactions between the HVC and NIf, we have proposed a neural network model based on previous biological evidence. The HVC is modeled by a recurrent neural network (RNN) that learns to generate temporal patterns of songs. The NIf is modeled as a mechanism that provides auditory feedback to the HVC and generates random noise that feeds into the HVC. The model showed that complex syntactical songs can be replicated by simple interactions between deterministic dynamics of the RNN and random noise. In the current study, the plausibility of the model is tested by the comparison between the changes in the songs of actual birds induced by pharmacological inhibition of the NIf and the changes in the songs produced by the model resulting from modification of parameters representing NIf functions. The efficacy of the model demonstrates that the changes of songs induced by pharmacological inhibition of the NIf can be interpreted as a trade-off between the effects of noise and the effects of feedback on the dynamics of the RNN of the HVC. These facts suggest that the current model provides a convincing hypothesis for the functional role of NIf–HVC interaction. PMID:21559065

A multi-model approach to nucleic acid-based drug development.

PubMed

Gautherot, Isabelle; Sodoyer, Regís

2004-01-01

With the advent of functional genomics and the shift of interest towards sequence-based therapeutics, the past decades have witnessed intense research efforts on nucleic acid-mediated gene regulation technologies. Today, RNA interference is emerging as a groundbreaking discovery, holding promise for development of genetic modulators of unprecedented potency. Twenty-five years after the discovery of antisense RNA and ribozymes, gene control therapeutics are still facing developmental difficulties, with only one US FDA-approved antisense drug currently available in the clinic. Limited predictability of target site selection models is recognized as one major stumbling block that is shared by all of the so-called complementary technologies, slowing the progress towards a commercial product. Currently employed in vitro systems for target site selection include RNAse H-based mapping, antisense oligonucleotide microarrays, and functional screening approaches using libraries of catalysts with randomized target-binding arms to identify optimal ribozyme/DNAzyme cleavage sites. Individually, each strategy has its drawbacks from a drug development perspective. Utilization of message-modulating sequences as therapeutic agents requires that their action on a given target transcript meets criteria of potency and selectivity in the natural physiological environment. In addition to sequence-dependent characteristics, other factors will influence annealing reactions and duplex stability, as well as nucleic acid-mediated catalysis. Parallel consideration of physiological selection systems thus appears essential for screening for nucleic acid compounds proposed for therapeutic applications. Cellular message-targeting studies face issues relating to efficient nucleic acid delivery and appropriate analysis of response. For reliability and simplicity, prokaryotic systems can provide a rapid and cost-effective means of studying message targeting under pseudo-cellular conditions, but such approaches also have limitations. To streamline nucleic acid drug discovery, we propose a multi-model strategy integrating high-throughput-adapted bacterial screening, followed by reporter-based and/or natural cellular models and potentially also in vitro assays for characterization of the most promising candidate sequences, before final in vivo testing.

IDM-PhyChm-Ens: intelligent decision-making ensemble methodology for classification of human breast cancer using physicochemical properties of amino acids.

PubMed

Ali, Safdar; Majid, Abdul; Khan, Asifullah

2014-04-01

Development of an accurate and reliable intelligent decision-making method for the construction of cancer diagnosis system is one of the fast growing research areas of health sciences. Such decision-making system can provide adequate information for cancer diagnosis and drug discovery. Descriptors derived from physicochemical properties of protein sequences are very useful for classifying cancerous proteins. Recently, several interesting research studies have been reported on breast cancer classification. To this end, we propose the exploitation of the physicochemical properties of amino acids in protein primary sequences such as hydrophobicity (Hd) and hydrophilicity (Hb) for breast cancer classification. Hd and Hb properties of amino acids, in recent literature, are reported to be quite effective in characterizing the constituent amino acids and are used to study protein foldings, interactions, structures, and sequence-order effects. Especially, using these physicochemical properties, we observed that proline, serine, tyrosine, cysteine, arginine, and asparagine amino acids offer high discrimination between cancerous and healthy proteins. In addition, unlike traditional ensemble classification approaches, the proposed 'IDM-PhyChm-Ens' method was developed by combining the decision spaces of a specific classifier trained on different feature spaces. The different feature spaces used were amino acid composition, split amino acid composition, and pseudo amino acid composition. Consequently, we have exploited different feature spaces using Hd and Hb properties of amino acids to develop an accurate method for classification of cancerous protein sequences. We developed ensemble classifiers using diverse learning algorithms such as random forest (RF), support vector machines (SVM), and K-nearest neighbor (KNN) trained on different feature spaces. We observed that ensemble-RF, in case of cancer classification, performed better than ensemble-SVM and ensemble-KNN. Our analysis demonstrates that ensemble-RF, ensemble-SVM and ensemble-KNN are more effective than their individual counterparts. The proposed 'IDM-PhyChm-Ens' method has shown improved performance compared to existing techniques.

Background sampling and transferability of species distribution model ensembles under climate change

NASA Astrophysics Data System (ADS)

Iturbide, Maialen; Bedia, Joaquín; Gutiérrez, José Manuel

2018-07-01

Species Distribution Models (SDMs) constitute an important tool to assist decision-making in environmental conservation and planning. A popular application of these models is the projection of species distributions under climate change conditions. Yet there are still a range of methodological SDM factors which limit the transferability of these models, contributing significantly to the overall uncertainty of the resulting projections. An important source of uncertainty often neglected in climate change studies comes from the use of background data (a.k.a. pseudo-absences) for model calibration. Here, we study the sensitivity to pseudo-absence sampling as a determinant factor for SDM stability and transferability under climate change conditions, focusing on European wide projections of Quercus robur as an illustrative case study. We explore the uncertainty in future projections derived from ten pseudo-absence realizations and three popular SDMs (GLM, Random Forest and MARS). The contribution of the pseudo-absence realization to the uncertainty was higher in peripheral regions and clearly differed among the tested SDMs in the whole study domain, being MARS the most sensitive - with projections differing up to a 40% for different realizations - and GLM the most stable. As a result we conclude that parsimonious SDMs are preferable in this context, avoiding complex methods (such as MARS) which may exhibit poor model transferability. Accounting for this new source of SDM-dependent uncertainty is crucial when forming multi-model ensembles to undertake climate change projections.

A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms.

PubMed

Leakey, Tatiana I; Zielinski, Jerzy; Siegfried, Rachel N; Siegel, Eric R; Fan, Chun-Yang; Cooney, Craig A

2008-06-01

DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites.

Environmental change makes robust ecological networks fragile

USGS Publications Warehouse

Strona, Giovanni; Lafferty, Kevin D.

2016-01-01

Complex ecological networks appear robust to primary extinctions, possibly due to consumers’ tendency to specialize on dependable (available and persistent) resources. However, modifications to the conditions under which the network has evolved might alter resource dependability. Here, we ask whether adaptation to historical conditions can increase community robustness, and whether such robustness can protect communities from collapse when conditions change. Using artificial life simulations, we first evolved digital consumer-resource networks that we subsequently subjected to rapid environmental change. We then investigated how empirical host–parasite networks would respond to historical, random and expected extinction sequences. In both the cases, networks were far more robust to historical conditions than new ones, suggesting that new environmental challenges, as expected under global change, might collapse otherwise robust natural ecosystems.

State estimator for multisensor systems with irregular sampling and time-varying delays

NASA Astrophysics Data System (ADS)

Peñarrocha, I.; Sanchis, R.; Romero, J. A.

2012-08-01

This article addresses the state estimation in linear time-varying systems with several sensors with different availability, randomly sampled in time and whose measurements have a time-varying delay. The approach is based on a modification of the Kalman filter with the negative-time measurement update strategy, avoiding running back the full standard Kalman filter, the use of full augmented order models or the use of reorganisation techniques, leading to a lower implementation cost algorithm. The update equations are run every time a new measurement is available, independently of the time when it was taken. The approach is useful for networked control systems, systems with long delays and scarce measurements and for out-of-sequence measurements.

MitoQ regulates autophagy by inducing a pseudo-mitochondrial membrane potential

PubMed Central

Sun, Chao; Liu, Xiongxiong; Di, Cuixia; Wang, Zhenhua; Mi, Xiangquan; Liu, Yang; Zhao, Qiuyue; Mao, Aihong; Chen, Weiqiang; Gan, Lu; Zhang, Hong

2017-01-01

ABSTRACT During the process of oxidative phosphorylation, protons are pumped into the mitochondrial intermembrane space to establish a mitochondrial membrane potential (MMP). The electrochemical gradient generated allows protons to return to the matrix through the ATP synthase complex and generates ATP in the process. MitoQ is a lipophilic cationic drug that is adsorbed to the inner mitochondrial membrane; however, the cationic moiety of MitoQ remains in the intermembrane space. We found that the positive charges in MitoQ inhibited the activity of respiratory chain complexes I, III, and IV, reduced proton production, and decreased oxygen consumption. Therefore, a pseudo-MMP (PMMP) was formed via maintenance of exogenous positive charges. Proton backflow was severely impaired, leading to a decrease in ATP production and an increase in AMP production. Excess AMP activates AMP kinase, which inhibits the MTOR (mechanistic target of rapamycin) pathway and induces macroautophagy/autophagy. Therefore, we conclude that MitoQ increases PMMP via proton displacement with exogenous positive charges. In addition, PMMP triggered autophagy in hepatocellular carcinoma HepG2 cells via modification of mitochondrial bioenergetics pathways. PMID:28121478

MitoQ regulates autophagy by inducing a pseudo-mitochondrial membrane potential.

PubMed

Sun, Chao; Liu, Xiongxiong; Di, Cuixia; Wang, Zhenhua; Mi, Xiangquan; Liu, Yang; Zhao, Qiuyue; Mao, Aihong; Chen, Weiqiang; Gan, Lu; Zhang, Hong

2017-04-03

During the process of oxidative phosphorylation, protons are pumped into the mitochondrial intermembrane space to establish a mitochondrial membrane potential (MMP). The electrochemical gradient generated allows protons to return to the matrix through the ATP synthase complex and generates ATP in the process. MitoQ is a lipophilic cationic drug that is adsorbed to the inner mitochondrial membrane; however, the cationic moiety of MitoQ remains in the intermembrane space. We found that the positive charges in MitoQ inhibited the activity of respiratory chain complexes I, III, and IV, reduced proton production, and decreased oxygen consumption. Therefore, a pseudo-MMP (PMMP) was formed via maintenance of exogenous positive charges. Proton backflow was severely impaired, leading to a decrease in ATP production and an increase in AMP production. Excess AMP activates AMP kinase, which inhibits the MTOR (mechanistic target of rapamycin) pathway and induces macroautophagy/autophagy. Therefore, we conclude that MitoQ increases PMMP via proton displacement with exogenous positive charges. In addition, PMMP triggered autophagy in hepatocellular carcinoma HepG2 cells via modification of mitochondrial bioenergetics pathways.

Effects of momentary self-monitoring on empowerment in a randomized controlled trial in patients with depression.

PubMed

Simons, C J P; Hartmann, J A; Kramer, I; Menne-Lothmann, C; Höhn, P; van Bemmel, A L; Myin-Germeys, I; Delespaul, P; van Os, J; Wichers, M

2015-11-01

Interventions based on the experience sampling method (ESM) are ideally suited to provide insight into personal, contextualized affective patterns in the flow of daily life. Recently, we showed that an ESM-intervention focusing on positive affect was associated with a decrease in symptoms in patients with depression. The aim of the present study was to examine whether ESM-intervention increased patient empowerment. Depressed out-patients (n=102) receiving psychopharmacological treatment who had participated in a randomized controlled trial with three arms: (i) an experimental group receiving six weeks of ESM self-monitoring combined with weekly feedback sessions, (ii) a pseudo-experimental group participating in six weeks of ESM self-monitoring without feedback, and (iii) a control group (treatment as usual only). Patients were recruited in the Netherlands between January 2010 and February 2012. Self-report empowerment scores were obtained pre- and post-intervention. There was an effect of group×assessment period, indicating that the experimental (B=7.26, P=0.061, d=0.44, statistically imprecise) and pseudo-experimental group (B=11.19, P=0.003, d=0.76) increased more in reported empowerment compared to the control group. In the pseudo-experimental group, 29% of the participants showed a statistically reliable increase in empowerment score and 0% reliable decrease compared to 17% reliable increase and 21% reliable decrease in the control group. The experimental group showed 19% reliable increase and 4% reliable decrease. These findings tentatively suggest that self-monitoring to complement standard antidepressant treatment may increase patients' feelings of empowerment. Further research is necessary to investigate long-term empowering effects of self-monitoring in combination with person-tailored feedback. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Random-walk enzymes.

PubMed

Mak, Chi H; Pham, Phuong; Afif, Samir A; Goodman, Myron F

2015-09-01

Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C→U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics.

Random-walk enzymes

PubMed Central

Mak, Chi H.; Pham, Phuong; Afif, Samir A.; Goodman, Myron F.

2015-01-01

Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C → U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics. PMID:26465508

Random-walk enzymes

NASA Astrophysics Data System (ADS)

Mak, Chi H.; Pham, Phuong; Afif, Samir A.; Goodman, Myron F.

2015-09-01

Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the conversion profiles produced by these enzymes, comparing an intrusive model, in which scanning and catalysis are tightly coupled, against a loosely coupled passive model. Diagrammatic theory and path-integral solutions of these models revealed clearly distinct predictions. Comparison to experimental data from catalyzed deaminations deposited on single-stranded DNA by the enzyme activation-induced deoxycytidine deaminase (AID) demonstrates that catalysis and diffusion are strongly intertwined, where the chemical conversions give rise to new stochastic trajectories that were absent if the substrate DNA was homogeneous. The C →U deamination profiles in both analytical predictions and experiments exhibit a strong contextual dependence, where the conversion rate of each target site is strongly contingent on the identities of other surrounding targets, with the intrusive model showing an excellent fit to the data. These methods can be applied to deduce sequence-dependent catalytic signatures of other DNA modification enzymes, with potential applications to cancer, gene regulation, and epigenetics.

Implementation of a quantum random number generator based on the optimal clustering of photocounts

NASA Astrophysics Data System (ADS)

Balygin, K. A.; Zaitsev, V. I.; Klimov, A. N.; Kulik, S. P.; Molotkov, S. N.

2017-10-01

To implement quantum random number generators, it is fundamentally important to have a mathematically provable and experimentally testable process of measurements of a system from which an initial random sequence is generated. This makes sure that randomness indeed has a quantum nature. A quantum random number generator has been implemented with the use of the detection of quasi-single-photon radiation by a silicon photomultiplier (SiPM) matrix, which makes it possible to reliably reach the Poisson statistics of photocounts. The choice and use of the optimal clustering of photocounts for the initial sequence of photodetection events and a method of extraction of a random sequence of 0's and 1's, which is polynomial in the length of the sequence, have made it possible to reach a yield rate of 64 Mbit/s of the output certainly random sequence.

Low rank approach to computing first and higher order derivatives using automatic differentiation

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

Reed, J. A.; Abdel-Khalik, H. S.; Utke, J.

2012-07-01

This manuscript outlines a new approach for increasing the efficiency of applying automatic differentiation (AD) to large scale computational models. By using the principles of the Efficient Subspace Method (ESM), low rank approximations of the derivatives for first and higher orders can be calculated using minimized computational resources. The output obtained from nuclear reactor calculations typically has a much smaller numerical rank compared to the number of inputs and outputs. This rank deficiency can be exploited to reduce the number of derivatives that need to be calculated using AD. The effective rank can be determined according to ESM by computingmore » derivatives with AD at random inputs. Reduced or pseudo variables are then defined and new derivatives are calculated with respect to the pseudo variables. Two different AD packages are used: OpenAD and Rapsodia. OpenAD is used to determine the effective rank and the subspace that contains the derivatives. Rapsodia is then used to calculate derivatives with respect to the pseudo variables for the desired order. The overall approach is applied to two simple problems and to MATWS, a safety code for sodium cooled reactors. (authors)« less

Scope of Various Random Number Generators in ant System Approach for TSP

NASA Technical Reports Server (NTRS)

Sen, S. K.; Shaykhian, Gholam Ali

2007-01-01

Experimented on heuristic, based on an ant system approach for traveling salesman problem, are several quasi- and pseudo-random number generators. This experiment is to explore if any particular generator is most desirable. Such an experiment on large samples has the potential to rank the performance of the generators for the foregoing heuristic. This is mainly to seek an answer to the controversial issue "which generator is the best in terms of quality of the result (accuracy) as well as cost of producing the result (time/computational complexity) in a probabilistic/statistical sense."

Real-time fast physical random number generator with a photonic integrated circuit.

PubMed

Ugajin, Kazusa; Terashima, Yuta; Iwakawa, Kento; Uchida, Atsushi; Harayama, Takahisa; Yoshimura, Kazuyuki; Inubushi, Masanobu

2017-03-20

Random number generators are essential for applications in information security and numerical simulations. Most optical-chaos-based random number generators produce random bit sequences by offline post-processing with large optical components. We demonstrate a real-time hardware implementation of a fast physical random number generator with a photonic integrated circuit and a field programmable gate array (FPGA) electronic board. We generate 1-Tbit random bit sequences and evaluate their statistical randomness using NIST Special Publication 800-22 and TestU01. All of the BigCrush tests in TestU01 are passed using 410-Gbit random bit sequences. A maximum real-time generation rate of 21.1 Gb/s is achieved for random bit sequences in binary format stored in a computer, which can be directly used for applications involving secret keys in cryptography and random seeds in large-scale numerical simulations.

Genetic Variation and Its Reflection on Posttranslational Modifications in Frequency Clock and Mating Type a-1 Proteins in Sordaria fimicola

PubMed Central

Arif, Rabia; Akram, Faiza; Jamil, Tazeen; Lee, Siu Fai

2017-01-01

Posttranslational modifications (PTMs) occur in all essential proteins taking command of their functions. There are many domains inside proteins where modifications take place on side-chains of amino acids through various enzymes to generate different species of proteins. In this manuscript we have, for the first time, predicted posttranslational modifications of frequency clock and mating type a-1 proteins in Sordaria fimicola collected from different sites to see the effect of environment on proteins or various amino acids pickings and their ultimate impact on consensus sequences present in mating type proteins using bioinformatics tools. Furthermore, we have also measured and walked through genomic DNA of various Sordaria strains to determine genetic diversity by genotyping the short sequence repeats (SSRs) of wild strains of S. fimicola collected from contrasting environments of two opposing slopes (harsh and xeric south facing slope and mild north facing slope) of Evolution Canyon (EC), Israel. Based on the whole genome sequence of S. macrospora, we targeted 20 genomic regions in S. fimicola which contain short sequence repeats (SSRs). Our data revealed genetic variations in strains from south facing slope and these findings assist in the hypothesis that genetic variations caused by stressful environments lead to evolution. PMID:28717646

Genetic Variation and Its Reflection on Posttranslational Modifications in Frequency Clock and Mating Type a-1 Proteins in Sordaria fimicola.

PubMed

Arif, Rabia; Akram, Faiza; Jamil, Tazeen; Mukhtar, Hamid; Lee, Siu Fai; Saleem, Muhammad

2017-01-01

Posttranslational modifications (PTMs) occur in all essential proteins taking command of their functions. There are many domains inside proteins where modifications take place on side-chains of amino acids through various enzymes to generate different species of proteins. In this manuscript we have, for the first time, predicted posttranslational modifications of frequency clock and mating type a-1 proteins in Sordaria fimicola collected from different sites to see the effect of environment on proteins or various amino acids pickings and their ultimate impact on consensus sequences present in mating type proteins using bioinformatics tools. Furthermore, we have also measured and walked through genomic DNA of various Sordaria strains to determine genetic diversity by genotyping the short sequence repeats (SSRs) of wild strains of S. fimicola collected from contrasting environments of two opposing slopes (harsh and xeric south facing slope and mild north facing slope) of Evolution Canyon (EC), Israel. Based on the whole genome sequence of S. macrospora , we targeted 20 genomic regions in S. fimicola which contain short sequence repeats (SSRs). Our data revealed genetic variations in strains from south facing slope and these findings assist in the hypothesis that genetic variations caused by stressful environments lead to evolution.

Effects of heart rate variability biofeedback during exposure to fear-provoking stimuli within spider-fearful individuals: study protocol for a randomized controlled trial.

PubMed

Schäfer, Sarah K; Ihmig, Frank R; Lara H, Karen A; Neurohr, Frank; Kiefer, Stephan; Staginnus, Marlene; Lass-Hennemann, Johanna; Michael, Tanja

2018-03-16

Specific phobias are among the most common anxiety disorders. Exposure therapy is the treatment of choice for specific phobias. However, not all patients respond equally well to it. Hence, current research focuses on therapeutic add-ons to increase and consolidate the effects of exposure therapy. One potential therapeutic add-on is biofeedback to increase heart rate variability (HRV). A recent meta-analysis shows beneficial effects of HRV biofeedback interventions on stress and anxiety symptoms. Therefore, the purpose of the current trial is to evaluate the effects of HRV biofeedback, which is practiced before and utilized during exposure, in spider-fearful individuals. Further, this trial is the first to differentiate between the effects of a HRV biofeedback intervention and those of a low-load working memory (WM) task. Eighty spider-fearful individuals participate in the study. All participants receive a training session in which they practice two tasks (HRV biofeedback and a motor pseudo-biofeedback task or two motor pseudo-biofeedback tasks). Afterwards, they train both tasks at home for 6 days. One week later, during the exposure session, they watch 16 1-min spider video clips. Participants are divided into four groups: group 1 practices the HRV biofeedback and one motor pseudo-task before exposure and utilizes HRV biofeedback during exposure. Group 2 receives the same training, but continues the pseudo-biofeedback task during exposure. Group 3 practices two pseudo-biofeedback tasks and continues one of them during exposure. Group 4 trains in two pseudo-biofeedback tasks and has no additional task during exposure. The primary outcome is fear of spiders (measured by the Fear of Spiders Questionnaire and the Behavioral Approach Test). Secondary outcomes are physiological measures based on electrodermal activity, electrocardiogram and respiration. This RCT is the first one to investigate the effects of using a pre-trained HRV biofeedback during exposure in spider-fearful individuals. The study critically contrasts the effects of the biofeedback intervention with those of pseudo-tasks, which also require WM capacity, but which do not have a physiological base. If HRV biofeedback is effective in reducing fear of spiders, it would represent an easy-to-use tool to improve exposure-therapy outcomes. Deutsches Register Klinischer Studien, DRKS00012278 . Registered on 23 May 2017, amendment on 5 October 2017.

Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes.

PubMed

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

2016-05-01

The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.

Weight loss with naltrexone SR/bupropion SR combination therapy as an adjunct to behavior modification: the COR-BMOD trial

USDA-ARS?s Scientific Manuscript database

This 56-week, randomized, placebo-controlled trial examined the efficacy and safety of naltrexone plus bupropion as an adjunct to intensive behavior modification (BMOD). A total of 793 participants (BMI = 36.5 +/- 4.2 kg/m(2)) was randomly assigned in a 1:3 ratio to: (i) placebo + BMOD (N = 202); or...

Progress of targeted genome modification approaches in higher plants.

PubMed

Cardi, Teodoro; Neal Stewart, C

2016-07-01

Transgene integration in plants is based on illegitimate recombination between non-homologous sequences. The low control of integration site and number of (trans/cis)gene copies might have negative consequences on the expression of transferred genes and their insertion within endogenous coding sequences. The first experiments conducted to use precise homologous recombination for gene integration commenced soon after the first demonstration that transgenic plants could be produced. Modern transgene targeting categories used in plant biology are: (a) homologous recombination-dependent gene targeting; (b) recombinase-mediated site-specific gene integration; (c) oligonucleotide-directed mutagenesis; (d) nuclease-mediated site-specific genome modifications. New tools enable precise gene replacement or stacking with exogenous sequences and targeted mutagenesis of endogeneous sequences. The possibility to engineer chimeric designer nucleases, which are able to target virtually any genomic site, and use them for inducing double-strand breaks in host DNA create new opportunities for both applied plant breeding and functional genomics. CRISPR is the most recent technology available for precise genome editing. Its rapid adoption in biological research is based on its inherent simplicity and efficacy. Its utilization, however, depends on available sequence information, especially for genome-wide analysis. We will review the approaches used for genome modification, specifically those for affecting gene integration and modification in higher plants. For each approach, the advantages and limitations will be noted. We also will speculate on how their actual commercial development and implementation in plant breeding will be affected by governmental regulations.

Random sequences generation through optical measurements by phase-shifting interferometry

NASA Astrophysics Data System (ADS)

François, M.; Grosges, T.; Barchiesi, D.; Erra, R.; Cornet, A.

2012-04-01

The development of new techniques for producing random sequences with a high level of security is a challenging topic of research in modern cryptographics. The proposed method is based on the measurement by phase-shifting interferometry of the speckle signals of the interaction between light and structures. We show how the combination of amplitude and phase distributions (maps) under a numerical process can produce random sequences. The produced sequences satisfy all the statistical requirements of randomness and can be used in cryptographic schemes.

UAV Control on the Basis of 3D Landmark Bearing-Only Observations

PubMed Central

Karpenko, Simon; Konovalenko, Ivan; Miller, Alexander; Miller, Boris; Nikolaev, Dmitry

2015-01-01

The article presents an approach to the control of a UAV on the basis of 3D landmark observations. The novelty of the work is the usage of the 3D RANSAC algorithm developed on the basis of the landmarks’ position prediction with the aid of a modified Kalman-type filter. Modification of the filter based on the pseudo-measurements approach permits obtaining unbiased UAV position estimation with quadratic error characteristics. Modeling of UAV flight on the basis of the suggested algorithm shows good performance, even under significant external perturbations. PMID:26633394

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

USDA-ARS?s Scientific Manuscript database

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylat...

The sensitivity of tropospheric chemistry to cloud interactions

NASA Technical Reports Server (NTRS)

Jonson, Jan E.; Isaksen, Ivar S. A.

1994-01-01

Clouds, although only occupying a relatively small fraction of the troposphere volume, can have a substantial impact on the chemistry of the troposphere. In newly formed clouds, or in clouds with air rapidly flowing through, the chemistry is expected to be far more active than in aged clouds with stagnant air. Thus, frequent cycling of air through shortlived clouds, i.e. cumulus clouds, is likely to be a much more efficient media for altering the composition of the atmosphere than an extensive cloud cover i.e. frontal cloud systems. The impact of clouds is tested out in a 2-D channel model encircling the globe in a latitudinal belt from 30 to 60 deg N. The model contains a detailed gas phase chemistry. In addition physiochemical interactions between the gas and aqueous phases are included. For species as H2O2, CH2O, O3, and SO2, Henry's law equilibria are assumed, whereas HNO3 and H2SO4 are regarded as completed dissolved in the aqueous phase. Absorption of HO2 and OH is assumed to be mass-transport limited. The chemistry of the aqueous phase is characterized by rapid cycling of odd hydrogen, (H2O2, HO2, and OH). O2(-) (produced through dissociation of HO2) reacting with dissolved O3 is a major source of OH in the aqueous phase. This reaction can be a significant sink for O3 in the troposphere. In the interstitial cloud air, odd hydrogen is depleted, whereas NO(x) remains in the gas phase, thus reducing ozone production due to the reaction between NO and HO2. Our calculations give markedly lower ozone levels when cloud interactions are included. This may in part explain the overpredictions of ozone levels often experienced in models neglecting cloud chemical interactions. In the present study, the existence of clouds, cloud types, and their lifetimes are modeled as pseudo random variables. Such pseudo random sequences are in reality deterministic and may, given the same starting values, be reproduced. The effects of cloud interactions on the overall chemistry of the troposphere are discussed. In particular, tests are performed to determine the sensitivity of cloud frequencies and cloud types.

Sequence-specific unusual (1-->2)-type helical turns in alpha/beta-hybrid peptides.

PubMed

Prabhakaran, Panchami; Kale, Sangram S; Puranik, Vedavati G; Rajamohanan, P R; Chetina, Olga; Howard, Judith A K; Hofmann, Hans-Jörg; Sanjayan, Gangadhar J

2008-12-31

This article describes novel conformationally ordered alpha/beta-hybrid peptides consisting of repeating l-proline-anthranilic acid building blocks. These oligomers adopt a compact, right-handed helical architecture determined by the intrinsic conformational preferences of the individual amino acid residues. The striking feature of these oligomers is their ability to display an unusual periodic pseudo beta-turn network of nine-membered hydrogen-bonded rings formed in the forward direction of the sequence by 1-->2 amino acid interactions both in solid-state and in solution. Conformational investigations of several of these oligomers by single-crystal X-ray diffraction, solution-state NMR, and ab initio MO theory suggest that the characteristic steric and dihedral angle restraints exerted by proline are essential for stabilizing the unusual pseudo beta-turn network found in these oligomers. Replacing proline by the conformationally flexible analogue alanine (Ala) or by the conformationally more constrained alpha-amino isobutyric acid (Aib) had an adverse effect on the stabilization of this structural architecture. These findings increase the potential to design novel secondary structure elements profiting from the steric and dihedral angle constraints of the amino acid constituents and help to augment the conformational space available for synthetic oligomer design with diverse backbone structures.

iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition.

PubMed

Chen, Wei; Feng, Peng-Mian; Lin, Hao; Chou, Kuo-Chen

2014-01-01

In eukaryotic genes, exons are generally interrupted by introns. Accurately removing introns and joining exons together are essential processes in eukaryotic gene expression. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapid and effective detection of splice sites that play important roles in gene structure annotation and even in RNA splicing. Although a series of computational methods were proposed for splice site identification, most of them neglected the intrinsic local structural properties. In the present study, a predictor called "iSS-PseDNC" was developed for identifying splice sites. In the new predictor, the sequences were formulated by a novel feature-vector called "pseudo dinucleotide composition" (PseDNC) into which six DNA local structural properties were incorporated. It was observed by the rigorous cross-validation tests on two benchmark datasets that the overall success rates achieved by iSS-PseDNC in identifying splice donor site and splice acceptor site were 85.45% and 87.73%, respectively. It is anticipated that iSS-PseDNC may become a useful tool for identifying splice sites and that the six DNA local structural properties described in this paper may provide novel insights for in-depth investigations into the mechanism of RNA splicing.

RNA-LIM: a novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure.

PubMed

Hall, Damien; Li, Songling; Yamashita, Kazuo; Azuma, Ryuzo; Carver, John A; Standley, Daron M

2015-03-01

RNA-LIM is a procedure that can analyze various pseudo-potentials describing the affinity between single-stranded RNA (ssRNA) ribonucleotides and surface amino acids to produce a coarse-grained estimate of the structure of the ssRNA at the protein interface. The search algorithm works by evolving an ssRNA chain, of known sequence, as a series of walks between fixed sites on a protein surface. Optimal routes are found by application of a set of minimal "limiting" restraints derived jointly from (i) selective sampling of the ribonucleotide amino acid affinity pseudo-potential data, (ii) limited surface path exploration by prior determination of surface arc lengths, and (iii) RNA structural specification obtained from a statistical potential gathered from a library of experimentally determined ssRNA structures. We describe the general approach using a NAST (Nucleic Acid Simulation Tool)-like approximation of the ssRNA chain and a generalized pseudo-potential reflecting the location of nucleic acid binding residues. Minimum and maximum performance indicators of the methodology are established using both synthetic data, for which the pseudo-potential defining nucleic acid binding affinity is systematically degraded, and a representative real case, where the RNA binding sites are predicted by the amplified antisense RNA (aaRNA) method. Some potential uses and extensions of the routine are discussed. RNA-LIM analysis programs along with detailed instructions for their use are available on request from the authors. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

Novel Colloidal Microstructures of β-Escin and the Liposomal Components Cholesterol and DPPC.

PubMed

de Groot, Carolin; Müsken, Mathias; Müller-Goymann, Christel C

2018-05-24

The discovery of immunostimulating complex formation by the saponin Quil A from the plant Quillaja saponaria with cholesterol and a phospholipid opened up new avenues for the development of drug delivery systems for vaccine application with additional adjuvant properties. In this study, β -escin, a monodesmosidic triterpene saponin from horse chestnut, was investigated in terms of its interaction with liposomal components (cholesterol, dipalmitoylphosphatidylcholine) by Langmuir film balance studies and with regard to particle formation visualized by transmission electron microscopy. A strong interaction of β -escin with cholesterol was observed by Langmuir isotherms due to the intercalation of the saponin into the monolayer, whereas no interaction occurred with dipalmitoylphosphatidylcholine. Transmission electron microscopy studies also confirmed the strong interaction of β -escin with cholesterol. In aqueous pseudo-ternary systems ( β -escin, dipalmitoylphosphatidylcholine, cholesterol) and in pseudo-binary systems ( β -escin, cholesterol), new colloidal structures built up from ring-like and worm-like subunits were observed with a size of about 100 - 200 nm. These colloidal structures are formed in pseudo-binary systems by aggregation of the subunits, whereas in pseudo-ternary systems, they are formed among others by attacking the liposomal membrane. The rehydration of the liposomal dispersions in NANOpure water or Tris buffer pH 7.4 (140 mM) resulted in the same particle formation. In contrast, the sequence of the dispersions' production process affected the particle formation. Unless adding the saponin to the other components from the beginning, just a liposomal dispersion was formed without any colloidal aggregates of the subunits mentioned above. Georg Thieme Verlag KG Stuttgart · New York.

Impulse radio ultra wideband wireless transmission of dopamine concentration levels recorded by fast-scan cyclic voltammetry.

PubMed

Ebrazeh, Ali; Bozorgzadeh, Bardia; Mohseni, Pedram

2015-01-01

This paper demonstrates the feasibility of utilizing impulse radio ultra wideband (IR-UWB) signaling technique for reliable, wireless transmission of dopamine concentration levels recorded by fast-scan cyclic voltammetry (FSCV) at a carbon-fiber microelectrode (CFM) to address the problem of elevated data rates in high-channel-count neurochemical monitoring. Utilizing an FSCV-sensing chip fabricated in AMS 0.35μm 2P/4M CMOS, a 3-5-GHz, IR-UWB transceiver (TRX) chip fabricated in TSMC 90nm 1P/9M RF CMOS, and two off-chip, miniature, UWB antennae, wireless transfer of pseudo-random binary sequence (PRBS) data at 50Mbps over a distance of <;1m is first shown with bit-error rates (BER) <; 10(-3). Further, IR-UWB wireless transmission of dopamine concentration levels prerecorded with FSCV at a CFM during flow injection analysis (FIA) is also demonstrated with transmitter (TX) power dissipation of only ~4.4μW from 1.2V, representing two orders of magnitude reduction in TX power consumption compared to that of a conventional frequency-shift-keyed (FSK) link operating at ~433MHz.

ViBe: a universal background subtraction algorithm for video sequences.

PubMed

Barnich, Olivier; Van Droogenbroeck, Marc

2011-06-01

This paper presents a technique for motion detection that incorporates several innovative mechanisms. For example, our proposed technique stores, for each pixel, a set of values taken in the past at the same location or in the neighborhood. It then compares this set to the current pixel value in order to determine whether that pixel belongs to the background, and adapts the model by choosing randomly which values to substitute from the background model. This approach differs from those based upon the classical belief that the oldest values should be replaced first. Finally, when the pixel is found to be part of the background, its value is propagated into the background model of a neighboring pixel. We describe our method in full details (including pseudo-code and the parameter values used) and compare it to other background subtraction techniques. Efficiency figures show that our method outperforms recent and proven state-of-the-art methods in terms of both computation speed and detection rate. We also analyze the performance of a downscaled version of our algorithm to the absolute minimum of one comparison and one byte of memory per pixel. It appears that even such a simplified version of our algorithm performs better than mainstream techniques.

Testing and performance analysis of a 650 Mbps QPPM modem for free-space laser communications

NASA Astrophysics Data System (ADS)

Mortensen, Dale J.

1994-08-01

The testing and performance of a prototype modem developed at NASA Lewis Research Center for high-speed free-space direct detection optical communications is described. The testing was performed under laboratory conditions using computer control with specially developed test equipment that simulates free-space link conditions. The modem employs quaternary pulse position modulation (QPPM) at 325 Megabits per second (Mbps) on two optical channels, which are multiplexed to transmit a single 650 Mbps data stream. The measured results indicate that the receiver's automatic gain control (AGC), phased-locked-loop slot clock recovery, digital symbol clock recovery, matched filtering, and maximum likelihood data recovery circuits were found to have only 1.5 dB combined implementation loss during bit-error-rate (BER) performance measurements. Pseudo random bit sequences and real-time high quality video sources were used to supply 650 Mbps and 325 Mbps data streams to the modem. Additional testing revealed that Doppler frequency shifting can be easily tracked by the receiver, that simulated pointing errors are readily compensated for by the AGC circuits, and that channel timing skew affects the BER performance in an expected manner. Overall, the needed technologies for a high-speed laser communications modem were demonstrated.

Normal-inverse bimodule operation Hadamard transform ion mobility spectrometry.

PubMed

Hong, Yan; Huang, Chaoqun; Liu, Sheng; Xia, Lei; Shen, Chengyin; Chu, Yannan

2018-10-31

In order to suppress or eliminate the spurious peaks and improve signal-to-noise ratio (SNR) of Hadamard transform ion mobility spectrometry (HT-IMS), a normal-inverse bimodule operation Hadamard transform - ion mobility spectrometry (NIBOHT-IMS) technique was developed. In this novel technique, a normal and inverse pseudo random binary sequence (PRBS) was produced in sequential order by an ion gate controller and utilized to control the ion gate of IMS, and then the normal HT-IMS mobility spectrum and the inverse HT-IMS mobility spectrum were obtained. A NIBOHT-IMS mobility spectrum was gained by subtracting the inverse HT-IMS mobility spectrum from normal HT-IMS mobility spectrum. Experimental results demonstrate that the NIBOHT-IMS technique can significantly suppress or eliminate the spurious peaks, and enhance the SNR by measuring the reactant ions. Furthermore, the gas CHCl 3 and CH 2 Br 2 were measured for evaluating the capability of detecting real sample. The results show that the NIBOHT-IMS technique is able to eliminate the spurious peaks and improve the SNR notably not only for the detection of larger ion signals but also for the detection of small ion signals. Copyright © 2018 Elsevier B.V. All rights reserved.

E-learning platform for automated testing of electronic circuits using signature analysis method

NASA Astrophysics Data System (ADS)

Gherghina, Cǎtǎlina; Bacivarov, Angelica; Bacivarov, Ioan C.; Petricǎ, Gabriel

2016-12-01

Dependability of electronic circuits can be ensured only through testing of circuit modules. This is done by generating test vectors and their application to the circuit. Testability should be viewed as a concerted effort to ensure maximum efficiency throughout the product life cycle, from conception and design stage, through production to repairs during products operating. In this paper, is presented the platform developed by authors for training for testability in electronics, in general and in using signature analysis method, in particular. The platform allows highlighting the two approaches in the field namely analog and digital signature of circuits. As a part of this e-learning platform, it has been developed a database for signatures of different electronic components meant to put into the spotlight different techniques implying fault detection, and from this there were also self-repairing techniques of the systems with this kind of components. An approach for realizing self-testing circuits based on MATLAB environment and using signature analysis method is proposed. This paper analyses the benefits of signature analysis method and simulates signature analyzer performance based on the use of pseudo-random sequences, too.

Long-reach transmission experiment of a wavelength division multiplexed-passive optical networks transmitter based on reflective semiconductor optical amplifiers

NASA Astrophysics Data System (ADS)

Jeon, Sie-Wook; Kim, Youngbok; Park, Chang-Soo

2012-01-01

We propose and demonstrate a long-reach wavelength division multiplexed-passive optical networks (WDM-PON) based on reflective semiconductor optical amplifiers (RSOAs) with easy maintenance of the optical source. Unlike previous studies the proposed WDM-PON uses two RSOAs: one for wavelength-selected light generation to provide a constant seed light to the second RSOA, the other for active external modulation. This method is free from intensity-fluctuated power penalties inherent to directly modulated single-RSOA sources, making long-reach transmission possible. Also, the wavelength of the modulated signal can easily be changed for the same RSOA by replacing the external feedback reflector, such as a fiber Bragg grating, or via thermal tuning. The seed light has a high-side-mode suppression ratio (SMSR) of 45 dB, and the bit error rate (BER) curve reveals that the upstream 1.25-Gb/s nonreturn-to-zero (NRZ) signal with a pseudo-random binary sequence (PRBS) of length of 215-1 has power penalties of 0.22 and 0.69 dB at BERs of 10-9 after 55-km and 110-km transmission due to fiber dispersion, respectively.

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

Yashchuk, V. V.; Fischer, P. J.; Chan, E. R.

We present a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) one-dimensional sequences and two-dimensional arrays as an effective method for spectral characterization in the spatial frequency domain of a broad variety of metrology instrumentation, including interferometric microscopes, scatterometers, phase shifting Fizeau interferometers, scanning and transmission electron microscopes, and at this time, x-ray microscopes. The inherent power spectral density of BPR gratings and arrays, which has a deterministic white-noise-like character, allows a direct determination of the MTF with a uniform sensitivity over the entire spatial frequency range and field of view of an instrument. We demonstrate themore » MTF calibration and resolution characterization over the full field of a transmission soft x-ray microscope using a BPR multilayer (ML) test sample with 2.8 nm fundamental layer thickness. We show that beyond providing a direct measurement of the microscope's MTF, tests with the BPRML sample can be used to fine tune the instrument's focal distance. Finally, our results confirm the universality of the method that makes it applicable to a large variety of metrology instrumentation with spatial wavelength bandwidths from a few nanometers to hundreds of millimeters.« less

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

Yashchuk, V. V., E-mail: VVYashchuk@lbl.gov; Chan, E. R.; Lacey, I.

We present a modulation transfer function (MTF) calibration method based on binary pseudo-random (BPR) one-dimensional sequences and two-dimensional arrays as an effective method for spectral characterization in the spatial frequency domain of a broad variety of metrology instrumentation, including interferometric microscopes, scatterometers, phase shifting Fizeau interferometers, scanning and transmission electron microscopes, and at this time, x-ray microscopes. The inherent power spectral density of BPR gratings and arrays, which has a deterministic white-noise-like character, allows a direct determination of the MTF with a uniform sensitivity over the entire spatial frequency range and field of view of an instrument. We demonstrate themore » MTF calibration and resolution characterization over the full field of a transmission soft x-ray microscope using a BPR multilayer (ML) test sample with 2.8 nm fundamental layer thickness. We show that beyond providing a direct measurement of the microscope’s MTF, tests with the BPRML sample can be used to fine tune the instrument’s focal distance. Our results confirm the universality of the method that makes it applicable to a large variety of metrology instrumentation with spatial wavelength bandwidths from a few nanometers to hundreds of millimeters.« less

Reflectively Coupled Waveguide Photodetector for High Speed Optical Interconnection

PubMed Central

Hsu*, Shih-Hsiang

2010-01-01

To fully utilize GaAs high drift mobility, techniques to monolithically integrate In0.53Ga0.47As p-i-n photodetectors with GaAs based optical waveguides using total internal reflection coupling are reviewed. Metal coplanar waveguides, deposited on top of the polyimide layer for the photodetector’s planarization and passivation, were then uniquely connected as a bridge between the photonics and electronics to illustrate the high-speed monitoring function. The photodetectors were efficiently implemented and imposed on the echelle grating circle for wavelength division multiplexing monitoring. In optical filtering performance, the monolithically integrated photodetector channel spacing was 2 nm over the 1,520–1,550 nm wavelength range and the pass band was 1 nm at the −1 dB level. For high-speed applications the full-width half-maximum of the temporal response and 3-dB bandwidth for the reflectively coupled waveguide photodetectors were demonstrated to be 30 ps and 11 GHz, respectively. The bit error rate performance of this integrated photodetector at 10 Gbit/s with 27-1 long pseudo-random bit sequence non-return to zero input data also showed error-free operation. PMID:22163502

Neural correlates of Korean proverb processing: A functional magnetic resonance imaging study.

PubMed

Yi, You Gyoung; Kim, Dae Yul; Shim, Woo Hyun; Oh, Joo Young; Kim, Sung Hyun; Kim, Ho Sung

2017-10-01

The Korean language is based on a syntactic system that is different from other languages. This study investigated the processing area of the Korean proverb in comparison with the literal sentence using functional magnetic resonance imaging. In addition, the effect of opacity and transparency of proverbs on the activation pattern, when familiarity is set to the same condition, was also examined. The experimental stimuli included 36 proverbs and 18 literal sentences. A cohort of 15 healthy participants silently read each sentence for 6 s. A total of 18 opaque proverbs, 18 transparent proverbs, and 18 literal sentences were presented pseudo-randomly in one of three predesigned sequences. Compared with the literal sentences, a significant activation pattern was observed in the left hemisphere, including the left inferior frontal gyrus, in association with the proverbs. Compared with the transparent proverbs, opaque proverbs elicited more activation in the right supramarginal gyrus and precuneus. Our study confirmed that the left inferior frontal gyrus mediates the retrieval and/or selection of semantic knowledge in the Korean language. The present findings indicated that the right precuneus and the right supramarginal gyrus may be involved in abstract language processing.

SU-F-J-169: A Feasibility Study of Using MRI Alone in Abdominal Radiotherapy

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

Zawisza, I; Hsu, S; Peng, Q

Purpose: To demonstrate the feasibility of a MRI alone workflow to support treatment planning and image guidance for abdominal radiotherapy. Methods: Abdominal MR images (in-phase/out-phase/fat/water) were acquired for a patient with breath-hold using a Dixon pulse sequence. Air masks were created on in-phase images using intensity thresholding and morphological processing methods in order to separate air from bone. Pseudo-CT and DRRs were generated using a published method. To investigate the effect of heterogeneity corrections on dose calculations using pseudo-CT, three different plans (3-field 3D, 5-field IMRT and 2-arc VMAT) were performed to mimic pancreatic treatments (1.8Gy/fraction over 28 fractions). Results:more » The DRRs created from pseudo-CT were of comparable quality as those created from CT. Comparing dose calculations with and without heterogeneity corrections between the 3 different plans, the biggest dosimetric differences were seen in the VMAT plan where modulation must occur across air-tissue interfaces such as those of the stomach and bowel. The DVHs for the VMAT plan showed ∼84cc difference at V50Gy in the small bowel. In terms of pseudo-CT quality, some small volumes of air in the bowel and stomach were misclassified as bone. The VMAT plan was re-optimized on pseudo-CT with 0 HU in the misclassified areas. The V50Gy in the small bowel differed by ∼90cc between the new VMAT plan with and without heterogeneity corrections. Conclusion: We found that the use of MRI alone is feasible for abdominal treatment planning and image guidance. A difference between calculations with and without heterogeneity corrections was found that is most pronounced for VMAT where the traversal of air-tissue interfaces is unavoidable. Future work will be performed to minimize misclassification between bone and air.« less

Somatic diversification of chicken immunoglobulin light chains by point mutations.

PubMed

Parvari, R; Ziv, E; Lantner, F; Heller, D; Schechter, I

1990-04-01

The light-chain locus of chicken has 1 functional V lambda 1 gene, 1 J gene, and 25 pseudo-V lambda-genes (where V = variable and J = joining). A major problem is which somatic mechanisms expand this extremely limited germ-line information to generate many different antibodies. Weill's group [Reynaud, C. A., Anquez, V., Grimal, H. & Weill, J. C. (1987) Cell 48, 379-388] has shown that the pseudo-V lambda-genes diversify the rearranged V lambda 1 by gene conversion. Here we demonstrate that chicken light chains are further diversified by somatic point mutations and by V lambda 1-J flexible joining. Somatic point mutations were identified in the J and 3' noncoding DNA of rearranged light-chain genes of chicken. These regions were analyzed because point mutations in V lambda 1 are obscured by gene conversion; the J and 3' noncoding DNA are presented in one copy per haploid genome and are not subject to gene conversion. In rodents point mutations occur as frequently in the V-J coding regions as in the adjacent flanking DNA. Therefore, we conclude that somatic point mutations diversify the V lambda 1 of chicken. The frequency (0-1%) and distribution of the mutations (decreasing in number with increased distance from the V lambda 1 segment) in chicken were as observed in rodents. Sequence variability at the V lambda 1-J junctions could be attributed to imprecise joining of the V lambda 1 and J genes. The modification by gene conversion of rearranged V lambda 1 genes in the bursa was similar in chicken aged 3 months (9.5%) or 3 weeks (9.1%)--i.e., gene conversion that generates the preimmune repertoire in the bursa seems to level off around 3 weeks of age. This preimmune repertoire can be further diversified by somatic point mutations that presumably lead to the formation of antibodies with increased affinity. A segment with structural features of a matrix association region [(A + T)-rich and four topoisomerase II binding sites] was identified in the middle of the J-C lambda intron (where C = constant).

Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing.

PubMed

Zhou, Katherine I; Clark, Wesley C; Pan, David W; Eckwahl, Matthew J; Dai, Qing; Pan, Tao

2018-05-11

The abundant RNA modification pseudouridine (Ψ) has been mapped transcriptome-wide by chemically modifying pseudouridines with carbodiimide and detecting the resulting reverse transcription stops in high-throughput sequencing. However, these methods have limited sensitivity and specificity, in part due to the use of reverse transcription stops. We sought to use mutations rather than just stops in sequencing data to identify pseudouridine sites. Here, we identify reverse transcription conditions that allow read-through of carbodiimide-modified pseudouridine (CMC-Ψ), and we show that pseudouridines in carbodiimide-treated human ribosomal RNA have context-dependent mutation and stop rates in high-throughput sequencing libraries prepared under these conditions. Furthermore, accounting for the context-dependence of mutation and stop rates can enhance the detection of pseudouridine sites. Similar approaches could contribute to the sequencing-based detection of many RNA modifications.

NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents.

PubMed

Liu, Sophia S; Hockenberry, Adam J; Lancichinetti, Andrea; Jewett, Michael C; Amaral, Luís A N

2016-11-01

The existence of over- and under-represented sequence motifs in genomes provides evidence of selective evolutionary pressures on biological mechanisms such as transcription, translation, ligand-substrate binding, and host immunity. In order to accurately identify motifs and other genome-scale patterns of interest, it is essential to be able to generate accurate null models that are appropriate for the sequences under study. While many tools have been developed to create random nucleotide sequences, protein coding sequences are subject to a unique set of constraints that complicates the process of generating appropriate null models. There are currently no tools available that allow users to create random coding sequences with specified amino acid composition and GC content for the purpose of hypothesis testing. Using the principle of maximum entropy, we developed a method that generates unbiased random sequences with pre-specified amino acid and GC content, which we have developed into a python package. Our method is the simplest way to obtain maximally unbiased random sequences that are subject to GC usage and primary amino acid sequence constraints. Furthermore, this approach can easily be expanded to create unbiased random sequences that incorporate more complicated constraints such as individual nucleotide usage or even di-nucleotide frequencies. The ability to generate correctly specified null models will allow researchers to accurately identify sequence motifs which will lead to a better understanding of biological processes as well as more effective engineering of biological systems.

m6ASNP: a tool for annotating genetic variants by m6A function.

PubMed

Jiang, Shuai; Xie, Yubin; He, Zhihao; Zhang, Ya; Zhao, Yuli; Chen, Li; Zheng, Yueyuan; Miao, Yanyan; Zuo, Zhixiang; Ren, Jian

2018-05-01

Large-scale genome sequencing projects have identified many genetic variants for diverse diseases. A major goal of these projects is to characterize these genetic variants to provide insight into their function and roles in diseases. N6-methyladenosine (m6A) is one of the most abundant RNA modifications in eukaryotes. Recent studies have revealed that aberrant m6A modifications are involved in many diseases. In this study, we present a user-friendly web server called "m6ASNP" that is dedicated to the identification of genetic variants that target m6A modification sites. A random forest model was implemented in m6ASNP to predict whether the methylation status of an m6A site is altered by the variants that surround the site. In m6ASNP, genetic variants in a standard variant call format (VCF) are accepted as the input data, and the output includes an interactive table that contains the genetic variants annotated by m6A function. In addition, statistical diagrams and a genome browser are provided to visualize the characteristics and to annotate the genetic variants. We believe that m6ASNP is a very convenient tool that can be used to boost further functional studies investigating genetic variants. The web server "m6ASNP" is implemented in JAVA and PHP and is freely available at [60].

Antibody performance in ChIP-sequencing assays: From quality scores of public data sets to quantitative certification.

PubMed

Mendoza-Parra, Marco-Antonio; Saravaki, Vincent; Cholley, Pierre-Etienne; Blum, Matthias; Billoré, Benjamin; Gronemeyer, Hinrich

2016-01-01

We have established a certification system for antibodies to be used in chromatin immunoprecipitation assays coupled to massive parallel sequencing (ChIP-seq). This certification comprises a standardized ChIP procedure and the attribution of a numerical quality control indicator (QCi) to biological replicate experiments. The QCi computation is based on a universally applicable quality assessment that quantitates the global deviation of randomly sampled subsets of ChIP-seq dataset with the original genome-aligned sequence reads. Comparison with a QCi database for >28,000 ChIP-seq assays were used to attribute quality grades (ranging from 'AAA' to 'DDD') to a given dataset. In the present report we used the numerical QC system to assess the factors influencing the quality of ChIP-seq assays, including the nature of the target, the sequencing depth and the commercial source of the antibody.  We have used this approach specifically to certify mono and polyclonal antibodies obtained from Active Motif directed against the histone modification marks H3K4me3, H3K27ac and H3K9ac for ChIP-seq. The antibodies received the grades AAA to BBC ( www.ngs-qc.org). We propose to attribute such quantitative grading of all antibodies attributed with the label "ChIP-seq grade".

WWC Review of the Report "Accommodations for English Language Learner Students: The Effect of Linguistic Modification of Math Test Item Sets"

ERIC Educational Resources Information Center

What Works Clearinghouse, 2012

2012-01-01

The research described in this report is a randomized controlled trial in which seventh- and eighth-grade students were randomly assigned to complete a set of 25 math questions delivered with either standard language or language that had undergone "linguistic modification" by the research team. The purpose of the study was to assess the…

Asymmetric histone modifications between the original and derived loci of human segmental duplications

PubMed Central

Zheng, Deyou

2008-01-01

Background Sequencing and annotation of several mammalian genomes have revealed that segmental duplications are a common architectural feature of primate genomes; in fact, about 5% of the human genome is composed of large blocks of interspersed segmental duplications. These segmental duplications have been implicated in genomic copy-number variation, gene novelty, and various genomic disorders. However, the molecular processes involved in the evolution and regulation of duplicated sequences remain largely unexplored. Results In this study, the profile of about 20 histone modifications within human segmental duplications was characterized using high-resolution, genome-wide data derived from a ChIP-Seq study. The analysis demonstrates that derivative loci of segmental duplications often differ significantly from the original with respect to many histone methylations. Further investigation showed that genes are present three times more frequently in the original than in the derivative, whereas pseudogenes exhibit the opposite trend. These asymmetries tend to increase with the age of segmental duplications. The uneven distribution of genes and pseudogenes does not, however, fully account for the asymmetry in the profile of histone modifications. Conclusion The first systematic analysis of histone modifications between segmental duplications demonstrates that two seemingly 'identical' genomic copies are distinct in their epigenomic properties. Results here suggest that local chromatin environments may be implicated in the discrimination of derived copies of segmental duplications from their originals, leading to a biased pseudogenization of the new duplicates. The data also indicate that further exploration of the interactions between histone modification and sequence degeneration is necessary in order to understand the divergence of duplicated sequences. PMID:18598352

RANDOMNESS of Numbers DEFINITION(QUERY:WHAT? V HOW?) ONLY Via MAXWELL-BOLTZMANN CLASSICAL-Statistics(MBCS) Hot-Plasma VS. Digits-Clumping Log-Law NON-Randomness Inversion ONLY BOSE-EINSTEIN QUANTUM-Statistics(BEQS) .

NASA Astrophysics Data System (ADS)

Siegel, Z.; Siegel, Edward Carl-Ludwig

2011-03-01

RANDOMNESS of Numbers cognitive-semantics DEFINITION VIA Cognition QUERY: WHAT???, NOT HOW?) VS. computer-``science" mindLESS number-crunching (Harrel-Sipser-...) algorithmics Goldreich "PSEUDO-randomness"[Not.AMS(02)] mea-culpa is ONLY via MAXWELL-BOLTZMANN CLASSICAL-STATISTICS(NOT FDQS!!!) "hot-plasma" REPULSION VERSUS Newcomb(1881)-Weyl(1914;1916)-Benford(1938) "NeWBe" logarithmic-law digit-CLUMPING/ CLUSTERING NON-Randomness simple Siegel[AMS Joint.Mtg.(02)-Abs. # 973-60-124] algebraic-inversion to THE QUANTUM and ONLY BEQS preferentially SEQUENTIALLY lower-DIGITS CLUMPING/CLUSTERING with d = 0 BEC, is ONLY VIA Siegel-Baez FUZZYICS=CATEGORYICS (SON OF TRIZ)/"Category-Semantics"(C-S), latter intersection/union of Lawvere(1964)-Siegel(1964)] category-theory (matrix: MORPHISMS V FUNCTORS) "+" cognitive-semantics'' (matrix: ANTONYMS V SYNONYMS) yields Siegel-Baez FUZZYICS=CATEGORYICS/C-S tabular list-format matrix truth-table analytics: MBCS RANDOMNESS TRUTH/EMET!!!

Fast physical-random number generation using laser diode's frequency noise: influence of frequency discriminator

NASA Astrophysics Data System (ADS)

Matsumoto, Kouhei; Kasuya, Yuki; Yumoto, Mitsuki; Arai, Hideaki; Sato, Takashi; Sakamoto, Shuichi; Ohkawa, Masashi; Ohdaira, Yasuo

2018-02-01

Not so long ago, pseudo random numbers generated by numerical formulae were considered to be adequate for encrypting important data-files, because of the time needed to decode them. With today's ultra high-speed processors, however, this is no longer true. So, in order to thwart ever-more advanced attempts to breach our system's protections, cryptologists have devised a method that is considered to be virtually impossible to decode, and uses what is a limitless number of physical random numbers. This research describes a method, whereby laser diode's frequency noise generate a large quantities of physical random numbers. Using two types of photo detectors (APD and PIN-PD), we tested the abilities of two types of lasers (FP-LD and VCSEL) to generate random numbers. In all instances, an etalon served as frequency discriminator, the examination pass rates were determined using NIST FIPS140-2 test at each bit, and the Random Number Generation (RNG) speed was noted.

Base modifications affecting RNA polymerase and reverse transcriptase fidelity.

PubMed

Potapov, Vladimir; Fu, Xiaoqing; Dai, Nan; Corrêa, Ivan R; Tanner, Nathan A; Ong, Jennifer L

2018-06-20

Ribonucleic acid (RNA) is capable of hosting a variety of chemically diverse modifications, in both naturally-occurring post-transcriptional modifications and artificial chemical modifications used to expand the functionality of RNA. However, few studies have addressed how base modifications affect RNA polymerase and reverse transcriptase activity and fidelity. Here, we describe the fidelity of RNA synthesis and reverse transcription of modified ribonucleotides using an assay based on Pacific Biosciences Single Molecule Real-Time sequencing. Several modified bases, including methylated (m6A, m5C and m5U), hydroxymethylated (hm5U) and isomeric bases (pseudouridine), were examined. By comparing each modified base to the equivalent unmodified RNA base, we can determine how the modification affected cumulative RNA polymerase and reverse transcriptase fidelity. 5-hydroxymethyluridine and N6-methyladenosine both increased the combined error rate of T7 RNA polymerase and reverse transcriptases, while pseudouridine specifically increased the error rate of RNA synthesis by T7 RNA polymerase. In addition, we examined the frequency, mutational spectrum and sequence context of reverse transcription errors on DNA templates from an analysis of second strand DNA synthesis.

Analysis of multivariate longitudinal kidney function outcomes using generalized linear mixed models.

PubMed

Jaffa, Miran A; Gebregziabher, Mulugeta; Jaffa, Ayad A

2015-06-14

Renal transplant patients are mandated to have continuous assessment of their kidney function over time to monitor disease progression determined by changes in blood urea nitrogen (BUN), serum creatinine (Cr), and estimated glomerular filtration rate (eGFR). Multivariate analysis of these outcomes that aims at identifying the differential factors that affect disease progression is of great clinical significance. Thus our study aims at demonstrating the application of different joint modeling approaches with random coefficients on a cohort of renal transplant patients and presenting a comparison of their performance through a pseudo-simulation study. The objective of this comparison is to identify the model with best performance and to determine whether accuracy compensates for complexity in the different multivariate joint models. We propose a novel application of multivariate Generalized Linear Mixed Models (mGLMM) to analyze multiple longitudinal kidney function outcomes collected over 3 years on a cohort of 110 renal transplantation patients. The correlated outcomes BUN, Cr, and eGFR and the effect of various covariates such patient's gender, age and race on these markers was determined holistically using different mGLMMs. The performance of the various mGLMMs that encompass shared random intercept (SHRI), shared random intercept and slope (SHRIS), separate random intercept (SPRI) and separate random intercept and slope (SPRIS) was assessed to identify the one that has the best fit and most accurate estimates. A bootstrap pseudo-simulation study was conducted to gauge the tradeoff between the complexity and accuracy of the models. Accuracy was determined using two measures; the mean of the differences between the estimates of the bootstrapped datasets and the true beta obtained from the application of each model on the renal dataset, and the mean of the square of these differences. The results showed that SPRI provided most accurate estimates and did not exhibit any computational or convergence problem. Higher accuracy was demonstrated when the level of complexity increased from shared random coefficient models to the separate random coefficient alternatives with SPRI showing to have the best fit and most accurate estimates.

PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition.

PubMed

Zuo, Yongchun; Li, Yuan; Chen, Yingli; Li, Guangpeng; Yan, Zhenhe; Yang, Lei

2017-01-01

The reduced amino acids perform powerful ability for both simplifying protein complexity and identifying functional conserved regions. However, dealing with different protein problems may need different kinds of cluster methods. Encouraged by the success of pseudo-amino acid composition algorithm, we developed a freely available web server, called PseKRAAC (the pseudo K-tuple reduced amino acids composition). By implementing reduced amino acid alphabets, the protein complexity can be significantly simplified, which leads to decrease chance of overfitting, lower computational handicap and reduce information redundancy. PseKRAAC delivers more capability for protein research by incorporating three crucial parameters that describes protein composition. Users can easily generate many different modes of PseKRAAC tailored to their needs by selecting various reduced amino acids alphabets and other characteristic parameters. It is anticipated that the PseKRAAC web server will become a very useful tool in computational proteomics and protein sequence analysis. Freely available on the web at http://bigdata.imu.edu.cn/psekraac CONTACTS: yczuo@imu.edu.cn or imu.hema@foxmail.com or yanglei_hmu@163.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes.

PubMed

Chou, Kuo-Chen

2005-01-01

With protein sequences entering into databanks at an explosive pace, the early determination of the family or subfamily class for a newly found enzyme molecule becomes important because this is directly related to the detailed information about which specific target it acts on, as well as to its catalytic process and biological function. Unfortunately, it is both time-consuming and costly to do so by experiments alone. In a previous study, the covariant-discriminant algorithm was introduced to identify the 16 subfamily classes of oxidoreductases. Although the results were quite encouraging, the entire prediction process was based on the amino acid composition alone without including any sequence-order information. Therefore, it is worthy of further investigation. To incorporate the sequence-order effects into the predictor, the 'amphiphilic pseudo amino acid composition' is introduced to represent the statistical sample of a protein. The novel representation contains 20 + 2lambda discrete numbers: the first 20 numbers are the components of the conventional amino acid composition; the next 2lambda numbers are a set of correlation factors that reflect different hydrophobicity and hydrophilicity distribution patterns along a protein chain. Based on such a concept and formulation scheme, a new predictor is developed. It is shown by the self-consistency test, jackknife test and independent dataset tests that the success rates obtained by the new predictor are all significantly higher than those by the previous predictors. The significant enhancement in success rates also implies that the distribution of hydrophobicity and hydrophilicity of the amino acid residues along a protein chain plays a very important role to its structure and function.

Using the concept of Chou's pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy.

PubMed

Jiang, Xiaoying; Wei, Rong; Zhang, Tongliang; Gu, Quan

2008-01-01

The function of protein is closely correlated with it subcellular location. Prediction of subcellular location of apoptosis proteins is an important research area in post-genetic era because the knowledge of apoptosis proteins is useful to understand the mechanism of programmed cell death. Compared with the conventional amino acid composition (AAC), the Pseudo Amino Acid composition (PseAA) as originally introduced by Chou can incorporate much more information of a protein sequence so as to remarkably enhance the power of using a discrete model to predict various attributes of a protein. In this study, a novel approach is presented to predict apoptosis protein solely from sequence based on the concept of Chou's PseAA composition. The concept of approximate entropy (ApEn), which is a parameter denoting complexity of time series, is used to construct PseAA composition as additional features. Fuzzy K-nearest neighbor (FKNN) classifier is selected as prediction engine. Particle swarm optimization (PSO) algorithm is adopted for optimizing the weight factors which are important in PseAA composition. Two datasets are used to validate the performance of the proposed approach, which incorporate six subcellular location and four subcellular locations, respectively. The results obtained by jackknife test are quite encouraging. It indicates that the ApEn of protein sequence could represent effectively the information of apoptosis proteins subcellular locations. It can at least play a complimentary role to many of the existing methods, and might become potentially useful tool for protein function prediction. The software in Matlab is available freely by contacting the corresponding author.

Reduction of display artifacts by random sampling

NASA Technical Reports Server (NTRS)

Ahumada, A. J., Jr.; Nagel, D. C.; Watson, A. B.; Yellott, J. I., Jr.

1983-01-01

The application of random-sampling techniques to remove visible artifacts (such as flicker, moire patterns, and paradoxical motion) introduced in TV-type displays by discrete sequential scanning is discussed and demonstrated. Sequential-scanning artifacts are described; the window of visibility defined in spatiotemporal frequency space by Watson and Ahumada (1982 and 1983) and Watson et al. (1983) is explained; the basic principles of random sampling are reviewed and illustrated by the case of the human retina; and it is proposed that the sampling artifacts can be replaced by random noise, which can then be shifted to frequency-space regions outside the window of visibility. Vertical sequential, single-random-sequence, and continuously renewed random-sequence plotting displays generating 128 points at update rates up to 130 Hz are applied to images of stationary and moving lines, and best results are obtained with the single random sequence for the stationary lines and with the renewed random sequence for the moving lines.

Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random.

PubMed

Tomasch, Jürgen; Wang, Hui; Hall, April T K; Patzelt, Diana; Preusse, Matthias; Petersen, Jörn; Brinkmann, Henner; Bunk, Boyke; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; Lang, Andrew S; Wagner-Döbler, Irene

2018-01-01

Gene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer in the world's oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other nonrandom process responsible for packaging genomic DNA into GTAs has been found. Here, we show that knock-out of an autoinducer synthase gene of Dinoroseobacter shibae resulted in overproduction and release of functional GTA particles (DsGTA). Next-generation sequencing of the 4.2-kb DNA fragments isolated from DsGTAs revealed that packaging was not random. DNA from low-GC conjugative plasmids but not from high-GC chromids was excluded from packaging. Seven chromosomal regions were strongly overrepresented in DNA isolated from DsGTA. These packaging peaks lacked identifiable conserved sequence motifs that might represent recognition sites for the GTA terminase complex. Low-GC regions of the chromosome, including the origin and terminus of replication, were underrepresented in DNA isolated from DsGTAs. DNA methylation reduced packaging frequency while the level of gene expression had no influence. Chromosomal regions found to be over- and underrepresented in DsGTA-DNA were regularly spaced. We propose that a "headful" type of packaging is initiated at the sites of coverage peaks and, after linearization of the chromosomal DNA, proceeds in both directions from the initiation site. GC-content, DNA-modifications, and chromatin structure might influence at which sides GTA packaging can be initiated. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random

PubMed Central

Wang, Hui; Hall, April T K; Patzelt, Diana; Preusse, Matthias; Petersen, Jörn; Brinkmann, Henner; Bunk, Boyke; Bhuju, Sabin; Jarek, Michael; Geffers, Robert; Lang, Andrew S; Wagner-Döbler, Irene

2018-01-01

Abstract Gene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer in the world’s oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other nonrandom process responsible for packaging genomic DNA into GTAs has been found. Here, we show that knock-out of an autoinducer synthase gene of Dinoroseobacter shibae resulted in overproduction and release of functional GTA particles (DsGTA). Next-generation sequencing of the 4.2-kb DNA fragments isolated from DsGTAs revealed that packaging was not random. DNA from low-GC conjugative plasmids but not from high-GC chromids was excluded from packaging. Seven chromosomal regions were strongly overrepresented in DNA isolated from DsGTA. These packaging peaks lacked identifiable conserved sequence motifs that might represent recognition sites for the GTA terminase complex. Low-GC regions of the chromosome, including the origin and terminus of replication, were underrepresented in DNA isolated from DsGTAs. DNA methylation reduced packaging frequency while the level of gene expression had no influence. Chromosomal regions found to be over- and underrepresented in DsGTA-DNA were regularly spaced. We propose that a “headful” type of packaging is initiated at the sites of coverage peaks and, after linearization of the chromosomal DNA, proceeds in both directions from the initiation site. GC-content, DNA-modifications, and chromatin structure might influence at which sides GTA packaging can be initiated. PMID:29325123

Comparative characterization of random-sequence proteins consisting of 5, 12, and 20 kinds of amino acids

PubMed Central

Tanaka, Junko; Doi, Nobuhide; Takashima, Hideaki; Yanagawa, Hiroshi

2010-01-01

Screening of functional proteins from a random-sequence library has been used to evolve novel proteins in the field of evolutionary protein engineering. However, random-sequence proteins consisting of the 20 natural amino acids tend to aggregate, and the occurrence rate of functional proteins in a random-sequence library is low. From the viewpoint of the origin of life, it has been proposed that primordial proteins consisted of a limited set of amino acids that could have been abundantly formed early during chemical evolution. We have previously found that members of a random-sequence protein library constructed with five primitive amino acids show high solubility (Doi et al., Protein Eng Des Sel 2005;18:279–284). Although such a library is expected to be appropriate for finding functional proteins, the functionality may be limited, because they have no positively charged amino acid. Here, we constructed three libraries of 120-amino acid, random-sequence proteins using alphabets of 5, 12, and 20 amino acids by preselection using mRNA display (to eliminate sequences containing stop codons and frameshifts) and characterized and compared the structural properties of random-sequence proteins arbitrarily chosen from these libraries. We found that random-sequence proteins constructed with the 12-member alphabet (including five primitive amino acids and positively charged amino acids) have higher solubility than those constructed with the 20-member alphabet, though other biophysical properties are very similar in the two libraries. Thus, a library of moderate complexity constructed from 12 amino acids may be a more appropriate resource for functional screening than one constructed from 20 amino acids. PMID:20162614

Interuser Interference Analysis for Direct-Sequence Spread-Spectrum Systems Part I: Partial-Period Cross-Correlation

NASA Technical Reports Server (NTRS)

Ni, Jianjun (David)

2012-01-01

This presentation discusses an analysis approach to evaluate the interuser interference for Direct-Sequence Spread-Spectrum (DSSS) Systems for Space Network (SN) Users. Part I of this analysis shows that the correlation property of pseudo noise (PN) sequences is the critical factor which determines the interuser interference performance of the DSSS system. For non-standard DSSS systems in which PN sequence s period is much larger than one data symbol duration, it is the partial-period cross-correlation that determines the system performance. This study reveals through an example that a well-designed PN sequence set (e.g. Gold Sequence, in which the cross-correlation for a whole-period is well controlled) may have non-controlled partial-period cross-correlation which could cause severe interuser interference for a DSSS system. Since the analytical derivation of performance metric (bit error rate or signal-to-noise ratio) based on partial-period cross-correlation is prohibitive, the performance degradation due to partial-period cross-correlation will be evaluated using simulation in Part II of this analysis in the future.

Using cellular automata to generate image representation for biological sequences.

PubMed

Xiao, X; Shao, S; Ding, Y; Huang, Z; Chen, X; Chou, K-C

2005-02-01

A novel approach to visualize biological sequences is developed based on cellular automata (Wolfram, S. Nature 1984, 311, 419-424), a set of discrete dynamical systems in which space and time are discrete. By transforming the symbolic sequence codes into the digital codes, and using some optimal space-time evolvement rules of cellular automata, a biological sequence can be represented by a unique image, the so-called cellular automata image. Many important features, which are originally hidden in a long and complicated biological sequence, can be clearly revealed thru its cellular automata image. With biological sequences entering into databanks rapidly increasing in the post-genomic era, it is anticipated that the cellular automata image will become a very useful vehicle for investigation into their key features, identification of their function, as well as revelation of their "fingerprint". It is anticipated that by using the concept of the pseudo amino acid composition (Chou, K.C. Proteins: Structure, Function, and Genetics, 2001, 43, 246-255), the cellular automata image approach can also be used to improve the quality of predicting protein attributes, such as structural class and subcellular location.

Atomistic simulation of laser-pulse surface modification: Predictions of models with various length and time scales

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

Starikov, Sergey V., E-mail: starikov@ihed.ras.ru; Pisarev, Vasily V.; Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow 125412

2015-04-07

In this work, the femtosecond laser pulse modification of surface is studied for aluminium (Al) and gold (Au) by use of two-temperature atomistic simulation. The results are obtained for various atomistic models with different scales: from pseudo-one-dimensional to full-scale three-dimensional simulation. The surface modification after laser irradiation can be caused by ablation and melting. For low energy laser pulses, the nanoscale ripples may be induced on a surface by melting without laser ablation. In this case, nanoscale changes of the surface are due to a splash of molten metal under temperature gradient. Laser ablation occurs at a higher pulse energymore » when a crater is formed on the surface. There are essential differences between Al ablation and Au ablation. In the first step of shock-wave induced ablation, swelling and void formation occur for both metals. However, the simulation of ablation in gold shows an additional athermal type of ablation that is associated with electron pressure relaxation. This type of ablation takes place at the surface layer, at a depth of several nanometers, and does not induce swelling.« less

Chemically Modified Polyvinyl Chloride for Removal of Thionine Dye (Lauth’s Violet)

PubMed Central

Silva, Cleuzilene V.; Royer, Betina; Rodrigues Filho, Guimes; Cerqueira, Daniel A.; Assunção, Rosana M. N.

2017-01-01

The chemical modification of hydrophobic polymer matrices is an alternative way to elchange their surface properties. The introduction of sulfonic groups in the polymer changes the surface properties such as adhesion, wettability, catalytic ability, and adsorption capacity. This work describes the production and application of chemically modified polyvinyl chloride (PVC) as adsorbent for dyes removal. Chemical modification of PVC was evaluated by infrared spectroscopy and elemental analysis, which indicated the presence of sulfonic groups on PVC. The chemically modified PVC (PVCDS) showed an ion exchange capacity of 1.03 mmol−1, and efficiently removed the thionine dye (Lauth’s violet) from aqueous solutions, reaching equilibrium in 30 min. The adsorption kinetics was better adjusted for a pseudo second order model. This result indicates that the adsorption of thionine onto PVCDS occurs by chemisorption. Among the models for the state of equilibrium, SIPS and Langmuir exhibited the best fit to the experimental results and PVCDS showed high adsorption capacities (370 mg−1). Thus, it is assumed that the system presents homogeneous characteristics to the distribution of active sites. The modification promoted the formation of surface characteristics favorable to the dye adsorption by the polymer. PMID:29137158

Introduction on Using the FastPCR Software and the Related Java Web Tools for PCR and Oligonucleotide Assembly and Analysis.

PubMed

Kalendar, Ruslan; Tselykh, Timofey V; Khassenov, Bekbolat; Ramanculov, Erlan M

2017-01-01

This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP). It also contains a built-in program to design oligonucleotide sets both for long sequence assembly by ligase chain reaction and for design of amplicons that tile across a region(s) of interest. The software calculates the melting temperature for the standard and degenerate oligonucleotides including locked nucleic acid (LNA) and other modifications. It also provides analyses for a set of primers with the prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, linguistic complexity as well as a primer dilution and resuspension calculator. The program consists of various bioinformatical tools for analysis of sequences with the GC or AT skew, CG% and GA% content, and the purine-pyrimidine skew. It also analyzes the linguistic sequence complexity and performs generation of random DNA sequence as well as restriction endonucleases analysis. The program allows to find or create restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It performs efficient and complete detection of various repeat types with visual display. The FastPCR software allows the sequence file batch processing that is essential for automation. The program is available for download at http://primerdigital.com/fastpcr.html , and its online version is located at http://primerdigital.com/tools/pcr.html .

Biopanning and characterization of peptides with Fe3O4 nanoparticles-binding capability via phage display random peptide library technique.

PubMed

You, Fei; Yin, Guangfu; Pu, Ximing; Li, Yucan; Hu, Yang; Huang, Zhongbin; Liao, Xiaoming; Yao, Yadong; Chen, Xianchun

2016-05-01

Functionalization of inorganic nanoparticles (NPs) play an important role in biomedical applications. A proper functionalization of NPs can improve biocompatibility, avoid a loss of bioactivity, and further endow NPs with unique performances. Modification with vairous specific binding biomolecules from random biological libraries has been explored. In this work, two 7-mer peptides with sequences of HYIDFRW and TVNFKLY were selected from a phage display random peptide library by using ferromagnetic NPs as targets, and were verified to display strong binding affinity to Fe3O4 NPs. Fourier transform infrared spectrometry, fluorescence microscopy, thermal analysis and X-ray photoelectron spectroscopy confirmed the presence of peptides on the surface of Fe3O4 NPs. Sequence analyses revealed that the probable binding mechanism between the peptide and Fe3O4 NPs might be driven by Pearson hard acid-hard base specific interaction and hydrogen bonds, accompanied with hydrophilic interactions and non-specific electrostatic attractions. The cell viability assay indicated a good cytocompatibility of peptide-bound Fe3O4 NPs. Furthermore, TVNFKLY peptide and an ovarian tumor cell A2780 specific binding peptide (QQTNWSL) were conjugated to afford a liner 14-mer peptide (QQTNWSLTVNFKLY). The binding and targeting studies showed that 14-mer peptide was able to retain both the strong binding ability to Fe3O4 NPs and the specific binding ability to A2780 cells. The results suggested that the Fe3O4-binding peptides would be of great potential in the functionalization of Fe3O4 NPs for the tumor-targeted drug delivery and magnetic hyperthermia. Copyright © 2016 Elsevier B.V. All rights reserved.

Beliefs about Child Support Modification Following Remarriage and Subsequent Childbirth

ERIC Educational Resources Information Center

Hans, Jason D.

2009-01-01

Framed by equity theory, fairness beliefs regarding child support modification to account for the financial impact of remarriage and subsequent childbirth were assessed. Based on a random sample of 407 Kentucky residents using a multiple segment factorial vignette approach, modification was supported by 57% of respondents following remarriage, but…

Mass Spectrometry to Identify New Biomarkers of Nerve Agent Exposure

DTIC Science & Technology

2009-04-01

covalent bond with the active site serine in the consensus sequence GXSXG of esterases and proteases. However, the site of attachment to proteins...that have no active site serine has only recently been recognized as tyrosine. In last year’s report we provided mass spectrometry evidence that...PMID: 18502412 Lockridge O, Xue W, Gaydess A, Grigoryan H, Ding SJ, Schopfer LM, Hinrichs SH, Masson P. Pseudo- esterase activity of human albumin

Relatively Random: Context Effects on Perceived Randomness and Predicted Outcomes

ERIC Educational Resources Information Center

Matthews, William J.

2013-01-01

This article concerns the effect of context on people's judgments about sequences of chance outcomes. In Experiment 1, participants judged whether sequences were produced by random, mechanical processes (such as a roulette wheel) or skilled human action (such as basketball shots). Sequences with lower alternation rates were judged more likely to…

Sparse sampling and reconstruction for electron and scanning probe microscope imaging

DOEpatents

Anderson, Hyrum; Helms, Jovana; Wheeler, Jason W.; Larson, Kurt W.; Rohrer, Brandon R.

2015-07-28

Systems and methods for conducting electron or scanning probe microscopy are provided herein. In a general embodiment, the systems and methods for conducting electron or scanning probe microscopy with an undersampled data set include: driving an electron beam or probe to scan across a sample and visit a subset of pixel locations of the sample that are randomly or pseudo-randomly designated; determining actual pixel locations on the sample that are visited by the electron beam or probe; and processing data collected by detectors from the visits of the electron beam or probe at the actual pixel locations and recovering a reconstructed image of the sample.

Ring correlations in random networks.

PubMed

Sadjadi, Mahdi; Thorpe, M F

2016-12-01

We examine the correlations between rings in random network glasses in two dimensions as a function of their separation. Initially, we use the topological separation (measured by the number of intervening rings), but this leads to pseudo-long-range correlations due to a lack of topological charge neutrality in the shells surrounding a central ring. This effect is associated with the noncircular nature of the shells. It is, therefore, necessary to use the geometrical distance between ring centers. Hence we find a generalization of the Aboav-Weaire law out to larger distances, with the correlations between rings decaying away when two rings are more than about three rings apart.

Predicting protein-protein interactions by combing various sequence- derived features into the general form of Chou's Pseudo amino acid composition.

PubMed

Zhao, Xiao-Wei; Ma, Zhi-Qiang; Yin, Ming-Hao

2012-05-01

Knowledge of protein-protein interactions (PPIs) plays an important role in constructing protein interaction networks and understanding the general machineries of biological systems. In this study, a new method is proposed to predict PPIs using a comprehensive set of 930 features based only on sequence information, these features measure the interactions between residues a certain distant apart in the protein sequences from different aspects. To achieve better performance, the principal component analysis (PCA) is first employed to obtain an optimized feature subset. Then, the resulting 67-dimensional feature vectors are fed to Support Vector Machine (SVM). Experimental results on Drosophila melanogaster and Helicobater pylori datasets show that our method is very promising to predict PPIs and may at least be a useful supplement tool to existing methods.

Environmental change makes robust ecological networks fragile

PubMed Central

Strona, Giovanni; Lafferty, Kevin D.

2016-01-01

Complex ecological networks appear robust to primary extinctions, possibly due to consumers' tendency to specialize on dependable (available and persistent) resources. However, modifications to the conditions under which the network has evolved might alter resource dependability. Here, we ask whether adaptation to historical conditions can increase community robustness, and whether such robustness can protect communities from collapse when conditions change. Using artificial life simulations, we first evolved digital consumer-resource networks that we subsequently subjected to rapid environmental change. We then investigated how empirical host–parasite networks would respond to historical, random and expected extinction sequences. In both the cases, networks were far more robust to historical conditions than new ones, suggesting that new environmental challenges, as expected under global change, might collapse otherwise robust natural ecosystems. PMID:27511722

77 FR 2679 - Defense Federal Acquisition Regulation Supplement: Order of Application for Modifications

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-19

... following methods: [cir] Regulations.gov : http://www.regulations.gov . Submit comments via the Federal e... contract. In order to determine the sequence of modifications to a contract or order, a method for... the numeric order of the modifications to a contract is not the order in which the changes to the...

REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.

PubMed

Roberts, Richard J; Vincze, Tamas; Posfai, Janos; Macelis, Dana

2015-01-01

REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The molecular biology of environmental aromatic hydrocarbons: Progress report for the period September 1, 1986 through July 31, 1987

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

Weiss, S.B.

Our laboratory has explored the use of short DNA oligomers as targets for activated polycyclic aromatic hydrocarbons, such as benzo(a)pyrene diol epoxide (BPDE), in order to detect alterations in DNA sequence arrangement. In this model system, oligomers alkylated with (+)-BPDE are ligated into M13 viral DNA and used to transfect Escherichia coli. These cells are plated on agar, incubated at 37/sup 0/C, progeny viral clones are selected, amplified, and the viral DNAs isolated are sequenced at the site of oligomer insertion. We have devised a procedure for the preparation of unique duplex DNA oligomers such that the site of oligomermore » alkylation is specific for a single deoxynucleotide species in the two DNA strands. The procedure for oligomer assembly also allows us to vary the position of the alkylated residue in each of the two strands. Using our model system, the results obtained over the past year can be summarized as follows. When nonalkylated oligomer constructs are ligated into M13 viral DNA and used to transfect E. coli, no modifications in DNA sequence arrangement are detected in progeny viral DNAs. On the other hand, with oligomer constructs containing BP-adducts two major types of modifications in DNA sequence arrangement were observed: (1) large deletions, and (2) nonhomologous (illegitimate) recombinants. Both of these DNA modifications result in the complete removal of the oligomer insert. Transfection of E. coli that are recA/sup -/ does not alter these DNA modifications, therefore, it appears that the deletions and recombinants induced by the alkylated inserts are not under control of the RecA gene. As the distance between the alkylated residues in the duplex strands is increased, the number of recombinant events detected is reduced. In addition to the above types of DNA modifications, restoration of the original nucleotide sequence in the alkylated construct was also observed in progeny viral DNAs. 7 refs., 6 figs., 2 tabs.« less

Predicting protein amidation sites by orchestrating amino acid sequence features

NASA Astrophysics Data System (ADS)

Zhao, Shuqiu; Yu, Hua; Gong, Xiujun

2017-08-01

Amidation is the fourth major category of post-translational modifications, which plays an important role in physiological and pathological processes. Identifying amidation sites can help us understanding the amidation and recognizing the original reason of many kinds of diseases. But the traditional experimental methods for predicting amidation sites are often time-consuming and expensive. In this study, we propose a computational method for predicting amidation sites by orchestrating amino acid sequence features. Three kinds of feature extraction methods are used to build a feature vector enabling to capture not only the physicochemical properties but also position related information of the amino acids. An extremely randomized trees algorithm is applied to choose the optimal features to remove redundancy and dependence among components of the feature vector by a supervised fashion. Finally the support vector machine classifier is used to label the amidation sites. When tested on an independent data set, it shows that the proposed method performs better than all the previous ones with the prediction accuracy of 0.962 at the Matthew's correlation coefficient of 0.89 and area under curve of 0.964.

Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta

DOE PAGES

Patil, Shrikant; Moeys, Sara; von Dassow, Peter; ...

2015-11-14

Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestralmore » loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. Lastly, our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.« less

Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta

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

Patil, Shrikant; Moeys, Sara; von Dassow, Peter

Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestralmore » loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. Lastly, our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.« less

Surface Development and Test Facility (SDTF) New R&D Simulator for Airport Operations

NASA Technical Reports Server (NTRS)

Dorighi, Nancy S.

1997-01-01

A new simulator, the Surface Development and Test Facility (SDTF) is under construction at the NASA Ames Research Center in Mountain View, California. Jointly funded by the FAA (Federal Aviation Administration) and NASA, the SDTF will be a testbed for airport surface automation technologies of the future. The SDTF will be operational in the third quarter of 1998. The SDTF will combine a virtual tower with simulated ground operations to allow evaluation of new technologies for safety, effectiveness, reliability, and cost benefit. The full-scale level V tower will provide a seamless 360 degree high resolution out-the-window view, and a full complement of ATC (air traffic control) controller positions. The imaging system will be generated by two fully-configured Silicon Graphics Onyx Infinite Reality computers, and will support surface movement of up to 200 aircraft and ground vehicles. The controller positions, displays and consoles can be completely reconfigured to match the unique layout of any individual airport tower. Dedicated areas will accommodate pseudo-airport ramp controllers, pseudo-airport operators, and pseudo-pilots. Up to 33 total personnel positions will be able to participate in simultaneous operational scenarios. A realistic voice communication infrastructure will emulate the intercom and telephone communications of a real airport tower. Multi-channel audio and video recording and a sophisticated data acquisition system will support a wide variety of research and development areas, such as evaluation of automation tools for surface operations, human factors studies, integration of terminal area and airport technologies, and studies of potential airport physical and procedural modifications.

Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta.

PubMed

Patil, Shrikant; Moeys, Sara; von Dassow, Peter; Huysman, Marie J J; Mapleson, Daniel; De Veylder, Lieven; Sanges, Remo; Vyverman, Wim; Montresor, Marina; Ferrante, Maria Immacolata

2015-11-14

Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestral loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. Our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.

Echo-Planar Imaging-Based, J-Resolved Spectroscopic Imaging for Improved Metabolite Detection in Prostate Cancer

DTIC Science & Technology

2016-12-01

tiple dimensions (20). Hu et al. employed pseudo-random phase-encoding blips during the EPSI readout to create nonuniform sampling along the spatial...resolved MRSI with Nonuniform Undersampling and Compressed Sensing 514 30.5 Prior-knowledge Fitting for Metabolite Quantitation 515 30.6 Future Directions... NONUNIFORM UNDERSAMPLING AND COMPRESSED SENSING Nonuniform undersampling (NUS) of k-space and subsequent reconstruction using compressed sensing (CS

Ballistic Missile Defense Glossary Version 3.0.

DTIC Science & Technology

1997-06-01

The suppression of background noise for the improvement of an object signal. Battlefield Area Evaluation (USA term). Best and Final Offer...field of the lens are focused. An FPA is a matrix of photon sensitive detectors which, when combined with low noise preamplifiers, provides image data...orbital planes with an orbit period of 12 hours at 10,900 nautical miles altitude. Each satellite transmits three L-band, pseudo-random noise -coded

Mining and Querying Multimedia Data

DTIC Science & Technology

2011-09-29

able to capture more subtle spatial variations such as repetitiveness. Local feature descriptors such as SIFT [74] and SURF [12] have also been widely...empirically set to s = 90%, r = 50%, K = 20, where small variations lead to little perturbation of the output. The pseudo-code of the algorithm is...by constructing a three-layer graph based on clustering outputs, and executing a slight variation of random walk with restart algorithm. It provided

Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore

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

Kou, Qiang; Zhu, Binhai; Wu, Si

Various proteoforms may be generated from a single gene due to primary structure alterations (PSAs) such as genetic variations, alternative splicing, and post-translational modifications (PTMs). Top-down mass spectrometry is capable of analyzing intact proteins and identifying patterns of multiple PSAs, making it the method of choice for studying complex proteoforms. In top-down proteomics, proteoform identification is often performed by searching tandem mass spectra against a protein sequence database that contains only one reference protein sequence for each gene or transcript variant in a proteome. Because of the incompleteness of the protein database, an identified proteoform may contain unknown PSAs comparedmore » with the reference sequence. Proteoform characterization is to identify and localize PSAs in a proteoform. Although many software tools have been proposed for proteoform identification by top-down mass spectrometry, the characterization of proteoforms in identified proteoform-spectrum matches still relies mainly on manual annotation. We propose to use the Modification Identification Score (MIScore), which is based on Bayesian models, to automatically identify and localize PTMs in proteoforms. Experiments showed that the MIScore is accurate in identifying and localizing one or two modifications.« less

Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS

NASA Astrophysics Data System (ADS)

Yang, Rong-Sheng; Tang, Weijuan; Sheng, Huaming; Meng, Fanyu

2018-01-01

Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. [Figure not available: see fulltext.

Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS

NASA Astrophysics Data System (ADS)

Yang, Rong-Sheng; Tang, Weijuan; Sheng, Huaming; Meng, Fanyu

2018-05-01

Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. [Figure not available: see fulltext.

Noise-Induced Synchronization among Sub-RF CMOS Analog Oscillators for Skew-Free Clock Distribution

NASA Astrophysics Data System (ADS)

Utagawa, Akira; Asai, Tetsuya; Hirose, Tetsuya; Amemiya, Yoshihito

We present on-chip oscillator arrays synchronized by random noises, aiming at skew-free clock distribution on synchronous digital systems. Nakao et al. recently reported that independent neural oscillators can be synchronized by applying temporal random impulses to the oscillators [1], [2]. We regard neural oscillators as independent clock sources on LSIs; i. e., clock sources are distributed on LSIs, and they are forced to synchronize through the use of random noises. We designed neuron-based clock generators operating at sub-RF region (<1GHz) by modifying the original neuron model to a new model that is suitable for CMOS implementation with 0.25-μm CMOS parameters. Through circuit simulations, we demonstrate that i) the clock generators are certainly synchronized by pseudo-random noises and ii) clock generators exhibited phase-locked oscillations even if they had small device mismatches.

Post-transcriptional modifications in the small subunit ribosomal RNA from Thermotoga maritima, including presence of a novel modified cytidine

PubMed Central

Guymon, Rebecca; Pomerantz, Steven C.; Ison, J. Nicholas; Crain, Pamela F.; McCloskey, James A.

2007-01-01

Post-transcriptional modifications of RNA are nearly ubiquitous in the principal RNAs involved in translation. However, in the case of rRNA the functional roles of modification are far less established than for tRNA, and are subject to less knowledge in terms of specific nucleoside identities and their sequence locations. Post-transcriptional modifications have been studied in the SSU rRNA from Thermotoga maritima (optimal growth 80°C), one of the most deeply branched organisms in the Eubacterial phylogenetic tree. A total of 10 different modified nucleosides were found, the greatest number reported for bacterial SSU rRNA, occupying a net of ∼14 sequence sites, compared with a similar number of sites recently reported for Thermus thermophilus and 11 for Escherichia coli. The relatively large number of modifications in Thermotoga offers modest support for the notion that thermophile rRNAs are more extensively modified than those from mesophiles. Seven of the Thermotoga modified sites are identical (location and identity) to those in E. coli. An unusual derivative of cytidine was found, designated N-330 (M r 330.117), and was sequenced to position 1404 in the decoding region of the rRNA. It was unexpectedly found to be identical to an earlier reported nucleoside of unknown structure at the same location in the SSU RNA of the archaeal mesophile Haloferax volcanii. PMID:17255199

Replication Protein A-1 Has a Preference for the Telomeric G-rich Sequence in Trypanosoma cruzi.

PubMed

Pavani, Raphael Souza; Vitarelli, Marcela O; Fernandes, Carlos A H; Mattioli, Fabio F; Morone, Mariana; Menezes, Milene C; Fontes, Marcos R M; Cano, Maria Isabel N; Elias, Maria Carolina

2018-05-01

Replication protein A (RPA), the major eukaryotic single-stranded binding protein, is a heterotrimeric complex formed by RPA-1, RPA-2, and RPA-3. RPA is a fundamental player in replication, repair, recombination, and checkpoint signaling. In addition, increasing evidences have been adding functions to RPA in telomere maintenance, such as interaction with telomerase to facilitate its activity and also involvement in telomere capping in some conditions. Trypanosoma cruzi, the etiological agent of Chagas disease is a protozoa parasite that appears early in the evolution of eukaryotes. Recently, we have showed that T. cruziRPA presents canonical functions being involved with DNA replication and DNA damage response. Here, we found by FISH/IF assays that T. cruziRPA localizes at telomeres even outside replication (S) phase. In vitro analysis showed that one telomeric repeat is sufficient to bind RPA-1. Telomeric DNA induces different secondary structural modifications on RPA-1 in comparison with other types of DNA. In addition, RPA-1 presents a higher affinity for telomeric sequence compared to randomic sequence, suggesting that RPA may play specific roles in T. cruzi telomeric region. © 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists.

Genomic and chromatin features shaping meiotic double-strand break formation and repair in mice

PubMed Central

Jasin, Maria; Lange, Julian

2017-01-01

ABSTRACT The SPO11-generated DNA double-strand breaks (DSBs) that initiate meiotic recombination occur non-randomly across genomes, but mechanisms shaping their distribution and repair remain incompletely understood. Here, we expand on recent studies of nucleotide-resolution DSB maps in mouse spermatocytes. We find that trimethylation of histone H3 lysine 36 around DSB hotspots is highly correlated, both spatially and quantitatively, with trimethylation of H3 lysine 4, consistent with coordinated formation and action of both PRDM9-dependent histone modifications. In contrast, the DSB-responsive kinase ATM contributes independently of PRDM9 to controlling hotspot activity, and combined action of ATM and PRDM9 can explain nearly two-thirds of the variation in DSB frequency between hotspots. DSBs were modestly underrepresented in most repetitive sequences such as segmental duplications and transposons. Nonetheless, numerous DSBs form within repetitive sequences in each meiosis and some classes of repeats are preferentially targeted. Implications of these findings are discussed for evolution of PRDM9 and its role in hybrid strain sterility in mice. Finally, we document the relationship between mouse strain-specific DNA sequence variants within PRDM9 recognition motifs and attendant differences in recombination outcomes. Our results provide further insights into the complex web of factors that influence meiotic recombination patterns. PMID:28820351

PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing.

PubMed

Malina, Abba; Cameron, Christopher J F; Robert, Francis; Blanchette, Mathieu; Dostie, Josée; Pelletier, Jerry

2015-12-08

In CRISPR-Cas9 genome editing, the underlying principles for selecting guide RNA (gRNA) sequences that would ensure for efficient target site modification remain poorly understood. Here we show that target sites harbouring multiple protospacer adjacent motifs (PAMs) are refractory to Cas9-mediated repair in situ. Thus we refine which substrates should be avoided in gRNA design, implicating PAM density as a novel sequence-specific feature that inhibits in vivo Cas9-driven DNA modification.

PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing

PubMed Central

Malina, Abba; Cameron, Christopher J. F.; Robert, Francis; Blanchette, Mathieu; Dostie, Josée; Pelletier, Jerry

2015-01-01

In CRISPR-Cas9 genome editing, the underlying principles for selecting guide RNA (gRNA) sequences that would ensure for efficient target site modification remain poorly understood. Here we show that target sites harbouring multiple protospacer adjacent motifs (PAMs) are refractory to Cas9-mediated repair in situ. Thus we refine which substrates should be avoided in gRNA design, implicating PAM density as a novel sequence-specific feature that inhibits in vivo Cas9-driven DNA modification. PMID:26644285

Lack of association between the pseudo deficiency mutation in the arylsulfatase A gene on chromosome 22 with schizophrenia

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

Chang, P.L.; Chetty, V.; Kasch, L.

Arylsulfatase-A deficiency causes the neurodegenerative lysosomal storage disease metachromatic leukodystrophy. In the late-onset variant, schizophrenia-like psychosis is a frequent finding and sometimes given as the initial diagnosis. A mutant allele, pseudo-deficiency, causes deficient enzyme activity but no apparent clinical effect. It occurs at a high frequency and consists of two tightly-linked A{r_arrow}G transitions: one causing the loss of a glycosylation site (PDg); and one causing the loss of a polyadenylation signal (PDa). Since this gene was mapped to chromosome 22q13-qter, a region implicated in a potential linkage with schizophrenia, we hypothesized that this common mutation may be a predisposing geneticmore » factor for schizophrenia. We studied a random sample of schizophrenic patients for possible increase in frequency of the pseudo-deficiency mutations and in multiplex families to verify if the mutations are linked to schizophrenia. Among 50 Caucasian patients identified through out-patient and in-patient clinics, the frequencies for the three alleles PDg + PDa together, PDg or PDa alone were 11%, 5% and 0%, respectively. The corresponding frequencies among 100 Caucasian controls were 7.5%, 6% and 0%, respectively, the differences between the patients and controls being insignificant ({chi}{sup 2}tests: 0.10« less

Modeling of batch sorber system: kinetic, mechanistic, and thermodynamic modeling

NASA Astrophysics Data System (ADS)

Mishra, Vishal

2017-10-01

The present investigation has dealt with the biosorption of copper and zinc ions on the surface of egg-shell particles in the liquid phase. Various rate models were evaluated to elucidate the kinetics of copper and zinc biosorptions, and the results indicated that the pseudo-second-order model was more appropriate than the pseudo-first-order model. The curve of the initial sorption rate versus the initial concentration of copper and zinc ions also complemented the results of the pseudo-second-order model. Models used for the mechanistic modeling were the intra-particle model of pore diffusion and Bangham's model of film diffusion. The results of the mechanistic modeling together with the values of pore and film diffusivities indicated that the preferential mode of the biosorption of copper and zinc ions on the surface of egg-shell particles in the liquid phase was film diffusion. The results of the intra-particle model showed that the biosorption of the copper and zinc ions was not dominated by the pore diffusion, which was due to macro-pores with open-void spaces present on the surface of egg-shell particles. The thermodynamic modeling reproduced the fact that the sorption of copper and zinc was spontaneous, exothermic with the increased order of the randomness at the solid-liquid interface.

The Effect of Interference on Temporal Order Memory for Random and Fixed Sequences in Nondemented Older Adults

ERIC Educational Resources Information Center

Tolentino, Jerlyn C.; Pirogovsky, Eva; Luu, Trinh; Toner, Chelsea K.; Gilbert, Paul E.

2012-01-01

Two experiments tested the effect of temporal interference on order memory for fixed and random sequences in young adults and nondemented older adults. The results demonstrate that temporal order memory for fixed and random sequences is impaired in nondemented older adults, particularly when temporal interference is high. However, temporal order…

Long-Term Predictive and Feedback Encoding of Motor Signals in the Simple Spike Discharge of Purkinje Cells

PubMed Central

Popa, Laurentiu S.; Streng, Martha L.

2017-01-01

Abstract Most hypotheses of cerebellar function emphasize a role in real-time control of movements. However, the cerebellum’s use of current information to adjust future movements and its involvement in sequencing, working memory, and attention argues for predicting and maintaining information over extended time windows. The present study examines the time course of Purkinje cell discharge modulation in the monkey (Macaca mulatta) during manual, pseudo-random tracking. Analysis of the simple spike firing from 183 Purkinje cells during tracking reveals modulation up to 2 s before and after kinematics and position error. Modulation significance was assessed against trial shuffled firing, which decoupled simple spike activity from behavior and abolished long-range encoding while preserving data statistics. Position, velocity, and position errors have the most frequent and strongest long-range feedforward and feedback modulations, with less common, weaker long-term correlations for speed and radial error. Position, velocity, and position errors can be decoded from the population simple spike firing with considerable accuracy for even the longest predictive (-2000 to -1500 ms) and feedback (1500 to 2000 ms) epochs. Separate analysis of the simple spike firing in the initial hold period preceding tracking shows similar long-range feedforward encoding of the upcoming movement and in the final hold period feedback encoding of the just completed movement, respectively. Complex spike analysis reveals little long-term modulation with behavior. We conclude that Purkinje cell simple spike discharge includes short- and long-range representations of both upcoming and preceding behavior that could underlie cerebellar involvement in error correction, working memory, and sequencing. PMID:28413823

Heterogeneous Suppression of Sequential Effects in Random Sequence Generation, but Not in Operant Learning.

PubMed

Shteingart, Hanan; Loewenstein, Yonatan

2016-01-01

There is a long history of experiments in which participants are instructed to generate a long sequence of binary random numbers. The scope of this line of research has shifted over the years from identifying the basic psychological principles and/or the heuristics that lead to deviations from randomness, to one of predicting future choices. In this paper, we used generalized linear regression and the framework of Reinforcement Learning in order to address both points. In particular, we used logistic regression analysis in order to characterize the temporal sequence of participants' choices. Surprisingly, a population analysis indicated that the contribution of the most recent trial has only a weak effect on behavior, compared to more preceding trials, a result that seems irreconcilable with standard sequential effects that decay monotonously with the delay. However, when considering each participant separately, we found that the magnitudes of the sequential effect are a monotonous decreasing function of the delay, yet these individual sequential effects are largely averaged out in a population analysis because of heterogeneity. The substantial behavioral heterogeneity in this task is further demonstrated quantitatively by considering the predictive power of the model. We show that a heterogeneous model of sequential dependencies captures the structure available in random sequence generation. Finally, we show that the results of the logistic regression analysis can be interpreted in the framework of reinforcement learning, allowing us to compare the sequential effects in the random sequence generation task to those in an operant learning task. We show that in contrast to the random sequence generation task, sequential effects in operant learning are far more homogenous across the population. These results suggest that in the random sequence generation task, different participants adopt different cognitive strategies to suppress sequential dependencies when generating the "random" sequences.

Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

PubMed Central

Chatterjee, Aniruddha; Rodger, Euan J.; Stockwell, Peter A.; Weeks, Robert J.; Morison, Ian M.

2012-01-01

Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background. PMID:23193365

Progress in the preparation and application of modified biochar for improved contaminant removal from water and wastewater.

PubMed

Ahmed, Mohammad Boshir; Zhou, John L; Ngo, Huu H; Guo, Wenshan; Chen, Mengfang

2016-08-01

Modified biochar (BC) is reviewed in its preparation, functionality, applications and regeneration. The nature of precursor materials, preparatory conditions and modification methods are key factors influencing BC properties. Steam activation is unsuitable for improving BC surface functionality compared with chemical modifications. Alkali-treated BC possesses the highest surface functionality. Both alkali modified BC and nanomaterial impregnated BC composites are highly favorable for enhancing the adsorption of different contaminants from wastewater. Acidic treatment provides more oxygenated functional groups on BC surfaces. The Langmuir isotherm model provides the best fit for sorption equilibria of heavy metals and anionic contaminants, while the Freundlich isotherm model is the best fit for emerging contaminants. The pseudo 2(nd) order is the most appropriate model of sorption kinetics for all contaminants. Future research should focus on industry-scale applications and hybrid systems for contaminant removal due to scarcity of data. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ammonia-nitrogen sorptional properties of banana peels.

PubMed

Chen, Yunnen; Ding, Lichao; Fan, Jingbiao

2011-04-01

Using modified banana peel as a biosorbent to treat water containing ammonia-nitrogen (NH4(+)-N) was studied. Related parameters in the sorptional process, such as chemical modification, pH, and contact time were investigated. The experimental results showed that banana peel modified by 30% sodium hydroxide (NaOH) and mesothermal microwaves (NMBPs) can greatly improve the sorption removal for NH4(+)-N. The kinetics study revealed that the sorption behavior better fit the pseudo-second-order equation than the Lagergren first-order equation. Fourier transform infrared absorption spectrum analysis of banana peels and NMBPs before and after NH4(+)-N sorption revealed that the activity of hydroxyl groups at the surface of the banana peels was strengthened after modification, and nitrogenous groups appeared after biosorpting the NH4(+)-N. In the end, metallurgical wastewater containing a low concentration of NH4(+)-N was treated by NMBPs. The initial NH4(+)-N concentration of 138 mg/L was reduced to 13 mg/L in 25 minutes by 4 g/L NMBPs at pH 10.

Measurement of Z0-boson production at large rapidities in Pb-Pb collisions at √{sNN } = 5.02TeV

NASA Astrophysics Data System (ADS)

Acharya, S.; Adamová, D.; Adolfsson, J.; Aggarwal, M. M.; Aglieri Rinella, G.; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahn, S. U.; Aiola, S.; Akindinov, A.; Al-Turany, M.; Alam, S. N.; Albuquerque, D. S. D.; Aleksandrov, D.; Alessandro, B.; Alfaro Molina, R.; Ali, Y.; Alici, A.; Alkin, A.; Alme, J.; Alt, T.; Altenkamper, L.; Altsybeev, I.; Andrei, C.; Andreou, D.; Andrews, H. A.; Andronic, A.; Angeletti, M.; Anguelov, V.; Anson, C.; Antičić, T.; Antinori, F.; Antonioli, P.; Apadula, N.; Aphecetche, L.; Appelshäuser, H.; Arcelli, S.; Arnaldi, R.; Arnold, O. W.; Arsene, I. C.; Arslandok, M.; Audurier, B.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Badalà, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Baldisseri, A.; Ball, M.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barioglio, L.; Barnaföldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Barth, K.; Bartsch, E.; Bastid, N.; Basu, S.; Batigne, G.; Batyunya, B.; Batzing, P. C.; Bazo Alba, J. L.; Bearden, I. 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A.; Carena, F.; Carena, W.; Carnesecchi, F.; Castillo Castellanos, J.; Castro, A. J.; Casula, E. A. R.; Ceballos Sanchez, C.; Chandra, S.; Chang, B.; Chang, W.; Chapeland, S.; Chartier, M.; Chattopadhyay, S.; Chattopadhyay, S.; Chauvin, A.; Cheshkov, C.; Cheynis, B.; Chibante Barroso, V.; Chinellato, D. D.; Cho, S.; Chochula, P.; Chojnacki, M.; Choudhury, S.; Chowdhury, T.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Chung, S. U.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Concas, M.; Conesa Balbastre, G.; Conesa Del Valle, Z.; Contreras, J. G.; Cormier, T. M.; Corrales Morales, Y.; Cortés Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Costanza, S.; Crkovská, J.; Crochet, P.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danisch, M. C.; Danu, A.; Das, D.; Das, I.; Das, S.; Dash, A.; Dash, S.; de, S.; de Caro, A.; de Cataldo, G.; de Conti, C.; de Cuveland, J.; de Falco, A.; de Gruttola, D.; De Marco, N.; de Pasquale, S.; de Souza, R. D.; Degenhardt, H. F.; Deisting, A.; Deloff, A.; Deplano, C.; Dhankher, P.; di Bari, D.; di Mauro, A.; di Nezza, P.; di Ruzza, B.; Dietel, T.; Dillenseger, P.; Ding, Y.; Divià, R.; Djuvsland, Ø.; Dobrin, A.; Domenicis Gimenez, D.; Dönigus, B.; Dordic, O.; Doremalen, L. V. R.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dudi, S.; Duggal, A. K.; Dukhishyam, M.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Endress, E.; Engel, H.; Epple, E.; Erazmus, B.; Erhardt, F.; Espagnon, B.; Eulisse, G.; Eum, J.; Evans, D.; Evdokimov, S.; Fabbietti, L.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Feliciello, A.; Feofilov, G.; Fernández Téllez, A.; Ferretti, A.; Festanti, A.; Feuillard, V. J. G.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Francisco, A.; Frankenfeld, U.; Fronze, G. G.; Fuchs, U.; Furget, C.; Furs, A.; Fusco Girard, M.; Gaardhøje, J. J.; Gagliardi, M.; Gago, A. M.; Gajdosova, K.; Gallio, M.; Galvan, C. D.; Ganoti, P.; Garabatos, C.; Garcia-Solis, E.; Garg, K.; Gargiulo, C.; Gasik, P.; Gauger, E. F.; Gay Ducati, M. B.; Germain, M.; Ghosh, J.; Ghosh, P.; Ghosh, S. K.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-Dziadus, E.; Glässel, P.; Goméz Coral, D. M.; Gomez Ramirez, A.; Gonzalez, A. S.; González-Zamora, P.; Gorbunov, S.; Görlich, L.; Gotovac, S.; Grabski, V.; Graczykowski, L. K.; Graham, K. L.; Greiner, L.; Grelli, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Gronefeld, J. M.; Grosa, F.; Grosse-Oetringhaus, J. F.; Grosso, R.; Guber, F.; Guernane, R.; Guerzoni, B.; Guittiere, M.; Gulbrandsen, K.; Gunji, T.; Gupta, A.; Gupta, R.; Guzman, I. B.; Haake, R.; Hadjidakis, C.; Hamagaki, H.; Hamar, G.; Hamon, J. C.; Haque, M. R.; Harris, J. W.; Harton, A.; Hassan, H.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Hellbär, E.; Helstrup, H.; Herghelegiu, A.; Hernandez, E. G.; Herrera Corral, G.; Herrmann, F.; Hess, B. A.; Hetland, K. F.; Hillemanns, H.; Hills, C.; Hippolyte, B.; Hohlweger, B.; Horak, D.; Hornung, S.; Hosokawa, R.; Hristov, P.; Hughes, C.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Iddon, J. P.; Iga Buitron, S. A.; Ilkaev, R.; Inaba, M.; Ippolitov, M.; Islam, M. S.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jacak, B.; Jacazio, N.; Jacobs, P. M.; Jadhav, M. B.; Jadlovska, S.; Jadlovsky, J.; Jaelani, S.; Jahnke, C.; Jakubowska, M. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jercic, M.; Jimenez Bustamante, R. T.; Jones, P. G.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kang, J. H.; Kaplin, V.; Kar, S.; Karasu Uysal, A.; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karczmarczyk, P.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Ketzer, B.; Khabanova, Z.; Khan, P.; Khan, S.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Khatun, A.; Khuntia, A.; Kielbowicz, M. M.; Kileng, B.; Kim, B.; Kim, D.; Kim, D. J.; Kim, E. J.; Kim, H.; Kim, J. S.; Kim, J.; Kim, M.; Kim, S.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein, J.; Klein-Bösing, C.; Klewin, S.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobdaj, C.; Kofarago, M.; Köhler, M. K.; Kollegger, T.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Konyushikhin, M.; Kopcik, M.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.; Králik, I.; Kravčáková, A.; Kreis, L.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kučera, V.; Kuhn, C.; Kuijer, P. G.; Kumar, A.; Kumar, J.; Kumar, L.; Kumar, S.; Kundu, S.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kushpil, S.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Lagana Fernandes, C.; Lai, Y. S.; Lakomov, I.; Langoy, R.; Lapidus, K.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lavicka, R.; Lea, R.; Leardini, L.; Lee, S.; Lehas, F.; Lehner, S.; Lehrbach, J.; Lemmon, R. C.; Leogrande, E.; León Monzón, I.; Lévai, P.; Li, X.; Li, X. L.; Lien, J.; Lietava, R.; Lim, B.; Lindal, S.; Lindenstruth, V.; Lindsay, S. W.; Lippmann, C.; Lisa, M. A.; Litichevskyi, V.; Liu, A.; Llope, W. J.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Loncar, P.; Lopez, X.; López Torres, E.; Lowe, A.; Luettig, P.; Luhder, J. R.; Lunardon, M.; Luparello, G.; Lupi, M.; Lutz, T. H.; Maevskaya, A.; Mager, M.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Malinina, L.; Mal'Kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Mao, Y.; Marchisone, M.; Mareš, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marín, A.; Markert, C.; Marquard, M.; Martin, N. A.; Martinengo, P.; Martinez, J. A. L.; Martínez, M. I.; Martínez García, G.; Martinez Pedreira, M.; Masciocchi, S.; Masera, M.; Masoni, A.; Massacrier, L.; Masson, E.; Mastroserio, A.; Mathis, A. M.; Matuoka, P. F. T.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzilli, M.; Mazzoni, M. A.; Meddi, F.; Melikyan, Y.; Menchaca-Rocha, A.; Meninno, E.; Mercado Pérez, J.; Meres, M.; Mhlanga, S.; Miake, Y.; Mieskolainen, M. M.; Mihaylov, D. L.; Mikhaylov, K.; Mischke, A.; Mishra, A. N.; Miśkowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, A. P.; Mohanty, B.; Mohisin Khan, M.; Moreira de Godoy, D. A.; Moreno, L. A. P.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Mühlheim, D.; Muhuri, S.; Mukherjee, M.; Mulligan, J. D.; Munhoz, M. G.; Münning, K.; Munoz, M. I. A.; Munzer, R. H.; Murakami, H.; Murray, S.; Musa, L.; Musinsky, J.; Myers, C. J.; Myrcha, J. W.; Nag, D.; Naik, B.; Nair, R.; Nandi, B. K.; Nania, R.; Nappi, E.; Narayan, A.; Naru, M. U.; Natal da Luz, H.; Nattrass, C.; Navarro, S. R.; Nayak, K.; Nayak, R.; Nayak, T. K.; Nazarenko, S.; Negrao de Oliveira, R. A.; Nellen, L.; Nesbo, S. V.; Neskovic, G.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Nobuhiro, A.; Noferini, F.; Nomokonov, P.; Nooren, G.; Noris, J. C. C.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, H.; Ohlson, A.; Olah, L.; Oleniacz, J.; Oliveira da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Orava, R.; Oravec, M.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Pachmayer, Y.; Pacik, V.; Pagano, D.; Paić, G.; Palni, P.; Pan, J.; Pandey, A. K.; Panebianco, S.; Papikyan, V.; Pareek, P.; Park, J.; Parmar, S.; Passfeld, A.; Pathak, S. P.; Patra, R. N.; Paul, B.; Pei, H.; Peitzmann, T.; Peng, X.; Pereira, L. G.; Pereira da Costa, H.; Peresunko, D.; Perez Lezama, E.; Peskov, V.; Pestov, Y.; Petráček, V.; Petrovici, M.; Petta, C.; Pezzi, R. P.; Piano, S.; Pikna, M.; Pillot, P.; Pimentel, L. O. D. L.; Pinazza, O.; Pinsky, L.; Piyarathna, D. B.; Płoskoń, M.; Planinic, M.; Pliquett, F.; Pluta, J.; Pochybova, S.; Podesta-Lerma, P. L. M.; Poghosyan, M. G.; Polichtchouk, B.; Poljak, N.; Poonsawat, W.; Pop, A.; Poppenborg, H.; Porteboeuf-Houssais, S.; Pozdniakov, V.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puccio, M.; Punin, V.; Putschke, J.; Raha, S.; Rajput, S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Rami, F.; Rana, D. B.; Raniwala, R.; Raniwala, S.; Räsänen, S. S.; Rascanu, B. T.; Rathee, D.; Ratza, V.; Ravasenga, I.; Read, K. F.; Redlich, K.; Rehman, A.; Reichelt, P.; Reidt, F.; Ren, X.; Renfordt, R.; Reshetin, A.; Reygers, K.; Riabov, V.; Richert, T.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Ristea, C.; Rodríguez Cahuantzi, M.; Røed, K.; Rogalev, R.; Rogochaya, E.; Rohr, D.; Röhrich, D.; Rokita, P. S.; Ronchetti, F.; Rosas, E. D.; Roslon, K.; Rosnet, P.; Rossi, A.; Rotondi, A.; Roukoutakis, F.; Roy, C.; Roy, P.; Rueda, O. V.; Rui, R.; Rumyantsev, B.; Rustamov, A.; Ryabinkin, E.; Ryabov, Y.; Rybicki, A.; Saarinen, S.; Sadhu, S.; Sadovsky, S.; Šafařík, K.; Saha, S. K.; Sahoo, B.; Sahoo, P.; Sahoo, R.; Sahoo, S.; Sahu, P. K.; Saini, J.; Sakai, S.; Saleh, M. A.; Salzwedel, J.; Sambyal, S.; Samsonov, V.; Sandoval, A.; Sarkar, A.; Sarkar, D.; Sarkar, N.; Sarma, P.; Sas, M. H. P.; Scapparone, E.; Scarlassara, F.; Schaefer, B.; Scheid, H. S.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schmidt, M. O.; Schmidt, M.; Schmidt, N. V.; Schukraft, J.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Šefčík, M.; Seger, J. E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Senyukov, S.; Serradilla, E.; Sett, P.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shahoyan, R.; Shaikh, W.; Shangaraev, A.; Sharma, A.; Sharma, A.; Sharma, M.; Sharma, M.; Sharma, N.; Sheikh, A. I.; Shigaki, K.; Shimomura, M.; Shirinkin, S.; Shou, Q.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silaeva, S.; Silvermyr, D.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singhal, V.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Song, J.; Soramel, F.; Sorensen, S.; Sozzi, F.; Sputowska, I.; Stachel, J.; Stan, I.; Stankus, P.; Stenlund, E.; Stocco, D.; Storetvedt, M. M.; Strmen, P.; Suaide, A. A. P.; Sugitate, T.; Suire, C.; Suleymanov, M.; Suljic, M.; Sultanov, R.; Šumbera, M.; Sumowidagdo, S.; Suzuki, K.; Swain, S.; Szabo, A.; Szarka, I.; Tabassam, U.; Takahashi, J.; Tambave, G. J.; Tanaka, N.; Tarhini, M.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Muñoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thakur, D.; Thakur, S.; Thomas, D.; Thoresen, F.; Tieulent, R.; Tikhonov, A.; Timmins, A. R.; Toia, A.; Toppi, M.; Torres, S. R.; Tripathy, S.; Trogolo, S.; Trombetta, G.; Tropp, L.; Trubnikov, V.; Trzaska, W. H.; Trzeciak, B. A.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Umaka, E. N.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vala, M.; van der Maarel, J.; van Hoorne, J. W.; van Leeuwen, M.; Vanat, T.; Vande Vyvre, P.; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Vázquez Doce, O.; Vechernin, V.; Veen, A. M.; Velure, A.; Vercellin, E.; Vergara Limón, S.; Vermunt, L.; Vernet, R.; Vértesi, R.; Vickovic, L.; Viinikainen, J.; Vilakazi, Z.; Villalobos Baillie, O.; Villatoro Tello, A.; Vinogradov, A.; Vinogradov, L.; Virgili, T.; Vislavicius, V.; Vodopyanov, A.; Völkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; von Haller, B.; Vorobyev, I.; Voscek, D.; Vranic, D.; Vrláková, J.; Wagner, B.; Wang, H.; Wang, M.; Watanabe, Y.; Weber, M.; Weber, S. G.; Wegrzynek, A.; Weiser, D. F.; Wenzel, S. C.; Wessels, J. P.; Westerhoff, U.; Whitehead, A. M.; Wiechula, J.; Wikne, J.; Wilk, G.; Wilkinson, J.; Willems, G. A.; Williams, M. C. S.; Willsher, E.; Windelband, B.; Witt, W. E.; Xu, R.; Yalcin, S.; Yamakawa, K.; Yang, P.; Yano, S.; Yin, Z.; Yokoyama, H.; Yoo, I.-K.; Yoon, J. H.; Yun, E.; Yurchenko, V.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zardoshti, N.; Zarochentsev, A.; Závada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zhalov, M.; Zhang, H.; Zhang, X.; Zhang, Y.; Zhang, C.; Zhang, Z.; Zhao, C.; Zhigareva, N.; Zhou, D.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zhu, J.; Zhu, Y.; Zichichi, A.; Zimmermann, M. B.; Zinovjev, G.; Zmeskal, J.; Zou, S.; Alice Collaboration

2018-05-01

The production of Z0 bosons at large rapidities in Pb-Pb collisions at √{sNN } = 5.02TeV is reported. Z0 candidates are reconstructed in the dimuon decay channel (Z0 →μ+μ-), based on muons selected with pseudo-rapidity - 4.0 < η < - 2.5 and pT > 20GeV/ c. The invariant yield and the nuclear modification factor, RAA, are presented as a function of rapidity and collision centrality. The value of RAA for the 0-20% central Pb-Pb collisions is 0.67 ± 0.11(stat.) ± 0.03(syst.) ± 0.06(corr. syst.), exhibiting a deviation of 2.6σ from unity. The results are well-described by calculations that include nuclear modifications of the parton distribution functions, while the predictions using vacuum PDFs deviate from data by 2.3σ in the 0-90% centrality class and by 3σ in the 0-20% central collisions.

Oligomerization of the protein tau in the Alzheimer's disease

NASA Astrophysics Data System (ADS)

Larini, Luca

The Alzheimer's disease is characterized by the formation of protein aggregates both within and outside of the brain's cells, the neurons. Within the neurons, the aggregation of the microtubule associated protein tau leads to the destruction of the microtubules in the axon of the neuron. Tau is extremely flexible and is classified as an intrinsically disordered protein due to its low propensity to form secondary structure. Tau promotes tubulin assembly into microtubules, which are an essential component of the cytoskeleton of the axon. The microtubule binding region of tau consists of 4 pseudo-repeats that are critical for aggregation as well. In this study, we focus on the aggregation propensity of different segments of the microtubule binding region as well as post-translational modifications that can alter tau dynamics and structure. We have performed replica exchange molecular dynamics simulations to characterize the ensemble of conformations of the monomer and small oligomers as well as how these structures are stabilized or destabilized by mutations and post-translational modifications.

Dissociation from DNA of Type III Restriction–Modification enzymes during helicase-dependent motion and following endonuclease activity

PubMed Central

Tóth, Júlia; van Aelst, Kara; Salmons, Hannah; Szczelkun, Mark D.

2012-01-01

DNA cleavage by the Type III Restriction–Modification (RM) enzymes requires the binding of a pair of RM enzymes at two distant, inversely orientated recognition sequences followed by helicase-catalysed ATP hydrolysis and long-range communication. Here we addressed the dissociation from DNA of these enzymes at two stages: during long-range communication and following DNA cleavage. First, we demonstrated that a communicating species can be trapped in a DNA domain without a recognition site, with a non-specific DNA association lifetime of ∼200 s. If free DNA ends were present the lifetime became too short to measure, confirming that ends accelerate dissociation. Secondly, we observed that Type III RM enzymes can dissociate upon DNA cleavage and go on to cleave further DNA molecules (they can ‘turnover’, albeit inefficiently). The relationship between the observed cleavage rate and enzyme concentration indicated independent binding of each site and a requirement for simultaneous interaction of at least two enzymes per DNA to achieve cleavage. In light of various mechanisms for helicase-driven motion on DNA, we suggest these results are most consistent with a thermally driven random 1D search model (i.e. ‘DNA sliding’). PMID:22523084

Modification of semi-coke powder and its adsorption mechanisms for Cr(VI) and methylene blue

NASA Astrophysics Data System (ADS)

Zhang, Linjiang; Liu, Zhuannian; Fan, Yidan; Fan, Aping; Han, Xiaogang

2018-02-01

In this paper, the semi-coke powder was modified by three kinds of physical or chemical methods and then modified semi-coke was used as adsorbent for removal of Cr6+ and methylene blue (MB) from aqueous solution. The effects of time, dosage and pH on removal rate were investigated using batch experiments. The process of Cr6+ and MB adsorption onto the modified semi-coke powder follows pseudo second-order kinetics. The analysis of SEM and BET showed the Specific surface area of modified semi-coke are 84.92 m2/g, which is higher than that of raw semi-coke powder.

System for the growth of bulk SiC crystals by modified CVD techniques

NASA Technical Reports Server (NTRS)

Steckl, Andrew J.

1994-01-01

The goal of this program was the development of a SiC CVD growth of films thick enough to be useful as pseudo-substrates. The cold-walled CVD system was designed, assembled, and tested. Extrapolating from preliminary evaluation of SiC films grown in the system at relatively low temperatures indicates that the growth rate at the final temperatures will be high enough to make our approach practical. Modifications of the system to allow high temperature growth and cleaner growth conditions are in progress. This program was jointly funded by Wright Laboratory, Materials Directorate and NASA LeRC and monitored by NASA.

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly.

PubMed

Patel, Sagar; Lu, Zhixiu; Jin, Xiaozhu; Swaminathan, Padmapriya; Zeng, Erliang; Fennell, Anne Y

2018-01-17

De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC). The three new assemblies were greater in size than the AP assembly. PLAT*_GC had the greatest number of scaffolds aligning with a minimum of 95% identity and ≥1000 bp alignment length to V. vinifera (PN40024 12X.v2) reference genome. SNP analysis also identified additional high quality SNPs. A greater number of sequence reads mapped back with zero-mismatch to the PLAT_d, MERGE, and PLAT*_GC (>94%) than was found in the AP assembly (87%) indicating a greater fidelity to the original sequence data in the new assemblies than in AP assembly. A de novo gene prediction conducted using seedless RNA-seq data predicted > 30,000 coding sequences for the three new de novo assemblies, with the greatest number (30,544) in PLAT*_GC and only 26,515 for the AP assembly. Transcription factor analysis indicated good family coverage, but some genes found in the VCOST.v3 annotation were not identified in any of the de novo assemblies, particularly some from  the MYB and ERF families. The PLAT_d and PLAT*_GC had a greater number of synteny blocks with the V. vinifera (PN40024 12X.v2) reference genome than AP or MERGE. PLAT*_GC provided the most contiguous assembly with only 1.2% scaffold N, in contrast to AP (10.7% N), PLAT_d (6.6% N) and Merge (6.4% N). A PLAT*_GC pseudo-chromosome assembly with chromosome alignment to the reference genome V. vinifera, (PN40024 12X.v2) provides new information for use in seedless grape genetic mapping studies. An annotated de novo gene prediction for the PLAT*_GC assembly, aligned with VitisNet pathways provides new seedless grapevine specific transcriptomic resource that has excellent fidelity with the seedless short read sequence data.

Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction.

PubMed

Tengs, Torstein; Zhang, Haibo; Holst-Jensen, Arne; Bohlin, Jon; Butenko, Melinka A; Kristoffersen, Anja Bråthen; Sorteberg, Hilde-Gunn Opsahl; Berdal, Knut G

2009-10-08

When generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown. We show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of Arabidopsis thaliana and published EST datasets from commercially relevant species (rice and papaya). We believe that computational subtraction represents a powerful new strategy for determining if an organism has been genetically modified as well as to define the nature of the modification. Fewer assumptions have to be made compared to methods currently in use and this is an advantage particularly when working with unknown GMOs.

Improving CRISPR-Cas specificity with chemical modifications in single-guide RNAs.

PubMed

Ryan, Daniel E; Taussig, David; Steinfeld, Israel; Phadnis, Smruti M; Lunstad, Benjamin D; Singh, Madhurima; Vuong, Xuan; Okochi, Kenji D; McCaffrey, Ryan; Olesiak, Magdalena; Roy, Subhadeep; Yung, Chong Wing; Curry, Bo; Sampson, Jeffrey R; Bruhn, Laurakay; Dellinger, Douglas J

2018-01-25

CRISPR systems have emerged as transformative tools for altering genomes in living cells with unprecedented ease, inspiring keen interest in increasing their specificity for perfectly matched targets. We have developed a novel approach for improving specificity by incorporating chemical modifications in guide RNAs (gRNAs) at specific sites in their DNA recognition sequence ('guide sequence') and systematically evaluating their on-target and off-target activities in biochemical DNA cleavage assays and cell-based assays. Our results show that a chemical modification (2'-O-methyl-3'-phosphonoacetate, or 'MP') incorporated at select sites in the ribose-phosphate backbone of gRNAs can dramatically reduce off-target cleavage activities while maintaining high on-target performance, as demonstrated in clinically relevant genes. These findings reveal a unique method for enhancing specificity by chemically modifying the guide sequence in gRNAs. Our approach introduces a versatile tool for augmenting the performance of CRISPR systems for research, industrial and therapeutic applications. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction

PubMed Central

Tengs, Torstein; Zhang, Haibo; Holst-Jensen, Arne; Bohlin, Jon; Butenko, Melinka A; Kristoffersen, Anja Bråthen; Sorteberg, Hilde-Gunn Opsahl; Berdal, Knut G

2009-01-01

Background When generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown. Results We show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of Arabidopsis thaliana and published EST datasets from commercially relevant species (rice and papaya). Conclusion We believe that computational subtraction represents a powerful new strategy for determining if an organism has been genetically modified as well as to define the nature of the modification. Fewer assumptions have to be made compared to methods currently in use and this is an advantage particularly when working with unknown GMOs. PMID:19814792

The "pseudo-craniovertebral articulation" in the deep-sea fish Stomias boa (Teleostei: Stomiidae).

PubMed

Schnell, Nalani K; Bernstein, Peter; Maier, Wolfgang

2008-05-01

Many predatory deep-sea fishes show highly specialized modifications of their feeding apparatus, e.g., elongate jaws studded with long daggerlike teeth, often combined with a very distensible stomach, to be capable of swallowing relatively large prey. These striking features can be observed in members of the marine teleost family Stomiidae. The present study gives a detailed morphological description of the mesopelagic predatory fish, Stomias boa, based on a combined approach of clearing and double staining, serial sections and dissection. In this genus, large pads made of dense connective tissue extend from the first enlarged neural arch to the ventral side of the chordal sheath, embracing the prominent exoccipitals and thus constituting a kind of double ball- and socket joint for the head. The notochordal occipito-vertebral gap is enlarged, probably not by loss of vertebral centra as is proposed for other genera of the stomiid family, e.g., in Astronesthes or Photostomias. We conclude that this "pseudo-craniovertebral articulation" serves as a functional substitute for the absent vertebrae and strengthens the flexible, anterior part of the vertebral column during extreme dorsal expansion of the gape during prey capture and swallowing. (c) 2007 Wiley-Liss, Inc.

Conformational sensitivity of conjugated poly(ethylene oxide)-poly(amidoamine) molecules to cations adducted upon electrospray ionization - a mass spectrometry, ion mobility and molecular modeling study.

PubMed

Tintaru, Aura; Chendo, Christophe; Wang, Qi; Viel, Stéphane; Quéléver, Gilles; Peng, Ling; Posocco, Paola; Pricl, Sabrina; Charles, Laurence

2014-01-15

Tandem mass spectrometry and ion mobility spectrometry experiments were performed on multiply charged molecules formed upon conjugation of a poly(amidoamine) (PAMAM) dendrimer with a poly(ethylene oxide) (PEO) linear polymer to evidence any conformational modification as a function of their charge state (2+ to 4+) and of the adducted cation (H(+)vs Li(+)). Experimental findings were rationalized by molecular dynamics simulations. The G0 PAMAM head-group could accommodate up to three protons, with protonated terminal amine group enclosed in a pseudo 18-crown-6 ring formed by the PEO segment. This particular conformation enabled a hydrogen bond network which allowed long-range proton transfer to occur during collisionally activated dissociation. In contrast, lithium adduction was found to mainly occur onto oxygen atoms of the polyether, each Li(+) cation being coordinated by a 12-crown-4 pseudo structure. As a result, for the studied polymeric segment (Mn=1500gmol(-1)), PEO-PAMAM hybrid molecules exhibited a more expanded shape when adducted to lithium as compared to proton. Copyright © 2013 Elsevier B.V. All rights reserved.

Resolution of model Holliday junctions by yeast endonuclease: effect of DNA structure and sequence.

PubMed Central

Parsons, C A; Murchie, A I; Lilley, D M; West, S C

1989-01-01

The resolution of Holliday junctions in DNA involves specific cleavage at or close to the site of the junction. A nuclease from Saccharomyces cerevisiae cleaves model Holliday junctions in vitro by the introduction of nicks in regions of duplex DNA adjacent to the crossover point. In previous studies [Parsons and West (1988) Cell, 52, 621-629] it was shown that cleavage occurred within homologous arm sequences with precise symmetry across the junction. In contrast, junctions with heterologous arm sequences were cleaved asymmetrically. In this work, we have studied the effect of sequence changes and base modification upon the site of cleavage. It is shown that the specificity of cleavage is unchanged providing that perfect homology is maintained between opposing arm sequences. However, in the absence of homology, cleavage depends upon sequence context and is affected by minor changes such as base modification. These data support the proposed mechanism for cleavage of a Holliday junction, which requires homologous alignment of arm sequences in an enzyme--DNA complex as a prerequisite for symmetrical cleavage by the yeast endonuclease. Images PMID:2653810

Genetic control of ColE1 plasmid stability that is independent of plasmid copy number regulation.

PubMed

Standley, Melissa S; Million-Weaver, Samuel; Alexander, David L; Hu, Shuai; Camps, Manel

2018-06-16

ColE1-like plasmid vectors are widely used for expression of recombinant genes in E. coli. For these vectors, segregation of individual plasmids into daughter cells during cell division appears to be random, making them susceptible to loss over time when no mechanisms ensuring their maintenance are present. Here we use the plasmid pGFPuv in a recA relA strain as a sensitized model to study factors affecting plasmid stability in the context of recombinant gene expression. We find that in this model, plasmid stability can be restored by two types of genetic modifications to the plasmid origin of replication (ori) sequence: point mutations and a novel 269 nt duplication at the 5' end of the plasmid ori, which we named DAS (duplicated anti-sense) ori. Combinations of these modifications produce a range of copy numbers and of levels of recombinant expression. In direct contradiction with the classic random distribution model, we find no correlation between increased plasmid copy number and increased plasmid stability. Increased stability cannot be explained by reduced levels of recombinant gene expression either. Our observations would be more compatible with a hybrid clustered and free-distribution model, which has been recently proposed based on detection of individual plasmids in vivo using super-resolution fluorescence microscopy. This work suggests a role for the plasmid ori in the control of segregation of ColE1 plasmids that is distinct from replication initiation, opening the door for the genetic regulation of plasmid stability as a strategy aimed at enhancing large-scale recombinant gene expression or bioremediation.

Treatment Sequencing for Childhood ADHD: A Multiple-Randomization Study of Adaptive Medication and Behavioral Interventions.

PubMed

Pelham, William E; Fabiano, Gregory A; Waxmonsky, James G; Greiner, Andrew R; Gnagy, Elizabeth M; Pelham, William E; Coxe, Stefany; Verley, Jessica; Bhatia, Ira; Hart, Katie; Karch, Kathryn; Konijnendijk, Evelien; Tresco, Katy; Nahum-Shani, Inbal; Murphy, Susan A

2016-01-01

Behavioral and pharmacological treatments for children with attention deficit/hyperactivity disorder (ADHD) were evaluated to address whether endpoint outcomes are better depending on which treatment is initiated first and, in case of insufficient response to initial treatment, whether increasing dose of initial treatment or adding the other treatment modality is superior. Children with ADHD (ages 5-12, N = 146, 76% male) were treated for 1 school year. Children were randomized to initiate treatment with low doses of either (a) behavioral parent training (8 group sessions) and brief teacher consultation to establish a Daily Report Card or (b) extended-release methylphenidate (equivalent to .15 mg/kg/dose bid). After 8 weeks or at later monthly intervals as necessary, insufficient responders were rerandomized to secondary interventions that either increased the dose/intensity of the initial treatment or added the other treatment modality, with adaptive adjustments monthly as needed to these secondary treatments. The group beginning with behavioral treatment displayed significantly lower rates of observed classroom rule violations (the primary outcome) at study endpoint and tended to have fewer out-of-class disciplinary events. Further, adding medication secondary to initial behavior modification resulted in better outcomes on the primary outcomes and parent/teacher ratings of oppositional behavior than adding behavior modification to initial medication. Normalization rates on teacher and parent ratings were generally high. Parents who began treatment with behavioral parent training had substantially better attendance than those assigned to receive training following medication. Beginning treatment with behavioral intervention produced better outcomes overall than beginning treatment with medication.

Simulations Using Random-Generated DNA and RNA Sequences

ERIC Educational Resources Information Center

Bryce, C. F. A.

1977-01-01

Using a very simple computer program written in BASIC, a very large number of random-generated DNA or RNA sequences are obtained. Students use these sequences to predict complementary sequences and translational products, evaluate base compositions, determine frequencies of particular triplet codons, and suggest possible secondary structures.…

Sequence Complexity of Chromosome 3 in Caenorhabditis elegans

PubMed Central

Pierro, Gaetano

2012-01-01

The nucleotide sequences complexity in chromosome 3 of Caenorhabditis elegans (C. elegans) is studied. The complexity of these sequences is compared with some random sequences. Moreover, by using some parameters related to complexity such as fractal dimension and frequency, indicator matrix is given a first classification of sequences of C. elegans. In particular, the sequences with highest and lowest fractal value are singled out. It is shown that the intrinsic nature of the low fractal dimension sequences has many common features with the random sequences. PMID:22919380

Complete genome sequence of Actinosynnema mirum type strain (101T)

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

Land, Miriam; Lapidus, Alla; Mayilraj, Shanmugam

2009-05-20

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together withmore » the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

Sequence Elucidation of an Unknown Cyclic Peptide of High Doping Potential by ETD and CID Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Guan, Fuyu; Uboh, Cornelius E.; Soma, Lawrence R.; Rudy, Jeffrey

2011-04-01

Identification of an unknown substance without any information remains a daunting challenge despite advances in chemistry and mass spectrometry. However, an unknown cyclic peptide in a sample with very limited volume seized at a Pennsylvania racetrack has been successfully identified. The unknown sample was determined by accurate mass measurements to contain a small unknown peptide as the major component. Collision-induced dissociation (CID) of the unknown peptide revealed the presence of Lys (not Gln, by accurate mass), Phe, and Arg residues, and absence of any y-type product ion. The latter, together with the tryptic digestion results of the unusual deamidation and absence of any tryptic cleavage, suggests a cyclic structure for the peptide. Electron-transfer dissociation (ETD) of the unknown peptide indicated the presence of Gln (not Lys, by the unusual deamidation), Phe, and Arg residues and their connectivity. After all the results were pieced together, a cyclic tetrapeptide, cyclo[Arg-Lys-N(C6H9)Gln-Phe], is proposed for the unknown peptide. Observations of different amino acid residues from CID and ETD experiments for the peptide were interpreted by a fragmentation pathway proposed, as was preferential CID loss of a Lys residue from the peptide. ETD was used for the first time in sequencing of a cyclic peptide; product ions resulting from ETD of the peptide identified were categorized into two types and named pseudo-b and pseudo-z ions that are important for sequencing of cyclic peptides. The ETD product ions were interpreted by fragmentation pathways proposed. Additionally, multi-stage CID mass spectrometry cannot provide complete sequence information for cyclic peptides containing adjacent Arg and Lys residues. The identified cyclic peptide has not been documented in the literature, its pharmacological effects are unknown, but it might be a "designer" drug with athletic performance-enhancing effects.

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

PubMed Central

2013-01-01

Background Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. Results Genotyping by Sequencing (GBS) was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs) linked these results to published maps for cross-validation and map comparison. Conclusions GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation distortion in R. idaeus, which may help to identify deleterious alleles that are the basis of inbreeding depression in the species. PMID:23324311

Propagation failures, breathing pulses, and backfiring in an excitable reaction-diffusion system.

PubMed

Manz, Niklas; Steinbock, Oliver

2006-09-01

We report results from experiments with a pseudo-one-dimensional Belousov-Zhabotinsky reaction that employs 1,4-cyclohexanedione as its organic substrate. This excitable system shows traveling oxidation pulses and pulse trains that can undergo complex sequences of propagation failures. Moreover, we present examples for (i) breathing pulses that undergo periodic changes in speed and size and (ii) backfiring pulses that near their back repeatedly generate new pulses propagating in opposite direction.

Analysis and prediction of presynaptic and postsynaptic neurotoxins by Chou's general pseudo amino acid composition and motif features.

PubMed

Mei, Juan; Zhao, Ji

2018-06-14

Presynaptic neurotoxins and postsynaptic neurotoxins are two important neurotoxins isolated from venoms of venomous animals and have been proven to be potential effective in neurosciences and pharmacology. With the number of toxin sequences appeared in the public databases, there was a need for developing a computational method for fast and accurate identification and classification of the novel presynaptic neurotoxins and postsynaptic neurotoxins in the large databases. In this study, the Multinomial Naive Bayes Classifier (MNBC) had been developed to discriminate the presynaptic neurotoxins and postsynaptic neurotoxins based on the different kinds of features. The Minimum Redundancy Maximum Relevance (MRMR) feature selection method was used for ranking 400 pseudo amino acid (PseAA) compositions and 50 top ranked PseAA compositions were selected for improving the prediction results. The motif features, 400 PseAA compositions and 50 PseAA compositions were combined together, and selected as the input parameters of MNBC. The best correlation coefficient (CC) value of 0.8213 was obtained when the prediction quality was evaluated by the jackknife test. It was anticipated that the algorithm presented in this study may become a useful tool for identification of presynaptic neurotoxin and postsynaptic neurotoxin sequences and may provide some useful help for in-depth investigation into the biological mechanism of presynaptic neurotoxins and postsynaptic neurotoxins. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Draft Genome and Transcriptome of Amaranthus hypochondriacus: A C4 Dicot Producing High-Lysine Edible Pseudo-Cereal

PubMed Central

Sunil, Meeta; Hariharan, Arun K.; Nayak, Soumya; Gupta, Saurabh; Nambisan, Suran R.; Gupta, Ravi P.; Panda, Binay; Choudhary, Bibha; Srinivasan, Subhashini

2014-01-01

Grain amaranths, edible C4 dicots, produce pseudo-cereals high in lysine. Lysine being one of the most limiting essential amino acids in cereals and C4 photosynthesis being one of the most sought-after phenotypes in protein-rich legume crops, the genome of one of the grain amaranths is likely to play a critical role in crop research. We have sequenced the genome and transcriptome of Amaranthus hypochondriacus, a diploid (2n = 32) belonging to the order Caryophyllales with an estimated genome size of 466 Mb. Of the 411 linkage single-nucleotide polymorphisms (SNPs) reported for grain amaranths, 355 SNPs (86%) are represented in the scaffolds and 74% of the 8.6 billion bases of the sequenced transcriptome map to the genomic scaffolds. The genome of A. hypochondriacus, codes for at least 24,829 proteins, shares the paleohexaploidy event with species under the superorders Rosids and Asterids, harbours 1 SNP in 1,000 bases, and contains 13.76% of repeat elements. Annotation of all the genes in the lysine biosynthetic pathway using comparative genomics and expression analysis offers insights into the high-lysine phenotype. As the first grain species under Caryophyllales and the first C4 dicot genome reported, the work presented here will be beneficial in improving crops and in expanding our understanding of angiosperm evolution. PMID:25071079

Depletion of Unwanted Nucleic Acid Templates by Selective Cleavage: LNAzymes, Catalytically Active Oligonucleotides Containing Locked Nucleic Acids, Open a New Window for Detecting Rare Microbial Community Members

PubMed Central

Dolinšek, Jan; Dorninger, Christiane; Lagkouvardos, Ilias; Wagner, Michael

2013-01-01

Many studies of molecular microbial ecology rely on the characterization of microbial communities by PCR amplification, cloning, sequencing, and phylogenetic analysis of genes encoding rRNAs or functional marker enzymes. However, if the established clone libraries are dominated by one or a few sequence types, the cloned diversity is difficult to analyze by random clone sequencing. Here we present a novel approach to deplete unwanted sequence types from complex nucleic acid mixtures prior to cloning and downstream analyses. It employs catalytically active oligonucleotides containing locked nucleic acids (LNAzymes) for the specific cleavage of selected RNA targets. When combined with in vitro transcription and reverse transcriptase PCR, this LNAzyme-based technique can be used with DNA or RNA extracts from microbial communities. The simultaneous application of more than one specific LNAzyme allows the concurrent depletion of different sequence types from the same nucleic acid preparation. This new method was evaluated with defined mixtures of cloned 16S rRNA genes and then used to identify accompanying bacteria in an enrichment culture dominated by the nitrite oxidizer “Candidatus Nitrospira defluvii.” In silico analysis revealed that the majority of publicly deposited rRNA-targeted oligonucleotide probes may be used as specific LNAzymes with no or only minor sequence modifications. This efficient and cost-effective approach will greatly facilitate tasks such as the identification of microbial symbionts in nucleic acid preparations dominated by plastid or mitochondrial rRNA genes from eukaryotic hosts, the detection of contaminants in microbial cultures, and the analysis of rare organisms in microbial communities of highly uneven composition. PMID:23263968

A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification.

PubMed

Cenik, Can; Chua, Hon Nian; Singh, Guramrit; Akef, Abdalla; Snyder, Michael P; Palazzo, Alexander F; Moore, Melissa J; Roth, Frederick P

2017-03-01

Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5 ' proximal- i ntron- m inus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5' cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the exon junction complex (EJC) at noncanonical 5' proximal positions. Finally, N 1 -methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising ∼20% of human transcripts. This class is defined by depletion of 5' proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N 1 -methyladenosines in the early coding region, and enrichment for noncanonical binding by the EJC. © 2017 Cenik et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Testability Design Rating System: Testability Handbook. Volume 1

DTIC Science & Technology

1992-02-01

4-10 4.7.5 Summary of False BIT Alarms (FBA) ............................. 4-10 4.7.6 Smart BIT Technique...Circuit Board PGA Pin Grid Array PLA Programmable Logic Array PLD Programmable Logic Device PN Pseudo-Random Number PREDICT Probabilistic Estimation of...11 4.7.6 Smart BIT ( reference: RADC-TR-85-198). " Smart " BIT is a term given to BIT circuitry in a system LRU which includes dedicated processor/memory

Whole-exome sequencing identifies USH2A mutations in a pseudo-dominant Usher syndrome family.

PubMed

Zheng, Sui-Lian; Zhang, Hong-Liang; Lin, Zhen-Lang; Kang, Qian-Yan

2015-10-01

Usher syndrome (USH) is an autosomal recessive (AR) multi-sensory degenerative disorder leading to deaf-blindness. USH is clinically subdivided into three subclasses, and 10 genes have been identified thus far. Clinical and genetic heterogeneities in USH make a precise diagnosis difficult. A dominant‑like USH family in successive generations was identified, and the present study aimed to determine the genetic predisposition of this family. Whole‑exome sequencing was performed in two affected patients and an unaffected relative. Systematic data were analyzed by bioinformatic analysis to remove the candidate mutations via step‑wise filtering. Direct Sanger sequencing and co‑segregation analysis were performed in the pedigree. One novel and two known mutations in the USH2A gene were identified, and were further confirmed by direct sequencing and co‑segregation analysis. The affected mother carried compound mutations in the USH2A gene, while the unaffected father carried a heterozygous mutation. The present study demonstrates that whole‑exome sequencing is a robust approach for the molecular diagnosis of disorders with high levels of genetic heterogeneity.

WWC Review of the Report "Closing the Achievement Gap through Modification of Neurocognitive and Neuroendocrine Function: Results from a Cluster Randomized Controlled Trial of an Innovative Approach to the Education of Children in Kindergarten." What Works Clearinghouse Single Study Review

ERIC Educational Resources Information Center

What Works Clearinghouse, 2015

2015-01-01

In the 2014 report, "Closing the Achievement Gap Through Modification of Neurocognitive and Neuroendocrine Function: Results from a Cluster Randomized Controlled Trial of an Innovative Approach to the Education of Children in Kindergarten," researchers examined the impacts of "Tools of the Mind" on cognitive and academic…

Gift from statistical learning: Visual statistical learning enhances memory for sequence elements and impairs memory for items that disrupt regularities.

PubMed

Otsuka, Sachio; Saiki, Jun

2016-02-01

Prior studies have shown that visual statistical learning (VSL) enhances familiarity (a type of memory) of sequences. How do statistical regularities influence the processing of each triplet element and inserted distractors that disrupt the regularity? Given that increased attention to triplets induced by VSL and inhibition of unattended triplets, we predicted that VSL would promote memory for each triplet constituent, and degrade memory for inserted stimuli. Across the first two experiments, we found that objects from structured sequences were more likely to be remembered than objects from random sequences, and that letters (Experiment 1) or objects (Experiment 2) inserted into structured sequences were less likely to be remembered than those inserted into random sequences. In the subsequent two experiments, we examined an alternative account for our results, whereby the difference in memory for inserted items between structured and random conditions is due to individuation of items within random sequences. Our findings replicated even when control letters (Experiment 3A) or objects (Experiment 3B) were presented before or after, rather than inserted into, random sequences. Our findings suggest that statistical learning enhances memory for each item in a regular set and impairs memory for items that disrupt the regularity. Copyright © 2015 Elsevier B.V. All rights reserved.

Variants in ACTG2 underlie a substantial number of Australasian patients with primary chronic intestinal pseudo-obstruction.

PubMed

Ravenscroft, G; Pannell, S; O'Grady, G; Ong, R; Ee, H C; Faiz, F; Marns, L; Goel, H; Kumarasinghe, P; Sollis, E; Sivadorai, P; Wilson, M; Magoffin, A; Nightingale, S; Freckmann, M-L; Kirk, E P; Sachdev, R; Lemberg, D A; Delatycki, M B; Kamm, M A; Basnayake, C; Lamont, P J; Amor, D J; Jones, K; Schilperoort, J; Davis, M R; Laing, N G

2018-05-21

Primary chronic intestinal pseudo-obstruction (CIPO) is a rare, potentially life-threatening disorder characterized by severely impaired gastrointestinal motility. The objective of this study was to examine the contribution of ACTG2, LMOD1, MYH11, and MYLK mutations in an Australasian cohort of patients with a diagnosis of primary CIPO associated with visceral myopathy. Pediatric and adult patients with primary CIPO and suspected visceral myopathy were recruited from across Australia and New Zealand. Sanger sequencing of the genes encoding enteric gamma-actin (ACTG2) and smooth muscle leiomodin (LMOD1) was performed on DNA from patients, and their relatives, where available. MYH11 and MYLK were screened by next-generation sequencing. We identified heterozygous missense variants in ACTG2 in 7 of 17 families (~41%) diagnosed with CIPO and its associated conditions. We also identified a previously unpublished missense mutation (c.443C>T, p.Arg148Leu) in one family. One case presented with megacystis-microcolon-intestinal hypoperistalsis syndrome in utero with subsequent termination of pregnancy at 28 weeks' gestation. All of the substitutions identified occurred at arginine residues. No likely pathogenic variants in LMOD1, MYH11, or MYLK were identified within our cohort. ACTG2 mutations represent a significant underlying cause of primary CIPO with visceral myopathy and associated phenotypes in Australasian patients. Thus, ACTG2 sequencing should be considered in cases presenting with hypoperistalsis phenotypes with suspected visceral myopathy. It is likely that variants in other genes encoding enteric smooth muscle contractile proteins will contribute further to the genetic heterogeneity of hypoperistalsis phenotypes. © 2018 John Wiley & Sons Ltd.

Fast carotid artery MR angiography with compressed sensing based three-dimensional time-of-flight sequence.

PubMed

Li, Bo; Li, Hao; Dong, Li; Huang, Guofu

2017-11-01

In this study, we sought to investigate the feasibility of fast carotid artery MR angiography (MRA) by combining three-dimensional time-of-flight (3D TOF) with compressed sensing method (CS-3D TOF). A pseudo-sequential phase encoding order was developed for CS-3D TOF to generate hyper-intense vessel and suppress background tissues in under-sampled 3D k-space. Seven healthy volunteers and one patient with carotid artery stenosis were recruited for this study. Five sequential CS-3D TOF scans were implemented at 1, 2, 3, 4 and 5-fold acceleration factors for carotid artery MRA. Blood signal-to-tissue ratio (BTR) values for fully-sampled and under-sampled acquisitions were calculated and compared in seven subjects. Blood area (BA) was measured and compared between fully sampled acquisition and each under-sampled one. There were no significant differences between the fully-sampled dataset and each under-sampled in BTR comparisons (P>0.05 for all comparisons). The carotid vessel BAs measured from the images of CS-3D TOF sequences with 2, 3, 4 and 5-fold acceleration scans were all highly correlated with that of the fully-sampled acquisition. The contrast between blood vessels and background tissues of the images at 2 to 5-fold acceleration is comparable to that of fully sampled images. The images at 2× to 5× exhibit the comparable lumen definition to the corresponding images at 1×. By combining the pseudo-sequential phase encoding order, CS reconstruction, and 3D TOF sequence, this technique provides excellent visualizations for carotid vessel and calcifications in a short scan time. It has the potential to be integrated into current multiple blood contrast imaging protocol. Copyright © 2017. Published by Elsevier Inc.

Absolute GPS Positioning Using Genetic Algorithms

NASA Astrophysics Data System (ADS)

Ramillien, G.

A new inverse approach for restoring the absolute coordinates of a ground -based station from three or four observed GPS pseudo-ranges is proposed. This stochastic method is based on simulations of natural evolution named genetic algorithms (GA). These iterative procedures provide fairly good and robust estimates of the absolute positions in the Earth's geocentric reference system. For comparison/validation, GA results are compared to the ones obtained using the classical linearized least-square scheme for the determination of the XYZ location proposed by Bancroft (1985) which is strongly limited by the number of available observations (i.e. here, the number of input pseudo-ranges must be four). The r.m.s. accuracy of the non -linear cost function reached by this latter method is typically ~10-4 m2 corresponding to ~300-500-m accuracies for each geocentric coordinate. However, GA can provide more acceptable solutions (r.m.s. errors < 10-5 m2), even when only three instantaneous pseudo-ranges are used, such as a lost of lock during a GPS survey. Tuned GA parameters used in different simulations are N=1000 starting individuals, as well as Pc=60-70% and Pm=30-40% for the crossover probability and mutation rate, respectively. Statistical tests on the ability of GA to recover acceptable coordinates in presence of important levels of noise are made simulating nearly 3000 random samples of erroneous pseudo-ranges. Here, two main sources of measurement errors are considered in the inversion: (1) typical satellite-clock errors and/or 300-metre variance atmospheric delays, and (2) Geometrical Dilution of Precision (GDOP) due to the particular GPS satellite configuration at the time of acquisition. Extracting valuable information and even from low-quality starting range observations, GA offer an interesting alternative for high -precision GPS positioning.

Design of a glutamine substrate tag enabling protein labelling mediated by Bacillus subtilis transglutaminase.

PubMed

Oteng-Pabi, Samuel K; Clouthier, Christopher M; Keillor, Jeffrey W

2018-01-01

Transglutaminases (TGases) are enzymes that catalyse protein cross-linking through a transamidation reaction between the side chain of a glutamine residue on one protein and the side chain of a lysine residue on another. Generally, TGases show low substrate specificity with respect to their amine substrate, such that a wide variety of primary amines can participate in the modification of specific glutamine residue. Although a number of different TGases have been used to mediate these bioconjugation reactions, the TGase from Bacillus subtilis (bTG) may be particularly suited to this application. It is smaller than most TGases, can be expressed in a soluble active form, and lacks the calcium dependence of its mammalian counterparts. However, little is known regarding this enzyme and its glutamine substrate specificity, limiting the scope of its application. In this work, we designed a FRET-based ligation assay to monitor the bTG-mediated conjugation of the fluorescent proteins Clover and mRuby2. This assay allowed us to screen a library of random heptapeptide glutamine sequences for their reactivity with recombinant bTG in bacterial cells, using fluorescence assisted cell sorting. From this library, several reactive sequences were identified and kinetically characterized, with the most reactive sequence (YAHQAHY) having a kcat/KM value of 19 ± 3 μM-1 min-1. This sequence was then genetically appended onto a test protein as a reactive 'Q-tag' and fluorescently labelled with dansyl-cadaverine, in the first demonstration of protein labelling mediated by bTG.

Subcortical roles in lexical task processing: Inferences from thalamic and subthalamic event-related potentials.

PubMed

Tiedt, Hannes O; Ehlen, Felicitas; Krugel, Lea K; Horn, Andreas; Kühn, Andrea A; Klostermann, Fabian

2017-01-01

Subcortical functions for language capacities are poorly defined, but may be investigated in the context of deep brain stimulation. Here, we studied event-related potentials recorded from electrodes in the subthalamic nucleus (STN) and the thalamic ventral intermediate nucleus (VIM) together with surface-EEG. Participants completed a lexical decision task (LDT), which required the differentiation of acoustically presented words from pseudo-words by button press. Target stimuli were preceded by prime-words. In recordings from VIM, a slow potential shift apparent at the lower electrode contacts persisted during target stimulus presentation (equally for words and pseudo-words). In contrast, recordings from STN electrodes showed a short local activation on prime-words but not target-stimuli. In both depth-recording regions, further components related to contralateral motor responses to target words were evident. On scalp level, mid-central activations on (pseudo)lexical stimuli were obtained, in line with the expression of N400 potentials. The prolonged activity recorded from VIM, exclusively accompanying the relevant LDT phase, is in line with the idea of thalamic "selective engagement" for supporting the realization of the behavioral focus demanded by the task. In contrast, the phasic prime related activity rather indicates "procedural" STN functions, for example, for trial sequencing or readiness inhibition of prepared target reactions. Hum Brain Mapp 38:370-383, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

[Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure].

PubMed

Bobrova, E V; Liakhovetskiĭ, V A; Borshchevskaia, E R

2011-01-01

The dependence of errors during reproduction of a sequence of hand movements without visual feedback on the previous right- and left-hand performance ("prehistory") and on positions in space of sequence elements (random or ordered by the explicit rule) was analyzed. It was shown that the preceding information about the ordered positions of the sequence elements was used during right-hand movements, whereas left-hand movements were performed with involvement of the information about the random sequence. The data testify to a central mechanism of the analysis of spatial structure of sequence elements. This mechanism activates movement coding specific for the left hemisphere (vector coding) in case of an ordered sequence structure and positional coding specific for the right hemisphere in case of a random sequence structure.

Recent advances in genetic modification of adenovirus vectors for cancer treatment.

PubMed

Yamamoto, Yuki; Nagasato, Masaki; Yoshida, Teruhiko; Aoki, Kazunori

2017-05-01

Adenoviruses are widely used to deliver genes to a variety of cell types and have been used in a number of clinical trials for gene therapy and oncolytic virotherapy. However, several concerns must be addressed for the clinical use of adenovirus vectors. Selective delivery of a therapeutic gene by adenovirus vectors to target cancer is precluded by the widespread distribution of the primary cellular receptors. The systemic administration of adenoviruses results in hepatic tropism independent of the primary receptors. Adenoviruses induce strong innate and acquired immunity in vivo. Furthermore, several modifications to these vectors are necessary to enhance their oncolytic activity and ensure patient safety. As such, the adenovirus genome has been engineered to overcome these problems. The first part of the present review outlines recent progress in the genetic modification of adenovirus vectors for cancer treatment. In addition, several groups have recently developed cancer-targeting adenovirus vectors by using libraries that display random peptides on a fiber knob. Pancreatic cancer-targeting sequences have been isolated, and these oncolytic vectors have been shown by our group to be associated with a higher gene transduction efficiency and more potent oncolytic activity in cell lines, murine models, and surgical specimens of pancreatic cancer. In the second part of this review, we explain that combining cancer-targeting strategies can be a promising approach to increase the clinical usefulness of oncolytic adenovirus vectors. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

A Node Linkage Approach for Sequential Pattern Mining

PubMed Central

Navarro, Osvaldo; Cumplido, René; Villaseñor-Pineda, Luis; Feregrino-Uribe, Claudia; Carrasco-Ochoa, Jesús Ariel

2014-01-01

Sequential Pattern Mining is a widely addressed problem in data mining, with applications such as analyzing Web usage, examining purchase behavior, and text mining, among others. Nevertheless, with the dramatic increase in data volume, the current approaches prove inefficient when dealing with large input datasets, a large number of different symbols and low minimum supports. In this paper, we propose a new sequential pattern mining algorithm, which follows a pattern-growth scheme to discover sequential patterns. Unlike most pattern growth algorithms, our approach does not build a data structure to represent the input dataset, but instead accesses the required sequences through pseudo-projection databases, achieving better runtime and reducing memory requirements. Our algorithm traverses the search space in a depth-first fashion and only preserves in memory a pattern node linkage and the pseudo-projections required for the branch being explored at the time. Experimental results show that our new approach, the Node Linkage Depth-First Traversal algorithm (NLDFT), has better performance and scalability in comparison with state of the art algorithms. PMID:24933123

Video Completion in Digital Stabilization Task Using Pseudo-Panoramic Technique

NASA Astrophysics Data System (ADS)

Favorskaya, M. N.; Buryachenko, V. V.; Zotin, A. G.; Pakhirka, A. I.

2017-05-01

Video completion is a necessary stage after stabilization of a non-stationary video sequence, if it is desirable to make the resolution of the stabilized frames equalled the resolution of the original frames. Usually the cropped stabilized frames lose 10-20% of area that means the worse visibility of the reconstructed scenes. The extension of a view of field may appear due to the pan-tilt-zoom unwanted camera movement. Our approach deals with a preparing of pseudo-panoramic key frame during a stabilization stage as a pre-processing step for the following inpainting. It is based on a multi-layered representation of each frame including the background and objects, moving differently. The proposed algorithm involves four steps, such as the background completion, local motion inpainting, local warping, and seamless blending. Our experiments show that a necessity of a seamless stitching occurs often than a local warping step. Therefore, a seamless blending was investigated in details including four main categories, such as feathering-based, pyramid-based, gradient-based, and optimal seam-based blending.

Phase-retrieval attack free cryptosystem based on cylindrical asymmetric diffraction and double-random phase encoding

NASA Astrophysics Data System (ADS)

Wang, Jun; Li, Xiaowei; Hu, Yuhen; Wang, Qiong-Hua

2018-03-01

A phase-retrieval attack free cryptosystem based on the cylindrical asymmetric diffraction and double-random phase encoding (DRPE) is proposed. The plaintext is abstract as a cylinder, while the observed diffraction and holographic surfaces are concentric cylinders. Therefore, the plaintext can be encrypted through a two-step asymmetric diffraction process with double pseudo random phase masks located on the object surface and the first diffraction surface. After inverse diffraction from a holographic surface to an object surface, the plaintext can be reconstructed using a decryption process. Since the diffraction propagated from the inner cylinder to the outer cylinder is different from that of the reversed direction, the proposed cryptosystem is asymmetric and hence is free of phase-retrieval attack. Numerical simulation results demonstrate the flexibility and effectiveness of the proposed cryptosystem.

Theta oscillations promote temporal sequence learning.

PubMed

Crivelli-Decker, Jordan; Hsieh, Liang-Tien; Clarke, Alex; Ranganath, Charan

2018-05-17

Many theoretical models suggest that neural oscillations play a role in learning or retrieval of temporal sequences, but the extent to which oscillations support sequence representation remains unclear. To address this question, we used scalp electroencephalography (EEG) to examine oscillatory activity over learning of different object sequences. Participants made semantic decisions on each object as they were presented in a continuous stream. For three "Consistent" sequences, the order of the objects was always fixed. Activity during Consistent sequences was compared to "Random" sequences that consisted of the same objects presented in a different order on each repetition. Over the course of learning, participants made faster semantic decisions to objects in Consistent, as compared to objects in Random sequences. Thus, participants were able to use sequence knowledge to predict upcoming items in Consistent sequences. EEG analyses revealed decreased oscillatory power in the theta (4-7 Hz) band at frontal sites following decisions about objects in Consistent sequences, as compared with objects in Random sequences. The theta power difference between Consistent and Random only emerged in the second half of the task, as participants were more effectively able to predict items in Consistent sequences. Moreover, we found increases in parieto-occipital alpha (10-13 Hz) and beta (14-28 Hz) power during the pre-response period for objects in Consistent sequences, relative to objects in Random sequences. Linear mixed effects modeling revealed that single trial theta oscillations were related to reaction time for future objects in a sequence, whereas beta and alpha oscillations were only predictive of reaction time on the current trial. These results indicate that theta and alpha/beta activity preferentially relate to future and current events, respectively. More generally our findings highlight the importance of band-specific neural oscillations in the learning of temporal order information. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Restriction/modification polypeptides, polynucleotides, and methods

DOEpatents

Westpheling, Janet; Chung, DaeHwan; Huddleston, Jennifer; Farkas, Joel A

2015-02-24

The present invention relates to the discovery of a novel restriction/modification system in Caldicellulosiruptor bescii. The discovered restriction enzyme is a HaeIII-like restriction enzyme that possesses a thermophilic activity profile. The restriction/modification system also includes a methyltransferase, M.CbeI, that methylates at least one cytosine residue in the CbeI recognition sequence to m.sup.4C. Thus, the invention provides, in various aspects, isolated CbeI or M.CbeI polypeptides, or biologically active fragments thereof; isolated polynucleotides that encode the CbeI or M.CbeI polypeptides or biologically active fragments thereof, including expression vectors that include such polynucleotide sequences; methods of digesting DNA using a CbeI polypeptide; methods of treating a DNA molecule using a M.CbeI polypeptide; and methods of transforming a Caldicellulosiruptor cell.

Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification

PubMed Central

Lech, Christopher Jacques

2017-01-01

Abstract Functionalized nanoparticles have seen valuable applications, particularly in the delivery of therapeutic and diagnostic agents in biological systems. However, the manufacturing of such nano-scale systems with the consistency required for biological application can be challenging, as variation in size and shape have large influences in nanoparticle behavior in vivo. We report on the development of a versatile nano-scaffold based on the modular functionalization of a DNA G-quadruplex. DNA sequences are functionalized in a modular fashion using well-established phosphoramidite chemical synthesis with nucleotides containing modification of the amino (N2) position of the guanine base. In physiological conditions, these sequences fold into well-defined G-quadruplex structures. The resulting DNA nano-scaffolds are thermally stable, consistent in size, and functionalized in a manner that allows for control over the density and relative orientation of functional chemistries on the nano-scaffold surface. Various chemistries including small modifications (N2-methyl-guanine), bulky aromatic modifications (N2-benzyl-guanine), and long chain-like modifications (N2-6-amino-hexyl-guanine) are tested and are found to be generally compatible with G-quadruplex formation. Furthermore, these modifications stabilize the G-quadruplex scaffold by 2.0–13.3 °C per modification in the melting temperature, with concurrent modifications producing extremely stable nano-scaffolds. We demonstrate the potential of this approach by functionalizing nano-scaffolds for use within the biotin–avidin conjugation approach. PMID:28499037

WE-AB-204-06: Pseudo-CT Generation Using Undersampled, Single-Acquisition UTE-MDixon and Direct-Mapping Artificial Neural Networks for MR-Based Attenuation Correction and Radiation Therapy Planning

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

Su, K; Kuo, J; Department of Radiology, University Hospitals Case Medical Center, Case Western Reserve University, Cleveland, Ohio

Purpose: Emerging technologies such as dedicated PET/MRI and MR-therapy systems require robust and clinically practical methods for determining photon attenuation. Herein, we propose using novel MR acquisition methods and processing for the generation of pseudo-CTs. Methods: A single acquisition, 190-second UTE-mDixon sequence with 25% (angular) sampling density and 3D radial readout was performed on nine volunteers. Three water-filled tubes were placed in the FOV for trajectory-delay correction. The MR data were reconstructed to generate three primitive images acquired at TEs of 0.1, 1.5 and 2.8 ms. In addition, three derived MR images were generated, i.e. two-point Dixon water/fat separation andmore » R2* (1/T2*) map. Furthermore, two spatial features, i.e. local binary pattern (S-1) and relative spatial coordinates (S-2), were incorporated. A direct-mapping operator was generated using Artificial Neural Networks (ANNs) for transforming the MR features to a pseudo-CT. CT images served as the training data and, using a leave-one-out method, for performance evaluation using mean prediction deviation (MPD), mean absolute prediction deviation (MAPD), and correlation coefficient (R). Results: The errors between measured CT and pseudo-CT declined dramatically when the spatial features, i.e. S-1 and S-2, were included. The MPD, MAPD, and R were, respectively, 5±57 HU, 141±41 HU, and 0.815±0.066 for results generated by the ANN trained without the spatial features and were 32±26 HU, 115±18 HU, and 0.869±0.035 with the spatial features. The estimation errors of the pseudo-CT were smaller when both the S-1 and S-2 were used together than when either the S-1 or the S-2 was used. Pseudo-CT generation (256×256×256 voxels) by ANN took < 0.5 s using a computer having an Intel i7 3.4GHz CPU and 16 GB RAM. Conclusion: The proposed direct-mapping ANN approach is a technically accurate, clinically practical method for pseudo-CT generation and can potentially help improve the accuracy of MR-AC and MR-RTP applications. Please note that the project was completed with partial funding from the Ohio Department of Development grant TECH 11-063 and a sponsored research agreement with Philips Healthcare that is managed by Case Western Reserve University. As noted in the affiliations, some of the authors are Philips employees.« less

Modification of bamboo-based activated carbon using microwave radiation and its effects on the adsorption of methylene blue

NASA Astrophysics Data System (ADS)

Liu, Qing-Song; Zheng, Tong; Li, Nan; Wang, Peng; Abulikemu, Gulizhaer

2010-03-01

Modification of bamboo-based activated carbon was carried out in a microwave oven under N 2 atmosphere. The virgin and modified activated carbons were characterized by means of low temperature N 2 adsorption, acid-base titration, point of zero charge (pH pzc) measurement, FTIR and XPS spectra. A gradual decrease in the surface acidic groups was observed during the modification, while the surface basicity was enhanced to some extent, which gave rise to an increase in the pH pzc value. The species of the functional groups and relative content of various elements and groups were given further analysis using FTIR and XPS spectra. An increase in the micropores was found at the start, and the micropores were then extended into larger ones, resulting in an increase in the pore volume and average pore size. Adsorption studies showed enhanced adsorption of methylene blue on the modified activated carbons, caused mainly by the enlargement of the micropores. Adsorption isotherm fittings revealed that Langmuir and Freundlich models were applicable for the virgin and modified activated carbons, respectively. Kinetic studies exhibited faster adsorption rate of methylene blue on the modified activated carbons, and the pseudo-second-order model fitted well for all of the activated carbons.

Characterization of the staphylococcal cassette chromosome composite island of Staphylococcus haemolyticus SH32, a methicillin-resistant clinical isolate from China.

PubMed

Yu, Dongliang; Pi, Borui; Chen, Yan; Wang, Yanfei; Ruan, Zhi; Otto, Michael; Yu, Yunsong

2014-01-01

Staphylococcal cassette chromosome (SCC) elements contribute considerably to virulence and resistance to antibiotic agents in staphylococci. SCC elements in coagulase-negative staphylococci (CoNS) are highly diverse and there is evidence suggesting that they serve as a reservoir for antibiotic resistance genes in methicillin-resistant Staphylococcus aureus (MRSA). However, only a small number of SCC elements have been characterized in CoNS and their exact roles in the emergence and evolution of MRSA remain to be demonstrated. Here, we determined the structure of an SCC composite island (CISH32) found in the clinical Staphylococcus haemolyticus isolate SH32 by whole-genome DNA sequencing. CISH32 was 48 kb in length and mainly composed of two imperfect SCC elements, namely (i) a ΨSCCmec(SH32) part containing a class C1 mec gene complex but lacking ccr genes and (ii) a SCCSH32 part with a ccrA5B3 gene complex but lacking mec genes. In addition, CISH32 contained a type III restriction-modification system and several resistance loci, for example genes conferring resistance to cadmium and arsenic. ΨSCCmec(SH32) is almost entirely identical to a pseudo SCCmec element found in S. haemolyticus WCH1 and shares pronounced sequence similarity to a ΨSCCmec element of S. haemolyticus JCSC1435. However, staphylococci other than S. haemolyticus, including S. aureus and S. epidermidis, contain homologs of SCCSH32 that are more similar to SCCSH32 than those elements found in S. haemolyticus, suggesting that CISH32 of S. haemolyticus SH32 was assembled in recent evolutionary events. Moreover, the composite structure of CISH32 indicates that the detection of class C1 mec and ccrA5B3 gene complexes in S. haemolyticus does not always indicate the existence of a UT9-type SCCmec element, which has remained questionable.

Characterization of the Staphylococcal Cassette Chromosome Composite Island of Staphylococcus haemolyticus SH32, a Methicillin-Resistant Clinical Isolate from China

PubMed Central

Yu, Dongliang; Pi, Borui; Chen, Yan; Wang, Yanfei; Ruan, Zhi; Otto, Michael; Yu, Yunsong

2014-01-01

Staphylococcal cassette chromosome (SCC) elements contribute considerably to virulence and resistance to antibiotic agents in staphylococci. SCC elements in coagulase-negative staphylococci (CoNS) are highly diverse and there is evidence suggesting that they serve as a reservoir for antibiotic resistance genes in methicillin-resistant Staphylococcus aureus (MRSA). However, only a small number of SCC elements have been characterized in CoNS and their exact roles in the emergence and evolution of MRSA remain to be demonstrated. Here, we determined the structure of an SCC composite island (CISH32) found in the clinical Staphylococcus haemolyticus isolate SH32 by whole-genome DNA sequencing. CISH32 was 48 kb in length and mainly composed of two imperfect SCC elements, namely (i) a ΨSCCmec(SH32) part containing a class C1 mec gene complex but lacking ccr genes and (ii) a SCCSH32 part with a ccrA5B3 gene complex but lacking mec genes. In addition, CISH32 contained a type III restriction-modification system and several resistance loci, for example genes conferring resistance to cadmium and arsenic. ΨSCCmec(SH32) is almost entirely identical to a pseudo SCCmec element found in S. haemolyticus WCH1 and shares pronounced sequence similarity to a ΨSCCmec element of S. haemolyticus JCSC1435. However, staphylococci other than S. haemolyticus, including S. aureus and S. epidermidis, contain homologs of SCCSH32 that are more similar to SCCSH32 than those elements found in S. haemolyticus, suggesting that CISH32 of S. haemolyticus SH32 was assembled in recent evolutionary events. Moreover, the composite structure of CISH32 indicates that the detection of class C1 mec and ccrA5B3 gene complexes in S. haemolyticus does not always indicate the existence of a UT9-type SCCmec element, which has remained questionable. PMID:24466348

Testing and performance analysis of a 650-Mbps quaternary pulse position modulation (QPPM) modem for free-space laser communications

NASA Astrophysics Data System (ADS)

Mortensen, Dale J.

1995-04-01

The testing and performance of a prototype modem developed at NASA Lewis Research Center for high-speed free-space direct detection optical communications is described. The testing was performed under laboratory conditions using computer control with specially developed test equipment that simulates free-space link conditions. The modem employs quaternary pulse position modulation at 325 Megabits per second (Mbps) on two optical channels, which are multiplexed to transmit a single 650 Mbps data stream. The measured results indicate that the receiver's automatic gain control (AGC), phased-locked-loop slot clock recovery, digital symbol clock recovery, matched filtering, and maximum likelihood data recovery circuits were found to have only 1.5 dB combined implementation loss during bit-error-rate (BER) performance measurements. Pseudo random bit sequences and real-time high quality video sources were used to supply 650 Mbps and 325 Mbps data streams to the modem. Additional testing revealed that Doppler frequency shifting can be easily tracked by the receiver, that simulated pointing errors are readily compensated for by the AGC circuits, and that channel timing skew affects the BER performance in an expected manner. Overall, the needed technologies for a high-speed laser communications modem were demonstrated.

Multi-iPPseEvo: A Multi-label Classifier for Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into Chou's General PseAAC via Grey System Theory.

PubMed

Qiu, Wang-Ren; Zheng, Quan-Shu; Sun, Bi-Qian; Xiao, Xuan

2017-03-01

Predicting phosphorylation protein is a challenging problem, particularly when query proteins have multi-label features meaning that they may be phosphorylated at two or more different type amino acids. In fact, human protein usually be phosphorylated at serine, threonine and tyrosine. By introducing the "multi-label learning" approach, a novel predictor has been developed that can be used to deal with the systems containing both single- and multi-label phosphorylation protein. Here we proposed a predictor called Multi-iPPseEvo by (1) incorporating the protein sequence evolutionary information into the general pseudo amino acid composition (PseAAC) via the grey system theory, (2) balancing out the skewed training datasets by the asymmetric bootstrap approach, and (3) constructing an ensemble predictor by fusing an array of individual random forest classifiers thru a voting system. Rigorous cross-validations via a set of multi-label metrics indicate that the multi-label phosphorylation predictor is very promising and encouraging. The current approach represents a new strategy to deal with the multi-label biological problems, and the software is freely available for academic use at http://www.jci-bioinfo.cn/Multi-iPPseEvo. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Early sensory encoding of affective prosody: neuromagnetic tomography of emotional category changes.

PubMed

Thönnessen, Heike; Boers, Frank; Dammers, Jürgen; Chen, Yu-Han; Norra, Christine; Mathiak, Klaus

2010-03-01

In verbal communication, prosodic codes may be phylogenetically older than lexical ones. Little is known, however, about early, automatic encoding of emotional prosody. This study investigated the neuromagnetic analogue of mismatch negativity (MMN) as an index of early stimulus processing of emotional prosody using whole-head magnetoencephalography (MEG). We applied two different paradigms to study MMN; in addition to the traditional oddball paradigm, the so-called optimum design was adapted to emotion detection. In a sequence of randomly changing disyllabic pseudo-words produced by one male speaker in neutral intonation, a traditional oddball design with emotional deviants (10% happy and angry each) and an optimum design with emotional (17% happy and sad each) and nonemotional gender deviants (17% female) elicited the mismatch responses. The emotional category changes demonstrated early responses (<200 ms) at both auditory cortices with larger amplitudes at the right hemisphere. Responses to the nonemotional change from male to female voices emerged later ( approximately 300 ms). Source analysis pointed at bilateral auditory cortex sources without robust contribution from other such as frontal sources. Conceivably, both auditory cortices encode categorical representations of emotional prosodic. Processing of cognitive feature extraction and automatic emotion appraisal may overlap at this level enabling rapid attentional shifts to important social cues. Copyright (c) 2009 Elsevier Inc. All rights reserved.

Kilowatt high-efficiency narrow-linewidth monolithic fiber amplifier operating at 1034 nm

NASA Astrophysics Data System (ADS)

Naderi, Nader A.; Flores, Angel; Anderson, Brian M.; Rowland, Ken; Dajani, Iyad

2016-03-01

Power scaling investigation of a narrow-linewidth, Ytterbium-doped all-fiber amplifier operating at 1034 nm is presented. Nonlinear stimulated Brillouin scattering (SBS) effects were suppressed through the utilization of an external phase modulation technique. Here, the power amplifier was seeded with a spectrally broadened master oscillator and the results were compared using both pseudo-random bit sequence (PRBS) and white noise source (WNS) phase modulation formats. By utilizing an optical band pass filter as well as optimizing the length of fiber used in the pre-amplifier stages, we were able to appreciably suppress unwanted amplified spontaneous emission (ASE). Notably, through PRBS phase modulation, greater than two-fold enhancement in threshold power was achieved when compared to the WNS modulated case. Consequently, by further optimizing both the power amplifier length and PRBS pattern at a clock rate of 3.5 GHz, we demonstrated 1 kilowatt of power with a slope efficiency of 81% and an overall ASE content of less than 1%. Beam quality measurements at 1 kilowatt provided near diffraction-limited operation (M2 < 1.2) with no sign of modal instability. To the best of our knowledge, the power scaling results achieved in this work represent the highest power reported for a spectrally narrow all-fiber amplifier operating at < 1040 nm in Yb-doped silica-based fiber.

3D single point imaging with compressed sensing provides high temporal resolution R 2* mapping for in vivo preclinical applications.

PubMed

Rioux, James A; Beyea, Steven D; Bowen, Chris V

2017-02-01

Purely phase-encoded techniques such as single point imaging (SPI) are generally unsuitable for in vivo imaging due to lengthy acquisition times. Reconstruction of highly undersampled data using compressed sensing allows SPI data to be quickly obtained from animal models, enabling applications in preclinical cellular and molecular imaging. TurboSPI is a multi-echo single point technique that acquires hundreds of images with microsecond spacing, enabling high temporal resolution relaxometry of large-R 2 * systems such as iron-loaded cells. TurboSPI acquisitions can be pseudo-randomly undersampled in all three dimensions to increase artifact incoherence, and can provide prior information to improve reconstruction. We evaluated the performance of CS-TurboSPI in phantoms, a rat ex vivo, and a mouse in vivo. An algorithm for iterative reconstruction of TurboSPI relaxometry time courses does not affect image quality or R 2 * mapping in vitro at acceleration factors up to 10. Imaging ex vivo is possible at similar acceleration factors, and in vivo imaging is demonstrated at an acceleration factor of 8, such that acquisition time is under 1 h. Accelerated TurboSPI enables preclinical R 2 * mapping without loss of data quality, and may show increased specificity to iron oxide compared to other sequences.

Frequency stabilization for multilocation optical FDM networks

NASA Astrophysics Data System (ADS)

Jiang, Quan; Kavehrad, Mohsen

1993-04-01

In a multi-location optical FDM network, the frequency of each user's transmitter can be offset-locked, through a Fabry-Perot, to an absolute frequency standard which is distributed to the users. To lock the local Fabry-Perot to the frequency standard, the standard has to be frequency-dithered by a sinusoidal signal and the sinusoidal reference has to be transmitted to the user location since the lock-in amplifier in the stabilization system requires the reference for synchronous detection. We proposed two solutions to avoid transmitting the reference. One uses an extraction circuit to obtain the sinusoidal signal from the incoming signal. A nonlinear circuit following the photodiode produces a strong second-order harmonic of the sinusoidal signal and a phase-locked loop is locked to it. The sinusoidal reference is obtained by a divide- by-2 circuit. The phase ambiguity (0 degree(s) or 180 degree(s)) is resolved by using a selection- circuit and an initial scan. The other method uses a pseudo-random sequence instead of a sinusoidal signal to dither the frequency standard and a surface-acoustic-wave (SAW) matched-filter instead of a lock-in amplifier to obtain the frequency error. The matched-filter serves as a correlator and does not require the dither reference.

Determining the Location of DNA Modification and Mutation Caused by UVB Light in Skin Cancer

DTIC Science & Technology

2013-09-01

we obtain cleavage patterns consistent with the administered UV dosage and that sequencing libraries generated for both yeast and human cells show...understanding the mutations they cause. 15. SUBJECT TERMS UV DNA modification, HeLa cells, Skin Cancer 16. SECURITY CLASSIFICATION OF: 17...of mutations that are caused by UV light in cells and correlate them to modification frequencies. Understanding the initial chemical changes

Two-Way Satellite Time and Frequency Transfer Using 1 MChips/s Codes

DTIC Science & Technology

2009-11-01

Abstract The Ku-band transatlantic and Europe-to-Europe two-way satellite time and frequency transfer ( TWSTFT ) operations used 2.5 MChip/s...pseudo-random codes with 3.5 MHz bandwidth until the end of July 2009. The cost of TWSTFT operation is associated with the bandwidth used on a...geostationary satellite. The transatlantic and Europe-to-Europe TWSTFT operations faced a significant increase in cost for using 3.5 MHz bandwidth on a new

Information Encoding on a Pseudo Random Noise Radar Waveform

DTIC Science & Technology

2013-03-01

quadrature mirror filter bank (QMFB) tree diagram [18] . . . . . . . . . . . 18 2.7 QMFB layer 3 contour plot for 7-bit barker code binary phase shift...test signal . . . . . . . . 20 2.9 Block diagram of the FFT accumulation method (FAM) time smoothing method to estimate the spectral correlation ... Samples A m pl itu de (b) Correlator output for an WGN pulse in a AWGN channel Figure 2.2: Effectiveness of correlation for SNR = -10 dB 10 2.3 Radar

Linkage analysis by genotyping of sibling populations: a genetic map for the potato cyst nematode constructed using a "pseudo-F2" mapping strategy.

PubMed

Rouppe van der Voort, J N; van Eck, H J; van Zandvoort, P M; Overmars, H; Helder, J; Bakker, J

1999-07-01

A mapping strategy is described for the construction of a linkage map of a non-inbred species in which individual offspring genotypes are not amenable to marker analysis. After one extra generation of random mating, the segregating progeny was propagated, and bulked populations of offspring were analyzed. Although the resulting population structure is different from that of commonly used mapping populations, we show that the maximum likelihood formula for a normal F2 is applicable for the estimation of recombination. This "pseudo-F2" mapping strategy, in combination with the development of an AFLP assay for single cysts, facilitated the construction of a linkage map for the potato cyst nematode Globodera rostochiensis. Using 12 pre-selected AFLP primer combinations, a total of 66 segregating markers were identified, 62 of which were mapped to nine linkage groups. These 62 AFLP markers are randomly distributed and cover about 65% of the genome. An estimate of the physical size of the Globodera genome was obtained from comparisons of the number of AFLP fragments obtained with the values for Caenorhabditis elegans. The methodology presented here resulted in the first genomic map for a cyst nematode. The low value of the kilobase/centimorgan (kb/cM) ratio for the Globodera genome will facilitate map-based cloning of genes that mediate the interaction between the nematode and its host plant.

Sorption reaction mechanism of some hazardous radionuclides from mixed waste by impregnated crown ether onto polymeric resin.

PubMed

Shehata, F A; Attallah, M F; Borai, E H; Hilal, M A; Abo-Aly, M M

2010-02-01

A novel impregnated polymeric resin was practically tested as adsorbent material for removal of some hazardous radionuclides from radioactive liquid waste. The applicability for the treatment of low-level liquid radioactive waste was investigated. The material was prepared by loading 4,4'(5')di-t-butylbenzo 18 crown 6 (DtBB18C6) onto poly(acrylamide-acrylic acid-acrylonitril)-N, N'-methylenediacrylamide (P(AM-AA-AN)-DAM). The removal of (134)Cs, (60)Co, (65)Zn , and ((152+154))Eu onto P(AM-AA-AN)-DAM/DtBB18C6 was investigated using a batch equilibrium technique with respect to the pH, contact time, and temperature. Kinetic models are used to determine the rate of sorption and to investigate the mechanism of sorption process. Five kinetics models, pseudo-first-order, pseudo-second-order, intra-particle diffusion, homogeneous particle diffusion (HPDM), and Elovich models, were used to investigate the sorption process. The obtained results of kinetic models predicted that, pseudo-second-order is applicable; the sorption is controlled by particle diffusion mechanism and the process is chemisorption. The obtained values of thermodynamics parameters, DeltaH degrees , DeltaS degrees , and DeltaG degrees indicated that the endothermic nature, increased randomness at the solid/solution interface and the spontaneous nature of the sorption processes. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

Assessing randomness and complexity in human motion trajectories through analysis of symbolic sequences

PubMed Central

Peng, Zhen; Genewein, Tim; Braun, Daniel A.

2014-01-01

Complexity is a hallmark of intelligent behavior consisting both of regular patterns and random variation. To quantitatively assess the complexity and randomness of human motion, we designed a motor task in which we translated subjects' motion trajectories into strings of symbol sequences. In the first part of the experiment participants were asked to perform self-paced movements to create repetitive patterns, copy pre-specified letter sequences, and generate random movements. To investigate whether the degree of randomness can be manipulated, in the second part of the experiment participants were asked to perform unpredictable movements in the context of a pursuit game, where they received feedback from an online Bayesian predictor guessing their next move. We analyzed symbol sequences representing subjects' motion trajectories with five common complexity measures: predictability, compressibility, approximate entropy, Lempel-Ziv complexity, as well as effective measure complexity. We found that subjects' self-created patterns were the most complex, followed by drawing movements of letters and self-paced random motion. We also found that participants could change the randomness of their behavior depending on context and feedback. Our results suggest that humans can adjust both complexity and regularity in different movement types and contexts and that this can be assessed with information-theoretic measures of the symbolic sequences generated from movement trajectories. PMID:24744716

Investigation of the contextual interference effect in the manipulation of the motor parameter of over-all force.

PubMed

Goodwin, J E; Meeuwsen, H J

1996-12-01

This investigation examined the contextual interference effect when manipulating over-all force in a golf-putting task. Undergraduate women (N = 30) were randomly assigned to a Random, Blocked-Random, or Blocked practice condition and practiced golf putting from distances of 2.43 m, 3.95 m, and 5.47 m during acquisition. Subjects in the Random condition practiced trials in a quasirandom sequence and those in the Blocked-Random condition practiced trials initially in a blocked sequence with the remainder of the trials practiced in a quasirandom sequence. In the Blocked condition subjects practiced trials in a blocked sequence. A 24-hr. transfer test consisted of 30 trials with 10 trials each from 1.67 m, 3.19 m, and 6.23 m. Transfer scores supported the Magill and Hall (1990) hypothesis that, when task variations involve learning parameters of a generalized motor program, the benefit of random practice over blocked practice would not be found.

Using Maximum Entropy to Find Patterns in Genomes

NASA Astrophysics Data System (ADS)

Liu, Sophia; Hockenberry, Adam; Lancichinetti, Andrea; Jewett, Michael; Amaral, Luis

The existence of over- and under-represented sequence motifs in genomes provides evidence of selective evolutionary pressures on biological mechanisms such as transcription, translation, ligand-substrate binding, and host immunity. To accurately identify motifs and other genome-scale patterns of interest, it is essential to be able to generate accurate null models that are appropriate for the sequences under study. There are currently no tools available that allow users to create random coding sequences with specified amino acid composition and GC content. Using the principle of maximum entropy, we developed a method that generates unbiased random sequences with pre-specified amino acid and GC content. Our method is the simplest way to obtain maximally unbiased random sequences that are subject to GC usage and primary amino acid sequence constraints. This approach can also be easily be expanded to create unbiased random sequences that incorporate more complicated constraints such as individual nucleotide usage or even di-nucleotide frequencies. The ability to generate correctly specified null models will allow researchers to accurately identify sequence motifs which will lead to a better understanding of biological processes. National Institute of General Medical Science, Northwestern University Presidential Fellowship, National Science Foundation, David and Lucile Packard Foundation, Camille Dreyfus Teacher Scholar Award.

Cloning, sequencing, and transgenic expression of Podospora curvicolla and Sordaria macrospora eEF1A genes: relationship between cytosolic translation and longevity in filamentous fungi.

PubMed

Gagny, B; Rossignol, M; Silar, P

1997-12-01

We have cloned and sequenced the gene encoding the translation elongation factor eEF1A from two filamentous fungi, Podospora curvicolla and Sordaria macrospora. These fungi are close relatives of Podospora anserina and also show senescence syndromes. Comparison of the sequences of the deduced proteins with that of P. anserina reveals that the three proteins differ in several positions. Replacement of the P. anserina gene by either of the two exogenous genes does not entail any modification in P. anserina physiology; the longevity of the fungus is not affected. No alteration of in vivo translational accuracy was detected; however, the exogenous proteins nonetheless promoted a modification of the resistance to the aminoglycoside antibiotic paromomycin. These data suggest that optimization of life span between these closely related fungi has likely not been performed during evolution through modifications of eEF1A activity, despite the fact that mutations in this factor can drastically affect longevity. Copyright 1997 Academic Press.

The methylome and virulence of bovine respiratory disease bacterial pathogens

USDA-ARS?s Scientific Manuscript database

With the advent of single molecule, real-time (SMRT®) sequencing, it is now possible to study complete microbial epigenomes. It has been known for decades that methylation and other types of epigenetic modifications in bacteria are responsible for much more than restriction-modification mechanics, b...

ChIP-Seq Analysis for Identifying Genome-Wide Histone Modifications Associated with Stress-Responsive Genes in Plants.

PubMed

Li, Guosheng; Jagadeeswaran, Guru; Mort, Andrew; Sunkar, Ramanjulu

2017-01-01

Histone modifications represent the crux of epigenetic gene regulation essential for most biological processes including abiotic stress responses in plants. Thus, identification of histone modifications at the genome-scale can provide clues for how some genes are 'turned-on' while some others are "turned-off" in response to stress. This chapter details a step-by-step protocol for identifying genome-wide histone modifications associated with stress-responsive gene regulation using chromatin immunoprecipitation (ChIP) followed by sequencing of the DNA (ChIP-seq).

Crystallization mechanisms of acicular crystals

NASA Astrophysics Data System (ADS)

Puel, François; Verdurand, Elodie; Taulelle, Pascal; Bebon, Christine; Colson, Didier; Klein, Jean-Paul; Veesler, Stéphane

2008-01-01

In this contribution, we present an experimental investigation of the growth of four different organic molecules produced at industrial scale with a view to understand the crystallization mechanism of acicular or needle-like crystals. For all organic crystals studied in this article, layer-by-layer growth of the lateral faces is very slow and clear, as soon as the supersaturation is high enough, there is competition between growth and surface-activated secondary nucleation. This gives rise to pseudo-twinned crystals composed of several needle individuals aligned along a crystallographic axis; this is explained by regular over- and inter-growths as in the case of twinning. And when supersaturation is even higher, nucleation is fast and random. In an industrial continuous crystallization, the rapid growth of needle-like crystals is to be avoided as it leads to fragile crystals or needles, which can be partly broken or totally detached from the parent crystals especially along structural anisotropic axis corresponding to weaker chemical bonds, thus leading to slower growing faces. When an activated mechanism is involved such as a secondary surface nucleation, it is no longer possible to obtain a steady state. Therefore, the crystal number, size and habit vary significantly with time, leading to troubles in the downstream processing operations and to modifications of the final solid-specific properties. These results provide valuable information on the unique crystallization mechanisms of acicular crystals, and show that it is important to know these threshold and critical values when running a crystallizer in order to obtain easy-to-handle crystals.

The effect of interference on temporal order memory for random and fixed sequences in nondemented older adults.

PubMed

Tolentino, Jerlyn C; Pirogovsky, Eva; Luu, Trinh; Toner, Chelsea K; Gilbert, Paul E

2012-05-21

Two experiments tested the effect of temporal interference on order memory for fixed and random sequences in young adults and nondemented older adults. The results demonstrate that temporal order memory for fixed and random sequences is impaired in nondemented older adults, particularly when temporal interference is high. However, temporal order memory for fixed sequences is comparable between older adults and young adults when temporal interference is minimized. The results suggest that temporal order memory is less efficient and more susceptible to interference in older adults, possibly due to impaired temporal pattern separation.

A Dog with Pseudo-Addison Disease Associated with Trichuris vulpis Infection.

PubMed

Venco, Luigi; Valenti, Valentina; Genchi, Marco; Grandi, Giulio

2011-01-01

A female Rottweiler dog was presented with a history of intermittent vomiting and diarrhoea, dysorexia, weakness, and weight loss. Haemocytometry and biochemistry values were within normal ranges except for electrolyte analyses, that demonstrated hyponatremia and hyperkalemia with a decreased sodium/potassium ratio. A diagnosis of hypoadrenocorticism was suspected. Basal and post-ACTH stimulation cortisolemia were within the normal values. Electrocardiography was normal, and thoracic radiography showed no significant modifications. On abdominal ultrasonography, adrenal glands appeared normal, while the bowel was distended, and several thin linear hyperechoic objects floating in the lumen were observed. Two adult female whipworms (Trichuris vulpis) were collected following bowel irrigation. Anthelmintic treatment against the parasite was curative.

Congenital zygomatico-mandibular fusion (pseudo-syngnathia?) in conjunction with unilateral anophthalmia: review of terminology and classification.

PubMed

Tauro, David P; Kallappanavar, N K; Kiran, H Y; Girhe, Vijaykumar J

2012-09-01

Syngnathia per se is a rare congenital disorder. A literature survey reveals a total of 26 cases of syngnathia in the English literature since 1936, of which only seven cases involved fusion of the ascending ramus of the mandible to the posterior portion of the maxilla and zygomatic complex. The remaining 19 involved fusion of the alveolar ridges of the maxilla and mandible. This is a unique case of fusion of the mandible to the zygomatic complex presenting with a unilateral anophthalmic orbit in an 18-day-old neonate. The use of the term syngnathia has been reviewed and a modification in classification has been suggested.

Removal of free fatty acid in Azadirachta indica (Neem) seed oil using phosphoric acid modified mordenite for biodiesel production.

PubMed

SathyaSelvabala, Vasanthakumar; Varathachary, Thiruvengadaravi Kadathur; Selvaraj, Dinesh Kirupha; Ponnusamy, Vijayalakshmi; Subramanian, Sivanesan

2010-08-01

In this study free fatty acids present in Azadirachta indica (Neem) oil were esterified with our synthesized phosphoric acid modified catalyst. During the esterification, the acid value was reduced from 24.4 to 1.8 mg KOH/g oil. Synthesized catalyst was characterized by NH(3) TPD, XRD, SEM, FTIR and TGA analysis. During phosphoric acid modification hydrophobic character and weak acid sites of the mordenite were increased, which lead to better esterification when compared to H-mordenite. A kinetic study demonstrates that the esterification reaction followed pseudo-first order kinetics. Thermodynamic studies were also done based on the Arrhenius model. (c) 2010 Elsevier Ltd. All rights reserved.

On hydromagnetic oscillations in a rotating cavity.

NASA Technical Reports Server (NTRS)

Gans, R. F.

1971-01-01

Time-dependent hydromagnetic phenomena in a rotating spherical cavity are investigated in the framework of an interior boundary-layer expansion. The first type of wave is a modification of the hydrodynamic inertial wave, the second is a pseudo-geostrophic wave and is involved in spinup, and the third is related to the MAC waves of Braginskii (1967). It is shown that the MAC waves must satisfy more than the usual normal boundary conditions, and that reference must be made to the boundary-layer solution to resolve the ambiguity regarding which conditions are to be taken. The boundary-layer structure is investigated in detail to display the interactions between applied field, viscosity, electrical conductivity, frequency and latitu de.

Study on the algorithm of computational ghost imaging based on discrete fourier transform measurement matrix

NASA Astrophysics Data System (ADS)

Zhang, Leihong; Liang, Dong; Li, Bei; Kang, Yi; Pan, Zilan; Zhang, Dawei; Gao, Xiumin; Ma, Xiuhua

2016-07-01

On the basis of analyzing the cosine light field with determined analytic expression and the pseudo-inverse method, the object is illuminated by a presetting light field with a determined discrete Fourier transform measurement matrix, and the object image is reconstructed by the pseudo-inverse method. The analytic expression of the algorithm of computational ghost imaging based on discrete Fourier transform measurement matrix is deduced theoretically, and compared with the algorithm of compressive computational ghost imaging based on random measurement matrix. The reconstruction process and the reconstruction error are analyzed. On this basis, the simulation is done to verify the theoretical analysis. When the sampling measurement number is similar to the number of object pixel, the rank of discrete Fourier transform matrix is the same as the one of the random measurement matrix, the PSNR of the reconstruction image of FGI algorithm and PGI algorithm are similar, the reconstruction error of the traditional CGI algorithm is lower than that of reconstruction image based on FGI algorithm and PGI algorithm. As the decreasing of the number of sampling measurement, the PSNR of reconstruction image based on FGI algorithm decreases slowly, and the PSNR of reconstruction image based on PGI algorithm and CGI algorithm decreases sharply. The reconstruction time of FGI algorithm is lower than that of other algorithms and is not affected by the number of sampling measurement. The FGI algorithm can effectively filter out the random white noise through a low-pass filter and realize the reconstruction denoising which has a higher denoising capability than that of the CGI algorithm. The FGI algorithm can improve the reconstruction accuracy and the reconstruction speed of computational ghost imaging.

Effect of increasing disorder on domains of the 2d Coulomb glass.

PubMed

Bhandari, Preeti; Malik, Vikas

2017-12-06

We have studied a two dimensional lattice model of Coulomb glass for a wide range of disorders at [Formula: see text]. The system was first annealed using Monte Carlo simulation. Further minimization of the total energy of the system was done using an algorithm developed by Baranovskii et al, followed by cluster flipping to obtain the pseudo-ground states. We have shown that the energy required to create a domain of linear size L in d dimensions is proportional to [Formula: see text]. Using Imry-Ma arguments given for random field Ising model, one gets critical dimension [Formula: see text] for Coulomb glass. The investigation of domains in the transition region shows a discontinuity in staggered magnetization which is an indication of a first-order type transition from charge-ordered phase to disordered phase. The structure and nature of random field fluctuations of the second largest domain in Coulomb glass are inconsistent with the assumptions of Imry and Ma, as was also reported for random field Ising model. The study of domains showed that in the transition region there were mostly two large domains, and that as disorder was increased the two large domains remained, but a large number of small domains also opened up. We have also studied the properties of the second largest domain as a function of disorder. We furthermore analysed the effect of disorder on the density of states, and showed a transition from hard gap at low disorders to a soft gap at higher disorders. At [Formula: see text], we have analysed the soft gap in detail, and found that the density of states deviates slightly ([Formula: see text]) from the linear behaviour in two dimensions. Analysis of local minima show that the pseudo-ground states have similar structure.

Comparative sequence analysis revealed altered chromosomal organization and a novel insertion sequence encoding DNA modification and potentially stress-related functions in an Escherichia coli O157:H7 foodborne isolate

USDA-ARS?s Scientific Manuscript database

We recently described the complete genome of enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain NADC 6564, an isolate of strain 86-24 linked to the 1986 disease outbreak. In the current study, we compared the chromosomal sequence of NADC 6564 to the well-characterized chromosomal sequences of ...

Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex

PubMed Central

Hand, Melanie L.; Spangenberg, German C.; Forster, John W.; Cogan, Noel O. I.

2013-01-01

Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL–psaI intergenic region, however, revealed a “hot-spot” of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses. PMID:23550121

Effects of Random Circuit Fabrication Errors on Small Signal Gain and on Output Phase In a Traveling Wave Tube

NASA Astrophysics Data System (ADS)

Rittersdorf, I. M.; Antonsen, T. M., Jr.; Chernin, D.; Lau, Y. Y.

2011-10-01

Random fabrication errors may have detrimental effects on the performance of traveling-wave tubes (TWTs) of all types. A new scaling law for the modification in the average small signal gain and in the output phase is derived from the third order ordinary differential equation that governs the forward wave interaction in a TWT in the presence of random error that is distributed along the axis of the tube. Analytical results compare favorably with numerical results, in both gain and phase modifications as a result of random error in the phase velocity of the slow wave circuit. Results on the effect of the reverse-propagating circuit mode will be reported. This work supported by AFOSR, ONR, L-3 Communications Electron Devices, and Northrop Grumman Corporation.

DNA damage induced by ascorbate in the presence of Cu2+.

PubMed

Kobayashi, S; Ueda, K; Morita, J; Sakai, H; Komano, T

1988-01-25

DNA damage induced by ascorbate in the presence of Cu2+ was investigated by use of bacteriophage phi X174 double-stranded supercoiled DNA and linear restriction fragments as substrates. Single-strand cleavage was induced when supercoiled DNA was incubated with 5 microM-10 mM ascorbate and 50 microM Cu2+ at 37 degrees C for 10 min. The induced DNA damage was analyzed by sequencing of fragments singly labeled at their 5'- or 3'-end. DNA was cleaved directly and almost uniformly at every nucleotide by ascorbate and Cu2+. Piperidine treatment after the reaction showed that ascorbate and Cu2+ induced another kind of DNA damage different from the direct cleavage. The damage proceeded to DNA cleavage by piperidine treatment and was sequence-specific rather than random. These results indicate that ascorbate induces two classes of DNA damage in the presence of Cu2+, one being direct strand cleavage, probably via damage to the DNA backbone, and the other being a base modification labile to alkali treatment. These two classes of DNA damage were inhibited by potassium iodide, catalase and metal chelaters, suggesting the involvement of radicals generated from ascorbate hydroperoxide.

Genome-wide Annotation and Comparative Analysis of Long Terminal Repeat Retrotransposons between Pear Species of P. bretschneideri and P. Communis

PubMed Central

Yin, Hao; Du, Jianchang; Wu, Jun; Wei, Shuwei; Xu, Yingxiu; Tao, Shutian; Wu, Juyou; Zhang, Shaoling

2015-01-01

Recent sequencing of the Oriental pear (P. bretschneideri Rehd.) genome and the availability of the draft genome sequence of Occidental pear (P. communis L.), has provided a good opportunity to characterize the abundance, distribution, timing, and evolution of long terminal repeat retrotransposons (LTR-RTs) in these two important fruit plants. Here, a total of 7247 LTR-RTs, which can be classified into 148 families, have been identified in the assembled Oriental pear genome. Unlike in other plant genomes, approximately 90% of these elements were found to be randomly distributed along the pear chromosomes. Further analysis revealed that the amplification timeframe of elements varies dramatically in different families, super-families and lineages, and the Copia-like elements have highest activity in the recent 0.5 million years (Mys). The data also showed that two genomes evolved with similar evolutionary rates after their split from the common ancestor ~0.77–1.66 million years ago (Mya). Overall, the data provided here will be a valuable resource for further investigating the impact of transposable elements on gene structure, expression, and epigenetic modification in the pear genomes. PMID:26631625

Randomizer for High Data Rates

NASA Technical Reports Server (NTRS)

Garon, Howard; Sank, Victor J.

2018-01-01

NASA as well as a number of other space agencies now recognize that the current recommended CCSDS randomizer used for telemetry (TM) is too short. When multiple applications of the PN8 Maximal Length Sequence (MLS) are required in order to fully cover a channel access data unit (CADU), spectral problems in the form of elevated spurious discretes (spurs) appear. Originally the randomizer was called a bit transition generator (BTG) precisely because it was thought that its primary value was to insure sufficient bit transitions to allow the bit/symbol synchronizer to lock and remain locked. We, NASA, have shown that the old BTG concept is a limited view of the real value of the randomizer sequence and that the randomizer also aids in signal acquisition as well as minimizing the potential for false decoder lock. Under the guidelines we considered here there are multiple maximal length sequences under GF(2) which appear attractive in this application. Although there may be mitigating reasons why another MLS sequence could be selected, one sequence in particular possesses a combination of desired properties which offsets it from the others.

Closing the evidence gap in infectious disease: point-of-care randomization and informed consent.

PubMed

Huttner, A; Leibovici, L; Theuretzbacher, U; Huttner, B; Paul, M

2017-02-01

The informed consent document is intended to provide basic rights to patients but often fails to do so. Patients' autonomy may be diminished by virtue of their illness; evidence shows that even patients who appear to be ideal candidates for understanding and granting informed consent rarely are, particularly those with acute infections. We argue that for low-risk trials whose purpose is to evaluate nonexperimental therapies or other measures towards which the medical community is in a state of equipoise, ethics committees should play a more active role in a more standardized fashion. Patients in the clinic are continually subject to spontaneous 'pseudo-randomizations' based on local dogma and the anecdotal experience of their physicians. Stronger ethics oversight would allow point-of-care trials to structure these spontaneous randomizations, using widely available informatics tools, in combination with opt-out informed consent where deemed appropriate. Copyright © 2016. Published by Elsevier Ltd.

47 CFR 1.947 - Modification of licenses.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 1 2014-10-01 2014-10-01 false Modification of licenses. 1.947 Section 1.947 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Grants by Random Selection Wireless Radio Services Applications and Proceedings Application Requirements and Procedures § 1.947...

47 CFR 1.947 - Modification of licenses.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 1 2012-10-01 2012-10-01 false Modification of licenses. 1.947 Section 1.947 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Grants by Random Selection Wireless Radio Services Applications and Proceedings Application Requirements and Procedures § 1.947...

47 CFR 1.947 - Modification of licenses.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 1 2013-10-01 2013-10-01 false Modification of licenses. 1.947 Section 1.947 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Grants by Random Selection Wireless Radio Services Applications and Proceedings Application Requirements and Procedures § 1.947...

Next-Generation DNA Sequencing of VH/VL Repertoires: A Primer and Guide to Applications in Single-Domain Antibody Discovery.

PubMed

Henry, Kevin A

2018-01-01

Immunogenetic analyses of expressed antibody repertoires are becoming increasingly common experimental investigations and are critical to furthering our understanding of autoimmunity, infectious disease, and cancer. Next-generation DNA sequencing (NGS) technologies have now made it possible to interrogate antibody repertoires to unprecedented depths, typically by sequencing of cDNAs encoding immunoglobulin variable domains. In this chapter, we describe simple, fast, and reliable methods for producing and sequencing multiplex PCR amplicons derived from the variable regions (V H , V H H or V L ) of rearranged immunoglobulin heavy and light chain genes using the Illumina MiSeq platform. We include complete protocols and primer sets for amplicon sequencing of V H /V H H/V L repertoires directly from human, mouse, and llama lymphocytes as well as from phage-displayed V H /V H H/V L libraries; these can be easily be adapted to other types of amplicons with little modification. The resulting amplicons are diverse and representative, even using as few as 10 3 input B cells, and their generation is relatively inexpensive, requiring no special equipment and only a limited set of primers. In the absence of heavy-light chain pairing, single-domain antibodies are uniquely amenable to NGS analyses. We present a number of applications of NGS technology useful in discovery of single-domain antibodies from phage display libraries, including: (i) assessment of library functionality; (ii) confirmation of desired library randomization; (iii) estimation of library diversity; and (iv) monitoring the progress of panning experiments. While the case studies presented here are of phage-displayed single-domain antibody libraries, the principles extend to other types of in vitro display libraries.

SNP-VISTA: An interactive SNP visualization tool

PubMed Central

Shah, Nameeta; Teplitsky, Michael V; Minovitsky, Simon; Pennacchio, Len A; Hugenholtz, Philip; Hamann, Bernd; Dubchak, Inna L

2005-01-01

Background Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it has become possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease in an attempt to identify causative mutations. In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental samples enables more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at [1]. Results We have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein evolutionary conservation visualization; and 5) display of automatically calculated recombination points that are user-editable. Conclusion The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNP data by the user. PMID:16336665

The subgenus Monotarsobius in the Iberian Peninsula with a description of a new pseudo-cryptic species from Northern Spain revealed by an integrative revision of Lithobius crassipes L. Koch, 1862 (Chilopoda, Lithobiomorpha, Lithobiidae)

PubMed Central

Voigtländer, Karin; Iorio, Etienne; Decker, Peter; Spelda, Jörg

2017-01-01

Abstract The widespread European centipede species Lithobius (Monotarsobius) crassipes L. Koch, 1862 was revised using an integrative approach incorporating sequence data and morphology. The partial mitochondrial cytochrome c oxidase subunit I (COI) barcoding gene was amplified and sequenced for 21 individuals from northern Spain, France and Germany as well as for individuals of three other species of the subgenus Monotarsobius Verhoeff, 1905. The dataset was used for molecular phylogenetic analysis and genetic distance determination. In addition, Monotarsobius specimens from more than 100 localities in northern Spain, France, and Germany were morphologically investigated. Both morphological and molecular data indicate that specimens from the Navarre and Gipuzkoa provinces, northern Spain, represent a distinct pseudo-cryptic species, only differing in some minor characters from L. crassipes. The new species L. (Monotarsobius) crassipesoides sp. n. is described and compared to L. crassipes in detail using morphology and morphometric statistics for body, head, and antennae length, number of ocelli and coxal pores, as well as the starting leg for legpair spines Vmt and DaP. The Iberian and European records of L. crassipes are discussed. The subspecies L. crassipes morenoi Garcia Ruiz, 2014 from Southern Spain is elevated to species as L. morenoi stat. n. A checklist, distribution map and key to all five species of Monotarsobius of the Iberian Peninsula are presented. PMID:28769719

Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification.

PubMed

Lech, Christopher Jacques; Phan, Anh Tuân

2017-06-20

Functionalized nanoparticles have seen valuable applications, particularly in the delivery of therapeutic and diagnostic agents in biological systems. However, the manufacturing of such nano-scale systems with the consistency required for biological application can be challenging, as variation in size and shape have large influences in nanoparticle behavior in vivo. We report on the development of a versatile nano-scaffold based on the modular functionalization of a DNA G-quadruplex. DNA sequences are functionalized in a modular fashion using well-established phosphoramidite chemical synthesis with nucleotides containing modification of the amino (N2) position of the guanine base. In physiological conditions, these sequences fold into well-defined G-quadruplex structures. The resulting DNA nano-scaffolds are thermally stable, consistent in size, and functionalized in a manner that allows for control over the density and relative orientation of functional chemistries on the nano-scaffold surface. Various chemistries including small modifications (N2-methyl-guanine), bulky aromatic modifications (N2-benzyl-guanine), and long chain-like modifications (N2-6-amino-hexyl-guanine) are tested and are found to be generally compatible with G-quadruplex formation. Furthermore, these modifications stabilize the G-quadruplex scaffold by 2.0-13.3 °C per modification in the melting temperature, with concurrent modifications producing extremely stable nano-scaffolds. We demonstrate the potential of this approach by functionalizing nano-scaffolds for use within the biotin-avidin conjugation approach. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A simple method for semi-random DNA amplicon fragmentation using the methylation-dependent restriction enzyme MspJI.

PubMed

Shinozuka, Hiroshi; Cogan, Noel O I; Shinozuka, Maiko; Marshall, Alexis; Kay, Pippa; Lin, Yi-Han; Spangenberg, German C; Forster, John W

2015-04-11

Fragmentation at random nucleotide locations is an essential process for preparation of DNA libraries to be used on massively parallel short-read DNA sequencing platforms. Although instruments for physical shearing, such as the Covaris S2 focused-ultrasonicator system, and products for enzymatic shearing, such as the Nextera technology and NEBNext dsDNA Fragmentase kit, are commercially available, a simple and inexpensive method is desirable for high-throughput sequencing library preparation. MspJI is a recently characterised restriction enzyme which recognises the sequence motif CNNR (where R = G or A) when the first base is modified to 5-methylcytosine or 5-hydroxymethylcytosine. A semi-random enzymatic DNA amplicon fragmentation method was developed based on the unique cleavage properties of MspJI. In this method, random incorporation of 5-methyl-2'-deoxycytidine-5'-triphosphate is achieved through DNA amplification with DNA polymerase, followed by DNA digestion with MspJI. Due to the recognition sequence of the enzyme, DNA amplicons are fragmented in a relatively sequence-independent manner. The size range of the resulting fragments was capable of control through optimisation of 5-methyl-2'-deoxycytidine-5'-triphosphate concentration in the reaction mixture. A library suitable for sequencing using the Illumina MiSeq platform was prepared and processed using the proposed method. Alignment of generated short reads to a reference sequence demonstrated a relatively high level of random fragmentation. The proposed method may be performed with standard laboratory equipment. Although the uniformity of coverage was slightly inferior to the Covaris physical shearing procedure, due to efficiencies of cost and labour, the method may be more suitable than existing approaches for implementation in large-scale sequencing activities, such as bacterial artificial chromosome (BAC)-based genome sequence assembly, pan-genomic studies and locus-targeted genotyping-by-sequencing.

Base modification strategies to modulate immune stimulation by an siRNA.

PubMed

Valenzuela, Rachel Anne P; Suter, Scott R; Ball-Jones, Alexi A; Ibarra-Soza, José M; Zheng, Yuxuan; Beal, Peter A

2015-01-19

Immune stimulation triggered by siRNAs is one of the major challenges in the development of safe RNAi-based therapeutics. Within an immunostimulatory siRNA sequence, this hurdle is commonly addressed by using ribose modifications (e.g., 2'-OMe or 2'-F), which results in decreased cytokine production. However, as immune stimulation by siRNAs is a sequence-dependent phenomenon, recognition of the nucleobases by the trigger receptor(s) is also likely. Here, we use the recently published crystal structures of Toll-like receptor 8 (TLR8) bound to small-molecule agonists to generate computational models for ribonucleotide binding by this immune receptor. Our modeling suggested that modification of either the Watson-Crick or Hoogsteen face of adenosine would disrupt nucleotide/TLR8 interactions. We employed chemical synthesis to alter either the Watson-Crick or Hoogsteen face of adenosine and evaluated the effect of these modifications in an siRNA guide strand by measuring the immunostimulatory and RNA interference properties. For the siRNA guide strand tested, we found that modifying the Watson-Crick face is generally more effective at blocking TNFα production in human peripheral blood mononuclear cells (PBMCs) than modification at the Hoogsteen edge. We also observed that modifications near the 5'-end were more effective at blocking cytokine production than those placed at the 3'-end. This work advances our understanding of how chemical modifications can be used to optimize siRNA performance. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Memory-Based Programmable Logic Device Using Look-Up Table Cascade with Synchronous Static Random Access Memories

NASA Astrophysics Data System (ADS)

Nakamura, Kazuyuki; Sasao, Tsutomu; Matsuura, Munehiro; Tanaka, Katsumasa; Yoshizumi, Kenichi; Nakahara, Hiroki; Iguchi, Yukihiro

2006-04-01

A large-scale memory-technology-based programmable logic device (PLD) using a look-up table (LUT) cascade is developed in the 0.35-μm standard complementary metal oxide semiconductor (CMOS) logic process. Eight 64 K-bit synchronous SRAMs are connected to form an LUT cascade with a few additional circuits. The features of the LUT cascade include: 1) a flexible cascade connection structure, 2) multi phase pseudo asynchronous operations with synchronous static random access memory (SRAM) cores, and 3) LUT-bypass redundancy. This chip operates at 33 MHz in 8-LUT cascades at 122 mW. Benchmark results show that it achieves a comparable performance to field programmable gate array (FPGAs).

Robust PRNG based on homogeneously distributed chaotic dynamics

NASA Astrophysics Data System (ADS)

Garasym, Oleg; Lozi, René; Taralova, Ina

2016-02-01

This paper is devoted to the design of new chaotic Pseudo Random Number Generator (CPRNG). Exploring several topologies of network of 1-D coupled chaotic mapping, we focus first on two dimensional networks. Two topologically coupled maps are studied: TTL rc non-alternate, and TTL SC alternate. The primary idea of the novel maps has been based on an original coupling of the tent and logistic maps to achieve excellent random properties and homogeneous /uniform/ density in the phase plane, thus guaranteeing maximum security when used for chaos base cryptography. In this aim two new nonlinear CPRNG: MTTL 2 sc and NTTL 2 are proposed. The maps successfully passed numerous statistical, graphical and numerical tests, due to proposed ring coupling and injection mechanisms.